Commit graph

29593 commits

Author SHA1 Message Date
Annop Wongwathanarat
ee3529fc10
lammps: enable linking with armpl-gcc FFT (#34980) 2023-01-18 11:25:41 -08:00
Harmen Stoppels
f050b1cf78
depfile: variable with all identifiers (#34678)
With the new variable [prefix/]SPACK_PACKAGE_IDS you can conveniently execute
things after each successful install.

For example push just-built packages to a buildcache

```
SPACK ?= spack
export SPACK_COLOR = always
MAKEFLAGS += -Orecurse
MY_BUILDCACHE := $(CURDIR)/cache

.PHONY: all clean

all: push

ifeq (,$(filter clean,$(MAKECMDGOALS)))
include env.mk
endif

# the relevant part: push has *all* example/push/<pkg identifier> as prereqs
push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
	$(SPACK) -e . buildcache update-index --directory $(MY_BUILDCACHE)
	$(info Pushed everything, yay!)

# and each example/push/<pkg identifier> has the install target as prereq,
# and the body can use target local $(HASH) and $(SPEC) variables to do
# things, such as pushing to a build cache
example/push/%: example/install/%
	@mkdir -p $(dir $@)
	$(SPACK) -e . buildcache create --allow-root --only=package --unsigned --directory $(MY_BUILDCACHE) /$(HASH) # push $(SPEC)
	@touch $@

spack.lock: spack.yaml
	$(SPACK) -e . concretize -f

env.mk: spack.lock
	$(SPACK) -e . env depfile -o $@ --make-target-prefix example

clean:
	rm -rf spack.lock env.mk example/
``
2023-01-18 19:19:46 +01:00
Stephen Sachs
6cf32110b9
[armpl-gcc] Make pkg-config files available (#34978)
* [armpl-gcc] Make pkg-config files available
  ARMpl pkgconfig files are located in a non-default location and do not have the
  .pc extension. Changing those both helps pkgconfig pick them up correctly, e.g.
  in the meson build of `py-scipy`.
* Address @annop-w comments
* symlink instead of cp.

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-18 07:57:55 -08:00
Annop Wongwathanarat
d841542b9c
acfl: update hash for 22.1 on RHEL-7 (#34997) 2023-01-18 15:55:29 +01:00
Harmen Stoppels
3bc943ae51
Remove verbose warning message from _try_install_from_binary_cache (#34994)
In the past we checked remote binary mirrors for existence of a spec
before attempting to download it. That changed to only checking local
copies of index.jsons (if available) to prioritize certain mirrors where
we expect to find a tarball. That was faster for CI since fetching
index.json and loading it just to order mirrors takes more time than
just attempting to fetch tarballs -- and also if we have a direct hit
there's no point to look at other mirrors.

Long story short: the info message only makes sense in the old version
of Spack, so it's better to remove it.
2023-01-18 08:25:48 -06:00
Dom Heinzeller
548aa21b18
Bug fix for duplicate rpath errors on macOS when creating build caches (#34375) 2023-01-18 13:32:16 +01:00
Adam J. Stewart
c9775df0a4
py-pytorch-lightning: add v1.9.0 (#34996) 2023-01-18 13:06:19 +01:00
Nate deVelder
6f11efe576
Add tiny profile cmake support (#34993) 2023-01-18 13:01:23 +01:00
Harmen Stoppels
fef0f47d65
spack mirror create takes local paths only (#34992)
spack mirror create cannot work with urls, so it shouldn't promote local
paths to file urls.
2023-01-18 11:45:58 +01:00
Adam J. Stewart
20575ca96a
Subclass PythonExtension instead of custom test method (#34985) 2023-01-17 19:47:16 -08:00
Glenn Johnson
13121b4c28
py-itk: add version 5.3.0 (#34968)
* py-itk: add version 5.3.0

* Remove wheels for unsupported python versions

* Fill out the version specs

* Drop th 'm' from the cp37 version strings
2023-01-17 17:42:17 -07:00
eugeneswalker
ef8214682c
py-h5py %oneapi@2023.0.0: -Wno-error=incompatible-function-pointer-types,pointer-types-discards-qualifiers (#34984) 2023-01-17 15:38:20 -08:00
Todd Gamblin
aca7dd6c2b
py-sphinx-immaterial: new package (#34948)
* py-sphinx-immaterial: new package

This is a new-ish theme for Sphinx that's based on MkDocs's `immaterial` theme. More on
the theme here: https://jbms.github.io/sphinx-immaterial/, but it seems to be very clear
and readable.  We *might* consider switching to it for Spack's docs.

* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-sphinx-immaterial/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* add note about node.js requirements

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-17 16:49:38 -06:00
eugeneswalker
c6d715c188
rempi: patch rempi_message_manager.h: include string (#34982) 2023-01-17 13:33:10 -08:00
Massimiliano Culpo
b148a43f08
CDashReporter: remove unused argument (#34869)
* CDashReporter: remove unused argument
* Removed extract_ctest_test_data
2023-01-17 11:09:38 -08:00
Massimiliano Culpo
74901a3d0d
Forward lookup of "test_log_file" and "test_failures" (#34882)
* Forward lookup of "test_log_file" and "test_failures"
  refers #34531
  closes #34487
  fixes #34440
* Add unit test
* py-libensemble: fix tests
* Support stand-alone tests with cached files as install-time tests

Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-01-17 10:59:48 -08:00
Annop Wongwathanarat
10d5f14c85
cp2k: enable linking with armpl-gcc for BLAS and FFT (#34981) 2023-01-17 09:34:43 -08:00
Harmen Stoppels
c0389ab3d0
python: 3.11.1, use -flto=thin when clang (#34951) 2023-01-17 17:26:38 +01:00
Harmen Stoppels
2fdd72094a
Bump gnupg & libksba, (CVE) (#34976)
* gnupg: 2.4.0

* libksba: 1.6.3 (CVE-2022-47629)
2023-01-17 14:27:12 +01:00
roottreej
7659912dc4
Reduce verbosity in mirrors.yaml (#34210)
Ensure `spack mirror add <name> <url/path>` without further arguments translates to `<name>: <url>` key value pairs in mirrors.yaml. If --s3-* flags are provided, only store the provided ones. 

Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-01-17 13:19:13 +00:00
Loïc Pottier
ff4cccbf6c
faiss: fixed error when importing faiss python package (#34672)
This is only a work-around for the actual problem that Python is used to install libraries instead of CMake, so we end up with BUILD_RPATH not INSTALL_RPATHs.

Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-01-17 13:43:35 +01:00
Harmen Stoppels
5074e72be8
bubblewrap: 0.7.0 (#34975) 2023-01-17 02:47:24 -08:00
Christopher Christofi
3d7674225f
perl-file-temp: add 0.2311 (#34866) 2023-01-17 01:47:28 -08:00
Glenn Johnson
873871bc62
libcroco: Get the doc variant working (#34735) 2023-01-17 10:43:12 +01:00
MatthewLieber
35d0dc8bb5
mvapich: add new package in preparation for v3.0 (#34276)
* Add new file for MVAPICH 3.0a release

Creating this as a new package since it requires some new configuration
options and because we are moving to the name "MVAPICH" and droping the
2 (following a similar move by MPICH).

Co-authored-by: Nat Shineman <shineman.5@osu.edu>
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2023-01-17 10:42:17 +01:00
Ashwin Kumar
331e3cd4e1
flexiblas: add versions up to v3.3.0 (#34874) 2023-01-17 10:36:27 +01:00
Marie Houillon
100134a2b1
New version for openCARP packages, v12.0 (#34710)
Co-authored-by: openCARP consortium <info@opencarp.org>
2023-01-17 10:31:15 +01:00
Axel Huebl
39ffef8363
Doc: config.yaml mention $env (#34905)
Add one more note on the $env variable in `config.yaml`.
2023-01-17 10:06:00 +01:00
dependabot[bot]
f0672bbaf8
build(deps): bump actions/checkout from 3.2.0 to 3.3.0 (#34829)
Bumps [actions/checkout](https://github.com/actions/checkout) from 3.2.0 to 3.3.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](755da8c3cf...ac59398561)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-01-17 10:02:31 +01:00
Cameron Smith
4fa0c1d11c
mfem: support pumi w/zoltan and parmetis (#34864) 2023-01-17 09:47:59 +01:00
Dom Heinzeller
9e845635ce
crtm: overhaul package, add crtm-fix (#34715)
Update crtm from JCSDA-EMC spack fork, add crtm-fix
2023-01-17 09:47:14 +01:00
dependabot[bot]
184a75ec54
build(deps): bump docker/build-push-action from 3.2.0 to 3.3.0 (#34972)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 3.2.0 to 3.3.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](c56af95754...37abcedcc1)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-01-17 09:44:00 +01:00
Dom Heinzeller
dbd425f0f8
ncview: bypass compiler check against netcdf-c compiler (#34580) 2023-01-17 09:30:52 +01:00
iarspider
3161784e9a
OpenCV: checksum for 4.5.5, make contrib optional (#34313)
* OpenCV: checksum for 4.5.5, make contrib optional

* [@spackbot] updating style on behalf of iarspider

* Add conflicts for contrib modules

* Fix typo

* Implement changes from review

* Update var/spack/repos/builtin/packages/opencv/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-17 00:22:00 -08:00
Glenn Johnson
a72a3fb2e0
gcc: add patch for noexcept declarations (#34964)
There are some declarations that need to be declared noexcept for
valarray. This affects gcc 9.5:11.2.
2023-01-17 08:58:45 +01:00
Marco De La Pierre
e253184886
Re adding 4th chunk of nf-tools deps (#34974)
* Revert "Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)"

This reverts commit 891a63cae6.

* fix to py-python-multipart, as per PR review
2023-01-16 23:12:00 -08:00
Glenn Johnson
d276a5f8e4
py-macs2: add version 2.2.7.1 and support python@3.10: (#34970)
* py-macs2: add version 2.2.7.1 and support python@3.10:

The tarball from PyPi includes the Cythonized C files. The tarball from
github does not. Remove the Cythonized C files from the source so that
they are rebuilt with the Spack Python/Cython combination. This is
necessary for python-3.10 but make sense for other combinations as well.

* Edits based on review

- set python version constraint on version 2.2.4
- removed all python-2 versions and related constraints.
2023-01-17 00:00:41 -06:00
Glenn Johnson
3ed219578b
py-xxhash: fix xxhash dependency (#34971)
* py-xxhash: fix xxhash dependency

The dependency should be xxhash@0.8.0:.

* Add version 3.2.0
2023-01-16 23:58:10 -06:00
Loïc Pottier
0040236cc6
rabbitmq-c: added RabbitMQ C interface (#34892)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-01-16 19:02:42 -08:00
Glenn Johnson
0629c8e5fa
itk: add version 5.3.0 (#34967)
* Add depends_on("mpi") to fix missing <mpi.h>
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-01-17 03:52:10 +01:00
Glenn Johnson
6f19eb5e67
hisat2: add version 2.2.1 and sra variant (#34966)
- add python dependency
- add perl dependency
- set python and perl interpreters in scripts
2023-01-17 03:31:00 +01:00
Glenn Johnson
b7e416046f
sra-tools: add version 3.0.3 and fix build (#34965) 2023-01-17 03:29:52 +01:00
Glenn Johnson
b2cc36109f
stringtie: add version 2.2.1 and fix build (#34973)
- stringtie uses internal samtools so remove dependency on samtools
- add dependency for zlib
- use make release target to get correct flags
2023-01-17 02:55:06 +01:00
Sergey Kosukhin
1262dcfb9f
intel-oneapi-mpi: fix setup_dependent_build_environment (#34956) 2023-01-16 23:11:43 +01:00
Benjamin Meyers
c3dc7a8349
py-fastfold add py-numpy upper bound (#34962) 2023-01-16 14:07:36 -08:00
iarspider
84d2c8a693
Add checksum for hwloc 2.9.0 (#34919) 2023-01-16 13:12:38 -08:00
Sebastian Ehlert
37b1bc9c26
Add package file for xtb and py-xtb (#34857)
* Add package file for xtb and py-xtb

* Retain maintainers from PythonPackage

* Update package files

- use extends("python") instead of tampering with PYTHONPATH
- use PyPI for downloading sdist of py-xtb
- add simple-dftd3 0.7.0
- add dftd4 3.5.0
- remove --wrap-mode=nodownload from toml-f

* Remove logic for download URL
2023-01-16 13:07:21 -08:00
Harmen Stoppels
3489cc0a9b
Refer to mirrors by name, path, or url (#34891)
With this change we get the invariant that `mirror.fetch_url` and
`mirror.push_url` return valid URLs, even when the backing config
file is actually using (relative) paths with potentially `$spack` and
`$env` like variables.

Secondly it avoids expanding mirror path / URLs too early,
so if I say `spack mirror add name ./path`, it stays `./path` in my
config. When it's retrieved through MirrorCollection() we
exand it to say `file://<env dir>/path` if `./path` was set in an
environment scope.

Thirdly, the interface is simplified for the relevant buildcache
commands, so it's more like `git push`:

```
spack buildcache create [mirror] [specs...]
```

`mirror` is either a mirror name, a path, or a URL.

Resolving the relevant mirror goes as follows:
    
- If it contains either / or \ it is used as an anonymous mirror with
   path or url.
- Otherwise, it's interpreted as a named mirror, which must exist.

This helps to guard against typos, e.g. typing `my-mirror` when there
is no such named mirror now errors with:

```
$ spack -e . buildcache create my-mirror
==> Error: no mirror named "my-mirror". Did you mean ./my-mirror?
```

instead of creating a directory in the current working directory. I
think this is reasonable, as the alternative (requiring that a local dir
exists) feels a bit pendantic in the general case -- spack is happy to
create the build cache dir when needed, saving a `mkdir`.

The old (now deprecated) format will still be available in Spack 0.20,
but is scheduled to be removed in 0.21:

```
spack buildcache create (--directory | --mirror-url | --mirror-name) [specs...]
```

This PR also touches `tmp_scope` in tests, because it didn't really
work for me, since spack fixes the possible --scope values once and
for all across tests, so tests failed when run out of order.
2023-01-16 10:14:41 -08:00
Auriane R
9a25e21da8
Add target propagation for pika package (#34924) 2023-01-16 17:57:50 +01:00
Alec Scott
d156e2ee91
Add py-python-lsp-server v1.7.0 (#34946) 2023-01-16 10:54:19 -06:00