Commit graph

22782 commits

Author SHA1 Message Date
bernhardkaindl
3c5a4157b0
py-anuga: add git main version to support build with python@3.5: (#26248)
* py-anuga: add git main version to support build with python@3.5:

py-anuga's main branch has been converted to Python-3 recently.

* py-triangle: use pypi, py-anuga: Fixed depends and test suite works now
2021-09-28 10:37:09 -05:00
bernhardkaindl
d00c9b47f2
py-tomopy: version bump and master, add new deps, make runtest pass (#26252)
Current py-tomopy has many features and dependencies, add them.
2021-09-28 10:33:29 -05:00
Manuela Kuhn
79808f92ae
py-numba: add 0.54.0 and restrict old dependencies (#26281)
* py-numba: add 0.54.0 and restrict old dependencies

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-28 10:32:44 -05:00
Manuela Kuhn
0f5c63b0c3
py-xlrd: add 2.0.1 (#26282) 2021-09-28 10:31:45 -05:00
Manuela Kuhn
b8dd8b07f9
py-appdirs: add 1.4.4 (#26298) 2021-09-28 10:26:23 -05:00
Diego Alvarez
f65a50d9f9
Update Nextflow (#26042) 2021-09-28 07:15:17 -04:00
Harmen Stoppels
4ce9c839ac
Add OpenSSL 3 (#26097)
* OpenSSL 3.0.0

* Remove openssl constraint in e4s to test 3.0.0

* Restrict openssl

* Restrict openssl to @:1 in unifyfs

* Revert "Remove openssl constraint in e4s to test 3.0.0"

This reverts commit 0f0355609771764280ab1b6a523c80843a4f85d6.

* Prefer 1.x
2021-09-28 10:36:55 +02:00
Massimiliano Culpo
aa8727f6f9
Move detection logic in its own package (#26119)
The logic to perform detection of already installed
packages has been extracted from cmd/external.py
and put into the spack.detection package.

In this way it can be reused programmatically for
other purposes, like bootstrapping.

The new implementation accounts for cases where the
executables are placed in a subdirectory within <prefix>/bin
2021-09-28 09:05:49 +02:00
bernhardkaindl
499d39f211
libp11: Fix build and add new version (#26135)
The build needs `pkgconfig` and `openssl`, `m4` is already added by `autoconf`.
Also add the current version of `libp11` to the list of versions.

Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-09-28 04:01:08 +02:00
Manuela Kuhn
cd8e85d802
py-dataclasses: add 0.8 (#26283) 2021-09-27 20:18:07 -05:00
Manuela Kuhn
c1cfbc5536
py-meshio: add 5.0.1 and 4.4.6 (#26285) 2021-09-27 20:17:22 -05:00
Manuela Kuhn
87b23cc9cd
py-deprecated: add 1.2.13 and get sources from pypi (#26286) 2021-09-27 20:15:35 -05:00
Harmen Stoppels
87450f3688
Use gnuconfig package for config file replacement (#26035)
* Use gnuconfig package for config file replacement

Currently the autotools build system tries to pick up config.sub and
config.guess files from the system (in /usr/share) on arm and power.
This is introduces an implicit system dependency which we can avoid by
distributing config.guess and config.sub files in a separate package,
such as the new `gnuconfig` package which is very lightweight/text only
(unlike automake where we previously pulled these files from as a
backup). This PR adds `gnuconfig` as an unconditional build dependency
for arm and power archs.

In case the user needs a system version of config.sub and config.guess,
they are free to mark `gnuconfig` as an external package with the prefix
pointing to the directory containing the config files:

```yaml
    gnuconfig:
      externals:
      - spec: gnuconfig@master
        prefix: /tmp/tmp.ooBlkyAKdw/lol
      buildable: false
```

Apart from that, this PR gives some better instructions for users when
replacing config files goes wrong.

* Mock needs this package too now, because autotools adds a depends_on

* Add documentation

* Make patch_config_files a prop, fix the docs, add integrations tests

* Make macOS happy
2021-09-27 18:38:14 -04:00
Tamara Dahlgren
c0da0d83ff
qhull: use secure github URLS instead of www.qhull.org downloads (#26211) 2021-09-27 14:50:43 -07:00
Manuela Kuhn
9b7a8f69fb
py-python-picard: add new package (#26268) 2021-09-27 23:39:30 +02:00
Brian Van Essen
acc8673e1a
Updated versions for cuDNN and NVSHMEM (#26272) 2021-09-27 13:54:15 -07:00
Adam J. Stewart
5c1e133d23
py-torchvision: add v0.10.1 (#26267) 2021-09-27 13:35:53 -07:00
Manuela Kuhn
1ad8c0d67d
py-llvmlite: add 0.37.0 (#26278) 2021-09-27 13:33:28 -07:00
Manuela Kuhn
044e2def4f
py-datalad: move datalad wtf test over from py-datalad-metalad (#26274)
* py-datalad: move datalad wtf test over from py-datalad-metalad

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-27 15:24:48 -05:00
Manuela Kuhn
44355a4f18
py-numexpr: add 2.7.3 (#26279) 2021-09-27 20:13:59 +00:00
Manuela Kuhn
6b94d7e6a3
py-tqdm: add 4.62.3 (#26277) 2021-09-27 19:55:22 +00:00
Manuela Kuhn
441c602d2d
py-nilearn: add 0.8.1 (#26276) 2021-09-27 14:50:13 -05:00
Thomas Madlener
285df128a1
[openloops][vbfnlo] Fix recipes and updated dependencies (#24461)
* [vbfnlo] Add doc variant to toggle building of docs

* [openloops] Add scons to dependencies

Make sure that the build_processes does not accidentally pick up a
non-suitable scons version from the underlying system

* [openloops] Set OLPYTHON to make sure the right scons is picked

* [openloops] Fix Flake8 style complaints
2021-09-27 11:40:33 -07:00
Richarda Butler
c68536e9d3
MPICH: Add E4S testsuite stand alone test (#25634) 2021-09-27 11:36:53 -07:00
Ben Darwin
c07af15946
mrtrix3: add version 3.0.3 (#25943) 2021-09-27 11:33:42 -07:00
iarspider
e256d02963
Update highfive (#26262)
* Add new versions of highfive
* Fix CMake option name
2021-09-27 11:24:37 -07:00
Marie Houillon
87c7a7e103
New packages for openCARP (#25909)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 11:21:43 -07:00
Melven Roehrig-Zoellner
6b2192ef96
source-highlight: allow to build the git master branch (#25947)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 11:16:55 -07:00
Miroslav Stoyanov
5130f43eb3
added workaround for rocm/cmake bug in tasmanian (#25949) 2021-09-27 11:14:21 -07:00
Edward Hartnett
c592e17d49
added package g2c from NOAAs NCEPLIBS project (#26190)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 11:03:54 -07:00
Olivier Cessenat
27c0b4a0f7
sundials package: @:5.7.0 requires hypre@:2.22.0 (#25903)
sundials@:5.7.0 fails to build with hypre@2.22.1
2021-09-27 10:58:54 -07:00
Steven Smith
ee63cfe0fd
New Package: EcoSLIM (#25975)
Co-authored-by: Steven Smith <Steven Smith>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 10:38:53 -07:00
psakievich
df9d1dd1cb
Correct path comparisons for fs view (#25891)
* Fix path comparisons in copy views

* Get correct permissions

* Set group id though os

Co-authored-by: Philip Sakievich <psakiev@sanida.gov>
2021-09-27 09:51:38 -07:00
jacorvar
33957f2745
add mantainer to bedops (#26141) 2021-09-27 16:23:50 +00:00
bernhardkaindl
0cc80f5118
spindle: It seems it needs mpi.h to compile, adding depends on mpi. (#26151)
Workaround this compile error for gcc by adding -Wno-narrowing for it:
spindle_logd.cc:65:76: error: narrowing conversion of '255' from 'int' to 'char'
spindle_logd.cc:65:76: error: narrowing conversion of '223' from 'int' to 'char'
spindle_logd.cc:65:76: error: narrowing conversion of '191' from 'int' to 'char'

spindle 0.8.1 wants to compile tests with mpi.h, newer versions need mpicc,
thus add: depends_on("mpi"). Spindle supports the --no-mpi to disable MPI.
2021-09-27 08:58:47 -07:00
Edward Hartnett
ffedc3637c
added NOAAs UPP package (#26198) 2021-09-27 08:56:05 -07:00
Adam J. Stewart
4d3becdfd9
py-torch: add v1.9.1 (#26159) 2021-09-27 09:30:47 -05:00
bernhardkaindl
4a130b9185
perl: Fix test case bug perl#15544: Don't fail with PATH >1000 chars (#26245)
Fix the perl test case bug Perl/perl5#15544
Variable PATH longer than 1000 characters (as is usual with spack) fails a perl test case
The fix is: Don't test PATH in testcase perlbug.t
Fixes `spack install --test=all` for specs triggering a build and test of perl!
2021-09-27 15:18:36 +02:00
Manuela Kuhn
2acfe55b74
exempi: fix expat dependency (#26221)
* exempi: fix expat dependency and fix test with --test=root

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-09-27 14:52:23 +02:00
iarspider
8710353336
pythia8: update to v8.306, change url, set environment variables for dependents (#26255) 2021-09-27 09:05:51 +00:00
Jen Herting
514d04c8f1
New package: r-klar (#25390) 2021-09-27 02:53:03 +00:00
Jen Herting
87e91178a6
New package: r-questionr (#25395) 2021-09-26 21:35:24 -05:00
Manuela Kuhn
e90534d45e
py-python-gitlab: add 2.10.1 (#26229) 2021-09-27 01:24:05 +02:00
Wouter Deconinck
caa33b7b05
[acts] eigen is not only a build dependency (#26257)
The ActsConfig.cmake includes a `find_dependency(Eigen3)` line. Requiring depends_on type='build' does not expose eigen to dependents during their build.

Ref: https://github.com/acts-project/acts/blob/v13.0.0/cmake/ActsConfig.cmake.in#L59
2021-09-27 01:23:44 +02:00
lorddavidiii
8fa6597d43
cfitsio: add version 4.0.0 (#26218) 2021-09-27 01:18:09 +02:00
Seth R. Johnson
7e2fc45354
trilinos: default gotype=long_long (#26253)
"Long long" is the default type when building trilinos on its own, and
many downstream packages (both in and out of spack) rely on it. E4S
already sets this explicitly to long_long.
2021-09-26 16:51:23 +02:00
Desmond Orton
3e7cee27d7
masurca: add versions up to v4.0.5 (#26171)
Co-authored-by: las_djorton <las_djorton@babybuild.las.iastate.edu>
2021-09-26 15:53:59 +02:00
Wouter Deconinck
798ef2bdb0
vtk: depends_on freetype @:2.10.2 through @:9.0.1 only (#26180)
The issues in https://gitlab.kitware.com/vtk/vtk/-/issues/18033 were fixed in:
- dae1718d50
- 31e8e4ebeb

These fixes are in vtk@9.0.2 https://github.com/Kitware/VTK/releases/tag/v9.0.2 and beyond.
2021-09-26 15:52:51 +02:00
Brian Van Essen
cc658c5f1e
lbann: add support for building with the ONNX C++ library (#26130) 2021-09-26 15:50:09 +02:00
Valentin Volkl
1f972f90c8
podio, edm4hep: fix tests (#26116)
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2021-09-26 15:49:10 +02:00