- constrain samtools to version 1.13
- replace lzma dependency with xz
- add missing dependencies for libdeflate and openssl
- explicitly set LD_FLAGS for dependencies in makefile
From the release announcement: "This is a special bugfix release ahead of
schedule to address a memory leak that was happening on certain function calls
when using Cython. The memory leak consisted of a small constant amount of bytes
in certain function calls from Cython code. Although in most cases this was not
very noticeable, it was very impactful for long-running applications and certain
usage patterns. Check bpo-46347 for more information."
* rivet: fix dependency build types
If it isn't a python package, there is no good reason to change the default build type to remove link
* rivet: turn swig into build dependency
Adds `spack external read-cray-manifest`, which reads a json file that describes a set of package DAGs. The parsed results are stored directly in the database. A user can see these installed specs with `spack find` (like any installed spec). The easiest way to use them right now as dependencies is to run `spack spec ... ^/hash-of-external-package`.
Changes include:
* `spack external read-cray-manifest --file <path/to/file>` will add all specs described in the file to Spack's installation DB and will also install described compilers to the compilers configuration (the expected format of the file is described in this PR as well including examples of the file)
* Database records now may include an "origin" (the command added in this PR registers the origin as "external-db"). In the future, it is assumed users may want to be able to treat installs registered with this command differently (e.g. they may want to uninstall all specs added with this command)
* Hash properties are now always preserved when copying specs if the source spec is concrete
* I don't think the hashes of installed-and-concrete specs should change and this was the easiest way to handle that
* also specs that are concrete preserve their `.normal` property when copied (external specs may mention compilers that are not registered, and without this change they would fail in `normalize` when calling `validate_or_raise`)
* it might be this should only be the case if the spec was installed
- [x] Improve testing
- [x] Specifically mark DB records added with this command (so that users can do something like "uninstall all packages added with `spack read-external-db`)
* This is now possible with `spack uninstall --all --origin=external-db` (this will remove all specs added from manifest files)
- [x] Strip variants that are listed in json entries but don't actually exist for the package
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
* Use same cxx value as root
* Remove pointer syntax from non-pointer type in source
* Run patch function before build
* Use raw string in filter_file and merge edit function with patch
* Escape parentheses
* Use gDirectory from ROOT instead of CurrentDirectory function
* Make boost composable
Currently Boost enables a few components through variants by default,
which means that if you want to use only what you need and no more, you
have to explicitly disable these variants, leading to concretization
errors whenever a second package explicitly needs those components.
For instance if package A only needs `+component_a` it might depend on
`boost +component_a ~component_b`. And if packge B only needs
`+component_b` it might depend on `boost ~component_a +component_b`. If
package C now depends on both A and B, this leads to unsatisfiable
variants and hence a concretization error.
However, if we default to disabling all components, package A can simply
depend on `boost +component_a` and package B on `boost +component_b` and
package C will concretize to depending on `boost +component_a
+component_b`, and whatever you install, you get the bare minimum.
* Fix style
* Added composable boost dependencies for folly
* fixing akantu merge issue
* hpctoolkit boost dependencies already defined
* Fix Styles
* Fixup style once more
* Adding isort fix
* isort one more time
* Fix for package audit issue
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Ryan O'Malley <rd.omalley@comcast.net>
* Incorporate new search location
* Add external user option
* proper doc string
* Explicit commands in getting started
* raise during chgrp on Win
recover installer changes
Notate admin privleges
Windows phase install hooks
Find external python and install ninja (#23496)
Allow external find python to find windows python and spack install ninja
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Betsy McPhail <betsy.mcphail@kitware.com>
CMake - Windows Bootstrap (#25825)
Remove hardcoded cmake compiler (#26410)
Revert breaking cmake changes
Ensure no autotools on Windows
Perl on Windows (#26612)
Python source build windows (#26313)
Reconfigure sysconf for Windows
Python2.6 compatibility
Fxixup new sbang tests for windows
Ruby support (#28287)
Add NASM support (#28319)
Add mock Ninja package for testing
MSVC's internal CMake and Ninja now detected by spack external find and added to packages.yaml
Saving progress on packaging zlib for Windows
Fixing the shared CMake flag
* Loading Intel's ifx Fortran compiler into MSVC; if there are multiple
versions of MSVC installed and detected, ifx will only be placed into
the first block written in compilers.yaml. The version number of ifx can
be detected using MSVC's version flag (instead of /QV) by using
ignore_version_errors. This commit also provides support for detection
of Intel compilers in their own compiler block by adding ifx.exe to the
fc/f77_name blocks inside intel.py
* Giving CMake a Fortran compiler argument
* Adding patch file for removing duplicated mangling header for versions 3.9.1 and older; static and shared now successfully building on Windows
* Have netlib-lapack depend on ninja@1.10
Co-authored-by: John R. Cary <cary@txcorp.com>
Co-authored-by: Jared Popelar <jpopelar@txcorp.com>
Making a default config.yaml for Windows
Small path length for build_stage
Provide more prerequisite details, mention default config.yaml
Killing an unnecessary setvars call
Replacing some lost changes, proofreading, updating windows-supported package list
Co-authored-by: John Parent <john.parent@kitware.com>
1. Forwarding sys.stdin, e.g. use input_multiprocess_fd,
gives an error on Windows. Skipping for now
3. subprocess_context needs to serialize for Windows, like it does
for Mac.
Co-authored-by: lou.lawrence@kitware.com <lou.lawrence@kitware.com>
Co-authored-by: John Parent <john.parent@kitware.com>
* python: allow versions with garbage suffix
Ubuntu 22.04 preview python prints version as 3.10.2+, the + causes
version parsing to fail and breaks detection.
* Add version comment
* match VALID_VERSION regex
* libiconv: compile with pic even when static build
* lmod: require shared lua
It seems to be unable to detect lua-posix when using a static lua:
```
Error: The follow lua module(s) are missing: posix
```
develop in the version string. The versions from the HDF5 code were not
matching because 'develop-' is not part of the HDF5 version. Also, the
develop-x.x versions in spack omit the release version (third) number
because the branch spans all of the release versions.
* Update: py-cmake
Add additional dependencies as declared by the `py-cmake` repository.
Note: for either from-source or from-binary builds, this downloads
additional software via the network. We might want to propose upstream
patches to make this work on nodes without internet connection.
* Add Review Comments + Newest Version
* Add: Ninja
Preferred generator according to outputs and upstream repo logic
* Attempt to use resource() for CMake source
* [py-watchdog] switched to pypi and audited dependencies
* [py-watchdog] added version 2.1.6
* [py-watchdog] updated dependencies for old versions
* [py-watchdog] added when for variant
* [py-watchdog] added some newlines to make flake8 happy
* hsa-rocr-dev, llvm-amdgpu: change dependency libelf to elf
Change the libelf dependency to the virtual elf for two rocm packages.
This allows other packages (hpctoolkit) to combine rocm and dyninst
(with elfutils) while still being able to build rocm with libelf when
needed, eg darwin.
* add comment describing include path for libelf vs elfutils
fixes#29446
The new setup_*_environment functions have been falling back
to calling the old functions and warn the user since #11115.
This commit removes the fallback behavior and any use of:
- setup_environment
- setup_dependent_environment
in the codebase
* new package: py-pytest-parallel
* depend on python@3.7:
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Change the internal representation of `Spec` to allow for multiple dependencies or
dependents stemming from the same package. This change permits to represent cases
which are frequent in cross compiled environments or to bootstrap compilers.
Modifications:
- [x] Substitute `DependencyMap` with `_EdgeMap`. The main differences are that the
latter does not support direct item assignment and can be modified only through its
API. It also provides a `select_by` method to query items.
- [x] Reworked a few public APIs of `Spec` to get list of dependencies or related edges.
- [x] Added unit tests to prevent regression on #11983 and prove the synthetic construction
of specs with multiple deps from the same package.
Since #22845 went in first, this PR reuses that format and thus it should not change hashes.
The same package may be present multiple times in the list of dependencies with different
associated specs (each with its own hash).
* The new version of Wonton requires the new version of Jali
* Wonton: versions after 1.2.10 don't require boost at all
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
* ECP-SDK/VTK-m: Update ROCm variant
VTK-m set contraint for when rocm/kokkos are available.
SDK Make ROCmPackage and propagate amdgpu_arch and rocm variant to
VTK-m.
Note: SDK has to check vtk-m@ 1.7: and :1.6 explicitly in orderer to have 1.7
be selected by default if +rocm in the SDK.
* ECP-SDK: Enable ROCm + VTK-m constraints
* Adding Panzer as Default
* Set Panzer as non-default
* Updated the conflict for Panzer.
* Updated the conflict for Panzer.
* Resolve the issue with Stratimikos and Thyra
* Fixing stk build issues.
* Fixing stk build issues.
* Adding another conflict for Thrya
* cray-libsci: only be a provider for scalapack with +mpi
If a package explicitly links the scalapack provider we might otherwise end up with different variants of libsci being linked: the explicitly linked one and the one added by the Cray compiler wrappers.
* cp2k: require cray-libsci+openmp with +openmp for consistency
otherwise we might get 2 different libsci linked: one explicitly, the other one via the Cray compiler wrappers, leading at least to segfaults during cleanup
* cp2k: depend on cray-fftw+openmp with +openmp
* hdf5: mark +fortran+shared conflict for older version
This version was only activated unintentionally by silo's conflict
statement, but `@1.8.15+shared+fortran+cxx` errors out in configure:
```
CMake Error at CMakeLists.txt:814 (message):
**** Shared FORTRAN libraries are unsupported ****
```
* silo: refine hdf5 conflicts to avoid building old version
Before this, `silo+hdf5` concretized to 1.10.7 or sometimes 1.8.15. Now
I've verified it works for the following configurations:
```
silo@4.10.2 patches=7b5a1dc,952d3c9
^ hdf5@1.10.7 api=default
silo@4.10.2 patches=7b5a1dc,952d3c9,eb2a3a0
^ hdf5@1.10.8 api=v18
silo@4.10.2 patches=7b5a1dc,952d3c9,eb2a3a0
^ hdf5@1.12.1 api=v110
silo@4.11-bsd patches=eb2a3a0
^ hdf5@1.12.1 api=v110
silo@4.11-bsd patches=eb2a3a0
^ hdf5@1.10.8 api=default
silo@4.11-bsd patches=eb2a3a0
^ hdf5@1.12.1 api=default
```
and verified that the following fail:
```
silo@4.10.2 ^hdf5@1.12.1 api=default
silo@4.11 ^hdf5 api=v18
silo@4.11-bsd ^hdf5@1.13.0 api=v12
silo@4.11-bsd ^hdf5@1.13.0 api=default
```
and have updated the constraints to match. Hdf5 no longer has to be
downgraded to work with Silo.
* silo: fix dependency conflicts
* py-h5py: shorten and add comments to py-h5py hdf5 dependencies
* e4s: remove slightly outdated hdf5 requirement
* e4s: remove excessive hdf5 variant constraints
These I think are holdovers from the old concretizer.
- `hdf5_compat` can be expressed as `+hdf5 ^hdf5@1.8`
- The extra variants on hdf5 shouldn't break conduit
- axom unnecessarily restricts hdf5 version
* conduit: restore hdf5_compat flag
New versions don't try to configure docs targets at all when the
BUILD_DOCS option is turned off. This avoids CMake warnings
when docs dependencies are not found.
* Bugfix in var/spack/repos/builtin/packages/esmf/package.py
* Bug fixes in var/spack/repos/builtin/packages/esmf/package.py to build ESMF on macOS with clang+gfortran and on cray
* Add maintainer to var/spack/repos/builtin/packages/esmf/package.py
* Fix style errors
* Fix more style errors
* py-jupytext: add version 0.13.6
From da3fcc305d:
markdown-it-py v2.0 implements some internal changes, but won't affect jupytext
* py-jupytext: keep mdit-py version restricted to 1
* py-jupytext: update dependencies
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
