Commit graph

24970 commits

Author SHA1 Message Date
Paul Ferrell
9d4291e590 Handle byte sequences which are not encoded as UTF8 while logging. (#21447)
Fix builds which produce a lines with non-UTF8 output while logging
The alternative is to read in binary mode, and then decode while
ignoring errors.
2021-12-23 16:02:09 +01:00
Harmen Stoppels
8f98f1d182 Use bash in setup_git.sh (#27676) 2021-12-23 16:02:09 +01:00
Harmen Stoppels
654f6839eb ci: run style unit tests only if we target develop (#27472)
Some tests assume the base branch is develop, but this branch may not
have been checked out.
2021-12-23 16:02:09 +01:00
Harmen Stoppels
c8daa7218d Turn some verbose messages into debug messages (#27408) 2021-12-23 16:02:09 +01:00
Harmen Stoppels
d862507bcf Fix overloaded argparse keys (#27379)
Commands should not reuse option names defined in main.
2021-12-23 16:02:09 +01:00
Jordan Galby
7c6b253d89 Fix log-format reporter ignoring install errors (#25961)
When running `spack install --log-format junit|cdash ...`, install
errors were ignored. This made spack continue building dependents of
failed install, ignoring `--fail-fast`, and exit 0 at the end.
2021-12-23 16:02:09 +01:00
Robert Underwood
abd418cc31 openmpi fix external find for 0.17 (#27255) 2021-12-23 16:02:09 +01:00
Dylan Simon
544826c825 make --enable-locks actually enable locks (#24675) 2021-12-23 16:02:09 +01:00
Vinícius
afd65a4cd0
simgrid package: add versions 3.28 and 3.29 (#28118) 2021-12-23 02:53:14 -07:00
Hadrien G
b6da473800
acts: add v15.1 and record incompatibility (#27942)
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2021-12-22 23:02:16 -07:00
Christoph Junghans
eee0f2b9d5
votca-*: merge packages into one (#28073)
* votca-*: merge packages into one

* Update package.py

* votca-*: make old version as deprecated

* votca-*: mark stable deprecated as well
2021-12-22 21:42:14 -07:00
Jen Herting
cb5d53e5a9
New package: py-qpth (#28047)
Co-authored-by: Doug Heckman <dahdco@rit.edu>
2021-12-22 20:29:08 -07:00
albestro
b5ba20ada4
New package: tree-sitter (#28110) 2021-12-22 19:18:09 -08:00
Bernhard Kaindl
d236b9438d
llvm: Fix the llvm versions for using the MicrosoftDemange patch (#28140) 2021-12-22 16:53:10 -07:00
Tom Scogland
b7b6542804
locks: allow locks to work under high contention (#27846)
* locks: allow locks to work under high contention

This is a bug found by Harshitha Menon.  

The `lock=None` line shouldn't be a release but should be 
```
return (lock_type, None)
``` 
to inform the caller it couldn't get the lock type requested without
disturbing the existing lock object in the database.  There were also a
couple of bugs due to taking write locks at the beginning without any
checking or release, and not releasing read locks before requeueing.
This version no longer gives me read upgrade to write errors, even
running 200 instances on one box.

* Change lock in check_deps_status to read, release if not installed,
  not sure why this was ever write, but read definitely is more
  appropriate here, and the read lock is only held out of the scope if
  the package is installed.

* Release read lock before requeueing to reduce chance of livelock, the
  timeout that caused the original issue now happens in roughly 3 of 200
  workers instead of 199 on average.
2021-12-22 16:25:05 +01:00
Joseph Snyder
34873f5fe7
Use consistent method of checking for presence of info in connection (#27694)
Fixes #27652

Ensure that mirror's to_dict function returns a syaml_dict object for all code
paths.

Switch to using the .get function for accessing the potential information from
the S3 mirror objects.  If the key is not there, it will gracefully return
None instead of failing with a KeyError

Additionally, check that the connection object is a dictionary before trying
to "get" from it.

Add a test for the capturing of the new S3 information.
2021-12-22 16:15:49 +01:00
Pat Riehecky
522a7c8ee0
New package: microsocks (#27859) 2021-12-21 16:55:15 -08:00
Mark Olesen
433f743074
openfoam package: add v2112 release and latest patched v2106 (#28108)
Also remove x86_64-only handling for Darwin
2021-12-21 16:47:39 -08:00
Seth R. Johnson
38196894db
perl: fix macOS build (#26290)
* perl: fix macOS build

With both 5.34.0 and 5.32.1 the build fails on macos-bigsur-skylake
%clang@12.0.5 and %clang13.0.0 :
```
2 errors found in build log:
     579013    /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-perl-5.34.0-tpha2u52qfwaraidpzzbf6u4dbqg7dk5/spack-src/cpan/
               Math-BigInt-FastCalc/../../miniperl "-I../../lib" -MExtUtils::Command::MM -e 'cp_nonempty' -- FastCalc.bs ../../lib/auto/Math/BigInt/FastCalc/Fas
               tCalc.bs 644
     579014
     579015    	Everything is up to date. Type '/Applications/Xcode.app/Contents/Developer/usr/bin/make test' to run test suite.
     579016    DYLD_LIBRARY_PATH=/private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-perl-5.34.0-tpha2u52qfwaraidpzzbf6u4dbqg7d
               k5/spack-src  ./perl -Ilib -I. installperl --destdir=
     579017    WARNING: You've never run 'make test' or some tests failed! (Installing anyway.)
     579018      /rnsdhpc/code/spack/opt/spack/apple-clang/perl/tpha2u5/bin/perl5.34.0
  >> 579019    install_name_tool: error: sh -c '/Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -sdk /Applications/Xcode.app/Contents/Developer/Pl
               atforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -find install_name_tool 2> /dev/null' failed with exit code 256: (null) (errno=Invalid argument
               )
     579020    xcode-select: Failed to locate 'install_name_tool', requesting installation of command line developer tools.
     579021    Cannot update /rnsdhpc/code/spack/opt/spack/apple-clang/perl/tpha2u5/bin/perl5.34.0 dependency paths
  >> 579022    make: *** [install-all] Error 72
```
This is due to SYSTEM_VERSION_COMPAT being set.

* perl: conditionally set SYSTEM_VERSION_COMPAT based on CLT

The version of command line tools is the only difference between
@alalazo and my builds: his (v11) works only when SYSTEM_VERSION_COMPAT
is set to 1, and mine (v12.5 and v13) only work when it is unset.
2021-12-21 22:22:35 +01:00
Harmen Stoppels
db69a291d4
Regenerate views when specs already installed (#28113)
With this commit:
```
$ spack env activate --temp
$ spack install zlib
==> All of the packages are already installed
==> Updating view at /tmp/spack-faiirgmt/.spack-env/view
$ spack install zlib
==> All of the packages are already installed
```

Before this PR:
```
$ spack env activate --temp
$ spack install zlib
==> All of the packages are already installed
$ spack install zlib
==> All of the packages are already installed
```

No view was generated
2021-12-21 18:41:12 +01:00
snehring
389beaef97
structure: fixing build errors with gcc10+ removing unused dep (#28097) 2021-12-21 18:39:26 +01:00
iarspider
8ebad6963b
New package: py-onnxmltools and dependencies (#28023)
* New package: py-onnxmltools and dependencies

* Small fix

* Changes from review

* Apply suggestions from code review

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

* Update recipe following review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-21 11:15:13 -06:00
dependabot[bot]
43042c14e0
build(deps): bump docker/login-action from 1.10.0 to 1.12.0 (#28100)
Bumps [docker/login-action](https://github.com/docker/login-action) from 1.10.0 to 1.12.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](f054a8b539...42d299face)

---
updated-dependencies:
- dependency-name: docker/login-action
  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>
2021-12-21 11:29:40 +01:00
snehring
6b91d3700b
soapdenovo2: fixing compiler errors in gcc10+ (#28098) 2021-12-21 10:51:47 +01:00
Adam J. Stewart
7aa2bdca44
py-build: add virtualenv variant (#28099) 2021-12-21 10:43:42 +01:00
snehring
5005e9a856
pcma: fixing compilation issues with gcc10+ (#28101) 2021-12-21 10:41:44 +01:00
Chris White
0a43dd1019
axom: add v0.6.1, fixed e4s builds (#28067) 2021-12-21 10:40:16 +01:00
Marie Houillon
a6d89853d4
openCARP packages: add version 8.2 (#28087)
Co-authored-by: openCARP consortium <info@opencarp.org>
2021-12-20 19:09:41 -08:00
Brian Spilner
116deb0386
CDO package: add version 2.0.2 (#28086)
Also fix URL for version 2.0.1 (sha256 is not changed)
2021-12-20 19:08:49 -08:00
Jen Herting
6647b2a4ca
New package: py-ctgan (#28050)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-20 19:07:21 -08:00
Valentin Volkl
6c62fa461e
harfbuzz package: add version 2.9.1 (#27927) 2021-12-20 18:29:52 -08:00
Jen Herting
e9edb5c96b
New package: py-liac-arff (#28046) 2021-12-20 18:18:09 -08:00
Jen Herting
9869a2d0da
New package: py-rdt (#28048)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-20 18:10:52 -08:00
Jen Herting
024c2b690a
New package: py-faker (#28049)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-20 18:08:53 -08:00
Enrico Usai
cd211acd80
aws-parallelcluster: add v2.11.4 (#28094)
Also remove tilne from admins.
2021-12-20 16:49:49 -08:00
Anton Kozhevnikov
494f0053ae
add sha256 sum (#28095) 2021-12-20 15:50:18 -07:00
Robert Cohn
d45280369f
Intel oneAPI packages: add 2022.1.1 release (#28096)
Co-authored-by: Egorov, Andrey <andrey.egorov@intel.com>
2021-12-20 14:06:32 -08:00
Adam J. Stewart
c68652c88c
py-torchgeo: add v0.1.1 (#28082) 2021-12-20 16:18:27 +01:00
Vanessasaurus
a94b4eef79
Fixing spacing of libabigail to : (#28085) 2021-12-20 03:56:03 -07:00
Erik Schnetter
94dd9685cc
nsimd: Declare missing py-chardet dependency (#28030)
Found by @stevenrbrandt.
2021-12-20 08:43:31 +01:00
Adam J. Stewart
a0f175f327
py-nbconvert: add v6.3.0 (#28075) 2021-12-20 07:57:27 +01:00
Wouter Deconinck
ea692ca6f7
assimp: add v5.1.4 (#28079) 2021-12-20 07:48:07 +01:00
Adam J. Stewart
02aab770db
py-kornia: add v0.6.2 (#28080) 2021-12-20 07:30:34 +01:00
Adam J. Stewart
cdc5c44bb1
py-numpy: add v1.21.5 (#28081) 2021-12-20 07:30:17 +01:00
Vanessasaurus
da9e152ed1
Fix bugs in spack monitor (#27511)
Updates to installer.py did not account for spack monitor, so as currently implemented
there are three cases of failure that spack monitor will not account for. To fix this we add additional
hooks, including an on cancel and also do a custom action on concretization fail.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-12-20 06:54:41 +01:00
Seth R. Johnson
ece1e3905e
cmake: new versions 3.22.x (#28077) 2021-12-19 19:59:00 -07:00
Todd Gamblin
bfc69f0e4b jsonschema: use more specific schema identifiers
The latest version of `jsonschema` fails if we're not specific about which schema draft
specification we're using.  Update all of them to use the latest one (draft-07).
2021-12-19 12:55:42 -08:00
Todd Gamblin
7703043195 externals: Upgrade jsonschema to v3.2.0
Our `jsonschema` external won't support Python 3.10, so we need to upgrade it.
It currently generates this warning:

    lib/spack/external/jsonschema/compat.py:6: DeprecationWarning: Using or importing the ABCs
        from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and
        in 3.10 it will stop working

This upgrades `jsonschema` to 3.2.0, the latest version with support for Python 2.7.  The next
version after this (4.0.0) drops support for 2.7 and 3.6, so we'll have to wait to upgrade to it.

Dependencies have been added in prior commits.
2021-12-19 12:55:42 -08:00
Todd Gamblin
f83e0fb81a externals: add attrs for new jsonschema
Updating `jsonschema` to 3.2.0 requires `attrs`. Add it to externals.
2021-12-19 12:55:42 -08:00
Todd Gamblin
90592b3cbe externals: add pyrsistent for new jsonschema
Updating `jsonschema` to 3.2.0 requires `pyrsistent`. Adding just the pieces of it
that are needed for `jsonschema`.
2021-12-19 12:55:42 -08:00