Currently lm-sensors defaults to the compiler specified in the Makefile
(gcc) rather than the one specified in the spec. This patch appends the
CC flag to the make invocation with the spec compiler to fix this
behavior.
* initial commit for rocm-5.5.0 release
* fix the hipsparse build error for 5.5.0
* fix build error for amrex .add hiprand as a dependency
* modify the patch for rocprofiler-dev
* add hiprand for +rocm build
* initial commit for rocm-5.5.1 release
* bump up the version for rocm-5.5.1 release.
* bump up the version for rocmlir.miopen to use this backend only till 5.5
* add new recipe py-barectf and add it as dependency for rocprofiler-dev
* revert the changes for rocprofiler-dev for 5.5.0/1 for now as it depends
on hsa-amdaqlprofile.so which is a closed source and no spack recipe is
available for now.
* add rocm-core as dependency for rocm packages from 5.5.0 onwards
* avoid download of the gtest for building unit tests
* feature (packages): implement `odgi` package
This commit re-implements odgi package (superseded by #38741)
* fix (packages): remove redundant `requires()` from odgi package
This commit removes redundant use of `requires()` for gcc version in the `odgi` package
libelf fails to build with clang16+ due to Wimplicit-int and
Wimplicit-function-declarations becoming errors by default. This breaks
the configuration stage, so no build takes place. This patch fixes this
by passing -Wno-error=implicit-int and
-Wno-error=implicit-function-declarations as cflags.
gcoff uses the register keyword in a couple different places which
causes errors when building with c++17, which is the default in clang
16. This patch adds the -Wno-register flag to ignore these errors when
when building with clang 16.
Clang 16's change to erroring out by default on implicit function
declarations and implicit integers causes the build script for unzip to
break. Since this project hasn't had a release since 2010, we need to
patch it downstream/pass additional flags to get the build to succeed.
With the release of clang 16, clang now treats implicit function
declarations and implicit integers as errors rather than warnings,
causing the build to fail. This patch adds flags to prevent build
failures.
The sanitization function is completely bogus as it tries to replace /
on unix after ... splitting on it. The way it's implemented is very
questionable: the input is a file name, not a path. It doesn't make
sense to interpret the input as a path and then make the components
valid -- you'll interpret / in a filename as a dir separator.
It also fails to deal with path components that contain just unsupported
characters (resulting in empty component).
The correct way to deal with this is to have a function that takes a
potential file name and replaces unsupported characters.
I'm not going to fix the other issues on Windows, such as reserved file
names, but left a note, and hope that @johnwparent can fix that
separately.
(Obviously we wouldn't have this problem at all if we just fixed the
filename in a safe way instead of trying to derive something from
the url; we could use the content digest when available for example)
* py-jaxlib: add conflict for missing cuda cuda_arch specification
* Update var/spack/repos/builtin/packages/py-jaxlib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-jaxlib: conflict missing cuda_arch value when with cuda
* Update var/spack/repos/builtin/packages/py-jaxlib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* commands: provide more information to Command
* fish: Add script to generate fish completion
* fish: auto prepend `spack` command to avoid duplication
* fish: impove completion generation code readability
* commands: replace match-case with if-else
* fish: fix optspec variable name prefix
* fish: fix return value in get_optspecs
* fish: fix return value in get_optspecs
* format: split long line and trim trailing space
* bugfix: replace f-string with interpolation
* fish: compete more specs and some fixes
* fish: complete hash spec starts with /
* fish: improve compatibility
* style: trim trailing whitespace
* commands: add fish to update args and update tests
* commands: add fish completion file
* style: merge imports
* fish: source completion in setup-env
* fish: caret only completes dependencies
* fish: make sure we always get same order of output
* fish: spack activate
only show installed packages that have extensions
* fish: update completion file
* fish: make dict keys sorted
* Blacken code
* Fix bad merge
* Undo style changes to setup-env.fish
* Fix unit tests
* Style fix
* Compatible with fish_indent
* Use list for stability of order
* Sort one more place
* Sort more things
* Sorting unneeded
* Unsort
* Print difference
* Style fix
* Help messages need quotes
* Arguments to -a must be quoted
* Update types
* Update types
* Update types
* Add type hints
* Change order of positionals
* Always expand help
* Remove shared base class
* Fix type hints
* Remove platform-specific choices
* First line of help only
* Remove unused maps
* Remove suppress
* Remove debugging comments
* Better quoting
* Fish completions have no double dash
* Remove test for deleted class
* Fix grammar in header file
* Use single quotes in most places
* Better support for remainder nargs
* No magic strings
* * and + can also complete multiple
* lower case, no period
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* tinygltf: new versions and release branch
for each minor release available, the newest patch release has been added
---------
Co-authored-by: aumuell <aumuell@users.noreply.github.com>
- drop use_xcode = True, as this would lead to an attempt install Xcode (#34064)
- don't automatically build Qt Location with +opengl, as this is
still broken
This built sucessfully with qt@5.15.10+opengl+dbus+phonon on ventura/arm without
Xcode installed (only command line tools) - I did not check with Xcode installed.
The user store is lazily evaluated. The change
in #38975 made it such that the first evaluation
was happening in the middle of swapping to user
configuration.
Ensure we construct the user store before that.
Use curly braces instead of quotes to enclose value or text in Tcl
modulefile. Within curly braces Tcl special characters like [, ] or $
are treated verbatim whereas they are evaluated within quotes.
Curly braces is Tcl recommended way to enclose verbatim content [1].
Note: if curly braces charaters are used within content, they must be
balanced. This point has been checked against current repository and no
unbalanced curly braces has been spotted.
Fixes#24243
[1] https://wiki.tcl-lang.org/page/Tcl+Minimal+Escaping+Style
* Fetching patches wouldn't result in acquiring a stage lock during install
* The installer would acquire a stage lock *after* fetching instead of
before, leading to races
* The name of the stage for patches was random, so on build failure
(where stage dirs are not removed), these directories would continue
to exist after a second successful install.
* There was this redundant "composite fetch" object -- there's already
a composite stage. Remove this.
* For some reason we do *double* shasum validation of patches, before
and after compression -- that's just too much? I removed it.
Spack heuristically adds `<install prefix>/lib` and `<install prefix>/lib64` as rpath entries, as it doesn't know what the install dir is going to be ahead of the build. This PR cleans up non-existing, absolute paths[^1], which
1. avoids redundant stat calls at runtime
2. drops redundant rpaths in `patchelf`, making it relocatable -- you don't need patchelf recursively then.
[^1]: It also removes relative paths not starting with `$` (so, `$ORIGIN/../lib` is retained -- we _could_ interpolate `$ORIGIN`, but that's hard to get right when symlinks have to be taken into account). Relative paths _are_ supported in glibc, but are relative to _the current working directory_, which is madness, and it would be better to drop those paths.
A LazyReference object is a reference to an attribute of a
lazily evaluated singleton. Its only purpose is to let developers
use shorter names to refer to such attribute.
This class does more harm than good, as it obfuscates the fact
that we are using the attribute of a global object. Also, it can easily
go out of sync with the singleton it refers to if, for instance, the
singleton is updated but the references are not.
This commit removes the LazyReference class entirely, and access
the attributes explicitly passing through the global value to which
they are attached.
Without the package name being present in the conflict messages, it is
significantly more difficult to debug concretization failures in
environments that contain many packages.
mesa-glu still has a couple instances of the register keyword which
causes build failures with clang on my platform. This patch removes the
register keyword which doesn't have any impact on correctness.
gperf still uses the register keyword in one place which makes
compilation fail with c++17. This patch adds in a patch file to remove
the usage of the reigster keyword so that it compiles properly.
In late 2021 elfutils was patched to make it build with clang, and these
patches ended up in version 0.186. This commit updates the conflicts to
specify this so elfutils can be built with clang.
These tests now work without any changes to core. Furthermore, it is
surprising that they had to be disabled (at least, as long as the
installer.py tests are run on Windows: these tests are more-basic
and their functionality would have been exercised automatically).
* py-poetry-core: add 1.6.1 and fix url
* Update var/spack/repos/builtin/packages/py-poetry-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Re-add python upper bound for older versions
* Update var/spack/repos/builtin/packages/py-poetry-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
In Clang 15, -Wint-conversion became an error instead of a warning,
breaking the fftw build for clang versions > 15. This patch fixes fftw
builds with clang 15+ by passing -Wno-error=int-conversion as a cflag.
Without --allow-root spack cannot push binaries that contain paths in
binaries. This flag is almost always needed, so there is no point of
requiring users to spell it out.
Even without --allow-root, rpaths would still have to be patched, so the
flag is not there to guarantee binaries are not modified on install.
This commit makes --allow-root the default, and drops the code
required for it. It also deprecates `spack buildcache preview`, since
the command made sense only with --allow-root.
As a side effect, Spack no longer depends on binutils for relocation
Add support for conflict directives in Lua modulefile like done for Tcl
modulefile.
Note that conflicts are correctly honored on Lmod and Environment
Modules <4.2 only if mutually expressed on both modulefiles that
conflict with each other.
Migrate conflict code from Tcl-specific classes to the common part. Add
tests for Lmod and split the conflict test case in two.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* When using system tools to unpack a .gz file, the input file needs a
different name than the output file. Normally, we generate this new
name by stripping off the .gz extension off of the file name.
This was not sufficient if the file name did not have an extension,
so we temporarily rename the file in that case.
* When using system tar utility to untar on Windows, we were (erroneously)
skipping the actual untar step if the filename was lacking a .tar
extension
* For foo.txz, we were not changing the extension of the decompressed file
(i.e. we would decompress foo.txz to foo.txz). This did not cause any
problems, but is confusing, so has been updated such that the output
filename reflects its decompressed state (i.e. foo.tar).
* Added test for strip_compression_extension
* Update test_native_unpacking to test each archive type with and without
an extension as part of the file name (i.e. we test "foo.tar.gz", but
also make sure we decompress properly if it is named "foo").
* py-pyside: fix build for version 1.2.2
* Remove check for python version
* Fix style
* Remove unnecessary patch
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-markupsafe conflict
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyside/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Move python check removal below suprocess patch
* Remove preference of 1.2.2
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* soapdenovo2: strip optimization flags from injected flags
* soapdenovo2: add maintainer
* soapdenovo2: only append on cflags
* soapdenovo2: clean up some wording and implementation
Running `spack test run <python package>` resulted in the error
```
'str' object is not callable
```
because the python executable was not set correctly.
* qt-base: always link to GSS framework on macOS
On macos, the code in src/network/kernel/qauthenticator.cpp
unconditionally includes the header from the GSS framework, so we should
link against it.
This applies two patches from the dev branch. They are to be cherry-picked
into the 6.5 (probably released with 6.5.2) and 6.6 branches, but they
apply against 6.3.2 as well.
* qt-base: disable libproxy on macOS
src/network/CMakeLists.txt disables it on MACOS anyway. And as it is not
found without pkg-config, building with +network would break because of
the feature being explicitly enabled.
* qt-base: don't depend on pkgconfig on macOS
On macOS, usage of pkg-config is disabled by unsetting
PKG_CONFIG_EXECUTABLE, unless the feature pkg-config is requested explicitly.
* qt-base: don't depend on at-spi2-core on macOS
Does not build on macOS and seems to be targeted at linux. Qt6 on
homebrew does not depend on it, either.
* qt-base: fix long lines
* qt-base: restrict use of pkgconfig to linux
yes, probably not needed on windows, either
Co-authored-by: Alec Scott <alec@bcs.sh>
* qt-base: disable libproxy on Windows as well
according to src/network/CMakeLists.txt it's only used on Unix
* qt-base: improvements based on reviewer suggestions
---------
Co-authored-by: Alec Scott <alec@bcs.sh>
* legion: Add 23.06.0, variants for UCX, max nodes, update CUDA version.
* legion: Make newer CUDA versions dependent on newer Legion.
* legion: Update CUDA arch list so that we can stop tracking manually.
* Added py-eprosima-fastdds package
* Fixed python extension and dependency version
* Added build type for swig
* Added minimum cmake support
* Added py-test dependency
* Added suggestion on python extension
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added suggestion on build type for cmake
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Lock objects can now be instantiated independently,
without being tied to the global configuration. The
same is true for database and store objects.
The database __init__ method has been simplified to
take a single lock configuration object. Some common
lock configurations (e.g. NO_LOCK or NO_TIMEOUT) have
been named and are provided as globals.
The use_store context manager keeps the configuration
consistent by pushing and popping an internal scope.
It can also be tuned by passing extra data to set up
e.g. upstreams or anything else that might be related
to the store.
Not having the package name in the conflict messages can make debugging
conflicts exceedingly hard when trying to concretize an environment with
a sufficient number of packages. This patch adds the package name to all
of the conflict messages so that it is easy to tell just from the
message which package is causing conflicts.
* py-jinja2: add conflict for py-markupsafe@2.0.2
* Update var/spack/repos/builtin/packages/py-jinja2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-shiboken: fix build by restricting dependencies
* Update var/spack/repos/builtin/packages/py-shiboken/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove conflict
* Remove py-markupsafe conflict
* Update var/spack/repos/builtin/packages/py-shiboken/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add a phist patch to avoid trying to compile SSE code if that is not available.
* phist: make the avoid-sse patch more robust because compiler on ARM system still tried to compile SSE code
* Bugfix: spack.yaml concretizer:unify needs to be read and used
* Optional: add environment test to ensure configuration scheme is used
* Activate environment in unit tests
A more proper solution would be to keep
an environment instance configuration as
an attribute, but that is a bigger refactor
* Delay evaluation of Environment.unify
* Slightly simplify unit tests
---------
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Update TensorFlow ecosystem
* Re-add +cpp
* Do not use system protobuf
* Let bazel auto-detect macOS SDK version
* Unnecessary duplicated dep
* Remove unused import
Allow the following formats:
```yaml
mirrors:
name: <url>
```
```yaml
mirrors:
name:
url: s3://xyz
access_pair: [x, y]
```
```yaml
mirrors:
name:
fetch: http://xyz
push:
url: s3://xyz
access_pair: [x, y]
```
And reserve two new properties to indicate the mirror type (e.g.
mirror.spack.io is a source mirror, not a binary cache)
```yaml
mirrors:
spack-public:
source: true
binary: false
url: https://mirror.spack.io
```
A few packages have version directives evaluated
within if statements, conditional on the value of
`platform.platform()`.
Sometimes there are no cases for e.g. platform=darwin and that
causes a lot of spurious failures with version existence
audits.
This PR allows expressing conditions to skip version
existence checks in audits and avoid these spurious reports.
### Rationale
While working on #29549, I noticed a lot of inconsistencies in our argparse help messages. This is important for fish where these help messages end up as descriptions in the tab completion menu. See https://github.com/spack/spack/pull/29549#issuecomment-1627596477 for some examples of longer or more stylized help messages.
### Implementation
This PR makes the following changes:
- [x] help messages start with a lowercase letter.
- [x] Help messages do not end with a period
- [x] the first line of a help message is short and simple
longer text is separated by an empty line
- [x] "help messages do not use triple quotes"
"""(except docstrings)"""
- [x] Parentheses not needed for string concatenation inside function call
- [x] Remove "..." "..." string concatenation leftover from black reformatting
- [x] Remove Sphinx argument docs from help messages
The first 2 choices aren't very controversial, and are designed to match the syntax of the `--help` flag automatically added by argparse. The 3rd choice is more up for debate, and is designed to match our package/module docstrings. The 4th choice is designed to avoid excessive newline characters and indentation. We may actually want to go even further and disallow docstrings altogether.
### Alternatives
Choice 3 in particular has a lot of alternatives. My goal is solely to ensure that fish tab completion looks reasonable. Alternatives include:
1. Get rid of long help messages, only allow short simple messages
2. Move longer help messages to epilog
3. Separate by 2 newline characters instead of 1
4. Separate by period instead of newline. First sentence goes into tab completion description
The number of commands with long help text is actually rather small, and is mostly relegated to `spack ci` and `spack buildcache`. So 1 isn't actually as ridiculous as it sounds.
Let me know if there are any other standardizations or alternatives you would like to suggest.
* ci: run spack list in power ci
Let's see if Spack itself is the bottleneck in CI...
* rebuild curl in CI
* more of the same please!
* drop the profiler
* undo rebuildme test in ci variant
* add comment for posterity
* enable profiling
* trigger CI
* See how it goes now that perf regressions are fixed on develop
* try shorter poll intervals
* Revert "try shorter poll intervals"
This reverts commit d60c34ad3eceead0c13a5277cf8e783fd42b7458.
* Remove spec.format call in Database._get_matching_spec_key
* once more in ci please
* undo irrelevant changes
* run spack list in before script
* test in ci
* -:
* Undo CI testing
The spdlog project precisely states/depends which fmt version should
be used for compatibility. Latest version 1.11.0 depends explictly on
fmt 9.1.0. Without fixed version micromamba build fails when using spack
install micromamba on e.g. Rockylinux 8.5.
The 'bison' executable requires libtextstyle to run. I think this was
usually satisfied because gettext is often installed with the OS, or
brought in accidentally via perl/m4.
Looks like the libtextstyle library dependency started in Bison 3.4
Refactor `TermTitle` into `InstallStatus` and use it to show progress
information both in the terminal title as well as inline. This also
turns on the terminal title status by default.
The inline output will look like the following after this change:
```
==> Installing m4-1.4.19-w2fxrpuz64zdq63woprqfxxzc3tzu7p3 [4/4]
```
* llvm: fix build with libcxx=none
* ispc: checksum 1.20.0
* ispc: ensure that it does not crash immediately
this would happen if linked to the wrong libc++
* ispc: fix build on macos
find ncurses instead of curses and link against tinfo in order to avoid
unresolved references to _del_curterm, _set_curterm, _setupterm, and
_tigetnum
* ispc: enable arm targets, if building on arm
* ispc: remove double cmake argument
I forgot to remove the constant -DARM_ENABLED=FALSE when adding
-DARM_ENABLED with a value depending on target architecture
* ispc: fix linux build
since 1.20, linux build uses TBB as default tasking system and thus
needs to depend on it
* ispc: try to fix link error on linux
link against both curses (as before) and tinfo (added because of macos)
* ispc: update for recent llvm changes
libcxx=none instead of ~libcxx
`mypy` will check *all* imported packages, even optional dependencies outside your
project, and this can cause issues if you are targeting python versions *older* than the
one you're running in. `mypy` will report issues in the latest versions of dependencies
as errors even if installing on some older python would have installed an older version
of the dependency.
We saw this problem before with `numpy` in #34732. We've started seeing it with IPython
in #38704. This fixes the issue by exempting `IPython` and a number of other imports of
Spack's from `mypy` checking.
* Setting library path as lib similar to other rocm packages.
* Fix style check failure
* Restricting changes to 5.4.3 and above
* Including comgr change
* initial commit for adding hip-examples package
* adding test to hip-examples
* fixed compile error on add4
* change standalone test to use new syntax
Spack-installed Perl always has opcode support, but external Perl
installations might not. This commit adds a +opcode variant and
updates the external detection logic to check for opcode support.
The postgresql package is updated to require perl+opcode (in
combination with the above, this helps detect when an external
Perl instance is sufficient for a Spack build of postgreqsql, or
if Spack needs to build its own Perl).
* Update cp2k recipe to use cmake or the current build system
Offers the possibility to build cp2k with the new cmake build system. commands like this are now supported
spack install cp2k@master build_system=cmake +.....
the recipe supports the following optional functionalities
- superlu, cosma, sirius, spglib, metis, spglib, libxc, libint, cuda/rocm, mkl/openblas/sci (and others), mpi, openmp, dbcsr
- dbcsr is built separately using the currently available recipe.
Two PRs need to be merged to be fully functional (cosma update in spack + one PR in cp2k github).
* Fix indentation
* Fix indentation
* Update libvori
* More typos
* Simplify BLAS/LAPACK
* Simplify BLAS/LAPACK
* Add A100 gpu value
* Fix typo
* Add the enable_regtests option
if -DCP2K_ENABLE_REGTESTS=ON (+enable_regtests with spack) then the location of the binary executables will be in the cp2k root directory under exe/build-cmake-*. This option is needed to run the regtests afterwards.
* Minor update
* more fixes
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
* small changes
* Remove any reference to nvidia architecture in the rocm list
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
* Final reformating
* Update py-fypp
---------
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
People frequently ask us how to pipe `spack find` output to other commands, and we tell
them to do things like this:
```console
$ spack find --format "/{hash}" | spack uninstall -ay
```
Sometimes users don't know about hash references and come up with potentially ambiguous
formulations like this:
```console
spack find --format {name}@{version}%{compiler} | spack uninstall -ay
```
Since this is a common enough thing to want to do, and to make it more obvious how, this
PR adds a `-H` / `--hashes` as a shortcut, so you can now just do:
```console
spack find -H | spack uninstall -ay
```
* Added packages bitstruct, callmonitor, and PYnvtx
* Revert "Added packages bitstruct, callmonitor, and PYnvtx"
This reverts commit 76d25aa76b.
* py-bitstruct: This module is intended to have a similar interface as the python struct module, but working on bits instead of primitive data types (char, int, …)
* Update package.py
To pass the style prechecks
* PyNVTX: new package
* Delete package.py
Accidentally added this package.
* Update var/spack/repos/builtin/packages/py-bitstruct/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* openssl: prefer 3.x
This PR is not intended to be merged immediately, but it would be good
to see what packages fail to build in CI so that we can get proper
version constraints on openssl (before all packages update and support
both openssl 1 and 3)
* Disable assembly for 3.x %oneapi
* cmake: depend on spack curl, to deal with curl - openssl compat
* also make zlib external
* remove overly strict & unsafe requirement on py-cryptographty patch version number
* update openssl compat bounds in py-cryptography
* smaller diff
* Make libssh2 an autotools/cmake package
* fix weird upperbound in libssh2 as there is not openssl v2
* libssh2: pc file lists plain -lssl -lcrypto w/o leading -L flag, confusing libgit2 parsing of pkg-config output
* Actually fix the issue in libssh2: its pc file looks broken
`"%s" % spec` formats the spec with deps included, which produces sometimes KBs
of data and is slow to run in pure Python. It can delay otherwise very short-lived
read/write locks on the database.
Discovered in #38762 where profile output showed about 2 seconds is spent in
`spec.format`, which is significant overhead when using multiprocessing to install
from binary cache in parallel (installation often takes <5s for small packages). With
this change, `spec.format` no longer shows up in profile output.
(This line hasn't changed since Spack v0.9 ;p)
* move format() call to custom NoSuchSpecError exception
* add a comment saying why, so we can eventually change `Spec.__str__`
* qt-base: new version 6.5.0
* qt-declarative: new version 6.5.0
* qt-quick3d: new version 6.5.0
* qt-quicktimeline: new version 6.5.0
* qt-shadertools: new version 6.5.0
* qt-*: new version 6.5.1
* qt-base: new version 6.5.1
* py-pyarrow: enable parquet variant by default
* Disable parquet variant by default
* Add conflict to enable parquet when dataset is active
* Disable dataset variant by default
* initial commit of nanobind package
* style fixes
* Update package.py
Typo
* addressed PR comments
* add v1.4.0
* Update var/spack/repos/builtin/packages/py-nanobind/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Matthew Archer <ma595@cam.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-astropy: fix import tests and restrict py-pip version
* Fix --install-option name in comments
* Rename variant and fix variant dependencies
* Remove parquet variant from py-pyarrow
1. Fix O(n^2) iteration in `_get_overwrite_specs`
2. Early exit `get_by_hash` on full hash
3. Fix O(n^2) double lookup in `all_matching_specs` with hashes
4. Fix some legibility issues
* mlpack: new package
mlpack is an intuitive, fast, and flexible header-only C++ machine learning library with bindings to other languages. It is meant to be a machine learning analog to LAPACK, and aims to implement a wide array of machine learning methods and functions as a "swiss army knife" for machine learning researchers.
* mlpack: upstream merged patch to allow python installation in spack
* Added v5.0.0 of PyAMG. This required v7.1.0 of setuptools_scm due to a bug in 7.0.5.
* Added comment about version requirement.
* Loosened dependency based on build experiments.
* Updated tomli deps.
* Update var/spack/repos/builtin/packages/py-setuptools-scm/package.py
Dependence for 7.0 only.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pyamg/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Swapped lines.
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pip: add 23.1.2
* Restrict py-pip version for py-protobuf
* Restrict py-pip version for straightforward packages
* Restrict py-pip version for nrm
* Fix --install-option name in comments
* Simplify py-pip restriction for py-scs
* nrm: fix wrong comment
* py-spglib: add 2.0.2
* Update var/spack/repos/builtin/packages/py-spglib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-setuptools as run dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add maintainers
* Updated cosma archive checksum and costa version
- updated cosma version (in the cosma build system)
- updated costa version
- use the default generic url for downloading packages
- do not build tiled-mm when the cpu only version is needed
Signed-off-by: Dr. Mathieu Taillefumier <mathieu.taillefumier@free.fr>
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
NAMD users expect the Tcl scripting interface to be enabled as it is used in many examples and tutorials in addition to being required for features such as multi-copy algorithms.
* When installing a package Spack will attempt to set group permissions on
the install prefix even when the configuration does not specify a group.
Co-authored-by: David Gomez <dvdgomez@users.noreply.github.com>
From the configure.ac file:
> H5VL_log is built on top of MPI. Configure option --without-mpi or
> --with-mpi=no should not be used. Abort.
This currently fails to build in the oneAPI pipeline on `develop`
* py-userpath: new package
* pipx: new package
* Update var/spack/repos/builtin/packages/pipx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* pipx: Remove incorrect dependency on py-platformdirs
* Update var/spack/repos/builtin/packages/pipx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-userpath: Remove version requirements to match upstream
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR removes deprecated versions for all packages that I'm maintaining. In future Spack releases, I'm planning to do this on a much larger scale, but we can hold off until we have better reproducibility.
I'm hoping that this will improve the maintainability of these packages. If any other maintainers of these recipes would like to retain any of these deprecated versions, or add new versions, speak now or forever hold your peace 😄
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
Windows runtime library loading searches PATH, and therefore bin/ is
the appropriate place to put .dll files. Prior to this change, XZ was
installing both .dll and .lib files to the lib/ directory.
Move the logic checking which mirrors have the specs we need closer
to where that information is needed. Also update the staging summary
to contain a brief description of why we scheduled or pruned each
job. If a spec was found on any mirrors, regardless of whether
we scheduled a job for it, print those mirrors.
* Change maintainer, add new version and deprecate old one
* Fix style issue
* Revert deprecation
---------
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
PowerShell requires explicit shell and env support in Spack.
This is due to the distinct differences in shell interactions between
cmd and pwsh. Add a doskey in pwsh piping 'spack' commands to a
powershell script similar to the sh function 'spack'. Add
support for PowerShell-specific shell interactions from Spack
(set/unset shell variables).
* py-ruamel-yaml: add 0.17.32 and py-ruamel-yaml-clib: add 0.2.7
* Update var/spack/repos/builtin/packages/py-ruamel-yaml/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix style
* Fix python dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* HDF5: is_enabled helper (ON)
Slightly generalize the `is_enabled` helper in the HDF5 package.
`ON` is the most typical CMake bool option passed, besides many
other possible `true` values, and should be included as a possible
check to the config.
* Simplify
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Support hardlinks/junctions on Windows systems without developer
mode enabled
* Generally, use of llnl.util.symlink.symlink is preferred over
os.symlink since it handles this automatically
* Generally an error is now reported if a user attempts to create a
symlink to a file that does not exist (this was previously allowed
on Linux/Mac).
* One exception to this: when Spack installs files from the source
into their final prefix, dangling symlinks are allowed (on
Linux/Mac - Windows does not allow this in any circumstance).
The intent behind this is to avoid generating failures for
installations on Linux/Mac that were succeeding before.
* Because Windows is strict about forbidding dangling symlinks,
`traverse_tree` has been updated to skip creating symlinks if they
would point to a file that is ignored. This check is not
transitive (i.e., a symlink to a symlink to an ignored file would
not be caught appropriately)
* Relocate function: resolve_link_target_relative_to_the_link
(this is not otherwise modified)
Co-authored-by: jamessmillie <smillie@txcorp.com>
Update list of excluded variables in `from_sourcing_file` function to
cover all variables specific to Environment Modules or Lmod. Add
specifically variables relative to the definition of `module()`, `ml()`
and `_module_raw()` Bash functions.
Fixes#13504
* Add new versions of Qthreads
* Add version URLs explicitly as it has recently changed
* Use function to extrapolate version URL for older versions
* Fix url formatter
llvm @13-15 is required for ispc, but fails to build with GCC 13.
14.0.6 and 15.0.7 built successfully with upstream patch, 13.0.1
still fails. Thus upstream patch is applied to 14 and 15 only.
Update `env.set` command and underlying `SetEnv` object to add the `raw`
boolean attribute. `raw` is optional and set to False by default. When
set to True, value format is skipped for object when generating
environment modifications.
With this change it is now possible to define environment variable
whose value contains variable reference syntax (like `{foo}` or `{}`)
that should be set as-is.
Fixes#29578
By default, `find_package(Python)` searches from highest version to lowest version, identifying the highest version that satisfies the requirements. This means that `/usr/bin/python3.11` will be found before `$(spack location -i python)/bin/python3.10`, even when other packages have been built with the `python` in spack.
This ensures that the `python` dependency is explicitly the `python` version that is used.
* libEnsemble: add v0.10.0
* Make new deps required
* Fixes to deps
* Update var/spack/repos/builtin/packages/py-libensemble/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix build, run
* Reorder required deps
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pytest: add 7.3.2
* [@spackbot] updating style on behalf of manuelakuhn
* Swap py-importlib-metadata dependency order
* Restrict python version for older versions
* Add recipe for iterative-stats
* Fix branch name and remove comment
* Add git link
* Add package maintainer
* Enforce multiple requested changes
* Update var/spack/repos/builtin/packages/py-iterative-stats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update checksum
* Fix openturns dependency specification
* Add python variant spec to openturns
---------
Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add rust v1.70.0 and simplify package logic by moving bootstrap to dedicated package
* Fix formatting of rust-bootstrap package file
* Re-enable Rust as extendable
* Add nightly version to rust and rust-bootstrap
* Manually inject openssl certs into environment
* Add master and beta versions to rust
* Add additional documentation for using rust development releases
* Remove @AndrewGaspar as maintainer
* py-notebook: add 6.5.4
* [@spackbot] updating style on behalf of manuelakuhn
* Update var/spack/repos/builtin/packages/py-notebook/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Fix version of py-nbclassic dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
It installs the LFortran runtime library and
LFortran can compile codes to binaries. The interactive mode does not
work yet with LLVM > 11, that has to be fixed upstream.
Co-authored-by: Wileam Y. Phan <50928756+wyphan@users.noreply.github.com>
No changes to the build system, no changes to `package.py` needed.
Changelog: https://github.com/qt/qtbase/compare/v5.15.9-lts-lgpl...v5.15.10-lts-lgpl
Main change taking up space:
- bundled 3rdparty/pcre2 updated from 10.39 to 10.40 (spack now includes 10.42, and we don't put specific version requirements in `package.py`)
* py-networkx: add 3.1
* Update var/spack/repos/builtin/packages/py-networkx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add default variant
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pycairo: add 1.24.0
* Change python dependency to 3.8
* Remove upper bound for python dependency
* Update var/spack/repos/builtin/packages/py-pycairo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add darshan 3.4.3 releases
* darshan-runtime 3.4.3
* darshan-util 3.4.3
* py-darshan 3.4.3.0
- add py-humanize as new dependency
* py-darshan has strict darshan-util version reqs
darshan-util version required is based on the first 3 parts of
the py-darshan version string
* remove support for python3.6
* py-humanize dependency for 3.4.3+ versions
* only enforce scipy dependency for 3.4.0.1
* drop optional lxml dependency
* drop matplotlib pinning
* importlib-resources not a dep in python-3.7+
* drop unnecessary numpy pin
* add build dep for pytest-runner
* fix typo in pytest-runner package name
* pip setuptools to match pydarsan setup.py
* spack style fix
* py-gsutil: add 5.24, fix and add dependencies
* Update var/spack/repos/builtin/packages/py-httplib2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add httplib2@0.20.4 and pin it in py-gsutil
* Add py-cryptography conflict
* Update var/spack/repos/builtin/packages/py-httplib2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-pyopenssl: fix py-cryptography conflict
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update mda and mdatests
* black
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* polish
* Update var/spack/repos/builtin/packages/py-mdanalysistests/package.py
* fixes
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`FFLAGS` and `FCFLAGS` are being ignored by WRF build system. Not only in version
`3.9.1.1`, but also `4.x`.
Also, I see no reason to explicitly add `-w` and `-O2` to compile lines when
using `gcc@10:`. Tested for version `3.9.1.1`, `4.2.2`, & `4.5.0`.
Tagging original authors of this part @MichaelLaufer and @giordano in case they
want to chime in.
* ncbi-rmblastn: patching to support building with %gcc@13:
* ncbi-rmblastn: patching to build with %gcc@13:
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
* py-pre-commit: add 3.3.3
* Update var/spack/repos/builtin/packages/py-pre-commit/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Spack flags supplied by users should supersede flags from package build systems and
other places in Spack. However, Spack currently adds user-supplied flags to the
beginning of the compile line, which means that in some cases build system flags will
supersede user-supplied ones.
The right place to add a flag to ensure it has highest precedence for the compiler really
depends on the type of flag. For example, search paths like `-L` and `-I` are examined
in order, so adding them first is highest precedence. Compilers take the *last* occurrence
of optimization flags like `-O2`, so those should be placed *after* other such flags. Shim
libraries with `-l` should go *before* other libraries on the command line, so we want
user-supplied libs to go first, etc.
`lib/spack/env/cc` already knows how to split arguments into categories like `libs_list`,
`rpath_dirs_list`, etc., so we can leverage that functionality to merge user flags into
the arg list correctly.
The general rules for injected flags are:
1. All `-L`, `-I`, `-isystem`, `-l`, and `*-rpath` flags from `spack_flags_*` to appear
before their regular counterparts.
2. All other flags ordered with the ones from flags after their regular counterparts,
i.e. `other_flags` before `spack_flags_other_flags`
- [x] Generalize argument categorization into its own function in the `cc` shell script
- [x] Apply the same splitting logic to injected flags and flags from the original compile line.
- [x] Use the resulting flag lists to merge user- and build-system-supplied flags by category.
- [x] Add tests.
Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
Co-authored-by: iermolae <igor.ermolaev@intel.com>
* py-vermin: add latest version 1.5.2
* Removed obsolete dep and setuptools is only for build-time
- setuptools are not used as runtime
- py27 isn't strictly necessary
The `unparser` that Spack uses for package hashing had several tweaks to ensure compatibility
with Python 2.7:
1. Currently, the unparser automatically moves `*` and `**` args to the end to preserve
compatibility with `python@:3.4`
2. `print a, b, c` statements and single-tuple `print((a, b, c))` function calls were
remapped to `print(a, b, c)` in the unparsed output for consistency across versions.
(1) is causing issues in our tests because a recent patch to the Python source code
(https://github.com/python/cpython/pull/102953/files#diff-7972dffec6674d5f09410c71766ac6caacb95b9bccbf032061806ae304519c9bR813-R823)
has a `**` arg before an named argument, and we round-trip the core python source code
as a test of our unparser. This isn't actually a break with our consistent unpausing -- it's still
consistent, the python source just doesn't unparse to the same thing anymore. It does makes
it harder to test, so it's not worth maintaining the Python2-specific stuff anymore.
Since we only support `python@3.6:`, this PR removes (1) and (2) from the unparser, but keeps
one last tweak for unicode AST inconsistencies, as it's still needed for Python 3.5-3.7.
This fixes the CI error we've been seeing on `python@3.11.4` and `python@3.10.12`. Again, that
bug exists only in the test system and doesn't affect our canonical hashing of Python code.
* WarpX 23.06
Update WarpX and related Python packages to the lastest releases.
WarpX 23.06 introduces multi-dimension support in a single package,
which will ease deployment in E4S et al. that can ship now a single,
full-feature module/package that is NOT incompatible with itself
anymore.
* e4s ci stacks: multiple specs for each dim variant no longer required
* [@spackbot] updating style on behalf of ax3l
* WarpX: Update CMake CLI and Test/Check
* Add Missing `build-directory`
* [@spackbot] updating style on behalf of ax3l
* Remove `build_directory` again
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Co-authored-by: ax3l <ax3l@users.noreply.github.com>
* star: add 2.7.10
* star: fix building for non-avx2 arch processors
* convert to MakefilePackage, second take at fixing for aarch64
* style
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
* DependencySpec: add virtuals attribute on edges
This works for both the new and the old concretizer. Also,
added type hints to involved functions.
* Improve virtual reconstruction from old format
* Reconstruct virtuals when reading from Cray manifest
* Reconstruct virtual information on test dependencies
* openradioss-starter,engine: new package
* openradioss-engine: change version name develop to main
* openradioss-starter: change version name develop to main
Update Tcl modulefile template to use the `depends-on` command to
autoload modules if Lmod is the current module tool.
Autoloading modules with `module load` command in Tcl modulefile does
not work well for Lmod at some extend. An attempt to unload then load
designated module is performed each time such command is encountered. It
may lead to a load storm that may not end correctly with large number of
module dependencies.
`depends-on` command should be used for Lmod instead of `module load`,
as it checks if module is already loaded, and does not attempt to reload
this module.
Lua modulefile template already uses `depends_on` command to autoload
dependencies. Thus it is already considered that to use Lmod with Spack,
it must support `depends_on` command (version 7.6+).
Environment Modules copes well with `module load` command to autoload
dependencies (version 3.2+). `depends-on` command is supported starting
version 5.1 (as an alias of `prereq-all` command) which was relased last
year.
This change introduces a test to determine if current module tool that
evaluates modulefile is Lmod. If so, autoload dependencies are defined
with `depends-on` command. Otherwise `module load` command is used.
Test is based on `LMOD_VERSION_MAJOR` environment variable, which is set
by Lmod starting version 5.1.
Fixes#36764
When interpreting local paths as relative URL endpoints, they were
formatted as Windows paths on Windows (i.e. with '\'). URLs should
always be POSIX-style.
Update modulefile templates to append a trailing delimiter to MANPATH
environment variable, if the modulefile sets it.
With a trailing delimiter at ends of MANPATH's value, man will search
the system man pages after searching the specific paths set.
Using append-path/append_path to add this element, the module tool
ensures it is appended only once. When modulefile is unloaded, the
number of append attempt is decreased, thus the trailing delimiter is
removed only if this number equals 0.
Disclaimer: no path element should be appended to MANPATH by generated
modulefiles. It should always be prepended to ensure this variable's
value ends with the trailing delimiter.
Fixes#11355.
* opencascade: new variants
OpenCascade has several major modules and not every
application needs all of them. This adds variants for
the various modules.
It also uodatws the 3rdparty dependency treatment.
* [@spackbot] updating style on behalf of wdconinc
* Update var/spack/repos/builtin/packages/opencascade/package.py
* opencascade: remove variant foundation_classes (always true)
* [@spackbot] updating style on behalf of wdconinc
* Update var/spack/repos/builtin/packages/opencascade/package.py
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Deprecate R packages for spatial analysis
* [@spackbot] updating style on behalf of adamjstewart
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
No changes to build system required. Changelog: https://github.com/xiaoyeli/superlu/compare/v5.3.0...v6.0.0
Since this new version adds "64-bit indexing support", and since at least one dependent package (`armadillo`) requires "32-bit integers" (faa6cbf895), the previous version remains preferred.
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* New version for openCARP packages
* Update carputils dependencies
* Update types of openCARP dependencies
* Add type "run" to setuptools dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add package py-common as carputils dependency
* Add setuptools dependency for py-common
* Remove spaces on blank line
* Restrict type of dependency setuptools to "build"
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: openCARP consortium <info@opencarp.org>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [gromacs] Fix intel (classic) libstdc++ path
Gromacs's `cmake` run will look for `--gcc-toolchain` (e.g. LLVM, icpx) or
`--gcc-name` (e.g. icpc) in `CMAKE_CXX_FLAGS`. Only if it does not find a good
g++ candidate there it will look for `GMX_GPLUSPLUS_PATH`:
cb6b311c39/cmake/FindLibStdCpp.cmake (L97)
Spack installed intel compilers already define a g++ for std libs. But in
`icp{c,x}.cfg` instead of the compile line. If we use the pre-defined g++ we not
only have less chance of mixing g++ versions, but also don't need to explicitly
add `gcc` as dependency to `gromacs`.
* Fix format
* Use a variant
As there is no way to check if a file exists at depends_on stage
* Fix format
* New name and fail if variant is used with other compiler
* Line too long.
The pcluster image has am internal buildcache without an index.
Also, we need to force reuse to avoid rebuilding GCC, since the default is
to only reuse dependencies - and that is subject to changes in the GCC
recipe.
* bedtools2: patching to build with gcc@13
* bedtools2: patching to build with gcc@13
* Update var/spack/repos/builtin/packages/bedtools2/package.py
Yep, sure. Makes sense.
Co-authored-by: Alec Scott <alec@bcs.sh>
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
* ensmallen: new package
ensmallen is a high-quality C++ library for non-linear numerical optimization.
* r-rcppensmallen: new package
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Improve lib/spack/spack/test/cmd/compiler.py
* Use "tmp_path" in the "mock_executable" fixture
* Return a pathlib.Path from mock_executable
* Fix mock_executable fixture on Windows
"mock_gcc" was very similar to mock_executable, so use the latter to reduce code duplication
* Remove wrong compiler cache, fix compiler removal
fixes#37996
_CACHE_CONFIG_FILES was both unneeded and wrong, if called
subsequently with different scopes.
Here we remove that cache, and we fix an issue with compiler
removal triggered by having the same compiler spec in multiple
scopes.
* e4s oneapi ci: use official intel oneapi-derived runner image
* update oneapi image
* tau builds ok, but only with libdrm - comment out for now, follow up with pr later
* Guard for define in netcdf 4.9.0 and later.
This code is already available in ParaView 5.11.0 so no patching
needed there.
* Add latest needed version (even if not in spack).
---------
Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
* llvm: add new versions and set default for libomptarget according to os
modified: var/spack/repos/builtin/packages/llvm/package.py
* Incorporate reviewer suggestions
Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
---------
Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
* e4s cray ci stack
* e4s ci: add cray
* add zen4 tag
* WIP: new defintions just for cray
* updates
* remove ci signing job overrride, not necessary
* echo $PATH and show modules loaded
* add mirror
* add external def for cray-libsci
* comment out quantum-espresso
* use /etc/protected-runner as key path
* cray ci stack: do not remove tags: [spack, public]
* make cray stack composable
* generate job should run on public tagged runner, override default config:install_tree:root
* CI: Use relative path in default script
* CI: Use relative includes paths for shell runners
* Use concrete_env_dir for relpath
* ml-darwin-aarch64-mps: jax has bazel codesign issue
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
#37592 updated cached cmake packages to set CMAKE_CUDA_ARCHITECTURES.
The condition `if archs != "none"` lead to `CMAKE_CUDA_ARCHITECTURES=none`
when cuda_arch=none (incorrect check on the value of a multi-valued
variant), i.e. CMAKE_CUDA_ARCHITECTURES is always set. This PR udpates
the condition to if archs[0] != "none" to ensure CMAKE_CUDA_ARCHITECTURES
is only set if cuda_arch is not none (which seems to be the pattern used
in other packages).
This does the same for HIP (although in general ROCmPackage disallows
amdgpu_target=none when +rocm).
* fastqc: add 0.12.1
* fastqc: add 0.12.1
* Update var/spack/repos/builtin/packages/fastqc/package.py
Yeah, had considered doing the same, I'd just opted to maintain the status quo. All good.
Co-authored-by: Alec Scott <alec@bcs.sh>
* Update package.py
Style fiddles to make the bot contented.
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
* py-htseq: add 0.12.3, switching over to new GitHub repo
* py-htseq: add 0.12.3, switching over to new GitHub repo
Style fixes
* py-htseq: add 2.0.3, switch to PyPI
* py-htseq: add 2.0.3, switch to PyPI
* Update package.py
* Update var/spack/repos/builtin/packages/py-htseq/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Removing SWIG
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* llvm: replace +omp_as_runtime with omp=runtime
* llvm: fetch 'libomp-libflags-as-list.patch' from upstream repo
* llvm: replace 'llvm14-hwloc-ompd.patch' with the official fix from upstream repo
* llvm: fix-up for the black reformatting
* llvm: fetch 'constexpr_longdouble.patch' from upstream repo
* llvm: optionally build libcxx as a runtime
* llvm: fetch 'llvm5-sanitizer-ustat.patch' from upstream repo
* llvm: update 'sanitizer-ipc_perm_mode.patch'
* llvm: refactor compiler conflicts when libcxx=project
* llvm: fetch 'llvm_python_path.patch' from upstream repo
* llvm: update comments and condition for 'xray_buffer_queue-cstddef.patch'
* llvm: optionally build compiler-rt as a runtime
* llvm: fetch 'lldb_external_ncurses-10.patch' from upstream repo
* llvm: fetch 'llvm_py37.patch' from upstream repo
* llvm: rename variant 'internal_unwind' to 'libunwind'
* llvm: optionally build libunwind as a runtime
* llvm: extend the list of maintainers
* llvm: allow for explicit '~clang~flang~libomptarget~lldb~omp_debug~z3'
* llvm: fetch 'llvm5-lld-ELF-Symbols.patch' from FreeBSD port repo
* llvm: fetch most of 'missing-includes.patch' from upstream repo and reuse 'llvm-gcc11.patch'
* llvm: regroup patches for missing include directives and drop compiler constraints for them
* llvm: fetch 'llvm-gcc11.patch' from upstream repo
* llvm: fetch 'no_cyclades.patch' from upstream repo
* llvm: update comments and condition for 'no_cyclades9.patch'
* llvm: rename variant 'omp' to 'openmp'
* llvm: constrain and rename variant 'omp_tsan' to 'libomp_tsan'
* llvm: rename variant 'omp_debug' to 'libomptarget_debug'
* llvm: do not apply same patch twice
* llvm: constrain and document the '*-thread.patch' patches
* llvm: document the '~lld+libomptarget' conflict
* llvm: update comments for the 'D133513.diff' patch
* py-future: add 0.18.3
* Update var/spack/repos/builtin/packages/py-future/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding libpsm3 package
* Make changes suggested by flake8
* Make one more flake8-suggested change, blank line after 'import os'
* Change to standard header to pass flake8 tests
* Update doc string, remove unnecessary comments
* Reviewer-recommende changes
* Alphabetize variants
* Use helper functions
* Change quotes to pass spack style check
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
- Add pkgconfig dependency from 1.23.0 onward.
- Add conflict of old versions with new gcc due to missing includes.
- Deprecate uneven minor versions because they are not regarded as stable.
- Add maintainer
* [xsdk-examples] Initial commit for v0.4.0
* [xsdk-examples] v0.4.0 depends on xsdk@0.8.0
* add in missing xsdk dependencies
* [xsdk-examples] remove repeated 'depends_on' directive
* [xsdk-examples] simplify and extend a bit the package
[mfem] process more optional dependencies of HiOp
[strumpack, superlu-dist] add a workaround for an issue on Mac
* [mfem] fix the handling of the hiop dependency
* [@spackbot] updating style on behalf of v-dobrev
* [xsdk-examples] enable 'heffte' and 'tasmanian' if enabled in 'xsdk'
* [xsdk-examples] Add PUMI dependency
* [xsdk-examples] Add preCICE dependency
* [xsdk-examples] add +rocm
* heffte: add in a backport fix for building xsdk-examples with cuda
* [xsdk] Remove the explicit requirement for deal.II to be built +hdf5
* ENABLE_ROCM -> ENABLE_HIP
* [hiop] Workaround for CMake not finding Cray's BLAS (libsci)
[xsdk-examples] Set CUDA/HIP architectures; sync cuda/rocm variants with xsdk
* [@spackbot] updating style on behalf of v-dobrev
* [exago] Workaround for CMake not finding Cray's LAPACK/BLAS, libsci
[mfem] Tweaks for running tests under Flux and PBS
* [slate] Pass CUDA/HIP architectures to CMake
* [heffte] For newer CMake versions, set CMAKE_CUDA_ARCHITECTURES
* [hypre] Patch v2.26.0 to fix sequential compilation in 'src/seq_mv'
* [xsdk-examples] Some tweaks in dependencies and compilers used
* [xsdk] Make the 'trilinos' variant sticky
[xsdk-examples] Tweak dependencies
* [slate] Fix copy-paste error
* [xsdk-examples] Workaround for CMakePackage not having the legacy
property 'build_directory'
* [xsdk-examples] Replace the testing branch used temporarily for v0.4.0 with
the official release
---------
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
* Add CMake options for building with CUDA/HIP support to
CachedCMakePackages (intended to reduce duplication across packages
building with +hip/+cuda and using CachedCMakePackage)
* Define generic variables like CMAKE_PREFIX_PATH for
CachedCMakePackages (so that a user may invoke "cmake" themselves
without needing to setthem on the command line).
* Make `lbann` a CachedCMakePackage.
Co-authored-by: Chris White <white238@llnl.gov>
fa7719a changed syntax for specifying exact versions, which are
required for some compiler specs (including those read as part
of parsing a Cray manifest). This fixes that and also makes a
couple other improvements to manifest parsing.
* Instantiate compiler specs with exact versions (fixes#37893)
* fix slingshot network detection (CPE 22.10+ has libcxi.so
in /usr/lib64)
* "spack external find": add arg to ignore default dir for cray
manifests
This will build flux-security separately to have a flux-imp
that can be defined in a flux broker.toml. Note that the user
that wants a multi-user setup is recommended to create a view,
and then a system/broker.toml in flux config directory that
points to it.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Sphinx is used to build Open MPI manpages, etc. as part of the make dist
process to create release tarballs. There should be no need/use to do
this within Spack. Also some sites have older Sphinx installs which
aren't compatible with the needs of the Open MPI documentation.
For example, attempts to install openmpi@main fail at NERSC owing to
such a situation.
Since Spack normally is used to build from release tarballs, in which
the docs have already been installed, this should present no issues.
This configuration option will be ignored for older than 5.0.0 Open MPI releases.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
This option is needed for DFT FE - or more accurately the check needs to
be checked off for a number of platforms or else the code doesn't work.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
Change default naming scheme for tcl modules for a more user-friendly
experience.
Change from flat projection to "per software name" projection.
Flat naming scheme restrains module selection capabilities. The
`{name}/{version}...` scheme make possible to use user-friendly
mechanisms:
* implicit defaults (`module load git`)
* extended default (`module load git/2`)
* advanced version specifiers (`module load git@2:`)
* py-cutadapt: add 4.4, 4.3, 4.2 versions
* Update var/spack/repos/builtin/packages/py-cutadapt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cutadapt/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update PennyLane ecosystem for 0.30 release
* Update package dep versions
* Fix formatting
* Update dep versions
* Remove PL hard pin and rely on PLQ to define version
* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py
Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>
* Convert pybind11 from build to link dep, and PL ver limit
---------
Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>
Note the win-sdk package is not installable and reports an error
which instructs the user how to add it. Without this fix, a
(more confusing) error occurs before this message can be generated.
"spack build-env" was not generating proper environment variable
definitions on Windows; this commit updates the generated commands
to succeed with batch/PowerShell.
Add a nightly job to attempt building all Paraview dependencies and
upload the results to cdash. This check doesn't affect the reported
build/test status of Spack. We are using this to monitor the state of
Windows support while working on more-robust checks (eventually the
Windows build will have to succeed to merge PRs to Spack).
* Dyninst: add standalone test
* Add docstring with description
* Don't use join_path for builtin path objects
* Whitespace
* Update format of docstring
Some requirements for @main version of environment-modules were missing:
* python (to build ChangeLog documentation file)
* py-sphinx@1.0: (to build man-pages, etc)
Also adding gzip, which is now required to build ChangeLog.gz (which is
now shipped instead of ChangeLog).
Other versions are not requiring these tools (as documentation is
pre-built in dist tarball).
* [devito] Move to version 4.8.1
* Fix: Adding patch file
* Update var/spack/repos/builtin/packages/py-devito/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-devito/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Addressing @adamjstewart comments
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add macOS ML CI stacks
* torchmeta is no longer maintained and requires ancient PyTorch
* Add MXNet
* update darwin aarch64 stacks
* add darwin-aarch64 scoped config.yaml
* remove unnecessary cleanup job
* fix specifications
* fix labels
* fix labels
* fix indent on tags specification
* no tags for trigger jobs
* try overriding tags in stack spack.yaml
* do not use CI_STACK_CONFIG_SCOPES
* incorporate config:install_tree:root: overrides and compiler defs
* copy relevant ci-scoped config settings directly into stack spack.yaml
* remove build-job-remove
* spack ci generate: add debug flag
* include cdash config directly in stack spack.yaml
* customize build-job script section to avoid absolute paths
* add any-job specification
* tags: use aarch64-macos instead of aarch64
* generate tags: use aarch64-macos instead of aarch64
* do not add morepadding
* use shared mirror; comment out known failures
* remove any-job
* nproc || true
* comment out specs failing due to bazel from cache codesign issue
---------
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
* py-babel: add 2.12.1
* Update var/spack/repos/builtin/packages/py-babel/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
When attempting to build paraview@5.10.1 using a recent Intel
compiler (Classic or OneAPI) or the IBM XL compiler, the build
fails if the version of protobuf used is > 3.18
* [pcluster pipeline] Use local buildcache instead of upstream spack
Spack currently does not relocate compiler references from upstream spack
installations. When using a buildcache we don't need an upstream spack.
* gcc needs to be installed via postinstall to get correct deps
* quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1
* Force gitlab to pull the new container
* Revert "Force gitlab to pull the new container"
This reverts commit 3af5f4cd88.
Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml
* Gitlab keeps picking up wrong container. Renaming
* Update containers once more after failed build
* add version 1.48.0 to bioconductor package r-a4
* add version 1.48.0 to bioconductor package r-a4base
* add version 1.48.0 to bioconductor package r-a4classif
* add version 1.48.0 to bioconductor package r-a4core
* add version 1.48.0 to bioconductor package r-a4preproc
* add version 1.48.0 to bioconductor package r-a4reporting
* add version 1.54.0 to bioconductor package r-absseq
* add version 1.30.0 to bioconductor package r-acde
* add version 1.78.0 to bioconductor package r-acgh
* add version 2.56.0 to bioconductor package r-acme
* add version 1.70.0 to bioconductor package r-adsplit
* add version 1.72.0 to bioconductor package r-affxparser
* add version 1.78.0 to bioconductor package r-affy
* add version 1.76.0 to bioconductor package r-affycomp
* add version 1.58.0 to bioconductor package r-affycontam
* add version 1.72.0 to bioconductor package r-affycoretools
* add version 1.48.0 to bioconductor package r-affydata
* add version 1.52.0 to bioconductor package r-affyilm
* add version 1.70.0 to bioconductor package r-affyio
* add version 1.76.0 to bioconductor package r-affyplm
* add version 1.46.0 to bioconductor package r-affyrnadegradation
* add version 1.48.0 to bioconductor package r-agdex
* add version 3.32.0 to bioconductor package r-agilp
* add version 2.50.0 to bioconductor package r-agimicrorna
* add version 1.32.0 to bioconductor package r-aims
* add version 1.32.0 to bioconductor package r-aldex2
* add version 1.38.0 to bioconductor package r-allelicimbalance
* add version 1.26.0 to bioconductor package r-alpine
* add version 2.62.0 to bioconductor package r-altcdfenvs
* add version 2.24.0 to bioconductor package r-anaquin
* add version 1.28.0 to bioconductor package r-aneufinder
* add version 1.28.0 to bioconductor package r-aneufinderdata
* add version 1.72.0 to bioconductor package r-annaffy
* add version 1.78.0 to bioconductor package r-annotate
* add version 1.62.0 to bioconductor package r-annotationdbi
* add version 1.24.0 to bioconductor package r-annotationfilter
* add version 1.42.0 to bioconductor package r-annotationforge
* add version 3.8.0 to bioconductor package r-annotationhub
* add version 3.30.0 to bioconductor package r-aroma-light
* add version 1.32.0 to bioconductor package r-bamsignals
* add version 2.16.0 to bioconductor package r-beachmat
* add version 2.60.0 to bioconductor package r-biobase
* add version 2.8.0 to bioconductor package r-biocfilecache
* add version 0.46.0 to bioconductor package r-biocgeneric
* add version 1.10.0 to bioconductor package r-biocio
* add version 1.18.0 to bioconductor package r-biocneighbors
* add version 1.34.0 to bioconductor package r-biocparallel
* add version 1.16.0 to bioconductor package r-biocsingular
* add version 2.28.0 to bioconductor package r-biocstyle
* add version 3.17.1 to bioconductor package r-biocversion
* add version 2.56.0 to bioconductor package r-biomart
* add version 1.28.0 to bioconductor package r-biomformat
* add version 2.68.0 to bioconductor package r-biostrings
* add version 1.48.0 to bioconductor package r-biovizbase
* add version 1.10.0 to bioconductor package r-bluster
* add version 1.68.0 to bioconductor package r-bsgenome
* add version 1.36.0 to bioconductor package r-bsseq
* add version 1.42.0 to bioconductor package r-bumphunter
* add version 2.66.0 to bioconductor package r-category
* add version 2.30.0 to bioconductor package r-champ
* add version 2.32.0 to bioconductor package r-champdata
* add version 1.50.0 to bioconductor package r-chipseq
* add version 4.8.0 to bioconductor package r-clusterprofiler
* add version 1.36.0 to bioconductor package r-cner
* add version 1.32.0 to bioconductor package r-codex
* add version 2.16.0 to bioconductor package r-complexheatmap
* add version 1.74.0 to bioconductor package r-ctc
* add version 2.28.0 to bioconductor package r-decipher
* add version 0.26.0 to bioconductor package r-delayedarray
* add version 1.22.0 to bioconductor package r-delayedmatrixstats
* add version 1.40.0 to bioconductor package r-deseq2
* add version 1.46.0 to bioconductor package r-dexseq
* add version 1.42.0 to bioconductor package r-dirichletmultinomial
* add version 2.14.0 to bioconductor package r-dmrcate
* add version 1.74.0 to bioconductor package r-dnacopy
* add version 3.26.0 to bioconductor package r-dose
* add version 2.48.0 to bioconductor package r-dss
* add version 3.42.0 to bioconductor package r-edger
* add version 1.20.0 to bioconductor package r-enrichplot
* add version 2.24.0 to bioconductor package r-ensembldb
* add version 1.46.0 to bioconductor package r-exomecopy
* add version 2.8.0 to bioconductor package r-experimenthub
* add version 1.26.0 to bioconductor package r-fgsea
* add version 2.72.0 to bioconductor package r-gcrma
* add version 1.36.0 to bioconductor package r-gdsfmt
* add version 1.82.0 to bioconductor package r-genefilter
* add version 1.36.0 to bioconductor package r-genelendatabase
* add version 1.72.0 to bioconductor package r-genemeta
* add version 1.78.0 to bioconductor package r-geneplotter
* add version 1.22.0 to bioconductor package r-genie3
* add version 1.36.0 to bioconductor package r-genomeinfodb
* update r-genomeinfodbdata
* add version 1.36.0 to bioconductor package r-genomicalignments
* add version 1.52.0 to bioconductor package r-genomicfeatures
* add version 1.52.0 to bioconductor package r-genomicranges
* add version 2.68.0 to bioconductor package r-geoquery
* add version 1.48.0 to bioconductor package r-ggbio
* add version 3.8.0 to bioconductor package r-ggtree
* add version 2.10.0 to bioconductor package r-glimma
* add version 1.12.0 to bioconductor package r-glmgampoi
* add version 5.54.0 to bioconductor package r-globaltest
* update r-go-db
* add version 1.20.0 to bioconductor package r-gofuncr
* add version 2.26.0 to bioconductor package r-gosemsim
* add version 1.52.0 to bioconductor package r-goseq
* add version 2.66.0 to bioconductor package r-gostats
* add version 1.78.0 to bioconductor package r-graph
* add version 1.62.0 to bioconductor package r-gseabase
* add version 1.32.0 to bioconductor package r-gtrellis
* add version 1.44.0 to bioconductor package r-gviz
* add version 1.28.0 to bioconductor package r-hdf5array
* add version 1.72.0 to bioconductor package r-hypergraph
* add version 1.36.0 to bioconductor package r-illumina450probevariants-db
* add version 0.42.0 to bioconductor package r-illuminaio
* add version 1.74.0 to bioconductor package r-impute
* add version 1.38.0 to bioconductor package r-interactivedisplaybase
* add version 2.34.0 to bioconductor package r-iranges
* add version 1.60.0 to bioconductor package r-kegggraph
* add version 1.40.0 to bioconductor package r-keggrest
* add version 3.56.0 to bioconductor package r-limma
* add version 2.52.0 to bioconductor package r-lumi
* add version 1.76.0 to bioconductor package r-makecdfenv
* add version 1.78.0 to bioconductor package r-marray
* add version 1.12.0 to bioconductor package r-matrixgenerics
* add version 1.8.0 to bioconductor package r-metapod
* add version 2.46.0 to bioconductor package r-methylumi
* add version 1.46.0 to bioconductor package r-minfi
* add version 1.34.0 to bioconductor package r-missmethyl
* add version 1.80.0 to bioconductor package r-mlinterfaces
* add version 1.12.0 to bioconductor package r-mscoreutils
* add version 2.26.0 to bioconductor package r-msnbase
* add version 2.56.0 to bioconductor package r-multtest
* add version 1.38.0 to bioconductor package r-mzid
* add version 2.34.0 to bioconductor package r-mzr
* add version 1.62.0 to bioconductor package r-oligoclasses
* update r-org-hs-eg-db
* add version 1.42.0 to bioconductor package r-organismdbi
* add version 1.40.0 to bioconductor package r-pathview
* add version 1.92.0 to bioconductor package r-pcamethods
* update r-pfam-db
* add version 1.44.0 to bioconductor package r-phyloseq
* add version 1.62.0 to bioconductor package r-preprocesscore
* add version 1.32.0 to bioconductor package r-protgenerics
* add version 1.34.0 to bioconductor package r-quantro
* add version 2.32.0 to bioconductor package r-qvalue
* add version 1.76.0 to bioconductor package r-rbgl
* add version 2.40.0 to bioconductor package r-reportingtools
* add version 2.44.0 to bioconductor package r-rgraphviz
* add version 2.44.0 to bioconductor package r-rhdf5
* add version 1.12.0 to bioconductor package r-rhdf5filters
* add version 1.22.0 to bioconductor package r-rhdf5lib
* add version 1.76.0 to bioconductor package r-roc
* add version 1.28.0 to bioconductor package r-rots
* add version 2.16.0 to bioconductor package r-rsamtools
* add version 1.60.0 to bioconductor package r-rtracklayer
* add version 0.38.0 to bioconductor package r-s4vectors
* add version 1.8.0 to bioconductor package r-scaledmatrix
* add version 1.28.0 to bioconductor package r-scater
* add version 1.14.0 to bioconductor package r-scdblfinder
* add version 1.28.0 to bioconductor package r-scran
* add version 1.10.0 to bioconductor package r-scuttle
* add version 1.66.0 to bioconductor package r-seqlogo
* add version 1.58.0 to bioconductor package r-shortread
* add version 1.74.0 to bioconductor package r-siggenes
* add version 1.22.0 to bioconductor package r-singlecellexperiment
* add version 1.34.0 to bioconductor package r-snprelate
* add version 1.50.0 to bioconductor package r-snpstats
* add version 2.36.0 to bioconductor package r-somaticsignatures
* add version 1.12.0 to bioconductor package r-sparsematrixstats
* add version 1.40.0 to bioconductor package r-spem
* add version 1.38.0 to bioconductor package r-sseq
* add version 1.30.0 to bioconductor package r-summarizedexperiment
* add version 3.48.0 to bioconductor package r-sva
* add version 1.38.0 to bioconductor package r-tfbstools
* add version 1.22.0 to bioconductor package r-tmixclust
* add version 2.52.0 to bioconductor package r-topgo
* add version 1.24.0 to bioconductor package r-treeio
* add version 1.28.0 to bioconductor package r-tximport
* add version 1.28.0 to bioconductor package r-tximportdata
* add version 1.46.0 to bioconductor package r-variantannotation
* add version 3.68.0 to bioconductor package r-vsn
* add version 2.6.0 to bioconductor package r-watermelon
* add version 2.46.0 to bioconductor package r-xde
* add version 1.58.0 to bioconductor package r-xmapbridge
* add version 0.40.0 to bioconductor package r-xvector
* add version 1.26.0 to bioconductor package r-yapsa
* add version 1.26.0 to bioconductor package r-yarn
* add version 1.46.0 to bioconductor package r-zlibbioc
* Revert "add version 1.82.0 to bioconductor package r-genefilter"
This reverts commit 1702071c6d.
* Revert "add version 0.38.0 to bioconductor package r-s4vectors"
This reverts commit 58a7df2387.
* add version 0.38.0 to bioconductor package r-s4vectors
* Revert "add version 1.28.0 to bioconductor package r-aneufinder"
This reverts commit 0a1f59de6c.
* add version 1.28.0 to bioconductor package r-aneufinder
* Revert "add version 2.16.0 to bioconductor package r-beachmat"
This reverts commit cd49fb8e4c.
* add version 2.16.0 to bioconductor package r-beachmat
* Revert "add version 4.8.0 to bioconductor package r-clusterprofiler"
This reverts commit 6e9a951cbe.
* add version 4.8.0 to bioconductor package r-clusterprofiler
* Fix syntax error
* r-genefilter: add version 1.82.0
* new package: r-basilisk-utils
* new package: r-basilisk
* new package: r-densvis
* new package: r-dir-expiry
* r-affyplm: add zlib dependency
* r-cner: add zlib dependency
* r-mzr: add zlib dependency
* r-rhdf5filters: add zstd dependency
* r-shortread: add zlib dependency
* r-snpstats: add zlib dependency
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
macOS doesn't have `getrandom`, and 1.10.2 fails to compile because of this.
There's an upstream fix at https://dev.gnupg.org/T6442 that will be in the next
`libgcrypt` release, but the patch is available now.
* py-argcomplete: add 3.0.8
* Update var/spack/repos/builtin/packages/py-argcomplete/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of manuelakuhn
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* aml: v0.2.1
* add version 0.2.1
* fix hip variant bug
* [fix] pkgconf required for all builds
On top of needing pkgconf for autoreconf builds, the release configure
scripts needs pkgconf do detect dependencies if any of the hwloc, ze, or
opencl variants are active.
* Remove deprecation for v0.2.0 based on PR advise.
* intel-xed: add version 2023.04.16
1. add version 2023.04.16
2. adjust the mbuild resource to better match the xed version at the time
3. replace three conflicts() with one new requires() for x86_64 target
4. add patch for libxed-ild for some new avx512 instructions
* [@spackbot] updating style on behalf of mwkrentel
* Fix the build for 2023.04.16. XED requires its source directory to be exactly 'xed', so add a symlink.
5. move the mbuild resource up one level, xed wants it to be in the same directory as the xed source dir
6. deprecate 10.2019.03
* semantic style fix: add OSError to except
* [@spackbot] updating style on behalf of mwkrentel
---------
Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
* py-jarvis-util: add a new package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update py-nltk
* [@spackbot] updating style on behalf of meyersbs
* Update var/spack/repos/builtin/packages/py-nltk/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add version 1.28.3 to r-hexbin
* add version 5.0-1 to r-hmisc
* add version 0.5.5 to r-htmltools
* add version 1.6.2 to r-htmlwidgets
* add version 1.4.2 to r-igraph
* add version 0.42.19 to r-imager
* add version 1.0-5 to r-inum
* add version 0.9-14 to r-ipred
* add version 1.3.2 to r-irkernel
* add version 2.2.0 to r-janitor
* add version 0.1-10 to r-jpeg
* add version 1.2.2 to r-jsonify
* add version 0.9-32 to r-kernlab
* add version 1.7-2 to r-klar
* add version 1.42 to r-knitr
* add version 1.14.0 to r-ks
* add version 2.11.0 to r-labelled
* add version 1.7.2.1 to r-lava
* add version 0.6-15 to r-lavaan
* add version 2.1.2 to r-leaflet
* add version 2.9-0 to r-lfe
* add version 1.1.6 to r-lhs
* add version 1.1-33 to r-lme4
* add version 1.5-9.7 to r-locfit
* add version 0.4.3 to r-log4r
* add version 5.6.18 to r-lpsolve
* add version 0.2-11 to r-lwgeom
* add version 2.7.4 to r-magick
* add version 1.22.1 to r-maldiquant
* add version 1.2.11 to r-mapproj
* add version 1.6 to r-markdown
* add version 7.3-59 to r-mass
* add version 1.5-4 to r-matrix
* add version 0.63.0 to r-matrixstats
* add version 4.2-3 to r-memuse
* add version 4.0-0 to r-metafor
* add version 1.8-42 to r-mgcv
* add version 3.15.0 to r-mice
* add version 0.4-5 to r-mitml
* add version 2.0.0 to r-mixtools
* add version 0.1.11 to r-modelr
* add version 1.4-23 to r-multcomp
* add version 0.1-9 to r-multcompview
* add version 0.1-13 to r-mutoss
* add version 1.18.1 to r-network
* add version 3.3.4 to r-nleqslv
* add version 3.1-162 to r-nlme
* add version 0.26 to r-nmf
* add version 0.60-17 to r-np
* add version 4.2.5.2 to r-openxlsx
* add version 2022.11-16 to r-ordinal
* add version 0.6.0.8 to r-osqp
* add version 0.9.1 to r-packrat
* add version 1.35.0 to r-parallelly
* add version 1.3-13 to r-party
* add version 1.2-20 to r-partykit
* add version 1.7-0 to r-pbapply
* add version 0.3-9 to r-pbdzmq
* add version 1.2 to r-pegas
* add version 1.5-1 to r-phytools
* add version 1.9.0 to r-pillar
* add version 1.4.0 to r-pkgbuild
* add version 2.1.0 to r-pkgcache
* add version 0.5.0 to r-pkgdepends
* add version 2.0.7 to r-pkgdown
* add version 1.3.2 to r-pkgload
* add version 0.1-8 to r-png
* add version 1.1.22 to r-polspline
* add version 1.0.1 to r-pool
* add version 1.4.1 to r-posterior
* add version 3.8.1 to r-processx
* add version 2023.03.31 to r-prodlim
* add version 1.0-12 to r-proj4
* add version 2.5.0 to r-projpred
* add version 0.1.6 to r-pryr
* add version 1.7.5 to r-ps
* add version 1.0.1 to r-purrr
* add version 1.3.2 to r-qqconf
* add version 0.25.5 to r-qs
* add version 1.60 to r-qtl
* add version 0.4.22 to r-quantmod
* add version 5.95 to r-quantreg
* add version 0.7.8 to r-questionr
* add version 1.2.5 to r-ragg
* add version 0.15.1 to r-ranger
* add version 3.6-20 to r-raster
* add version 2.2.13 to r-rbibutils
* add version 1.0.10 to r-rcpp
* add version 0.12.2.0.0 to r-rcpparmadillo
* add version 0.1.7 to r-rcppde
* add version 0.3.13 to r-rcppgsl
* add version 1.98-1.12 to r-rcurl
* add version 1.2-1 to r-rda
* add version 2.1.4 to r-readr
* add version 1.4.2 to r-readxl
* add version 1.0.6 to r-recipes
* add version 1.1.6 to r-repr
* add version 1.2.16 to r-reproducible
* add version 0.3.0 to r-require
* add version 1.28 to r-reticulate
* add version 2.0.7 to r-rfast
* add version 1.6-6 to r-rgdal
* add version 0.6-2 to r-rgeos
* add version 1.1.3 to r-rgl
* add version 0.2.18 to r-rinside
* add version 4-14 to r-rjags
* add version 1.3-1.8 to r-rjsonio
* add version 2.21 to r-rmarkdown
* add version 0.9-2 to r-rmpfr
* add version 0.7-1 to r-rmpi
* add version 6.6-0 to r-rms
* add version 0.10.25 to r-rmysql
* add version 0.8.7 to r-rncl
* add version 2.4.11 to r-rnexml
* add version 0.95-1 to r-robustbase
* add version 1.3-20 to r-rodbc
* add version 7.2.3 to r-roxygen2
* add version 1.4.5 to r-rpostgres
* add version 0.7-5 to r-rpostgresql
* add version 0.8.29 to r-rsconnect
* add version 0.4-15 to r-rsnns
* add version 2.3.1 to r-rsqlite
* add version 0.7.2 to r-rstatix
* add version 1.1.2 to r-s2
* add version 0.4.5 to r-sass
* add version 0.1.9 to r-scatterpie
* add version 0.3-43 to r-scatterplot3d
* add version 3.2.4 to r-scs
* add version 1.6-4 to r-segmented
* add version 4.2-30 to r-seqinr
* add version 0.26 to r-servr
* add version 4.3.0 to r-seurat
* add version 1.0-12 to r-sf
* add version 0.4.2 to r-sfheaders
* add version 1.1-15 to r-sfsmisc
* add version 1.7.4 to r-shiny
* add version 1.9.0 to r-signac
* add version 1.6.0.3 to r-smoof
* add version 0.1.7-1 to r-sourcetools
* add version 1.6-0 to r-sp
* add version 1.3-0 to r-spacetime
* add version 7.3-16 to r-spatial
* add version 2.0-0 to r-spatialeco
* add version 1.2-8 to r-spatialreg
* add version 3.0-5 to r-spatstat
* add version 3.0-1 to r-spatstat-data
* add version 3.1-0 to r-spatstat-explore
* add version 3.1-0 to r-spatstat-geom
* add version 3.1-0 to r-spatstat-linnet
* add version 3.1-4 to r-spatstat-random
* add version 3.0-1 to r-spatstat-sparse
* add version 3.0-2 to r-spatstat-utils
* add version 2.2.2 to r-spdata
* add version 1.2-8 to r-spdep
* add version 0.6-1 to r-stars
* add version 1.5.0 to r-statmod
* add version 4.8.0 to r-statnet-common
* add version 1.7.12 to r-stringi
* add version 1.5.0 to r-stringr
* add version 1.9.1 to r-styler
* add version 3.5-5 to r-survival
* add version 1.5-4 to r-tclust
* add version 1.7-29 to r-terra
* add version 3.1.7 to r-testthat
* add version 1.1-2 to r-th-data
* add version 1.2 to r-tictoc
* add version 1.3.2 to r-tidycensus
* add version 1.2.3 to r-tidygraph
* add version 1.3.0 to r-tidyr
* add version 2.0.0 to r-tidyverse
* add version 0.2.0 to r-timechange
* add version 0.45 to r-tinytex
* add version 0.4.1 to r-triebeard
* add version 1.0-9 to r-truncnorm
* add version 0.10-53 to r-tseries
* add version 0.8-1 to r-units
* add version 4.3.0 to r-v8
* add version 1.4-11 to r-vcd
* add version 1.14.0 to r-vcfr
* add version 0.6.2 to r-vctrs
* add version 1.1-8 to r-vgam
* add version 0.4.0 to r-vioplot
* add version 1.6.1 to r-vroom
* add version 1.72-1 to r-wgcna
* add version 0.4.1 to r-whisker
* add version 0.7.2 to r-wk
* add version 0.39 to r-xfun
* add version 1.7.5.1 to r-xgboost
* add version 1.0.7 to r-xlconnect
* add version 3.99-0.14 to r-xml
* add version 0.13.1 to r-xts
* add version 2.3.7 to r-yaml
* add version 2.3.0 to r-zip
* add version 1.8-12 to r-zoo
* r-bigmem: dependency on uuid
* r-bio3d: dependency on zlib
* r-devtools: dependency cleanup
* r-dose: dependency cleanup
* r-dss: dependency cleanup
* r-enrichplot: dependency cleanup
* r-fgsea: dependency cleanup
* r-geor: dependency cleanup
* r-ggridges: dependency cleanup
* r-lobstr: dependency cleanup
* r-lubridate: dependency cleanup
* r-mnormt: dependency cleanup
* r-sctransform: version format correction
* r-seuratobject: dependency cleanup
* r-tidyselect: dependency cleanup
* r-tweenr: dependency cleanup
* r-uwot: dependency cleanup
* new package: r-clock
* new package: r-conflicted
* new package: r-diagram
* new package: r-doby
* new package: r-httr2
* new package: r-kableextra
* new package: r-mclogit
* new package: r-memisc
* new package: r-spatstat-model
* r-rmysql: use mariadb-client
* r-snpstats: add zlib dependency
* r-qs: add zstd dependency
* r-rcppcnpy: add zlib dependency
* black reformatting
* Revert "r-dose: dependency cleanup"
This reverts commit 4c8ae8f5615ee124fff01ce43eddd3bb5d06b9bc.
* Revert "r-dss: dependency cleanup"
This reverts commit a6c5c15c617a9a688fdcfe2b70c501c3520d4706.
* Revert "r-enrichplot: dependency cleanup"
This reverts commit 65e116c18a94d885bc1a0ae667c1ef07d1fe5231.
* Revert "r-fgsea: dependency cleanup"
This reverts commit ffe2cdcd1f73f69d66167b941970ede0281b56d7.
* r-rda: this package is back in CRAN
* r-sctransform: fix copyright
* r-seurat: fix copyright
* r-seuratobject: fix copyright
* Revert "add version 6.0-94 to r-caret"
This reverts commit 236260597de97a800bfc699aec1cd1d0e3d1ac60.
* add version 6.0-94 to r-caret
* Revert "add version 1.8.5 to r-emmeans"
This reverts commit 64a129beb0bd88d5c88fab564cade16c03b956ec.
* add version 1.8.5 to r-emmeans
* Revert "add version 5.0-1 to r-hmisc"
This reverts commit 517643f4fd8793747365dfcfc264b894d2f783bd.
* add version 5.0-1 to r-hmisc
* Revert "add version 1.42 to r-knitr"
This reverts commit 2a0d9a4c1f0ba173f7423fed59ba725bac902c37.
* add version 1.42 to r-knitr
* Revert "add version 1.6 to r-markdown"
This reverts commit 4b5565844b5704559b819d2e775fe8dec625af99.
* add version 1.6 to r-markdown
* Revert "add version 0.26 to r-nmf"
This reverts commit 4c44a788b17848f2cda67b32312a342c0261caec.
* add version 0.26 to r-nmf
* Revert "add version 2.3.1 to r-rsqlite"
This reverts commit 5722ee2297276e4db8beee461d39014b0b17e420.
* add version 2.3.1 to r-rsqlite
* Revert "add version 1.0-12 to r-sf"
This reverts commit ee1734fd62cc02ca7a9359a87ed734f190575f69.
* add version 1.0-12 to r-sf
* fix syntax error
* Add FNAL Spack team to maintainers
* New variants and configuration improvements
* Version dependent "no-systemd" patches.
* New variants `client_only`, and `davix`
* Better handling of `cxxstd` for different versions, including
improved patching and CMake options.
* Version-specific CMake requirements.
* Better version-specific handling of `openssl` dependency.
* `py-setuptools` required for `+python` build.
* Specific enable/disable of CMake options and use of
`-DFORCE_ENABLED=TRUE` to prevent unwanted/non-portable activation
of features.
* Better handling of `+python` configuration.
* New version 5.5.5
Add aws-plcuster[-aarch64] stacks. These stacks build packages defined in
https://github.com/spack/spack-configs/tree/main/AWS/parallelcluster
They use a custom container from https://github.com/spack/gitlab-runners which
includes necessary ParallelCluster software to link and build as well as an
upstream spack installation with current GCC and dependencies.
Intel and ARM software is installed and used during the build stage but removed
from the buildcache before the signing stage.
Files `configs/linux/{arch}/ci.yaml` select the necessary providers in order to
build for specific architectures (icelake, skylake, neoverse_{n,v}1).
Make it clear that copy-only pipelines are not supported while still
using the deprecated ci config format. Also ensure that the deprecated
stack does not fail on spack pipelines for tags.
* Fix reporting of packageless specs as having no tests
* Add test_test_output_multiple_specs with update to simple-standalone-test (and tests)
* Refactored test status summary; added more tests or checks
MSVC compiler logic was using string parsing to extract version
from compiler spec, which was fragile. This broke in #37572, so has
been fixed and made more robust by using attribute access.
* CI: Expand E4S ROCm stack to include missing DaV packages
Ascent: Fixup for VTK-m with Kokkos backend
* DaV SDK: Removed duplicated openmp variant for ascent
* Drop visit and add conflict for Kokkos
* E4S: Drop ascent from CUDA builds
Ensure that requirements `packages:*:require:@x` and preferences `packages:*:version:[x]`
fail concretization when no version defined in the package satisfies `x`. This always holds
except for git versions -- they are defined on the fly.
In the past, Spack did not allow two different versions of the
same package within a DAG. That led to difficulties with packages
that still required Python 2 while other packages had already
switched to Python 3.
The libxcb and xcb-proto packages did not have Python 3 support
for a time. To get around this issue, Spack maintainers disabled
their dependency on an internal (i.e., Spack-provided) Python
(see #4145),forcing these packages to look for a system-provided
Python (see #7646).
This has worked for us all right, but with the arrival of our most
recent platform we seem to be missing the critical xcbgen Python
module on the system. Since most software has largely moved on to
Python 3 now, let's re-enable internal Spack dependencies for the
libxcb and xcb-proto packages.
Two bugs came in from #37438
1. `unify: when_possible` was broken, because of an incorrect assertion. abstract/concrete
spec pairs were compared against the results that were in the process of being computed,
rather than against the previous results.
2. `unify: true` had an ordering bug that could mix the association between abstract and
concrete specs
- [x] 1 is resolved by creating a lookup from old concrete specs to old abstract specs,
and we use that to associate the "new" concrete specs that happen to be the old
ones with their abstract specs (since those are stripped out for concretization
- [x] 2 is resolved by combining the new and old abstract as lists instead of combining
them as sets. This is important because `set() | set()` does not make any ordering
promises, even though set ordering is otherwise guaranteed in `python@3.7:`
* Upgrading kosh to 3.0.
* Accidentally regressed the package, changing back.
* Updating py-hdbscan versions for kosh.
* Fixing bug in patch.
* Adding 3.0.1
* Removing 3.0.
* Updating package deps for hdbscan to match requirements.txt.
* Version reqs for 3.0.*, need newer numpy and networkx
* spack style
* Reordering to match setup.py, adding "type" to python depends.
* trilinos@develop fixes
* Update var/spack/repos/builtin/packages/trilinos/package.py
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
---------
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
Spack displays package code context when it shouldn't (e.g., on `FetchError`s)
and doesn't display it when it should (e.g., when errors occur in builder classes.
The line attribution can sometimes be off by one, as well.
- [x] Display package context when errors occur in a subclass of `PackageBase`
- [x] Display package context when errors occur in a subclass of `BaseBuilder`
- [x] Do not display package context when errors occur in `PackageBase`,
`BaseBuilder` or other core code that is not in a `package.py` file.
- [x] Fix off-by-one error for core code (don't subtract one from the line number *unless*
it's in an actual `package.py` file.
---------
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
We currently throw a nasty error if you try to reuse packages from some other namespace
(e.g., OLCF), but we should be able to reuse patched local versions of builtin packages.
Right now the only obstacle to that is that we try to look up virtual info for unknown
namespaces, and we can't get the package from the repo to do that. We *can* assume that
a package with a known namespace is similar, and that its virtual provider information
is reasonably accurate, so we now do that. This isn't 100% accurate, but neither is
relying on the package itself, as it may have gone out of date.
The real solution here is virtual edge information, but this is a stopgap until we have
that.
`spec_clauses()` attempts to look up package information for concrete specs in order to
determine which virtuals they may provide. This fails for renamed/deleted dependencies
of buildcaches and installed packages.
This will eventually be fixed by #35258, which adds virtual information on edges, but we
need a workaround to make older buildcaches usable.
- [x] make an exception for renamed packages and omit their virtual constraints
- [x] add a note that this will be solved by adding virtuals to edges
The concretizer can fail with `reuse:true` if a buildcache or installation contains a
package with a dependency that has been renamed or deleted in the main repo (e.g.,
`netcdf` was refactored to `netcdf-c`, `netcdf-fortran`, etc., but there are still
binary packages with dependencies called `netcdf`).
We should still be able to install things for which we are missing `package.py` files.
`Spec.inject_patches_variant()` was failing this requirement by attempting to look up
the package class for concrete specs. This isn't needed -- we can skip it.
- [x] swap two conditions in `Spec.inject_patches_variant()`
I will follow this up with a variant to flux-core to add flux-security, and then automation in the flux-framework/spack repository.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
The @= in `spack find` output adds a bit of noise. Remove it as we
did for `spack spec` and `spack concretize`.
This modifies display_specs so it actually covers other places we use that routine, as
well, e.g., `spack buildcache list`.
before:
```
-- linux-ubuntu20.04-aarch64 / gcc@=11.1.0 -----------------------
ofdlcpi libpressio@0.88.0
```
after:
```
-- linux-ubuntu20.04-aarch64 / gcc@11.1.0 -----------------------
ofdlcpi libpressio@0.88.0
```
If a user does not explicitly `--force` the concretization of an entire environment,
Spack will try to reuse the concrete specs that are already in the lockfile.
---------
Co-authored-by: becker33 <becker33@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* gitlab ci: release fixes and improvements
- use rules to reduce boilerplate in .gitlab-ci.yml
- support copy-only pipeline jobs
- make pipelines for release branches rebuild everything
- make pipelines for protected tags copy-only
* gitlab ci: remove url changes used in testing
* gitlab ci: tag mirrors need public key
Make sure that mirrors associated with release branches and tags
contain the public key needed to verify the signed binaries. This
also ensures that when stack-specific mirror contents are copied
to the root, the root mirror has the public key as well.
* review: be more specific about tags, curl flags
* Make the check in ci.yaml consistent with the .gitlab-ci.yml
---------
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
Currently, specs on buildcache mirrors must be referenced by their full description. This PR allows buildcache specs to be referenced by their hashes, rather than their full description.
### How it works
Hash resolution has been moved from `SpecParser` into `Spec`, and now includes the ability to execute a `BinaryCacheQuery` after checking the local store, but before concluding that the hash doesn't exist.
### Side-effects of Proposed Changes
Failures will take longer when nonexistent hashes are parsed, as mirrors will now be scanned.
### Other Changes
- `BinaryCacheIndex.update` has been modified to fail appropriately only when mirrors have been configured.
- Tests of hash failures have been updated to use `mutable_empty_config` so they don't needlessly search mirrors.
- Documentation has been clarified for `BinaryCacheQuery`, and more documentation has been added to the hash resolution functions added to `Spec`.
* py-rsatoolbox: add 0.0.5, 0.1.0 and 0.1.2 from wheels
* py-setuptools: add 63.4.3
* remove wheels and open up requirements
* Fix style
* Update var/spack/repos/builtin/packages/py-rsatoolbox/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-rsatoolbox/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Change version for python restriction
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-mne: add 1.4.0 and py-importlib-resources: add 5.12.0
* Fix style
* Update var/spack/repos/builtin/packages/py-mne/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This PR ensures that we'll get a comprehensible error message whenever an old
version of Spack tries to use a DB or a lockfile that is "too new".
* Fix error message when using a too new DB
* Add a unit-test to ensure we have a comprehensible error message
* py-pysam: adding version 0.21.0
* Update var/spack/repos/builtin/packages/py-pysam/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Add a section to the lock file to track the Spack version/commit that produced
an environment. This should (eventually) enhance reproducibility, though we
do not currently do anything with the information. It just adds to provenance
at the moment.
Changes include:
- [x] adding the version/commit to `spack.lock`
- [x] refactor `spack.main.get_version()
- [x] fix a couple of environment lock file-related typos
* add a virtual dependency name instead of complete package name
* add OneAPI components as providers of virtual packages
* Revert the default of tbb
---------
Co-authored-by: Nisarg Patel <nisarg.patel@lrz.de>
The flags --mirror-name / --mirror-url / --directory were deprecated in
favor of just passing a positional name, url or directory, and letting spack
figure it out.
---------
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Prior to this PR, the HOMEDRIVE environment variable was used to
detect what drive we are operating in. This variable is not available
for service account logins (like what is used for CI), so switch to
extracting the drive from PROGRAMFILES (which is more-widely defined).
On Windows, several commonly available system tools for decompression
are unreliable (gz/bz2/xz). This commit refactors `decompressor_for`
to call out to a Windows or Unix-specific method:
* The decompressor_for_nix method behaves the same as before and
generally treats the Python/system support options for decompression
as interchangeable (although avoids using Python's built-in tar
support since that has had issues with permissions).
* The decompressor_for_win method can only use Python support for
gz/bz2/xz, although for a tar.gz it does use system support for
untar (after the decompression step). .zip uses the system tar
utility, and .Z depends on external support (i.e. that the user
has installed 7zip).
A naming scheme has been introduced for the various _decompression
methods:
* _system_gunzip means to use a system tool (and fail if it's not
available)
* _py_gunzip means to use Python's built-in support for decompressing
.gzip files (and fail if it's not available)
* _gunzip is a method that can do either
* fix(hdf5): h5pfc link failure
develop branch doesn't need linking any more.
See: acb186f6e5
* [@spackbot] updating style on behalf of hyoklee
---------
Co-authored-by: hyoklee <hyoklee@users.noreply.github.com>
This is a refactor of Spack's stand-alone test process to be more spack- and pytest-like.
It is more spack-like in that test parts are no longer "hidden" in a package's run_test()
method and pytest-like in that any package method whose name starts test_
(i.e., a "test" method) is a test part. We also support the ability to embed test parts in a
test method when that makes sense.
Test methods are now implicit test parts. The docstring is the purpose for the test part.
The name of the method is the name of the test part. The working directory is the active
spec's test stage directory. You can embed test parts using the test_part context manager.
Functionality added by this commit:
* Adds support for multiple test_* stand-alone package test methods, each of which is
an implicit test_part for execution and reporting purposes;
* Deprecates package use of run_test();
* Exposes some functionality from run_test() as optional helper methods;
* Adds a SkipTest exception that can be used to flag stand-alone tests as being skipped;
* Updates the packaging guide section on stand-alone tests to provide more examples;
* Restores the ability to run tests "inherited" from provided virtual packages;
* Prints the test log path (like we currently do for build log paths);
* Times and reports the post-install process (since it can include post-install tests);
* Corrects context-related error message to distinguish test recipes from build recipes.
* hip: get_paths for hipify-clang
* fix: need to actually use get_paths now to get hipify-clang path
* set hipify-clang path differentluy for external vs spack-installed case
* [@spackbot] updating style on behalf of eugeneswalker
fixes#22341
Using double quotes creates issues with shell variable substitutions,
in particular when the manifest has "definitions:" in it. Use single
quotes instead.
Add a "require" directive to packages, which functions exactly like
requirements specified in packages.yaml (uses the same fact-generation
logic); update both to allow making the requirement conditional.
* Packages may now use "require" to add constraints. This can be useful
for something like "require(%gcc)" (where before we had to add a
conflict for every compiler except gcc).
* Requirements (in packages.yaml or in a "require" directive) can be
conditional on a spec, e.g. "require(%gcc, when=@1.0.0)" (version
1.0.0 can only build with gcc).
* Requirements may include a message which clarifies why they are needed.
The concretizer assigns a high priority to errors which generate these
messages (in particular over errors for unsatisfied requirements that
do not produce messages, but also over a number of more-generic
errors).
## Version types, parsing and printing
- The version classes have changed: `VersionBase` is removed, there is now a
`ConcreteVersion` base class. `StandardVersion` and `GitVersion` both inherit
from this.
- The public api (`Version`, `VersionRange`, `ver`) has changed a bit:
1. `Version` produces either `StandardVersion` or `GitVersion` instances.
2. `VersionRange` produces a `ClosedOpenRange`, but this shouldn't affect the user.
3. `ver` produces any of `VersionList`, `ClosedOpenRange`, `StandardVersion`
or `GitVersion`.
- No unexpected type promotion, so that the following is no longer an identity:
`Version(x) != VersionRange(x, x)`.
- `VersionList.concrete` now returns a version if it contains only a single element
subtyping `ConcreteVersion` (i.e. `StandardVersion(...)` or `GitVersion(...)`)
- In version lists, the parser turns `@x` into `VersionRange(x, x)` instead
of `Version(x)`.
- The above also means that `ver("x")` produces a range, whereas
`ver("=x")` produces a `StandardVersion`. The `=` is part of _VersionList_
syntax.
- `VersionList.__str__` now outputs `=x.y.z` for specific version entries,
and `x.y.z` as a short-hand for ranges `x.y.z:x.y.z`.
- `Spec.format` no longer aliases `{version}` to `{versions}`, but pulls the
concrete version out of the list and prints that -- except when the list is
is not concrete, then is falls back to `{versions}` to avoid a pedantic error.
For projections of concrete specs, `{version}` should be used to render
`1.2.3` instead of `=1.2.3` (which you would get with `{versions}`).
The default `Spec` format string used in `Spec.__str__` now uses
`{versions}` so that `str(Spec(string)) == string` holds.
## Changes to `GitVersion`
- `GitVersion` is a small wrapper around `StandardVersion` which enriches it
with a git ref. It no longer inherits from it.
- `GitVersion` _always_ needs to be able to look up an associated Spack version
if it was not assigned (yet). It throws a `VersionLookupError` whenever `ref_version`
is accessed but it has no means to look up the ref; in the past Spack would
not error and use the commit sha as a literal version, which was incorrect.
- `GitVersion` is never equal to `StandardVersion`, nor is satisfied by it. This
is such that we don't lose transitivity. This fixes the following bug on `develop`
where `git_version_a == standard_version == git_version_b` does not imply
`git_version_a == git_version_b`. It also ensures equality always implies equal
hash, which is also currently broken on develop; inclusion tests of a set of
versions + git versions would behave differently from inclusion tests of a
list of the same objects.
- The above means `ver("ref=1.2.3) != ver("=1.2.3")` could break packages that branch
on specific versions, but that was brittle already, since the same happens with
externals: `pkg@1.2.3-external` suffixes wouldn't be exactly equal either. Instead,
those checks should be `x.satisfies("@1.2.3")` which works both for git versions and
custom version suffixes.
- `GitVersion` from commit will now print as `<hash>=<version>` once the
git ref is resolved to a spack version. This is for reliability -- version is frozen
when added to the database and queried later. It also improves performance
since there is no need to clone all repos of all git versions after `spack clean -m`
is run and something queries the database, triggering version comparison, such
as potentially reuse concretization.
- The "empty VerstionStrComponent trick" for `GitVerison` is dropped since it wasn't
representable as a version string (by design). Instead, it's replaced by `git`,
so you get `1.2.3.git.4` (which reads 4 commits after a tag 1.2.3). This means
that there's an edge case for version schemes `1.1.1`, `1.1.1a`, since the
generated git version `1.1.1.git.1` (1 commit after `1.1.1`) compares larger
than `1.1.1a`, since `a < git` are compared as strings. This is currently a
wont-fix edge case, but if really required, could be fixed by special casing
the `git` string.
- Saved, concrete specs (database, lock file, ...) that only had a git sha as their
version, but have no means to look the effective Spack version anymore, will
now see their version mapped to `hash=develop`. Previously these specs
would always have their sha literally interpreted as a version string (even when
it _could_ be looked up). This only applies to databases, lock files and spec.json
files created before Spack 0.20; after this PR, we always have a Spack version
associated to the relevant GitVersion).
- Fixes a bug where previously `to_dict` / `from_dict` (de)serialization would not
reattach the repo to the GitVersion, causing the git hash to be used as a literal
(bogus) version instead of the resolved version. This was in particularly breaking
version comparison in the build process on macOS/Windows.
## Installing or matching specific versions
- In the past, `spack install pkg@3.2` would install `pkg@=3.2` if it was a
known specific version defined in the package, even when newer patch releases
`3.2.1`, `3.2.2`, `...` were available. This behavior was only there because
there was no syntax to distinguish between `3.2` and `3.2.1`. Since there is
syntax for this now through `pkg@=3.2`, the old exact matching behavior is
removed. This means that `spack install pkg@3.2` constrains the `pkg` version
to the range `3.2`, and `spack install pkg@=3.2` constrains it to the specific
version `3.2`.
- Also in directives such as `depends_on("pkg@2.3")` and their when
conditions `conflicts("...", when="@2.3")` ranges are ranges, and specific
version matches require `@=2.3.`.
- No matching version: in the case `pkg@3.2` matches nothing, concretization
errors. However, if you run `spack install pkg@=3.2` and this version
doesn't exist, Spack will define it; this allows you to install non-registered
versions.
- For consistency, you can now do `%gcc@10` and let it match a configured
`10.x.y` compiler. It errors when there is no matching compiler.
In the past it was interpreted like a specific `gcc@=10` version, which
would get bootstrapped.
- When compiler _bootstrapping_ is enabled, `%gcc@=10.2.0` can be used to
bootstrap a specific compiler version.
## Other changes
- Externals, compilers, and develop spec definitions are backwards compatible.
They are typically defined as `pkg@3.2.1` even though they should be
saying `pkg@=3.2.1`. Spack now transforms `pkg@3` into `pkg@=3` in those cases.
- Finally, fix strictness of `version(...)` directive/declaration. It just does a simple
type check, and now requires strings/integers. Floats are not allowed because
they are ambiguous `str(3.10) == "3.1"`.
`spack buildcache create` is a misnomer cause it's the only way to push to
an existing buildcache (and it in fact calls binary_distribution.push).
Also we have `spack buildcache update-index` but for create the flag is
`--rebuild-index`, which is confusing (and also... why "rebuild"
something if the command is "create" in the first place, that implies it
wasn't there to begin with).
So, after this PR, you can use either
```
spack buildcache create --rebuild-index
```
or
```
spack buildcache push --update-index
```
Also, alias `spack buildcache rebuild-index` to `spack buildcache
update-index`.
Spack never parsed `nagfor` linker arguments put on the compiler line:
```
nagfor -Wl,-Wl,,-rpath,,/path
````
so, let's continue not attempting to parse that.
`buildcache create --rel`: deprecate this because there is no point in
making things relative before tarballing; on install you need to expand
`$ORIGIN` / `@loader_path` / relative symlinks anyways because some
dependencies may actually be in an upstream, or have different
projections.
`buildcache install --allow-root`: this flag was propagated through a
lot of functions but was ultimately unused.
* py-amici, py-python-libsbml: new packages
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Swig and cmake are build-only dependencies
* cmake as a run dependency after all
* py-amici: default boost and hdf5 variants to True
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
When building perl with posix jobserver, it seems to eat jobs, which
reduces parallelism to 1 in many cases, and is rather annoying. This is
solved in GNU Make 4.4 (fifo is more stable than file descriptors), but
that version is typically not available.
So, fix this issue by simply unsetting MAKEFLAGS for the duration of
./Configure. That's enough, and the build phase runs perfectly in
parallel again.
This switches the default Make build type to `build_type=Release`.
This offers:
- higher optimization level, including loop vectorization on older GCC
- adds NDEBUG define, which disables assertions, which could cause speedups if assertions are in loops etc
- no `-g` means smaller install size
Downsides are:
- worse backtraces (though this does NOT strip symbols)
- perf reports may be useless
- no function arguments / local variables in debugger (could be of course)
- no file path / line numbers in debugger
The downsides can be mitigated by overriding to `build_type=RelWithDebInfo` in `packages.yaml`,
if needed. The upside is that builds will be MUCH smaller (and faster) with this change.
---------
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* Vendor ruamel.yaml v0.17.21
* Add unit test for whitespace regression
* Add an abstraction layer in Spack to wrap ruamel.yaml
All YAML operations are routed through spack.util.spack_yaml
The custom classes have been adapted to the new ruamel.yaml
class hierarchy.
Fixed line annotation issue in "spack config blame"
This ensures that:
a) no externals are added to the tarball metadata file
b) no externals are added to the prefix to prefix map on install, also
for old tarballs that did include externals
c) ensure that the prefix -> prefix map is always string to string, and
doesn't contain None in case for some reason a hash is missing
* libiconv can be provided by libc, so update packages which depend on
libiconv to require the iconv virtual instead
* Many packages need special consideration when locating iconv depending
on whether it is provided by libc (no prefix provided) or the libiconv
package (in that case we want to provide a prefix)
* It was also noticed that when an iconv external was provided, that
there was interference with linking (this should generally be handled
by Spack's compiler wrappers and bears further investigation)
* Like iconv, libintl can be provided by libc or another package, namely
gettext. It is not converted to a provider like libiconv because it
provides additional routines. The logic is similar to that of iconv
but instead of checking the provider, we check whether the gettext
installation includes libintl.
* Provide openmp from rocm-open-extras for roblas test
* Addressing the prechecks/audit/package-audits check
* Correcting style check errors.
* rocm-openmp-extras path veriable restricting for test
* Correcting the env variable to run_tests
* Guard use of OpenMP to make it optional in rocblas test
* Removing unused patch
* Patch to handle file reorg changes for the tests
* Correcting patch file name
* Limiting hipify-clang path to 5.4 and later
* Set hipify-clang path env in CMake
* Disable module generation by default (#35564)
a) It's used by site administrators, so it's niche
b) If it's used by site administrators, they likely need to modify the config anyhow, so the default config only serves as an example to get started
c) it's too arbitrary to enable tcl, but disable lmod
* Remove leftover from old module file schema
* Warn if module file config is detected and generation is disabled
---------
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Change the signature of the Environment.__init__ method to have
a single argument, i.e. the directory where the environment manifest
is located. Initializing that directory is now delegated to a function
taking care of all the error handling upfront. Environment objects
require a "spack.yaml" to be available to be constructed.
Add a class to manage the environment manifest file. The environment
now delegates to an attribute of that class the responsibility of keeping
track of changes modifying the manifest. This allows simplifying the
updates of the manifest file, and helps keeping in sync the spec lists in
memory with the spack.yaml on disk.
* generax: adding new package generax
* muscle5: adding new package muscle5
* py-custom-inherit: adding new package py-custom-inherit
* py-ete3: adding new package py-ete3
* py-itolapi: adding new package py-itolapi
* py-opentree: adding new package py-opentree
* py-pypng: adding new package py-pypng
* py-toyplot: adding new package py-toyplot
* py-toytree: adding new package py-toytree
* py-pastml: adding new package py-pastml
* raxml-ng: adding new version 1.1.0
* py-topiary: adding new package py-topiary
* generax: adding master branch version
generax: adding version 2.0.1
generax: add mpi variant
* py-topiary: add main
* generax: correcting commit for 2.0.1
* Update var/spack/repos/builtin/packages/py-itolapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-opentree/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-topiary-asr: rename package, requested changes.
* Update var/spack/repos/builtin/packages/py-topiary-asr/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Make sure to append additional flags needed for specific compilers
in the flag_handler instead of adding them as separate cmake define
lines that override the main spack cflags.
Spack comes to a crawl post-install of nvhpc, which is partly thanks to
this post install hook which has a lot of redundancy, and isn't correct.
1. There's no need to store "type" because that _is_ "mode".
2. There are more file types than "symlink", "dir", "file".
3. Don't checksum device type things
4. Don't run 3 stat calls (exists, stat, isdir/islink), but one lstat
call
5. Don't read entire files into memory
I also don't know why `spack.crypto` wasn't used for checksumming, but I
guess it's too late for that now. Finally md5 would've been the faster
algorithm, which would've been fine given that a non cryptographicall
checksum was used anyways.
The bricks package uses header from the opencl-clhpp package when built with
the cuda variant activated. In order to find the header files, the bricks
CMakeLists.txt uses the `find_package(OpenCL 2.0)` statement. The CMake
FindOpenCL module searches several paths to find the header files. Eventually
it will search for header files in the local /usr/include directories. If
OpenCL headers are found, but CUDA is not installed locally, then the build
will fail.
One of the CMake variables searched for a path to the OpenCL headers is
OCL_ROOT. This fix utilizes the OCL_ROOT variable to identify the correct path
to the install opencl-clhpp package within Spack. Also, if the cuda variant is
not used, then the OpenCL build is disabled to prevent a build failure due to
improperly-identified locally-installed OpenCL header files.
The default behavior of the build process has not changed. An external variable
definitions must be made to activate these features. Specifically, to disable
the OpenCL build, this flag must be provided to CMake:
-DBRICK_USE_OPENCL=OFF
The Spack build process explicitly uses this option unless the cuda variant is
specified. If the cuda variant is specified, then the BRICK_USE_OPENCL variable
is set to ON and the OCL_ROOT variable is set to the path of the opencl-clhpp
include directory.
* "new py-subword-nmt package"
* [@spackbot] updating style on behalf of Sangu-Mbekelu
* Update package.py
updating package based on review
* [@spackbot] updating style on behalf of Sangu-Mbekelu
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
* [py-breathe] New version 4.35.0
* Update var/spack/repos/builtin/packages/py-breathe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [py-sphinx-design] New versions 0.4.0, 0.4.1
* conflicts() -> depends_on()
Per @adamjstewart
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Adding py-ipyrad for testing
* py-ipyrad: placating flake8
* py-ipyrad: adding version 0.9.90, fixing hard coded path.
* py-ipyrad: use join_path instead of hard coded linux path
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipyrad: Removing unneeded dependencies
* py-ipyrad: Readded future (see ipyrad setup.py)
* py-ipyrad: Switch to an anchored link in the docs
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipyrad: Removed patch decorator
---------
Co-authored-by: snehring <snehring@iastate.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* elfutils cannot build against libarchive@3.62+iconv
* elfutils needs libmicrohttpd version 0.9.50 or older
* elfutils: explicitly depend on pkg-config
* libmicrohttpd: Add several new versions
* Add patch for MacOS M1/M2 machines to fix segfault when using gmp
* Update var/spack/repos/builtin/packages/gmp/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Restrict patch to v6.2.1
* Update var/spack/repos/builtin/packages/gmp/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The patch for the zziplib package applied for version 0.13.69 and
earlier includes a reference to Creative Commons
Attribution-NonCommercial-ShareAlike 2.0 Generic license, which
causes Flexera's ~expensive perl script~ FlexNet Code Insights open
source license and compliance tool to flag Spack as a non-commercial
product. This patch narrows the diff context in the patch to exclude
this text. The semantics of the patch file are unchanged.
We have successfully been building silo@4.10.2 against hdf5@1.10.4 from
some time. Refinement of #34275 (which was concerned with 4.11 but
unnecessarily restricted 4.10).
* py-numpy: set openblas `symbol_suffix` in site.cfg
This writes the correct `symbol_suffix` variant value from the `openblas` in the spec into the `site.cfg`. Fixes#37133.
* py-numpy: fix style
* py-numpy: handle symbol_suffix == "none"
* py-codecov: deprecate since not on pypi anymore
* codecov: new package
* [@spackbot] updating style on behalf of wdconinc
* codecov: use github URL instead, multi-platform
* fix: install to prefix.bin.codecov
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* codecov: use versions lookup dict
* codecov: versions -> _versions, fix style
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Silence make
Set a fixed and large NUM_THREADS by default, to avoid that it gets initialized with the host # CPUs.
Set OMP_NUM_THREADS/OPENBLAS_NUM_THREADS in terms of make_jobs so that tests don't need excessive CPU.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
If we modify both Path and PATH, on Windows they will clobber one
another. This PR updates the shell modification logic to automatically
convert variable names to upper-case on Windows.
Paths with spaces are an issue on Windows and our current powershell
scripts are not sufficiently hardended against their use.
This PR removes promlematic commandlets that do not work well with paths
with spaces and adds escape quotes in other areas where this could be an
issue.
* glib: new version 2.76.1
This adds a new stable version of glib, 2.76.1 (skipping the 2.75 unstable series).
`mkenums.py` check now is specified as a dict, after r62dca6c1cf. The `filter_file` should disable both old and new. Better (maybe, but more complicated) would be to add the `can_fail` flag for this test.
The `iconv` argument was already deprecated and has now been removed. It is now resolved through meson itself, e71ecc8771.
Builds successfully on my system (and several dependents on top of it):
```console
==> glib: Successfully installed glib-2.76.1-7iy4mee2evabd357gviozbtyh5yxi27t
```
as does the previous 2.74.6 version
* glib: patch for 2.76.1, new version 2.74.7
Replace my initial libintl check with the much nicer check for
"intl" in self.spec["gettext"].libs.names. Thanks to Chris Green!
Co-authored-by: Bernhard Kaindl <bkaindl@gmail.com>
* initial commit for enabling test for rccl hsakmt-roct and rocm-opencl
* fix styling and cleaning code
* adding missing imports and minor fixes
* minor style fix
* moidfying hsakmt-roct test to run right after installation
* osg-ca-certs: igtf link should point to version, not 'current'
* osg-ca-certs: new version 1.110.igtf.1.119
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* ants: add version 2.4.3
- add version 2.4.3
- deprecate old git version
* [@spackbot] updating style on behalf of glennpj
---------
Co-authored-by: glennpj <glennpj@users.noreply.github.com>
* Add new package MozJPEG
MozJPEG is a patched version of libjpeg-turbo which improves JPEG compression efficiency achieving higher visual quality and smaller file sizes at the same time.
* MozJPEG: Add myself as a maintainer and fix style
* google-cloud-cli: add new package
* black fixes
* Less verbose
* [@spackbot] updating style on behalf of adamjstewart
* More robust if ver doesn't exist for platform
* Deprecate ancient GEE
* Fix ppc64le bug
---------
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
- [x] Replace `version(ver, checksum=None, **kwargs)` signature with
`version(ver, checksum=None, *, sha256=..., ...)` explicitly listing all arguments.
- [x] Fix various issues in packages:
- `tags` instead of `tag`
- `default` instead of `preferred`
- `sha26` instead of `sha256`
- etc
Also, use `sha256=...` consistently.
Note: setting `sha256` currently doesn't validate the checksum length, so you could do
`sha256="a"*32` and it would get checked as `md5`... but that's something for another PR.
* py-torch: define property cmake_prefix_paths
`py-torch` installs `libtorch` and a cmake config in a non-standard location. This points downstream code to the relevant locations. From there it should pick up the correctly library and include paths for C++ projects.
* py-torch: python_platlib suggestion
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of wdconinc
* py-torch: back to self.spec["python"].package.platlib
* [@spackbot] updating style on behalf of wdconinc
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
* Add mfem v4.5.2 and related updates/tweaks in other packages
* [mfem] Add the release source link for MFEM v4.5.2
* [mfem] Remove 'goxberry' (his request) from MFEM's maintainers list
This means that `spack install` will now build the minimal set of packages
required to install the root(s).
To opt out of build edge pruning, use `spack install --include-build-deps`.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Other tools like git support `GIT_EDITOR` which takes higher precedence than the
standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the
`SPACK_EDITOR` env var.
- [x] consolidate editor code from hooks into `spack.util.editor`
- [x] add more editor tests
- [x] add support for `SPACK_EDITOR`
- [x] add a documentation section for controlling the editor and reference it
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We
really only want one place where editor search logic is implemented. This consolidates
the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`.
- [x] consolidate editor search logic in spack.util.editor
- [x] add tests for licensing case, where `Executable` is used instead of `os.execv`
- [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg
- [x] add type annotations
fixes#36628
Fix using compilers that declare "target: any" in their
configuration. This should happen only on Cray with the
module based programming environment.
* Simplify test/cmd/ci.py::test_ci_generate_with_custom_scripts
* Rearrange the build-job logic in generate_gitlab_ci_yaml
* Preserve all unknown attributes in build jobs
* Slip tests for custom attributes in the tests for other job types
* Support custom artifacts
* [@spackbot] updating style on behalf of blue42u
* Don't bother sorting needs
---------
Co-authored-by: blue42u <blue42u@users.noreply.github.com>
* DaV SDK: Enable ParaView raytracing with in SDK
* CI: Drop swr testing from Data Vis SDK
* ISPC: extend LLVM requirement to main
* DaV SDK: Disallow concretizing develop unifyfs
No longer needed after mochi-margo patch
* New packages: py-ogb, py-outdated, py-littleutils
* Update var/spack/repos/builtin/packages/py-outdated/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Other tools like git support `GIT_EDITOR` which takes higher precedence than the
standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the
`SPACK_EDITOR` env var.
- [x] consolidate editor code from hooks into `spack.util.editor`
- [x] add more editor tests
- [x] add support for `SPACK_EDITOR`
- [x] add a documentation section for controlling the editor and reference it
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We
really only want one place where editor search logic is implemented. This consolidates
the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`.
- [x] consolidate editor search logic in spack.util.editor
- [x] add tests for licensing case, where `Executable` is used instead of `os.execv`
- [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg
- [x] add type annotations
* lmod modules: allow users to remove items from hierarchy per-spec
This allows MPI wrappers that depend on MPI to be removed from the MPI portion of
the hierarchy and be made available when the appropriate compiler is loaded.
module load gcc
module load mpi-wrapper # implicitly loads mpi
module load hdf5
This allows users to treat an mpi wrapper like an mpi program
This adds the new LTS version of Qt5. No build system changes needed.
The bundled libjpeg and sqlite versions were updated, but it is unclear if these are actual build requirements, and we have not been tracking these specific versions in the version dependencies (likely due to exactly this lack of clarity).
Compare: https://github.com/qt/qtbase/compare/v5.15.8-lts-lgpl...v5.15.9-lts-lgpl
* Add NetCDF95 package.
NetCDF95 is an alternative Fortran interface to the NetCDF library which uses Fortran 2003 features.
* [@spackbot] updating style on behalf of RemiLacroix-IDRIS
---------
Co-authored-by: RemiLacroix-IDRIS <RemiLacroix-IDRIS@users.noreply.github.com>
* libmypaint: change extend to append
For same reason as #36939, `extend` takes a list as argument, while `append` takes list entry. Here `append` should be used.
* libmypaint: depends_on intltool
starting with the 5.0.x release stream the cuda related configury
items in Open MPI once again need --with-cuda-libdir so that
libcuda.so can be found at configure time, otherwise no cuda
support unless someone copies libcuda.so to
$CUDA_HOME/lib64
related to #36760
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Updating torchgeo to 0.4.1
* Added some commas
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Changed fiona bounds
* Update var/spack/repos/builtin/packages/py-torchgeo/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* upcxx: Enhance auto-detection for HPE Cray EX platforms
1. Some Cray EX systems use ALPS instead of SLURM, ensure we default
the pmi-runcmd appropriately.
2. Some Cray EX systems run a stock kernel and lack a Cray PrgEnv
(yes, really), so add a check for libfabric CXI provider as a
last resort for detecting Cray EX, and ensure we don't choke on
a lack of `$CRAYPE_DIR`.
* upcxx: Cray XC improvements
1. Future-proof Cray XC detection, in case Spack ever starts reporting
it as "linux".
2. Revert cray-libsci workaround for ALCF Theta. The workaround no longer
appears to be necessary, and is actually causing failures on Theta now.
* upcxx: Add level_zero variant detection
This commit changes the environment modifications class to escape
strings with double quotes instead of single quotes.
Single quotes prevent the expansion of enviornment variables that are
nested within environment variable definitions.
Fixes#36689
- The "base" builder class should be last in the MRO
- `filter_compiler_wrappers` needs to be moved to builders
- Decorating a function from a mixin class require using
the correct metaclass for the mixin
* py-dask-mpi: remove jupyter-server-proxy
This dependency isn't a 'hard' one; it optionally simplifies getting access to the web consoles.
See: https://github.com/dask/dask-mpi/pull/102
* Add patch to remove unnecessary dependency
* review comments
* pass formatting
* Update m4
For %oneapi & %intel, we explicitly set -O0 so dependents of m4 do not break
# The default optimization level for icx/icpx is "-O2",
# but building m4 with this level breaks the build of dependents.
# So we set it explicitely to "-O0".
* [@spackbot] updating style on behalf of hpcnpatel
This aims to resolve#34164 by resolving the <include-fragment> tags
that GitHub has started using for their release pages, see
https://github.github.io/include-fragment-element/.
This feels a bit hacky but intended as a starting point for discussion.
After reading a page during spidering, it first parses for
include-fragments, gets them all, and treats them all as separate pages.
Then it looks for href links in both the page itself and the fragments.
Co-authored-by: Alec Scott <alec@bcs.sh>
* py-torch: Update conflicts for +/~tensorpipe
* [@spackbot] updating style on behalf of blue42u
* Update var/spack/repos/builtin/packages/py-torch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of blue42u
---------
Co-authored-by: blue42u <blue42u@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
MSVC compilers rely on vcvars environment setup scripts to establish
build environement variables neccesary for all projects to build
successfully. Prior to this we were only piping LIB, INCLUDE, and PATH
change through.
Instead we need to propegate all changes to the env variables made by
VCVARs in order to establish robust support for the MSVC compiler.
This most significantly impacts projects that need to be build with
NMake and MSBuild
No changes to the build recipe required. Changelog at https://github.com/xrootd/xrootd/compare/v5.5.3...v5.5.4.
Built successfully on my test system:
```console
[+] /opt/software/linux-ubuntu23.04-skylake/gcc-12.2.0/xrootd-5.5.4-cgyz43ivwwqkc7bhdofnxhl2fusysg3m
```
* CI: Fixup docs for bootstrap.
* CI: Add compatibility shim
* Add an update method for CI
Update requires manually renaming section to `ci`. After
this patch, updating and using the deprecated `gitlab-ci` section
should be possible.
* Fix typos in generate warnings
* Fixup CI schema validation
* Add unit tests for legacy CI
* Add deprecated CI stack for continuous testing
* Allow updating gitlab-ci section directly with env update
* Make warning give good advice for updating gitlab-ci
* Fix typo in CI name
* Remove white space
* Remove unneeded component of deprected-ci
* cppzmq: new versions 4.8.1, 4.9.0 (updated cmake dependency)
No important changes in the build system, https://github.com/zeromq/cppzmq/compare/v4.7.1...v4.9.0, other than the more recent cmake required starting with 4.8.0.
There is also a patch version 4.8.0, but presumably 4.8.1 is preferred.
* cppzmq: add maintainer
* Extract a method to warn when the manifest is not up-to-date
* Extract methods to update the repository and ensure dir exists
* Simplify further the write method, add failing unit-test
* Fix the function computing YAML equivalence between two instances
* ECP-SDK: enable hdf5 VOL adapters
- When +hdf5, enable VOL adapters suitable for the SDK.
- Each VOL package must prepend to the HDF5_PLUGIN_PATH.
- hdf5: 1.13.3 will break existing VOL packages, constrain
VOLs related to SDK and add note to keep 1.13.2 available.
- hdf5-vol-async:
- Do not set HDF5_VOL_CONNECTOR, consumers must opt-in.
- Enforce DAG constraints on MPI to require threaded version.
- Depend on an explicit version of argbots to relax
concretization issues in other spack environments.
- paraview: fix compiler flag usage for the 110 ABI (followup to #33617).
* ECP Data and ViS: Add constraits for HDF5 VOLS
* CI: HDF5 1.14 builds without VisIt
* hdf5-vol-async: Update docs string
---------
Co-authored-by: Stephen McDowell <stephen.mcdowell@kitware.com>
* Fix py-torch build on Linux >=6.0.3
* Update var/spack/repos/builtin/packages/py-torch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
VeloC/SCR component releases needed for upcoming VeloC release.
* AXL v0.8.0
* ER v0.4.0
* KVTree v1.4.0
* Rankstr v0.3.0
* Redset v0.3.0
* Shuffile v0.3.0
* Spath v0.3.0
Added some dependency compatibility restraints as the new componenet
versions have a change to how their cmake config works.
* add cuDNN variant and make RDKit optional
* [@spackbot] updating style on behalf of RMeli
* add newer version of rdkit
---------
Co-authored-by: RMeli <RMeli@users.noreply.github.com>
* archspec: add v0.2.0, deprecate old versions
* Simplify version ranges
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Remove py-setuptools
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Rename PIKA_WITH_P2300_REFERENCE_IMPLEMENTATION CMake option in pika package
* Remove unnecessary use of self in pika package
* Use append instead of list += for single options in pika package
* Add pika 0.14.0
* add tandem package
* apply black
* fix import
* fix year of license
* add version 1.0 and associated compile fix
* change git to property
* add conflict to intel
* Kokkos: add release 4.0.0
* Kokkos: updating default c++ standard requirement
Now Kokkos requires c++17 as its new minimum c++ standard library.
* Kokkos: adding support for new GPU architectures
The new updates include NVIDIA Hopper and AMD Navi
* Kokkos: fixing style...
* paraview +rocm: constrain kokkos dep to @:3.7.01
---------
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
* initial commit for enabling test for rocm-smi-lib, rocm-cmake and rocm-clang-ocl
* fix styling and cleaning code
* disabling some tests for rocm-smi-lib
* fix style errors
* msmpi has no wrappers so don't set MPI_CXX_COMPILER etc. for that
MPI implementation
* hdf5 on Windows does not have h5cc etc., so do not try to filter
them on Windows
* py-uproot: new versions 5.0.4, 5.0.5
No changed in dependency versions
* py-awkward-cpp: new versions
* py-awkward: new versions
* py-awkward: new version in 1.10.* series
Previously `spack -e bla config update <section>` would treat the
environment config scope as standard config file instead of a single
file config scope. This fixes that.
When app is uninstalled, if it matches a default, then remove the
default symlink targeting its modulefile.
Until now, when a default were uninstalled, the default symlink were
left pointing to a nonexistent modulefile.
- Update default image to Ubuntu 22.04 (previously was still Ubuntu 18.04)
- Optionally use depfiles to install the environment within the container
- Allow extending Dockerfile Jinja2 template
- Allow extending Singularity definition file Jinja2 template
- Deprecate previous options to add extra instructions
Unless the amdgpu_target is overriden, the libraries will default to
being built for cuda, since amdgpu_target=none is both default and in
conflict with +rocm. This requires a custom Disjoint set to include
both the 'auto' variant used by the rocm mathlibs and the 'none'
variant used by ROCmPackage.
* Fix search for hip+cuda in hipcub@5.1 and later
This patch is not strictly necessary, but it may fix the search for HIP
in certain environments.
* Backport fix for CUDA 11.5 to hipsparse
* Reduce effort on grounding by employing cardinality constraints
If we use a cardinality constraint instead of a rule
using pair of values, we'll end up grounding 1 rule
instead of all the possible pair combinations of the
allowed values.
* Display all errors from concretization, instead of just one
If clingo produces multiple "error" facts, we now print all
of them in the error message. Before we were printing just
the one with the least priority.
Consolidate a few common patterns in concretize.lp to ensure
that certain node attributes have one and only one value
assigned.
All errors are displayed, so use a single criterion
instead of three.
* Account for weights in concretize.lp
To recover the optimization order we had before, account
for weights of errors when minimizing.
The priority is mapped to powers of 10, so to effectively
get back the same results as with priorities.
openblas likes to concurrently writes to the same archive from different
targets, and solves that through .NOTPARALLEL: all
We run `make x y z` which is not affected by `NOTPARALLEL`, running into
races.
When generating modulefile, correctly detect software installation asked
by user as explicit installation.
Explicit installation status were previously fetched from database
record of spec, which was only set after modulefile generation.
Code is updated to pass down the explicit status of software
installation to the object that generates modulefiles.
Fixes#34730.
Fixes#12105.
A value for the explicit argument has to be set when creating a new
installation, but for operations on existing installation, this value is
retrieved from database. Such operations are: module rm, module refresh,
module setdefaults or when get_module function is used.
Update on the way tests that mimics an installation, thus explicit
argument has to be set under such situation.
Original Author of this change: Chris Green <greenc@fnal.gov>
Two changes:
- Remove adding the library path using -L: It is obsolete now
that we have the library paths in before the system paths.
- Link with -linto only if the gettext recipe provides it:
When we are on a glibc system, we can use external gettext,
which means we use the libintl inside libc.so: no -lintl then.
This change was already submitted in #35450 and reviewed but is
stuck in this big PR which is trying to do too in a single PR.
This fixes a bug in the Windows build of Perl.
An attribute defined in package class is inaccessible from the install
method due to builder: refactor it to be a method.
Add `config:stage_name` which is a Spec format string that can
customize the names of stages created by Spack. This was primarily
created to allow generating shorter stage names on Windows (along
with `config:build_stage`, this can be used to create stages with
short absolute paths).
By default, this is not set and the prior name stage format is used.
This also removes the username component that is always added to
Stage paths on Windows (if users want to include this, they can
add it to the `build_stage`).
* py-aioitertools: add v0.11.0
* Update var/spack/repos/builtin/packages/py-aioitertools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* compiler wrapper: fix -Xlinker parsing
* handle the case of -rpath without value; avoid that we drop the flag
* also handle the -Xlinker -rpath -Xlinker without further args case...
* fix test
* get rid of global $rp var, reduce branching
* Ascent: Drop VTK-h dependency for 0.9
* Ascent: Remove duplicate OpenMP constraints
* Ascent: 0.9.0 cannot build with vtk-m@2
* Ascent: Only needs vtkm when using vtkh
* Ascent: Require fides when building with ADIOS2
* QE v7.1 add post-processing tools installation
Quantum-Espersso@7.1 ships with an incoplete CMakeLists.txt that prevents the installation of post-processing tools.
Added patches, is fixed in two different commits in upstream.
* fixed style
* removed spaces
* added MR references
* Add new libfabric versions 1.17.1, 1.17.0, 1.16.0, 1.15.2.
* Add libfabric dependency on numactl and linux-headers when building
with OPX provider support.
* Set libfabric flag_handler to pass compiler flags as arguments to
configure.
Fix patching old boost versions to account for builders.
Add a proper version constraint on boost for recent dyninst.
The constraint can be found in dyninst source code under
"cmake/Boost.cmake" which contains:
set(_boost_min_version 1.70.0)
Co-authored-by: Greg Becker <becker33@llnl.gov>
* Current develop spack.bat file cannot handle any reserved characters
being passed via the CLI, particularly '=' and '?'. To address this,
re-do the CLI parsing for loop to use custom logic to allow for more
granular handling of CLI args.
* We take a less-than-ideal approach to escaping local scope and
handling unset variables as well as the actual parsing of CL
arguments. To address this, don't quote the args and then try to
parse the quotes we just added (resulting in spack flags being
undefined). Instead, leverage batch script features. Since we are
not unnecessarily quoting things, we don't need to think about
removing them, and in the case of paths with spaces, we should _not_
be removing the quotes as we currently do.
Corrects libs detection with a more specific root, otherwise there
can be inconsistencies between version of WGL requested and the
version picked up by `find_libraries`.
Corrects headers detection - win-sdk, win-wdk, and WGL headers all
exist under the same directory, so we can compute the headers for WGL
without querying the spec for win-sdk (which causes errors).
This commit also removes the `plat` variant of `wgl`, which is
redundant with the Spec's target.
- [x] Specs that define 'new' versions in the require: section need to generate associated facts to indicate that those versions are valid.
- [x] add test to verify success with unknown versions.
- [x] remove unneeded check that was leading to extra complexity and test
failures (at this point, all `hash=version` does not require listing out that version
in `packages.yaml`)
- [x] unique index for origin (dont reuse 0)
Co-authored-by: Peter Josef Scheibel <scheibel1@llnl.gov>
* Add v8.4.1, and a few other changes.
Minor adjustments for better alignment between Spack and ESMF native
build. For ESMF >= 8.3.1 now Spack defaults to using
external-parallelio. Before use internal version, which was PIO-1 all
the way up to v8.3.0b10 anyway! Xerces is disabled by default.
* Deal with two long lines flagged by prechecks/style.
* Try to satisfy prechecks/style.
* Try to satisfy flake8 rules wrt indentation of continuation lines.
* Now trying to satisfy "black reformatting".
* For "black" formatting really put that ugly comma at the end before
closing parentheses. Interesting.
* Support building against external-parallelio even w/o mpi, but select the
external-parallelio dependency accordingly.
* Correct C compiler setting.
* Handle `pnetcdf` variant consistent with how `ParallelIO` does it. And
also pass the `pnetcdf` variant down to the `external-parallelio`
dependency if set.
* Long line formatting again.
* Simplify handling of tarball URL construction and update sha256
checksums.
* Align version check with recommended self.spec.satisfies().
* Deprecate v8.4.0 which has a bug that can cause memory corruption, fixed
in v8.4.1.
* Use double quotes vs single quotes as per style-check... although
https://spack-tutorial.readthedocs.io/en/latest/tutorial_packaging.html#querying-spec-versions
clearly shows it with single quotes.
* ispc: attempts at getting more recent versions to work
* ispc: more attempts to get newer versions to build
* ispc: cleanup
* llvm: remove ispc_patches variant again
* ispc: unpin ncurses
* ispc: satisfy style checks
* ispc: 1.19 is only compatible with LLVM 13-15
otherwise it would not build against develop, as this now has LLVM 16
* ispc: relax LLVM version to what ispc requires itself
verified that it builds against LLVM 13, 14, 15, but not 12 and 16
* ispc: use spec.satisfies instead of version comparison
according to suggestions from review and docs, this is the canonical way to do it
* ispc: checksum 1.18.1
just in order to include all versions, also checked that it builds
---------
Co-authored-by: Martin Aumüller <aumuell@reserv.at>
Add a `find_first` method that locates one instance of a file
that matches a specified pattern by recursively searching a directory
tree. Unlike other `find` methods, this only locates one file at most,
so can use optimizations that avoid searching the entire tree:
Typically the relevant files are at low depth, so it makes sense to
locate files through iterative deepening and early exit.
Update tcl and lmod modulefile template to provide more information on
help message (name, version and target) like done on whatis for lmod
modulefiles.
This resolves a loose end from #36241 (missed due to package name). `libpthread-stubs` is another package from the xcb project that is now tracked through https://gitlab.freedesktop.org/xorg/ instead. No new versions; no changed hashes.
* py-iniconfig: new version 2.0.0 (-> hatchling)
py-iniconfig switched to hatchling with v2.0.0:
https://github.com/pytest-dev/iniconfig/blob/v2.0.0/pyproject.toml
```
==> py-iniconfig: Successfully installed py-iniconfig-2.0.0-ttoip2aalmxqqybv3vnozcabk47vg2yn
```
* Update var/spack/repos/builtin/packages/py-iniconfig/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Adapt tcl and lmod modulefile templates to generate append-path or
remove-path commands in modulefile when respectively append_flags or
remove_flags commands are defined in package for run environment.
Fixes#10299.
* Add option to optionally build with CMake
* Autotools is preferred where available
* Unlike the autotools-based build, the CMake-based build creates
either static or shared libs, not both (the default is shared
and is controlled with a new "shared" variant that only exists
when building with cmake)
* Note that `cmake~ownlibs` depends on expat, so would require
`expat build_system=autotools` (to avoid a cyclic dependency)
Simplify environment modification block in modulefile Tcl template by
always setting a path delimiter to the prepend-path, append-path and
remove-path commands.
Remove --delim option to the setenv command as this command does not
allow such option.
Update test_prepend_path_separator test to explicitly check the 6
path-like commands that should be present in generated modulefile.
* Add a pre-check job that just bootstrap the environment on Python 3.6
* py-typing-extension: restore information on Python 3.6 installation
* Fix job name, try to run quick test on installed python packages
fixes#36339
We were missing a rule that enforced a match between
the `node_compiler` and the compiler used to satisfy
a requirement.
Fix compiler with custom, made up version too
* gcc: fix for apple-clang conflict
* Update var/spack/repos/builtin/packages/gcc/package.py
Use variant by @adamjstewart
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Specs that define 'new' versions in the require: section need to generate
associated facts to indicate that those versions are valid.
* add test to verify success with unknown versions.
Since environment-modules has support for autoloading since 4.2,
and Spack-builds of it enable it by default, use the same autoload
default for tcl as lmod.
* add opppy-0_1_6 and opppy-0_1_7 releases to the spack recipes
* update urls
* remove sphinx from the dependency list
* cleanup OPPPY versions to capture OPPPY-0_1_1 tag descrepency
* one more attempt at fixing the url for opppy-0_1_1 (simpler fix)
---------
Co-authored-by: Cleveland <cleveland@lanl.gov>
Co-authored-by: clevelam <clevelam@users.noreply.github.com>
* update python package
* change package inheritance
* small update
* enable cpp tests
* small update
* Add flaky package
* Restructure PennyLane deps and order
* Change Lightning defaults and add libomp support for MacOS
* Replace explicit git url with PyPI
* Add Flaky support
* Update PennyLane and PennyLane Lightning support
* fix format
* update packages versioning
* Add patching and default updates for lightning package
* Format
* fix patch version
* update py-flaky package
* update py-pennylane-lightning package
* update py-pennylane package
* remove explicity python dependence
* Remove redundant lines from patch-file
* Update SHA for new patch
* Initial commit for PLLKokkos.
* Comment verbose variant.
* Update develop commit version and restore verbose option.
* Add backends.
* Add mesa package dep (libxml2). Fix rocm install for py-pennylane-lightning-kokkos.
* Restore sycl backend.
* Revert mesa package.
* Make py-pe-li-kokkos into CudaPackage, ROCmPackage.
* Do not force kokkos+wrapper when +cuda
* Few mods following comments on py-pll.
* Update versions of py-pennylane*.
* Remove py-pennylane-lightning patch.
* Remove redundant preferred=True.
* Fix lint in py-pennylane-lightning-kokkos.
* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Ninja and pip not required at runtime. Set lower bound on PL/PLL versions.
* Remove v0.29.0 from pennylane.
* Add AmintorDusko as maintainer.
---------
Co-authored-by: AmintorDusko <amintor_dusko@hotmail.com>
Co-authored-by: Lee J. O'Riordan <lee@xanadu.ai>
Co-authored-by: Amintor Dusko <87949283+AmintorDusko@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The xcb-utils have been migrated to the gitlab.freedesktop.org, from the
previous separate location. That means that a URL change is needed to
pick up newer version
([ref](https://lists.freedesktop.org/archives/xcb/2022-October/011422.html)).
This replaces the `homepage` and `url` with the latest (to an `xz`
file), adds a `url_for_version` function to resolve past versions, and
add the latest versions. Because of the `url_for_version` I don't think
we can use the `xorg_mirror_path` approach here.
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
netcdf-cxx and netcdf-c now build with CMake rather than Autotools.
netcdf-c can still optionally build with Autotools (but defaults to
CMake). With some additional patches to the CMake files, netcdf-c
can use CMake to build on Windows.
* abinit: add version 9.8.3
* require hdf5 up to 1.8 and libxc up to version 5
* abinit: constrained versions of libxc and hdf5
* fixed bad syntax for format
* fixed error looking for fftw in spec.
* Changed to look for fftw-api in spec.
* Update var/spack/repos/builtin/packages/abinit/package.py
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Xorg apps: updated versions to current latest
This updates all xorg apps to the latest versions, adding updated
requirements where needed.
No major version increases in any packages.
Minor version increases in some packages (build changes, if any, are
indicated below):
- rgb
- xauth
- xcalc
- xclock
- xeyes: xi >= 1.7, x11-xcb xcb-present >= 1.9 xcb-xfixes xcb-damage
- xfontsel
- xfs: xfont2 >= 2.0.1
- xinit
- xpr
- xrdb
Bugfix version increases in many packages, with no expected impact on
dependencies or interfaces.
Summary of dependency changes:
- xeyes:
- depends_on("libxi@1.7:", when="@1.2:")
- depends_on("libxcb@1.9:", when="@1.2:")
- xfs:
- depends_on("libxfont@1.4.5:", when="@:1.1")
- depends_on("libxfont2@2.0.1:", when="@1.2:")
* setxkbmap: depends_on libxrandr when @1.3.3:
* constype: new version
Add support for building with CMake and make it the default build
system on all platforms. By doing this, lz4 can now be built on
Windows. The makefile-based build remains as an option.
* wayland: new versions, new build system (meson)
* wayland-protocols: new version, new build system (meson)
* [@spackbot] updating style on behalf of wdconinc
* wayland-protocols: added maintainer
* wayland: added maintainer
* wayland-protocols: no need to import build systems, per flake8
* wayland: no need to import build system, per flake8
* Update var/spack/repos/builtin/packages/wayland/package.py
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
If you have a "require:" section in your packages config, and you
use it to specify a list of requirements, the list elements can
now include strings (before this, each element in the list had to
be a `one_of` or `any_of` specification, which is awkward if you
wanted to apply just one spec with no alternatives).
* py-pdf2image: new package
* py-pdf2image: 1.16.3 source now available on pypi
* Update var/spack/repos/builtin/packages/py-pdf2image/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Example one:
```
spack install --add x y z
```
is equivalent to
```
spack add x y z
spack concretize
spack install --only-concrete
```
where `--only-concrete` installs without modifying spack.yaml/spack.lock
Example two:
```
spack install
```
concretizes current spack.yaml if outdated and installs all specs.
Example three:
```
spack install x y z
```
concretizes current spack.yaml if outdated and installs *only* concrete
specs in the environment that match abstract specs `x`, `y`, or `z`.
* update versions and arch flags
* style update
* more style issues
* fix hashes and testing problem
* return the old versions, but they are really bad
* fix style
---------
Co-authored-by: Gerald Ragghianti <gerald@ragghianti.com>
The `ignore` parameter was only used for `spack activate/deactivate`, and it isn't used
by Spack Environments which have their own handling of file conflicts. We should remove it.
Everything that handles `ignore=` was removed in #29317 and included in 0.19, when we
removed `spack activate` and `spack deactivate` in favor of environments. So all of these
usages removed here were already being ignored by Spack.
Adapt tcl modulefile template to call "module load" on autoload
dependency without testing if this dependency is already loaded or not.
The is-loaded test is not necessary, as module commands know how to cope
with an already loaded module. With environment-modules 4.2+ (released
in 2018) it is also important to have this "module load" command even if
dependency is already loaded in order to record that the modulefile
declares such dependency. This is important if you want to keep a
consistent environment when a dependent module is unloaded.
The "Autoloading" verbose message is also removed as recent module
commands will report such information to the user (depending on the
verbosity configured for the module command).
Such change has been test successfully with Modules 3.2 (EL7), 4.5 (EL8)
and 5.2 (latest) and also with Lmod 7 and 8 (as it is mentionned in
Spack docs that Lmod can be used along with tcl modules). Dependencies
are correctly loaded or unloaded, whether they are loaded/unloaded or
not.
This change fixes Tcl quoting issue introduced in #32853.
Fixes#19155.
* py-setuptools-git-versioning: new package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-hepunits: new versions 2.2.0, 2.2.1, 2.3.0, 2.3.1
Python 2 support dropped in 2.2 series.
Ref: https://github.com/scikit-hep/hepunits/compare/v2.1.1...v2.3.1
* py-hepunits: py-hatchling as of version 2.3
* [@spackbot] updating style on behalf of wdconinc
* py-hepunits: only depends_on toml through 2.1.1
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
In the Windows filesystem logic for creating a symlink, we intend to
fall back to a copy when the symlink cannot be created (for some
configuration settings on Windows it is not possible for the user
to create a symlink). It turns out we were overly-broad in which
exceptions lead to this fallback, and the subsequent copy would
also fail: at least one case where this occurred is when we
attempted to create a symlink that already existed.
The updated logic expressly avoids falling back to a copy when the
file/symlink already exists.
* Bazel: limit parallelism
* Patch packages that don't directly invoke bazel
* Style fixes
* flag comes after build, not bazel
* flag comes after build, not bazel
* command is only attribute if specific package
* ASP-based solver: use satisfies instead of intersects
They are semantically equivalent for concrete versions,
but the GitVersion.intersects implementation is buggy
* Mitigation for git version bug
fixes#36134
This commit works around the issue in #36134, by using
GitVersion.satisfies instead of GitVersion.intersects
There are still underlying issues when trying to infer the
"reference version" when no explicit one is given, but:
1. They are not reproducible with our synthetic repo
2. They occur only when the `git.<xxx>` form of Git version
is used
Here we just work around the user facing issue and ensure
the tests are correct with our synthetic repository.
* py-pytorch-lightning: add v2.0.0
* py-lightning-utilities: add v0.8.0
* Update all PyTorch packages
* Open-CE does not yet have patches for PyTorch 2 on ppc64le
For `spack install --test=all gromacs`
* remove the `test` target from the `check()` call and just use
the `check` target, in accordance with usual GROMACS test protocol
* build the test binaries explicitly during the build phase
Additional minor updates are necessary. This change
updates the package structure to the newer format with a
separate Builder class so we can override `check()`.
However, note that additional modernization should be
undertaken with care.
This PR does 2 unrelated things:
1. It changes the encoding of the compilers
2. It tweaks the heuristic for the solves in a0d8817907
Both were initially motivated by trying to get a performance gain but, while 2 showed significant speed-ups[^1], 1 instead didn't. I kept it anyhow, since I think the code related to compilers is more consolidated with the new encoding and we might get some performance improvement out of it if we can base our errors on the `node_compiler(Package, CompilerID)` atoms instead of `attrs`.
[^1]: In general the changes in the heuristic brought a ~10% speed-up on the tests I did. I'll post detailed results below.
Add a warning about compilers.yaml that is triggered if there are multiple compilers with the same spec, os and
target (since they can't be selected by users with the spec syntax only).
* [openmpi] 5.0.0.rc10 onwards needs munge
This is the error you will see when munge is missing from `PKG_CONFIG_PATH`:
```
configure:63942: checking for pmix pkg-config cflags
configure:63956: check_package_pkgconfig_run_results=Package munge was not found in the pkg-config search path.
Perhaps you should add the directory containing `munge.pc'
to the PKG_CONFIG_PATH environment variable
Package 'munge', required by 'pmix', not found
configure:63959: $? = 1
configure:63966: pkg-config output: Package munge was not found in the pkg-config search path.
Perhaps you should add the directory containing `munge.pc'
to the PKG_CONFIG_PATH environment variable
Package 'munge', required by 'pmix', not found
configure:63972: result: error
configure:63974: error: An error occurred retrieving pmix cppflags from pkg-config
```
* Use same PKG_CONFIG_PATH defaults for ompi+pmix+prrte
The issue I tried to fix in https://github.com/spack/spack/pull/36105 comes from
different default search paths in different `pkg-config` executables used in
`openmpi` and `pmix` package. As these tools (`openmpi`, `pmix`, and `prrte`)
all use the same mechanisms to detect dependencies, the `pkg-config` environment
they use should also be equal.
Since GPG clear-sign cannot deal with lines longer than 19995 characters
and doesn't even error but simply truncates those linese (don't ask me
why...), we have to be careful not to hit that line limit when reducing
the filesize.
So, instead this PR sets the indent level to 0 and drops the whitespace
after `: `, which still reduces file size by 50% or so.
Per feedback from the UCX community, we rarely do update
releases to anything but the current and one previous main
release stream.
Update comments in the UCX spack file to reflect this.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* py-pyshacl: patch dependency typo
* py-pyshacl: satisfy flake8
* Update var/spack/repos/builtin/packages/py-pyshacl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Adds builders appropriate for building these packages on Windows.
It is intended that builds on other platforms are unaffected (e.g.
they build with Autotools as before on Linux).
* py-pint: new versions
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pint/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-antspyx: new package
Also adds required dependencies.
Requires options to ITK to enable the right support libraries, and
patches to remove tune the setup and provide resources rather than
downloading libraries/"submodules" on the fly.
* Fix patch URL
* Style fixes.
* bump version and re-include `git clone ...` as resource
... and use colors in disambiguate message for clarity.
This commit avoids the loop:
```
for root in roots:
for dep in deps(root):
...
```
instead it ensures each node is visited once and only once.
Also adds a small optimization when searching for concrete specs, since
we can assume uniqueness of dag hash, so it's fine to early exit.
This adds a new mode for `concretizer:reuse` called `dependencies`,
which only reuses dependencies. Currently, `spack install foo` will
reuse older versions of `foo`, which might be surprising to users.
* update mda dependencies
* apply black
* mdanalysis draft
* update
* small fixes
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mdanalysis/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* ci: version bump for ghcr.io/spack/e4s-amazonlinux-2
This new image comes with GnuPG v2.4.0
* py-cython: upperbounds for Python versions
* fix py-gevent nonsense
---------
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
* CI configuration boilerplate reduction and refactor
Configuration:
- New notation for list concatenation (prepend/append)
- New notation for string concatenation (prepend/append)
- Break out configuration files for: ci.yaml, cdash.yaml, view.yaml
- Spack CI section refactored to improve self-consistency and
composability
- Scripts are now lists of lists and/or lists of strings
- Job attributes are now listed under precedence ordered list that are
composed/merged using Spack config merge rules.
- "service-jobs" are identified explicitly rather than as a batch
CI:
- Consolidate common, platform, and architecture configurations for all CI stacks into composable configuration files
- Make padding consistent across all stacks (256)
- Merge all package -> runner mappings to be consistent across all
stacks
Unit Test:
- Refactor CI module unit-tests for refactor configuration
Docs:
- Add docs for new notations in configuration.rst
- Rewrite docs on CI pipelines to be consistent with refactored CI
workflow
* Script verbose environ, dev bootstrap
* Port #35409
By setting the traversal depth to 1, only specs matching the changed
package and direct dependents of those (and of course all dependencies
of that set) are removed from pruning candidacy.
* py-deap: newer version can use newer setuptools
* Update var/spack/repos/builtin/packages/py-deap/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The overlapping dependency version ranges caused the concretizer to pick
version 7.1 even though version 8.0 is available:
```
==> Error: No version for 'cubelib' satisfies '@4.7.1' and '@4.8'
```
Moreover, Score-P 8.0 requires libbfd:
```
configure: error: bfd.h required
```
* Provide openmp from rocm-open-extras when tensile uses openmp
* Correcting audit check failure in rocm-openmp-extras dependency
* Fixing style check error
* rocm-openmp-extras required instead of llvm-amdgpu both varient
When untouched spec pruning is enabled, specs possibly affected
by a change cannot be pruned from a pipeline.
Previously spack looked at all specs matching changed package
names, and traversed dependents of each, all the way to the
environment root, to compute the set of environment specs
possibly affected by a change (and thus, not candidates for
pruning).
With this PR, when untouched spec pruning is enabled, a new
environment variable can control how far towards the root spack
traverses to compute the set of specs possibly affected by a
change. SPACK_UNTOUCHED_PRUNING_DEPENDENT_DEPTH can be set
to any numeric value before the "spack ci generate" command
is called to control this traversal depth parameter. Setting
it to "0" traverses only touched specs, setting it to "1"
traverses only touched specs and their direct dependents, and
so on. Omitting the variable results in the previous behavior
of traversing all the way to the root. Setting it to a negative
value means no traversal is done, and always yields an empty
set of possibly affected specs (which would result in the max
pruning possible).
Currently `spack buildcache create` creates compressed tarballs that
differ between each invocation, thanks to:
1. The gzip header containing mtime set to time.time()
2. The generated buildinfo file which has a different mtime every time.
To avoid this, you have to explicitly construct GZipFile yourself, since
the Python API doesn't expose the mtime arg, and we have to manually
create the tarinfo object for the buildinfo metadata file.
Normalize mode: regular files & hardlinks executable by user, dirs, symlinks: set 0o755 permissions in tarfile; other files use 0o644
* "new py-thop package"
* [@spackbot] updating style on behalf of Sangu-Mbekelu
* Update package.py
modified the url and dependencies
---------
Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
* py-openmesh: new package
* Update var/spack/repos/builtin/packages/py-openmesh/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit formalizes `satisfies(lhs, rhs, strict=True/False)`
and splits it into two functions: `satisfies(lhs, rhs)` and
`intersects(lhs, rhs)`.
- `satisfies(lhs, rhs)` means: all concrete specs matching the
left hand side also match the right hand side
- `intersects(lhs, rhs)` means: there exist concrete specs
matching both lhs and rhs.
`intersects` now has the property that it's commutative,
which previously was not guaranteed.
For abstract specs, `intersects(lhs, rhs)` implies that
`constrain(lhs, rhs)` works.
What's *not* done in this PR is ensuring that
`intersects(concrete, abstract)` returns false when the
abstract spec has additional properties not present in the
concrete spec, but `constrain(concrete, abstract)` will
raise an error.
To accomplish this, some semantics have changed, as well
as bugfixes to ArchSpec:
- GitVersion is now interpreted as a more constrained
version
- Compiler flags are interpreted as strings since their
order is important
- Abstract specs respect variant type (bool / multivalued)
* New package: py-imbalanced-learn
* Fix typo
* [@spackbot] updating style on behalf of meyersbs
* Update var/spack/repos/builtin/packages/py-imbalanced-learn/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update/fix py-meldmd; update openmm
* Restrict filter_file based on openmm version
* Updates based on Adam's feedback
* [@spackbot] updating style on behalf of meyersbs
* Break up long filter_file
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The Cray fortran compiler names fortran modules in uppercase by
default. Compile with the "-ef" flag to produce the lowercase
name that singularity-eos is expecting.
Two fixes:
1. `-Wl,a,b,c,d` is a comma separated list of linker arguments, we
incorrectly assume key/value pairs, which runs into issues with for
example `-Wl,--enable-new-dtags,-rpath,/x`
2. `-Xlinker,xxx` is not a think, so it shouldn't be parsed.
* httpie: add v3.2.1
* Add additional 3.2.1 dependencies to httpie
* Add version condition to dependency
* Reorder dependencies for efficiency
* Update var/spack/repos/builtin/packages/httpie/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* awscli: add v1.27.84
* Add botocore dependency to awscli
* Update var/spack/repos/builtin/packages/awscli/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-botocore@1.29.84 dependency
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update mda dependencies
* apply black
* Update var/spack/repos/builtin/packages/py-gsd/package.py
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove numpy upper bound
* Update var/spack/repos/builtin/packages/py-griddataformats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gsd/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update proj
* re-add autotools support
* style
* Setup env in builders
* Drop direct windows conflict for older versions
* Default to CMake
Add new style class definiton
* Proj: setup_run_environment in package not builder
* Proj: move run env changes to pkg, rm cmake arg
* Set PROJ_LIB during build
* Style
* Rm redundant configure arg
Currently, if two compilers with the same spec differ on the flags, the concretizer will:
1. mix both sets of flags for the spec in the ASP program
2. error noting that the set of flags from the compiler (both of them) doesn't match the set from the lower priority compiler
This PR fixes both -- only flags from the highest priority compiler with a given spec are considered.
* py-elasticsearch: new versions
Also add py-elastic-transport as a new dependency
* py-elasticsearch: py-urllib3 is no longer a dependency
* Update var/spack/repos/builtin/packages/py-elasticsearch/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`mypy` only understands `sys.platform == "win32"`, not indirect assignments of that
value to things like `is_windows`. If we don't use the accepted platform checks, `mypy`
registers many Windows-only symbols as not present on Linux, when it should skip the
checks for platform-specific code.
* add 2.14.2 py-astroid version
* add py-pylint 2.26.2
* fix black
* fix py-dill depends_on
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix py-astroid minor versionning
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* modify typing_extensions depends_on
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Start using paths found in extra_rpaths in compilers.yaml when building
* running black and changing maintainer list
* changing import order to pass isort
---------
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
Update `spack.util.environment` to remove legacy idioms.
* Remove kwargs from method signature and use a class for traces
* Uppercase a few global variables
* spack.util.environment: add type-hints
* Improve docstrings
* Fixed most style issues reported by pylint
* py-ipdb: updating versions
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* py-ipdb: fixing versions problem and deleting 10.1 which is too old for Python > 3.6
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipdb: removed useless dependencies
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-ipdb: missing @
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
* Update var/spack/repos/builtin/packages/py-ipdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* e3sm-scorpio: add e3sm-scorpio package
This is the Scorpio package from the e3sm.org site.
* fixed style errors
* removed unneeded dependency on cmake
Use correct `shlib_symbol_version` for Julia 1.8, work around issue where libuv-julia's git checkout has arbitrary mtime, causing make to regenerate configure scripts, sometimes.
* Add a `py-gmxapi` package.
This package provides the Python package for the GROMACS
public API. The Python package is not strongly coupled to
a specific GROMACS _version_, but its compiled extension module
is strongly coupled to a specific GROMACS _installation_.
* Update conflict info.
In order to allow `^gromacs@2022.1` while rejecting `^gromacs@2022`,
we need to compare to `gromacs@2022.0`.
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Apply suggestions from code review.
* Simplify build system structure.
* Update dependencies for completeness.
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Per code review, pretend gmxapi <0.4 doesn't exist, for simplicity.
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
a shared library /lib64/libcxi.so, which seems to also appear on other
non-slingshot systems. This patch also checks to make sure that there
is a Cray programming enviornment in /opt/cray/pe in addition to the
shared library.
* py-pygments 2.12; fix py-docutils, again
`2.12` is the latest for which our style hack works, beyond that we need
our own package to make a plugin.
Old docutils needs old setuptools
* py-setuptools is always a dep
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update the range
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The Intel OneAPI's extreme pickiness continues to bring out
buggy/noncompliant code.
This patch fixes an error in the configure.in embedded 'c' test code
and also in a file with an initialized, but unused, variable.
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* Updates to release 0.6.
* Dep updates
* Dep version fix
* Another version fix
* Fix typo
* UFL version fix
* Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fenics-ffcx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Some updates following review
* Update var/spack/repos/builtin/packages/py-fenics-dolfinx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* More updates
* More updates
* build/run updates
* Small fix
* Fix version number.
* specify lower bounds for python dependencies
* address style issues
* address style issues
* address PR comments
* amend setuptools dependency to be of type build only
* amend setuptools dependency to be of type run and build for ffcx and ufl
* add build dependency to ensure import tests pass
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Matthew Archer <ma595@cam.ac.uk>
* py-dask-mpi: new package with dependencies
* py-hatch-jupyter-builder is not needed after all
* skip_modules seems cleaner
* Update var/spack/repos/builtin/packages/py-jupyter-server-proxy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-simpervisor/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Flags `-fallow-argument-mismatch -fallow-invalid-boz` set in `FFLAGS`/`FCFLAGS`
environment variables don't really have effect in older versions of WRF, we need
to force them in the compiler wrappers.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
With the last merge request for OOMMF [1], the intention was to have version
20b0_20220930 as the preferred version, and provide 20b0_20220930-vanilla as an
additional version for the unlikely case anybody needed that.
I made the (wrong) assumption that the `version` listed first in the `package.py` file
would be the preferred version. This merge request is to correct that by
explicitly tagging the preferred version with `preferred=True`.
[1] https://github.com/spack/spack/pull/33072/files
If the docbook packages
- docbook-xml
- docbook-xsl
are installed in a spack environment view the catalog files will be in
conflict in the view directory. This PR resolves that by adding an
appropriate prefix to each catalog name so that they are unique in the
view. The resulting XML_CATALOG_FILES environment variable will then be
able to point to both of them.
1. add version 2023.03.01
2. add variant 'python' that supports unwinding python source
3. clean up some things with the cray variant
4. require the latest libmonitor
5. fix sha256 checksum for url patch
6. delete rocm 5.3 from older versions
* cleaned up style, linked to external htslib
* removed htslib/bcfrools/samtools deps, use bundled libs instead
the pysam package includes the necessary libs to link to, so it wasn't even using linked libs when building
* fixed style
* revert to using external htslib
currently uses bundled samtools and bcftools, and there is no way to use external versions for those dependencies
* added libs property to htslibs package
added support for lib64
* added htslib name
* onednn: add variant to use Arm Compute Library on aarch64
* Update cmake version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Shorten macro definition
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update cpu/gpu_runtime variants
* Update acl variant when 1.7+
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [@spackbot] updating style on behalf of annop-w
* Add dependencies for new runtimes
* Fix dependency package name to oneapi-level-zero
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-awkward: new version 1.10.*, 2.0.*
Lots of changes in 2.0.*, see https://github.com/scikit-hep/awkward/releases. This will need some extra testing.
* py-awkward: hatchling
* Update var/spack/repos/builtin/packages/py-awkward/package.py
* Update var/spack/repos/builtin/packages/py-awkward/package.py
* py-scikit-build-core: new and improved py-scikit-build
* py-awkward-cpp: new package
* py-awkward: add depends_on py-awkward-cpp
* py-awkward: depends_on py-packaging
* py-awkward-cpp: new versions pinned by py-awkward
* py-scikit-build-core: additional depends_on
* py-awkward: branch master deprecated
* py-pytest-subprocess: new package
* py-pytest: new version 7.2.1
* py-scikit-build-core: add tests dependencies
* [@spackbot] updating style on behalf of wdconinc
* py-scikit-build-core: two more test dependencies
* py-pytest: depends_on py-exceptiongroup
* py-awkward: add pytest support
* py-pytest: suggestions from review
* py-scikit-build-core: suggestions from review
* Update var/spack/repos/builtin/packages/py-awkward-cpp/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-awkward: depends_on pyyaml when @:1, order old deps last
* [@spackbot] updating style on behalf of wdconinc
* py-awkward: move some opt deps to test, order test deps
* py-awkward: remove test dependencies
---------
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
if dump file existed it was not truncating the file, resulting in
a file with unaltered filesize, with the new content at the beginning,
"padded" with the tail of the old content, since the new content was
not enough to overwrite it.
`colify` is an old module in Spack that still uses `**kwargs` liberally.
We should be more explicit. Doing this eliminates the need for many
checks (can't pass the wrong arg if it isn't allowed) and makes the
function documentation more clear.
Fixes a bug introduced in 44ed0de8c0
where the push method of binary_distribution now takes named args
include_root and include_depedencies, to avoid the **kwarg hole.
But the call site wasn't update and we passed a dict of keys/values instead
of arguments, which resulted in a call like this:
```
push(include_root={"include_root": True, "include_dependencies": False})
```
This commit fixes that, and adds a test to see if we push the correct packages.
This error shows up a lot, typically it's harmless because an error
happened before the source build even started, in which case we don't
have build logs to copy. So, warn instead of error, cause it distracts
from the actual CI error.
Currently we attempt to setup the build environment even when
dependencies are not installed, which typically results in error while
searching for libraries or executables in a dependency's prefix.
With this change, we get a more user friendly error:
```
$ spack build-env perl
==> Error: Not all dependencies of perl are installed, cannot setup build environment:
- qpj6dw5 perl@5.36.0%apple-clang@14.0.0+cpanm+open+shared+threads build_system=generic arch=darwin-ventura-m1
- jq2plbe ^berkeley-db@18.1.40%apple-clang@14.0.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=darwin-ventura-m1
...
$ echo $?
1
```
* Allow users to specify root env dir
Environments managed by spack have some advantages over anonymous Environments
but they are tucked away inside spack's directory tree. This PR gives
users the ability to specify where the environments should live.
See #32823
This is also taken as an opportunity to ensure that all references are to "managed environments",
rather than "named environments". Prior to this PR some references to the latter persisted.
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* Update exago w/ 1.5.1 and small updates to hiop.
* Fix styling.
* Add RAJA back to ExaGO package.
* Update RAJA requirement for ExaGO and HiOp.
* Update last RAJA requirement in HiOp.
* Add new sphinx rtd theme release 1.2.0
The new release helps with supporting more recent version of docutils
* set docutils officially supported version
* add jquery dependency for sphinx-rtd-theme
* add conflict with jquery version
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* correct dependency
* fix version dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* set sphinx version
* fix sha256
* add version for flit-core
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The call:
```
x.satisfies(y[, strict=False])
```
is commutative, and tests non-empty intersection, whereas:
```
x.satsifies(y, strict=True)
```
is not commutative, and tests set-inclusion.
There are 2 fast paths. When strict=False both self and other need to
be concrete, when strict=True we can optimize when other is concrete.
a) It's used by site administrators, so it's niche
b) If it's used by site administrators, they likely need to modify the config anyhow, so the default config only serves as an example to get started
c) it's too arbitrary to enable tcl, but disable lmod
Spack generally ignores file-file projection clashes in environment
views, but would eventually error when linking the `.spack` directory
for two specs of the same package.
This leads to obscure errors where users have no clue what the issue is
and how to fix it. On top of that, the error comes very late, since it
happens when the .spack dir contents are linked (which happens after
everything else)
This PR improves that by doing a quick check ahead of time if clashes
are going to be anticipated (by simply checking for clashes in the
projection of each spec's .spack metadir). If there are clashes, a
human-readable error is thrown which shows two of the conflicting specs,
and tells users to user unify:true, view:false, or set up custom
projections.
* add pytng
* black
* add setuptools
* fix
* Update var/spack/repos/builtin/packages/py-pytng/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pytng/package.py
* Update var/spack/repos/builtin/packages/py-pytng/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Kokkos when compiled by spack without +wrapper could potentially capture the spack compiler wrappers, resulting in cmake configs and kokkos_launch_compiler trying to run the spack compiler wrapper after installation.
The checksum exception was not detailed enough and not reraised when using cache only, resulting in useless error messages.
Now it dumps the file path, expected
hash, computed hash, and the downloaded file summary.
Batch scripts in general will not function without carriage return line
endings on Windows. We rely on these scripts to support cmd, so we
should not allow these scripts to be converted to lf.
Note: Windows 11 supports lf line endings due to the use of Windows
Terminal. Once support for Windows 10 is dropped, this change can be
reverted.
When running many concurrent spack install processes that need to write
to the db, Spack regularly times out. This is because writing to the DB
after another process has written to it requires deserialization of the
db, mutating it in memory, and serializing it again, which takes some
time. On top of that, I believe there's a 1 second retry when a write
lock cannot be obtained, so I think this means only 3 processes can
really write to the DB at the same time before timing out.
* Style: black 23, skip magic trailing commas
* isort should use same line length as black
* Fix unused import
* Update version of black used in CI
* Update new packages
* Update new packages
* Update package.py
Initial new stuff
* Update package.py
* Update package.py
* Update package.py
* fix targets
* non-llvm backends
* ooops
* fix style
* Somehow that was not caught?
Somehow that was not caught?
* style
* Last fix
make capitalization consistent with Halide not LLVM...
* py-cmake-format: new version, new variants
* Update var/spack/repos/builtin/packages/py-cmake-format/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-cufflinks: new package version with 0.17.3
* Update var/spack/repos/builtin/packages/py-cufflinks/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
---------
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Specs that did not contribute any files to an env view caused a problem
where zip(specs, files grouped by prefix) got "out of sync", causing the
wrong merge map to be passed to a package's `add_files_to_view`, which
specifically caused an issue where *sometimes* bin/python ended up as a
symlink instead of a copy.
One such example is kokkos + kokkos-nvcc-wrapper, as the latter package
only provides the file bin/nvcc_wrapper, which is also added to view by
kokkos, causing kokkos-nvcc-wrapper to contribute 0 files.
The test feels a bit contrived, but it captures the problem... pkg a is
added first and has 0 files to contribute, pkg b adds a single file, and
we check if pkg b receives a merge map (and a does not).
* pfunit: add v4.6.3
* pfunit: use CMakePackage methods to define arguments
* pfunit: deprecate v3.X, make a variant conditional
* pfunit: simplify setting up environment variables
Reading the docs it seems only v3
needs F90_VENDOR to be set
* pfunit: fix option names
The names set before were unused
* pfunit: shared libraries seem not to be supported
See https://github.com/Goddard-Fortran-Ecosystem/pFUnit/issues/308#issuecomment-874725759
* Add py-mlflow and its dependencies
* mlflow: fix syntax error in package.py
* py-mlflow: cleanup
Process review remarks, add missing dependencies, add skinny variant
* Apply suggestions from code review
* Fix flake8 issues
* More formatting fixes
* Fix py-waitress dependency version
* py-mlflow: platform-specific dependency
* Update var/spack/repos/builtin/packages/py-mlflow/package.py
* Update var/spack/repos/builtin/packages/py-mlflow/package.py
* Process review remarks
* Fix typo in dependency version
* py-shap: fix dependencies
* py-arrow: fix dependencies
* py-slicer: remove py-setuptools explicit version
* py-pyarrow: dataset variant and pass options through environment
It appears there are some issues when using `pip install` instead of
`python setup.py` - this setup_build_environment should fix that.
* py-pyarrow: review remark
* Decouple setup_build_environment from install_options
* py-pyarrow: style
* Bump licenses to 2023
---------
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Matthias Wolf <matthias.wolf@epfl.ch>
`spack gc` removes build deps of explicitly installed specs, but somehow
if you take one of the specs that `spack gc` would remove, and feed it
to `spack uninstall /<hash>` by hash, it complains about all the
dependents that still rely on it.
This resolves the inconsistency by only following run/link type deps in
spack uninstall.
That way you can finally do `spack uninstall cmake` without having to
remove all packages built with cmake.
Default package requirements might contain
variants that are not defined in each package,
so we shouldn't verify them when emitting facts
for the ASP solver.
Account for group when enforcing requirements
packages:all : don't emit facts for requirement conditions
that can't apply to current spec
* Update package.py
Several libraries are need to be present at run time so that the code can be run in parallel.
I have added them as dependencies and to LD_LIBRARY_PATH. Orca comes as a binary so the libraries cannot be added as RPATH at compilation time.
Also, orca 5.0.3 was compiled against 4.1.1, not 4.1.2.
2023-02-14 16:17:37 -08:00
3835 changed files with 86232 additions and 47436 deletions
Thanks for taking the time to report this build failure. To proceed with the report please:
1. Title the issue `Installation issue: <name-of-the-package>`.
2. Provide the information required below.
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
- type:textarea
id:reproduce
@@ -29,7 +29,9 @@ body:
description:|
Please post the error message from spack inside the `<details>` tag below:
value:|
<details><summary>Error message</summary><pre>
<details><summary>Error message</summary>
<pre>
...
</pre></details>
validations:
@@ -53,7 +55,7 @@ body:
Please upload the following files:
* **`spack-build-out.txt`**
* **`spack-build-env.txt`**
They should be present in the stage directory of the failing build. Also upload any `config.log` or similar file if one exists.
description:Suggest adding a feature that is not yet in Spack
labels:[feature]
body:
@@ -29,13 +29,11 @@ body:
attributes:
label:General information
options:
- label:I have run `spack --version` and reported the version of Spack
required:true
- label:I have searched the issues of this repo and believe this is not a duplicate
required:true
- type:markdown
attributes:
value:|
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on [our Slack](https://slack.spack.io/) first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
@@ -942,7 +942,7 @@ first ``libelf`` above, you would run:
$ spack load /qmm4kso
To see which packages that you have loaded to your enviornment you would
To see which packages that you have loaded to your environment you would
use ``spack find --loaded``.
..code-block::console
@@ -1103,16 +1103,31 @@ Below are more details about the specifiers that you can add to specs.
Version specifier
^^^^^^^^^^^^^^^^^
A version specifier comes somewhere after a package name and starts
with ``@``. It can be a single version, e.g. ``@1.0``, ``@3``, or
``@1.2a7``. Or, it can be a range of versions, such as ``@1.0:1.5``
(all versions between ``1.0`` and ``1.5``, inclusive). Version ranges
can be open, e.g. ``:3`` means any version up to and including ``3``.
This would include ``3.4`` and ``3.4.2``. ``4.2:`` means any version
above and including ``4.2``. Finally, a version specifier can be a
set of arbitrary versions, such as ``@1.0,1.5,1.7`` (``1.0``, ``1.5``,
or ``1.7``). When you supply such a specifier to ``spack install``,
it constrains the set of versions that Spack will install.
A version specifier ``pkg@<specifier>`` comes after a package name
and starts with ``@``. It can be something abstract that matches
multiple known versions, or a specific version. During concretization,
Spack will pick the optimal version within the spec's constraints
according to policies set for the particular Spack installation.
The version specifier can be *a specific version*, such as ``@=1.0.0`` or
``@=1.2a7``. Or, it can be *a range of versions*, such as ``@1.0:1.5``.
Version ranges are inclusive, so this example includes both ``1.0``
and any ``1.5.x`` version. Version ranges can be unbounded, e.g. ``@:3``
means any version up to and including ``3``. This would include ``3.4``
and ``3.4.2``. Similarly, ``@4.2:`` means any version above and including
``4.2``. As a short-hand, ``@3`` is equivalent to the range ``@3:3`` and
includes any version with major version ``3``.
Notice that you can distinguish between the specific version ``@=3.2`` and
the range ``@3.2``. This is useful for packages that follow a versioning
scheme that omits the zero patch version number: ``3.2``, ``3.2.1``,
``3.2.2``, etc. In general it is preferable to use the range syntax
``@3.2``, since ranges also match versions with one-off suffixes, such as
``3.2-custom``.
A version specifier can also be a list of ranges and specific versions,
separated by commas. For example, ``@1.0:1.5,=1.7.1`` matches any version
in the range ``1.0:1.5`` and the specific version ``1.7.1``.
For packages with a ``git`` attribute, ``git`` references
may be specified instead of a numerical version i.e. branches, tags
@@ -1121,36 +1136,35 @@ reference provided. Acceptable syntaxes for this are:
..code-block::sh
# branches and tags
foo@git.develop # use the develop branch
foo@git.0.19 # use the 0.19 tag
# commit hashes
foo@abcdef1234abcdef1234abcdef1234abcdef1234 # 40 character hashes are automatically treated as git commits
foo@git.abcdef1234abcdef1234abcdef1234abcdef1234
Spack versions from git reference either have an associated version supplied by the user,
or infer a relationship to known versions from the structure of the git repository. If an
associated version is supplied by the user, Spack treats the git version as equivalent to that
version for all version comparisons in the package logic (e.g. ``depends_on('foo', when='@1.5')``).
# branches and tags
foo@git.develop # use the develop branch
foo@git.0.19 # use the 0.19 tag
The associated version can be assigned with ``[git ref]=[version]`` syntax, with the caveat that the specified version is known to Spack from either the package definition, or in the configuration preferences (i.e. ``packages.yaml``).
Spack always needs to associate a Spack version with the git reference,
which is used for version comparison. This Spack version is heuristically
taken from the closest valid git tag among ancestors of the git ref.
Once a Spack version is associated with a git ref, it always printed with
the git ref. For example, if the commit ``@git.abcdefg`` is tagged
``0.19``, then the spec will be shown as ``@git.abcdefg=0.19``.
If the git ref is not exactly a tag, then the distance to the nearest tag
is also part of the resolved version. ``@git.abcdefg=0.19.git.8`` means
that the commit is 8 commits away from the ``0.19`` tag.
In cases where Spack cannot resolve a sensible version from a git ref,
users can specify the Spack version to use for the git ref. This is done
by appending ``=`` and the Spack version to the git ref. For example:
..code-block::sh
foo@git.my_ref=3.2 # use the my_ref tag or branch, but treat it as version 3.2 for version comparisons
foo@git.abcdef1234abcdef1234abcdef1234abcdef1234=develop # use the given commit, but treat it as develop for version comparisons
If an associated version is not supplied then the tags in the git repo are used to determine
the most recent previous version known to Spack. Details about how versions are compared
and how Spack determines if one version is less than another are discussed in the developer guide.
If the version spec is not provided, then Spack will choose one
according to policies set for the particular spack installation. If
the spec is ambiguous, i.e. it could match multiple versions, Spack
will choose a version within the spec's constraints according to
policies set for the particular Spack installation.
Details about how versions are compared and how Spack determines if
one version is less than another are discussed in the developer guide.
Clone `spack-configs <https://github.com/spack/spack-configs>`_ repo and activate Intel oneAPI CPU environment::
git clone https://github.com/spack/spack-configs
spack env activate spack-configs/INTEL/CPU
spack concretize -f
`Intel oneAPI CPU environment <https://github.com/spack/spack-configs/blob/main/INTEL/CPU/spack.yaml>`_ contains applications tested and validated by Intel, this list is constantly extended. And currently it supports:
-`GROMACS <https://www.gromacs.org/>`_
-`HPCG <https://www.hpcg-benchmark.org/>`_
-`HPL <https://netlib.org/benchmark/hpl/>`_
-`LAMMPS <https://www.lammps.org/#gsc.tab=0>`_
-`OpenFOAM <https://www.openfoam.com/>`_
-`STREAM <https://www.cs.virginia.edu/stream/>`_
-`WRF <https://github.com/wrf-model/WRF>`_
To build lammps with oneAPI compiler from this environment just run::
spack install lammps
Compiled binaries can be find using::
spack cd -i lammps
You can do the same for all other applications from this environment.
"warnings":"Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors",
"flags":"-msse2"
}
]
],
"nvhpc":[]
}
},
"bulldozer":{
@@ -1451,6 +1532,12 @@
"warnings":"Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors",
"flags":"-msse3"
}
],
"nvhpc":[
{
"versions":":",
"flags":"-tp {name}"
}
]
}
},
@@ -1519,6 +1606,12 @@
"warnings":"Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors",
"flags":"-msse3"
}
],
"nvhpc":[
{
"versions":":",
"flags":"-tp {name}"
}
]
}
},
@@ -1588,6 +1681,13 @@
"warnings":"Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors",
warnings.warn("configobj_walker has move to ruamel.yaml.util, please update your code")
returnnew_configobj_walker(cfg)
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