Commit graph

19946 commits

Author SHA1 Message Date
Tomoyasu Nojiri
2648fe902d
bpp-seq: add v2.4.1 (#22171) 2021-03-08 10:19:54 +01:00
Tomoyasu Nojiri
39e30520ce
bpp-core: add v2.4.1 (#22172) 2021-03-08 10:19:19 +01:00
Andrew W Elble
a0b5dcca3c
py-tensorflow-probability: new package (#22165)
* py-tensorflow-probability: new package

* setuptools dep, quoting syntax
2021-03-08 02:23:49 +00:00
Todd Gamblin
8d3272f82d
spack python: add --path option (#22006)
This adds a `--path` option to `spack python` that shows the `python`
interpreter that Spack is using.

e.g.:

```console
$ spack python --path
/Users/gamblin2/src/spack/var/spack/environments/default/.spack-env/view/bin/python
```

This is useful for debugging, and we can ask users to run it to
understand what python Spack is picking up via preferences in `bin/spack`
and via the `SPACK_PYTHON` environment variable introduced in #21222.
2021-03-07 13:37:26 -08:00
Todd Gamblin
7aa5cc241d
add spack test list --all (#22032)
`spack test list` will show you which *installed* packages can be tested
but it won't show you which packages have tests.

- [x] add `spack test list --all` to show which packages have test methods
- [x] update `has_test_method()` to handle package instances *and*
      package classes.
2021-03-07 11:44:17 -08:00
darmac
e9c399110e
Add new package: r-mockery (#22125) 2021-03-06 13:51:53 -06:00
darmac
18ba1b8923
Add new package: r-lobstr (#22069) 2021-03-06 03:49:39 +00:00
Vanessasaurus
ef9a607c4c
libabigail: new package (#22092)
* adding package for libabigail, which we likely will need to use it for an analysis!
* includes variant for documentation (doxygen and pysphinx are associated dependencies)
2021-03-05 22:09:08 +00:00
Glenn Johnson
b5916451fd
Improve R package creation (#21861)
* Improve R package creation

This PR adds the `list_url` attribute to CRAN R packages when using
`spack create`. It also adds the `git` attribute to R Bioconductor
packages upon creation.

* Switch over to using cran/bioc attributes

The cran/bioc entries are set to have the '=' line up with homepage
entry, but homepage does not need to exist in the package file. If it
does not, that could affect the alignment.

* Do not have to split bioc

* Edit R package documentation

Explain Bioconductor packages and add `cran` and `bioc` attributes.

* Update lib/spack/docs/build_systems/rpackage.rst

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

* Update lib/spack/docs/build_systems/rpackage.rst

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

* Simplify the cran attribute

The version can be faked so that the cran attribute is simply equal to
the CRAN package name.

* Edit the docs to reflect new `cran` attribute format

* Use the first element of self.versions() for url

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-03-05 21:19:15 +00:00
Adam J. Stewart
89a4c9bb6d
gtkplus: add new version, convert to meson (#21914)
* gtkplus: add new version, convert to meson

* Add suggestions from aweits
2021-03-05 16:04:40 -05:00
Asher Mancinelli
da69f6eda8
Added support for disabling mumps in ipopt (#21592) 2021-03-05 11:32:11 -08:00
Martin Pokorny
4097a0c93f
casacore: use a modern CMake's version of FindHDF5.cmake (#21882)
Remove casacore's old version of the file with a package patch()
function, and depend on a modern CMake for the build.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-03-05 16:05:37 +00:00
iarspider
ad9db839cf
syscalc: fix recipe and URL (extension) (#22112) 2021-03-05 16:21:12 +01:00
David Böhme
098b7b2e50
Add Caliper 2.5.0 and Adiak 0.3.0 (#20718) 2021-03-05 15:30:57 +01:00
emai-imcs
71dd8ed265
FEniCS: update of packages to support 2019.1.0 (#21207) 2021-03-05 07:27:35 -07:00
Vasileios Karakasis
3b1b51e90d
reframe: add v3.4.2 and v3.4.1, enable autocompletion (#22114) 2021-03-05 13:57:21 +00:00
Mathew Cleveland
ca3171d002
py-oppy: add v0_1_5 (#22061)
Co-authored-by: Cleveland <cleveland@lanl.gov>
2021-03-05 06:09:35 -07:00
thelfer
aa8079556a
tfel: add v3.3.1, fix typo in checksum of v3.4.0 (#22062) 2021-03-05 12:27:05 +01:00
iarspider
ea45b95039
pythia6: extra patch provided by CERN's EP-SFT (#22055) 2021-03-05 04:14:36 -07:00
snehring
daf2ef9682
mcl: fixing missing extern in global variables (#22094)
Revealed by GCC 10 see https://gcc.gnu.org/gcc-10/porting_to.html
2021-03-05 12:01:18 +01:00
darmac
3c1b305752
rtags: add v2.20 (#22068) 2021-03-05 11:28:45 +01:00
Valentin Volkl
70cd948852
dd4hep: add v0.16 and geant4units variant (#22064) 2021-03-05 11:28:05 +01:00
Mark W. Krentel
290df7a14a
hpcviewer: add version 2021.03 (#22107) 2021-03-05 10:08:09 +00:00
Tomoyasu Nojiri
d7c4f7b7e6
xfsprogs: add --with-systemd-unit-dir option (#22075) 2021-03-05 10:39:36 +01:00
Tomoyasu Nojiri
d3b10b04c1
freeipmi: add --with-systemdsystemunitdir option (#22096) 2021-03-05 10:38:19 +01:00
Tomoyasu Nojiri
97afb34ac3
keepalived: add --with-systemdsystemunitdir option (#22098) 2021-03-05 10:37:39 +01:00
Tomoyasu Nojiri
dc275e1f83
moosefs: add --with-systemdsystemunitdir option (#22099) 2021-03-05 10:36:32 +01:00
Tomoyasu Nojiri
346e6b3b77
rrdtool: add --with-systemdsystemunitdir option (#22100) 2021-03-05 10:30:34 +01:00
Adam J. Stewart
5fb0ff3906
py-torch: add v1.8.0 (#22101) 2021-03-05 10:21:39 +01:00
Adam J. Stewart
4261de5434
py-torchvision: add v0.9.0 (#22102) 2021-03-05 10:21:15 +01:00
Axel Huebl
c2925a1704
SLATE: Default ~cuda (#22110)
Same as BLAS++ since more GPU backends are coming and cuda
is usually off as a variant default in Spack, unless requested.
2021-03-05 10:11:16 +01:00
Tomoyasu Nojiri
03756583c3
py-python-ldap: add link dependency on cyrus-sasl (#22105) 2021-03-05 10:07:02 +01:00
Mark W. Krentel
c6b632a1f9
hpctoolkit: add version 2021.03.01 (#22106)
1. Add version 2021.03.01.
2. Cleanup the binutils dependencies now that 2.35.2 and 2.36 are available.
3. Require gcc 7.x or later for current 2021 version.
4. Simplify the xz depends to always require +pic.
   This works around a glitch in the original concretizer.
2021-03-05 10:06:11 +01:00
h-denpo
c460013a91
flexi: allow building on aarch64 (#22109) 2021-03-05 10:02:15 +01:00
Valentin Volkl
e112a26513
py-awkward1: add v1.1.2 (#22081)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-03-05 09:52:57 +01:00
Greg Becker
92b7805e40
Allow relative paths in config files (relative to file dirname) (#21996)
This allows users to use relative paths for mirrors and repos and other things that may be part of a Spack environment.  There are two ways to do it.

1. Relative to the file

    ```yaml
    spack:
      repos:
      - local_dir/my_repository
    ```

    Which will refer to a repository like this in the directory where `spack.yaml` lives:

    ```
    env/
      spack.yaml  <-- the config file above
      local_dir/
        my_repository/  <-- this repository
          repo.yaml
          packages/
    ```

2. Relative to the environment

    ```yaml
    spack:
      repos:
      - $env/local_dir/my_repository
    ```

Both of these would refer to the same directory, but they differ for included files.  For example, if you had this layout:

```
env/
    spack.yaml
    repository/
    includes/
        repos.yaml
        repository/
```

And this `spack.yaml`:

```yaml
spack:
    include: includes/repos.yaml
```

Then, these two `repos.yaml` files are functionally different:

```yaml
repos:
    - $env/repository    # refers to env/repository/ above

repos:
    - repository    # refers to env/includes/repository/ above
```
    
The $env variable will not be evaluated if there is no active environment. This generally means that it should not be used outside of an environment's spack.yaml file. However, if other aspects of your workflow guarantee that there is always an active environment, it may be used in other config scopes.
2021-03-04 22:29:48 -08:00
Larry Knox
8bdd6c6f6d
hdf5: add v1.8.22. (#22089) 2021-03-04 20:04:52 +00:00
darmac
10c7831366
Add new package: perl-test-more (#22076)
* Add new package: perl-test-more

* perl-test-more: refine description
2021-03-04 10:04:57 -08:00
darmac
459b991e78
perl-test-output: new package at v1.033 (#22077) 2021-03-04 18:11:28 +01:00
Michael Kuron
7f01d1dc40
py-ase: add a build dependency on py-setuptools (#22078) 2021-03-04 18:09:37 +01:00
darmac
e9dfc50d1b
py-sqlparse: add v0.4.1 (#22080) 2021-03-04 17:44:33 +01:00
Dr. Christian Tacke
04cd884c95
poke: new package at v1.0 (#22085) 2021-03-04 17:41:48 +01:00
Dr. Christian Tacke
71954d9665
xrootd: add v5.1.0 (#22084) 2021-03-04 17:39:58 +01:00
Tomoyasu Nojiri
d7dd12edab
unifyfs: Fix strncpy build error of version 0.9.1 (#22066) 2021-03-04 07:46:18 -08:00
Axel Huebl
49c015e391
BLAS++: CUDA default (false) (#22067)
For opt-in packages in Spack, its common that the `cuda` variant
is disabled by default.

This also simplifies downstream usage in multi-variants for
backends in user code.
2021-03-04 12:07:48 +01:00
Mosè Giordano
7e143bab6a
libblastrampoline: Add version 3.0.2 (#22065) 2021-03-04 11:05:32 +01:00
darmac
f1d0a819e9
py-adb-enhanced: update version to fix runtime error (#22036)
* py-adb-enhanced: update version to fix runtime error

* py-adb-enhanced: fix dependencies
2021-03-03 20:57:41 -06:00
Andrew W Elble
631598014a
py-pycuda: new version 2020.1 (#22057)
* py-pycuda: new version 2020.1

* dep updates

* deal with lib/lib64 issue
2021-03-03 22:06:02 +00:00
Massimiliano Culpo
10e9e142b7
Bootstrap clingo from sources (#21446)
* Allow the bootstrapping of clingo from sources

Allow python builds with system python as external
for MacOS

* Ensure consistent configuration when bootstrapping clingo

This commit uses context managers to ensure we can
bootstrap clingo using a consistent configuration
regardless of the use case being managed.

* Github actions: test clingo with bootstrapping from sources

* Add command to inspect and clean the bootstrap store

 Prevent users to set the install tree root to the bootstrap store

* clingo: documented how to bootstrap from sources

Co-authored-by: Gregory Becker <becker33@llnl.gov>
2021-03-03 09:37:46 -08:00
Frédéric Simonis
6d54df1ba4
precice: add pkgconfig as a build dependency (#22059) 2021-03-03 17:10:00 +00:00