Commit Graph

36510 Commits

Author SHA1 Message Date
Wouter Deconinck
8dc91a7a5c
py-ipython: add latest bugfixes from v8.15.0 through v8.25.0 (#44499) 2024-06-06 14:07:16 +02:00
Teague Sterling
4c195b1a06
py-azure-mgmt-storage: add v20.0.0, v20.1.0 (#44511) 2024-06-06 14:05:08 +02:00
Teague Sterling
c6fb6bf5f8
py-nest-asyncio: v1.5.8, v1.5.9, v1.6.0 (#44512) 2024-06-06 14:03:28 +02:00
Teague Sterling
ed6161b80c
py-rich: add v12.6.0,13.7.1 (#44515) 2024-06-06 14:02:50 +02:00
Derek Ryan Strong
93424e4565
hwloc: add v2.9.2, v2.9.3, v2.10.0 (#44577) 2024-06-06 04:00:46 -06:00
Teague Sterling
ca00e42f1d
py-aiohttp: add 3.9.0, 3.9.4, 3.9.5 (#44510) 2024-06-06 11:22:31 +02:00
Teague Sterling
357ee1c632
py-uvloop: add v0.17.0,v0.18.0,v0.19.0 (#44513) 2024-06-06 11:15:22 +02:00
Derek Ryan Strong
cb0a3eaade
neovim: add v0.10.0, v0.9.5 (#44365) 2024-06-06 11:11:45 +02:00
dependabot[bot]
a20d34b8aa
build(deps): bump pytest from 8.2.1 to 8.2.2 in /lib/spack/docs (#44553)
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.2.1 to 8.2.2.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.2.1...8.2.2)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2024-06-06 08:38:54 +02:00
Derek Ryan Strong
329910a620
ffmpeg: add v7.0, master (#44107)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-06-06 07:57:29 +02:00
Derek Ryan Strong
c374d04b0d
wget: add v1.21.4 and v1.24.5 (#44574) 2024-06-06 07:56:22 +02:00
Derek Ryan Strong
b68cf16c85
Add gmake build dependency for unibilium (#44575) 2024-06-06 07:54:46 +02:00
Alex Richert
391c4cf099
netcdf-c: add logging variant (#43380)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2024-06-05 17:48:27 +02:00
Michael Kuhn
8260599e98
py-netcdf4: fix build with gcc@14 (#44134) 2024-06-05 17:38:54 +02:00
Brian Vanderwende
3433c8b8a5
ncl: consolidate patch methods (#44333) 2024-06-05 17:37:25 +02:00
Harmen Stoppels
e53bc780e4
libuuid: deprecate entirely (#44525)
There hasn't been a release in almost a decade, and build failures with
GCC 14 were reported. I don't think it makes sense to patch it, since
the project moved over to `util-linux`, and Spack's default provider is
that package. Better to just get rid of it in the next Spack release.
2024-06-05 17:36:09 +02:00
Teague Sterling
53346dbaa6
libuuid: address #44479 (#44481)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2024-06-05 08:14:20 -06:00
Chris Green
99994ea245
[root] New version 6.32.00 (#44550) 2024-06-05 08:27:13 -05:00
Harmen Stoppels
3ffe02a2fe
spack edit: allow edit multiple files at once (#44416) 2024-06-05 14:19:11 +02:00
Carlos Bederián
9b77502360
openblas: add v0.3.27 (#44312) 2024-06-05 13:18:32 +02:00
Vanessasaurus
96a97328cf
Automated deployment to update package flux-core 2024-06-05 (#44554)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2024-06-05 12:44:31 +02:00
Mikael Simberg
1a400383c0
valgrind: Add 3.21.0, 3.22.0, and 3.23.0 (#44557) 2024-06-05 12:33:00 +02:00
Harmen Stoppels
4f8ab19355
mold: unvendor (#44539) 2024-06-05 12:12:41 +02:00
Chris Marsh
8919677faf
Work around the linker incompatibility that exists with fortran and apple-clang (#44547) 2024-06-05 02:16:52 -07:00
Chris Marsh
858b185a0e
Armadillo: fix for linker error with apple-clang 15 (#44551)
* Armadillo needs to use -ld_classic with apple-clang 15
2024-06-05 01:02:43 -07:00
Tony Weaver
bc738cea32
py-your: new package (#44448)
* py-your: new package

Spack package recipe for YOUR, Your Unified Reader.  YOUR processes pulsar data in different formats.

Output below from spack install py-your
spack install py-your
[+] /usr (external glibc-2.28-oj2wjfl2ao5inhfz4qehw6hlck2hizvp)
[+] /opt/apps/spack/gcc-runtime-8.5.0-5k6kvi5
[+] /opt/apps/spack/libxcrypt-4.4.35-zigqpjo
[+] /opt/apps/spack/ncurses-6.4-xbvwv2w
[+] /opt/apps/spack/erfa-2.0.0-4qkta2n
[+] /opt/apps/spack/zlib-ng-2.1.6-ccn5qny
[+] /opt/apps/spack/pcre-8.45-33dfhul
[+] /opt/apps/spack/libpciaccess-0.17-2qdxdjo
[+] /opt/apps/spack/libmd-1.0.4-zbdiprt
[+] /opt/apps/spack/qhull-2020.2-klc7ewb
[+] /opt/apps/spack/bzip2-1.0.8-t65bq3t
[+] /opt/apps/spack/xz-5.4.6-axoznvt
[+] /opt/apps/spack/alsa-lib-1.2.3.2-a7icjdy
[+] /opt/apps/spack/zstd-1.5.6-nyk6gt6
[+] /opt/apps/spack/libffi-3.4.6-ibucrfe
[+] /opt/apps/spack/yasm-1.3.0-v4etmmm
[+] /opt/apps/spack/openblas-0.3.26-pfyk2vi
[+] /opt/apps/spack/pkgconf-1.9.5-ckjdqjm
[+] /opt/apps/spack/wcslib-7.3-zvcqq7o
[+] /opt/apps/spack/libiconv-1.17-jskazis
[+] /opt/apps/spack/unzip-6.0-mqftjtp
[+] /opt/apps/spack/libjpeg-turbo-3.0.0-vjvivme
[+] /opt/apps/spack/readline-8.2-2ys6ede
[+] /opt/apps/spack/openssl-3.2.1-4lqdgni
[+] /opt/apps/spack/pigz-2.8-rx263bp
[+] /opt/apps/spack/libpng-1.6.39-kiuku4y
[+] /opt/apps/spack/libbsd-0.12.1-njt5grs
[+] /opt/apps/spack/swig-4.0.2-fortran-z3sbnze
[+] /opt/apps/spack/binutils-2.42-vkjcvfr
[+] /opt/apps/spack/util-linux-uuid-2.38.1-w3kgjq3
[+] /opt/apps/spack/hdf5-1.14.3-sbuiw6q
[+] /opt/apps/spack/libedit-3.1-20230828-676jwbd
[+] /opt/apps/spack/nghttp2-1.57.0-u72gxms
[+] /opt/apps/spack/ffmpeg-6.1.1-2vhrbda
[+] /opt/apps/spack/libxml2-2.10.3-37klvxv
[+] /opt/apps/spack/gdbm-1.23-cylmqwx
[+] /opt/apps/spack/sqlite-3.43.2-axuxulg
[+] /opt/apps/spack/tar-1.34-wjzs4wj
[+] /opt/apps/spack/freetype-2.13.2-in4taxi
[+] /opt/apps/spack/expat-2.6.2-7kfe3hb
[+] /opt/apps/spack/curl-8.6.0-gpzsr3p
[+] /opt/apps/spack/hwloc-2.9.1-fhoz6al
[+] /opt/apps/spack/gettext-0.22.4-zjsp346
[+] /opt/apps/spack/lua-5.3.6-47356ia
[+] /opt/apps/spack/cfitsio-3.49-mmy3dbr
[+] /opt/apps/spack/python-3.10.13-fz7fymx
[+] /opt/apps/spack/elfutils-0.190-uswzaiw
[+] /opt/apps/spack/py-pytz-2023.3-ojdlhrd
[+] /opt/apps/spack/py-cycler-0.11.0-b7mjvv7
[+] /opt/apps/spack/py-pip-23.0-lxkcvby
[+] /opt/apps/spack/python-venv-1.0-2cz5c3s
[+] /opt/apps/spack/py-numpy-1.26.4-t5acjcv
[+] /opt/apps/spack/llvm-14.0.6-3nosumn
[+] /opt/apps/spack/py-packaging-23.1-wkeyuk6
[+] /opt/apps/spack/py-six-1.16.0-iv6iv3q
[+] /opt/apps/spack/py-pybind11-2.12.0-5rvupjv
[+] /opt/apps/spack/py-setuptools-69.2.0-3do76jw
[+] /opt/apps/spack/py-pyparsing-3.1.2-fq6imlt
[+] /opt/apps/spack/py-wheel-0.41.2-brm3k3h
[+] /opt/apps/spack/py-llvmlite-0.41.1-qom3l5h
[+] /opt/apps/spack/py-astropy-4.0.1.post1-xbojixg
[+] /opt/apps/spack/py-python-dateutil-2.8.2-kzdfskc
[+] /opt/apps/spack/py-numexpr-2.8.4-fc5xc5s
[+] /opt/apps/spack/py-h5py-3.11.0-y6drk3j
[+] /opt/apps/spack/py-tifffile-2023.8.30-oof4try
[+] /opt/apps/spack/py-pygments-2.16.1-stgrccl
[+] /opt/apps/spack/py-mdurl-0.1.2-nqk43ry
[+] /opt/apps/spack/py-scipy-1.13.0-vxjgfov
[+] /opt/apps/spack/py-contourpy-1.0.7-jg5lhss
[+] /opt/apps/spack/py-pillow-10.3.0-ijh2cju
[+] /opt/apps/spack/py-kiwisolver-1.4.5-vdh5sq5
[+] /opt/apps/spack/py-fonttools-4.39.4-x5ydbox
[+] /opt/apps/spack/py-bottleneck-1.3.7-ztsm4lg
[+] /opt/apps/spack/py-lazy-loader-0.4-k7hgvka
[+] /opt/apps/spack/py-numba-0.58.1-hzvrjwj
[+] /opt/apps/spack/py-markdown-it-py-3.0.0-l4p4qv5
[+] /opt/apps/spack/py-imageio-2.34.0-z5hu4yc
[+] /opt/apps/spack/py-matplotlib-3.8.4-azq2fzm
[+] /opt/apps/spack/py-pandas-1.5.3-p3gnh6t
[+] /opt/apps/spack/py-rich-13.4.2-okhgwwz
[+] /opt/apps/spack/py-networkx-3.1-b54br7r
[+] /opt/apps/spack/py-scikit-image-0.23.2-cvyzh3t
==> Installing py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x [83/83]
==> No binary for py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x found: installing from source
==> Fetching https://github.com/thepetabyteproject/your/archive/refs/tags/0.6.7.tar.gz
==> No patches needed for py-your
==> py-your: Executing phase: 'install'
==> py-your: Successfully installed py-your-0.6.7-djfzsn2lutp24ik6wrk6tjx5f7hil76x
  Stage: 1.43s.  Install: 0.99s.  Post-install: 0.12s.  Total: 3.12s

* Removed setup_run_environment

After some testing, both spack load and module load for the package will include the bin directory generated by py-your as well as the path to the version of python the package was built with, without the need for the setup_run_environment function.

I removed that function (Although, like Tamara I thought it would be necessary based on other package setups I used as a  basis for this package).

Note: I also updated the required version of py-astropy from py-astropy@4.0: to @py-astropy@6.1.0:  In my test builds, the install was picking up version py-astropy@4.0.1.post1 and numpy1.26.  However when I  tried to run some of the code I was getting errors about py-astropy making numpy calls that are now removed.  The newer version of py-astropy corrects these.  Ideally this would be handled in the py-astropy package to make sure numpy isn't too new
2024-06-04 21:38:38 -05:00
Teague Sterling
c2196f7d3a
py-humanize: add v1.0.0, v1.1.0, v2.6.0, v3.14.0, v4.8.0, v4.9.0 (#44516)
* py-humanize: add v1.0.0, v1.1.0, v2.6.0, v3.14.0, v4.8.0, v4.9.0
2024-06-04 17:34:12 -07:00
Kyle Knoepfel
d45c27fdbd
[intel-tbb] Speed up build and add versions (#44549)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2024-06-04 15:33:53 -06:00
Teague Sterling
173084de19
py-python-json-logger: add v2.0.2 (#44517)
* py-uvloop: add v3.8.14, v3.9.15, v3.10.3 and dependencies
* py-python-json-logger: add v2.0.2
2024-06-04 11:20:47 -07:00
Teague Sterling
fd2c5fa247
py-maturin: fix rust version dependencies to build (#44518)
* py-uvloop: add v3.8.14, v3.9.15, v3.10.3 and dependencies
* rollback
* py-maturin: fix rust version dependencies to build
2024-06-04 11:09:37 -07:00
kenche-linaro
73e0e9bdff
linaro-forge: added 24.0.1 version (#44538) 2024-06-04 11:00:54 -07:00
snehring
4442414d74
kallisto: add version 0.50.1 (#44544)
Signed-off-by: Shane Nehring <snehring@iastate.edu>
2024-06-04 10:21:54 -07:00
Chris Marsh
8dbf9005f0
proj@7: support the new tiff interface in cmake@3.19 (#44535)
Add patch for proj@7 to support the new tiff interface shipped in cmake@3.19: This compliments the existing patch for @8  in #43780
2024-06-04 13:09:49 -04:00
Scott Wittenburg
0c3da1b498
gitlab ci: Remove protected publish job (#44304) 2024-06-04 11:54:05 -05:00
Todd Gamblin
278f5818b7
python: make every view a venv (#44382)
#40773 introduced python-venv, which improved build isolation and avoids issues with,
e.g., `ubuntu`'s system python modifying `sysconfig` to include a (very unwanted)
`local` directory within the default install layout.

This addresses a few cases where #40773 removed functionality, without harming the
default cases where we use `python-venv`.

Traditionally, *every* view with `python` in it was essentially a virtual environment,
because we would copy the `python` interpreter and `os.py` into every view when linking.
We now rely on `python-venv` to do that, but only when it's used (i.e. new builds) and
only for packages that have an `extends("python")` directive.

This again makes every view with `python` in it a virtual environment, but only
if we're not already using a package like `python-venv`. This uses a different
mechanism from before -- instead of using the `virtualenv` trick of copying `python`
into the prefix, we instead create a `pyvenv.cfg` like `venv` (the more modern way
to do it).

This fixes two things:
1. If you already had an environment before Spack `v0.22` that worked, it would
   stop working without a reconcretize and rebuild in `v0.22`, because we no longer
   copy the python interpreter on link. Adding `pyvenv.cfg` fixes this in a more
   modern way, so old views will keep working.

2. If you have an env that only includes python packages that use `depends_on("python")`
   instead of `extends("python")`, those packages will now be importable as before,
   though they won't have the same level of build isolation you'd get with `extends`
   and `python-venv`.

* views: avoid making client code deal with link functions

Users of views and ViewDescriptors shouldn't have to deal with link functions -- they
should just say what type of linking they want.

- [x] views take a link_type, not a link function
- [x] views work out the link function from the link type
- [x] view descriptors and commands now just tell the view what they want.

* python: simplify logic for avoiding pyvenv.cfg in copy views

Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
2024-06-04 09:52:21 -06:00
John W. Parent
c2e85202c7
CMake: add 3.28.6 && 3.29.4 (#44532)
* Add CMake 3.28.6

* Add 3.29.4
2024-06-04 09:08:09 -06:00
Mikael Simberg
b021b12043
gcc: add mold variant to use mold by default (#44117) 2024-06-04 16:46:01 +02:00
Todd Gamblin
89a0c9f4b3
nvhpc: Do not use -Wno-error with nvhpc (#44142)
In #30882, we made Spack ignore `-Werror` calls so that it could more easily build
projects that inject `-Werror` into their builds. We did this by translating them to
`-Wno-error` in the compiler wrapper. However, some compilers (like `nvhpc`) do not
support `-Wno-error`. We need to exclude them from this feature until they do.

- [x] make a property on `PackageBase` for `keep_werror` that knows not to use it for
      `nvhpc`.

- [x] update property so that it keeps only the specific `-Werror=...` args for newer nvhpc's,
      which support `-Wno-error` but not `-Wno-error=...`

---------

Co-authored-by: William Mou <william.mou1024@gmail.com>
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
2024-06-04 03:46:35 -07:00
Weiqun Zhang
259629c300
amrex: add v24.06 (#44495) 2024-06-03 17:52:18 -07:00
Teague Sterling
1ce2baf7a2
duckdb: add v1.0.0, v0.10.3 (#44531)
* duckdb: add v1.0.0, v0.10.3
* Adding issue reference
2024-06-04 02:33:36 +02:00
Garth N. Wells
4576a42a0f
py-fenics-dolfinx: dependency update (#44524)
* Update nanobind dependency
* Update py-nanobind dependency
2024-06-03 17:24:40 -07:00
Nils Vu
4fba351b92
charmpp: enable darwin arm build (#44103) 2024-06-03 17:44:29 -06:00
Garth N. Wells
706737245a
py-nanobind: add v2.0.0 (#44371)
* Add nanobind 2.0.0
* Add dependency
* Fix dependency name
* Change "_" -> "-"
2024-06-03 15:25:03 -07:00
吴坎
0dbdf49075
Update py-vl-convert-python (#44527)
* Update py-vl-convert-python:
  1. set version to 1.4.0
  2. set version 1.3.0 deprecated since its rust dependency curve@4.1.1 is not able to compile
2024-06-03 15:07:16 -07:00
Owen Solberg
641075539c
hugo: add v0.126.3 (#44530)
Co-authored-by: Owen Solberg <owen.solberg@sana.com>
2024-06-03 23:37:51 +02:00
Diego Alvarez S
9428d99991
seqfu: new package (#44445)
* Add seqfu

---------

Co-authored-by: dialvarezs <dialvarezs@users.noreply.github.com>
2024-06-03 14:30:00 -07:00
eugeneswalker
f3cf2e94c4
hip@6.1: fix reference to hsa-rocr-dev so it works when externally defined (#44528) 2024-06-03 14:11:47 -07:00
Todd Gamblin
85f13442d2
Consolidate concretization output for environments (#44489)
When Spack concretizes environments, it prints every (newly concretized) root spec
individually with all of its dependencies. For most reasonably sized environments, this
is too much output. This is true for three commands:

* `spack concretize` when concretizing an environment with newly added specs
* `spack install` when installing an environment with newly added specs
* `spack spec` with no arguments in an environment

The output dates back to before we had unified environments or nicer spec traversal
routines, and we can improve it.

This PR makes environment concretization output analogous to what we do for regular
specs. Just like `spack spec` for a single spec, we show all root specs with no
indentation, so you can easily see the specs you explicitly requested. Dependencies are
shown:

1. With indentation according to their depth in a breadth-first traversal starting at
   the roots;
2. Only once if they appear on paths from multiple roots

So, the default is now consistent with `spack spec` for one spec--it's `--cover=nodes`.
i.e., if there are 100 specs in your environment, you'll get 100 lines of output.

If you want to see more details, you can do that with `spack spec` using the arguments
you're already familiar with. For example, if you wanted to see dependency types and
*all* dependencies, you could use `spack spec -l --cover=edges`. Or you could add
deptypes and namespaces with, e.g. `spack spec -ltN`.

With no arguments in an environment, `spack spec` concretizes (if necessary) and shows
the concretized environment. If you run `spack concretize` *first*, inspecting the
environment repeatedly with `spack spec` will be fast, as everything is already in the
`spack.lock` file.

- [x] factor most logic of `Spec.tree()` out of `Spec` class into `spack.spec.tree()`,
      which can take multiple specs as roots.
- [x] make `Spec.tree()` call `spack.spec.tree()`
- [x] `spack.environment.display_specs()` now uses `spack.spec.tree()`
- [x] Update `spack concretize`
- [x] Update `spack install`
- [x] Update `spack spec` to call `spack.spec.tree()` for environments.
- [x] Continue to output specs individually for `spack spec` when using
      `--yaml` or `--json`
2024-06-03 13:29:14 -07:00
James Taliaferro
f478a65635
nb: new package (#44456)
* new package: nb
* only one filter_file, install completions
* completions now implicit, merged by the view
2024-06-03 12:57:47 -07:00
Rocco Meli
eca44600c5
rdkit (#44476) 2024-06-03 12:53:08 -07:00