Commit graph

26722 commits

Author SHA1 Message Date
eugeneswalker
3cb6fd140c
update e4s to reflect june status (#31032) 2022-07-14 22:05:57 +00:00
Joseph Snyder
64b41b012c
Bug/fix credentials s3 buildcache update (#31391)
* Add connection information to buildcache update command

Ensure that the s3 connection made when attempting to update the content
of a buildcache attempts to use the extra connection information
from the mirror creation.

* Add unique help for endpoint URL argument

Fix copy/paste error for endpoint URL help which was the same as
the access token

* Re-work URL checking for S3 mirrors

Due to the fact that nested bucket URLs would never match the string used
for checking that the mirror is the same, switch the check used.

Sort all mirror URLs by length to have the most specific cases first
and see if the desired URL "starts with" the mirror URL.

* Long line style fixes

Add execptions for long lines and fix other style errors

* Use format() function to rebuild URL

Use the format command to rebuild the url instead of crafing a
formatted string out of known values

* Add early exit for URL checking

When a valid mirror is found, break from the loop
2022-07-14 20:49:46 +00:00
Todd Gamblin
3d0347ddd3
Deprecate blacklist/whitelist in favor of include/exclude (#31569)
For a long time the module configuration has had a few settings that use
`blacklist`/`whitelist` terminology. We've been asked by some of our users to replace
this with more inclusive language. In addition to being non-inclusive, `blacklist` and
`whitelist` are inconsistent with the rest of Spack, which uses `include` and `exclude`
for the same concepts.

- [x] Deprecate `blacklist`, `whitelist`, `blacklist_implicits` and `environment_blacklist`
      in favor of `exclude`, `include`, `exclude_implicits` and `exclude_env_vars` in module
      configuration, to be removed in Spack v0.20.
- [x] Print deprecation warnings if any of the deprecated names are in module config.
- [x] Update tests to test old and new names.
- [x] Update docs.
- [x] Update `spack config update` to fix this automatically, and include a note in the error
      that you can use this command.
2022-07-14 20:42:33 +00:00
Jen Herting
875b032151
[py-tensorflow-hub] full_index=1 caused checksum change (#31585) 2022-07-14 11:47:30 -07:00
snehring
c7e49ea5a0
interproscan: new version 5.56-89.0 (#31565)
* interproscan: new version 5.56-89.0

* interproscan: add maintainer
2022-07-14 09:53:12 -07:00
Adam J. Stewart
a1f07b68a8
py-statsmodels: add v0.13.2 (#31571) 2022-07-14 09:30:43 -07:00
Axel Huebl
c4efeab976
ADIOS2: 2.8.2 (#31564)
Add the latest ADIOS2 release.
2022-07-14 03:17:38 -06:00
Peter Scheibel
7741bfb7d1
Decompression: use tar exe vs. built-in Python tarfile support (#31563)
Python's built-in tarfile support doesn't address some general
cases of malformed tarfiles that are already handled by the system
'tar' utility; until these can be addressed, use that exclusively.
2022-07-13 14:12:21 -07:00
Stephen Sachs
d25315c2f6
Add package py-devito and it's dependencies (#31495)
* [py-devito] Add package

Also add dependencies:
- py-nbval
- py-cgen
- py-codepy
- py-contexttimer
- py-pyrevolve

* [py-devito] Fix some typos

* [py-devito] Fix: include examples directory

Upstream issue: https://github.com/devitocodes/devito/issues/1954

* [py-devito] clean up

* [py-devito] clean up dependency packages

* [py-devito] flake8: line too long

* Address @adamjstewart comments

* Make flake8 happy

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-07-13 13:12:28 -07:00
Jonathon Anderson
8e00aa7c79
m4: Add build dependency on diffutils (#31232) 2022-07-13 22:02:17 +02:00
Adam J. Stewart
752697add2
GDAL: CMake support and dependency variants (#31197)
Add support for CMake builds while preserving autotools support
for older versions of GDAL

* Add GDAL 3.5.0
* Remove GDAL 1
* Add support for new CMake build system
* Change defaults to build all recommended dependencies
* Simplify Autotools flag handling
* Determine version range for drivers
2022-07-13 11:58:39 -07:00
Ben Darwin
f7ed9092e5
ants: add version 2.4.0 (#31562) 2022-07-13 17:35:04 +00:00
Emil Briggs
5da8bae2a9
Add versions 4.3.0 and 4.3.1. Update boost reqs with component/versions. (#31559) 2022-07-13 10:08:29 -07:00
Erik Schnetter
a78e8bc54e
mpitrampoline: New version 4.1.2 (#31560) 2022-07-13 10:06:04 -07:00
Chris White
cdf541ac4a
Cppcheck: fix install and convert to cmake build system (#31488)
* fix cppcheck install and convert to cmake build system

* add white238 as a maintainer
2022-07-13 07:32:48 -07:00
Rémi Lacroix
0e783b2c47
ghostscript-fonts: fix URL (#31360) 2022-07-13 10:11:22 +02:00
H. Joe Lee
9c5ef2aafe
Hermes: add v0.7.0-beta, remove older versions (#31544) 2022-07-13 09:25:45 +02:00
Vicente Bolea
1f7ee4957b
vtk-m: add v1.8.0 (#31220) 2022-07-13 09:21:56 +02:00
Elizabeth Sherrock
6fbb01fe31
py-ford: add v6.1.13 (#31483) 2022-07-13 09:19:23 +02:00
Adam J. Stewart
a36c05068f
Open3D: fix build with external fmt (#31547) 2022-07-13 09:17:07 +02:00
Adam J. Stewart
16e079aa52
py-pytorch-lightning: add v1.6.5 (#31548) 2022-07-13 09:07:52 +02:00
Marco De La Pierre
79f67ba92b
Tower Agent / Tower CLI: new packages (#31539) 2022-07-13 09:05:03 +02:00
Massimiliano Culpo
7f2b5e8e57
spack.repo.get() can only be called on concrete specs (#31411)
The goal of this PR is to make clearer where we need a package object in Spack as opposed to a package class.

We currently instantiate a lot of package objects when we could make do with a class.  We should use the class
when we only need metadata, and we should only instantiate and us an instance of `PackageBase` at build time.

Modifications:
- [x] Remove the `spack.repo.get` convenience function (which was used in many places, and not really needed)
- [x] Use `spack.repo.path.get_pkg_class` wherever possible
- [x] Try to route most of the need for `spack.repo.path.get` through `Spec.package`
- [x] Introduce a non-data descriptor, that can be used as a decorator, to have "class level properties"
- [x] Refactor unit tests that had to be modified to reduce code duplication
- [x] `Spec.package` and `Repo.get` now require a concrete spec as input
- [x] Remove `RepoPath.all_packages` and `Repo.all_packages`
2022-07-12 19:45:24 -04:00
Seth R. Johnson
6ceb274de0
trilinos: add new release 13.4.0 and use sha256 instead of commit hashes (#31277) 2022-07-12 14:57:39 -06:00
Richard Berger
8e25fd4f16
spiner: update dependencies (#31486) 2022-07-12 11:16:34 -07:00
Adam J. Stewart
3fc8c3d18b
py-nbmake: add v1.3.0; py-nbclient: add v0.6.6, 0.5.13; py-traitlets: add v5.3.0 (#31513)
* py-nbmake: add v1.3.0

* Add newer versions
2022-07-12 11:03:40 -07:00
Carlos Bederián
bfe058aa57
amdblis: add 3.2 (#31518) 2022-07-12 10:40:54 -07:00
Carlos Bederián
45b77a2215
amdlibflame: add 3.2 (#31519) 2022-07-12 10:37:26 -07:00
Carlos Bederián
7dd22e93c6
amdfftw: add 3.2 (#31520) 2022-07-12 10:24:59 -07:00
nicolas le goff
cdb7c7a1db
fixed the cgal recipe and added the latest release. (#31523)
* fixed the cgal recipe and added the latest release.

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

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

* updated cgal recipe to new URL for tarballs

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-07-12 09:04:51 -07:00
Harmen Stoppels
ea91e8f4ca
file_cache.py: idempotent remove without races (#31477)
There's a race condition in `remove()` as the lockfile is removed after
releasing the lock, which is a problem when another process acquires a
write lock during deletion.

Also simplify life a bit in multiprocessing when a file is possibly
removed multiple times, which currently is an error on the second
deletion, so the proposed fix is to make remove(...) idempotent and not
error when deleting non-existing cache entries.

Don't tests for existence of lockfile, cause windows/linux behavior is different
2022-07-12 15:03:48 +00:00
Harmen Stoppels
74e2625dcf
compression.py: buffered copy (#31533) 2022-07-12 16:49:59 +02:00
RichardABunt
a4f0522468
arm-forge: add 22.0.2 and 22.0.3. (#31432) 2022-07-12 16:21:07 +02:00
Marco De La Pierre
ff67e10f60
lammps package: added fftw_precision variant (#31459) 2022-07-12 16:14:58 +02:00
Axel Huebl
c8931e390a
WarpX: 22.07 (#31508)
Update `warpx` & `py-warpx` to the latest release, `22.07`.
2022-07-12 16:13:51 +02:00
Harmen Stoppels
b2c519470b
environment.py: only acquire write lock when necessary (#31493) 2022-07-12 16:12:43 +02:00
marcosmazz
9087224e04
OpenMX: add v3.9 (#31466)
Co-authored-by: Marcos Mazzini - <mmazzini@serafin.ccad.unc.edu.ar>
2022-07-12 15:44:02 +02:00
Stephen Sachs
110a35a520
py-gevent: deprecated compiler flags (#31469)
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-07-12 15:23:26 +02:00
miheer vaidya
ea9151b2a5
abseil: add v20220623 (#31507) 2022-07-12 15:21:31 +02:00
Nicholas Brunhart-Lupo
9708afc3b3
amr-wind: add "ascent" variant (#31376) 2022-07-12 14:38:24 +02:00
Harmen Stoppels
d904a789d5
env depfile: add missing touch (#31494)
Oversight in #31433, the non-phony `env` target was missing a file being
created for it, which can cause make to infinitely loop when including
multiple generated makefiles.
2022-07-12 14:16:31 +02:00
Erik Schnetter
7917f87c63
cuda: New version 11.5.2 (#31463) 2022-07-12 13:52:12 +02:00
dependabot[bot]
e33a57ab65
build(deps): bump actions/setup-python from 4.0.0 to 4.1.0 (#31526)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](d09bd5e600...c4e89fac7e)

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

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-07-12 13:50:30 +02:00
Mark W. Krentel
7f830295ae
hpcviewer: add v2022.06 (#31532) 2022-07-12 13:41:13 +02:00
Massimiliano Culpo
89b8d33d05
Remove os.getcwd from function signature (#31480)
fixes #29730

This is also wrong since it binds the directory at the time
of module import, rather than the one at the time of function
call.
2022-07-12 10:08:37 +02:00
Jonathon Anderson
25f198aa91
Sanitize ownership when extracting tarfiles (#31524) 2022-07-12 09:28:24 +02:00
Adam J. Stewart
5bd1074afb
py-hatchling: add new packages, document new build backend (#31512)
* py-hatchling: add new package, document new build backend

* Minor doc changes

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-07-11 16:23:28 -07:00
Michael Kuhn
18b51e19df
glib: add 2.72.3 (#31516) 2022-07-11 17:09:43 -06:00
renjithravindrankannath
21822f233c
Fix for sanity check failure in spack upstream code: atmi, hip-rocclr (#31454)
* Fix for sanity check failure in spack upstream code

* Style check failure correction

* Correction as per the review comments
2022-07-11 15:01:47 -07:00
Keita Iwabuchi
5f7f8ce1eb
Metall package: add v0.21 (#31482)
* Metall package: add dependency to GCC for build test

* Package Metall: add v.017

* Package Metall: update the package file

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

Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>

* Metall package: add v0.18 and v0.19

* Metall Package: add v0.20

* Metall package: add v0.21

Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-07-11 14:54:57 -07:00