Commit graph

29558 commits

Author SHA1 Message Date
Massimiliano Culpo
033cb86fd6 Add vendored packages back 2023-01-04 09:43:04 -08:00
Massimiliano Culpo
5175189412 Delete outdated externals 2023-01-04 09:43:04 -08:00
Massimiliano Culpo
86378502f9 Use "vendoring" to manage 3rd party dependencies 2023-01-04 09:43:04 -08:00
Sinan
2530c7828b
add_new_package: py-file-magic (#34486)
* add_new_package: py-file-magic

* re-order depends...

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

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

* [@spackbot] updating style on behalf of Sinan81

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
2023-01-04 11:08:58 -06:00
Erik Heeren
ab2f842424
Add py-svgpath and py-trimesh (#34471)
* Add py-svgpath and dependency

* Update copyright expiration

* [@spackbot] updating style on behalf of heerener

* Process review remarks

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

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

* Fix style issue

* py-trimesh: cleanup and optional dependencies

* Fix formatting issue

* py-trimesh: complete dependency list for easy variant

Two new packages: py-mapbox-earcut and py-pycollada

* Some more missing dependencies

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-04 11:00:00 -06:00
Harmen Stoppels
b9f48da560
e4s: move default values for rocm/cuda arch into packags:all:variants (#34772) 2023-01-04 16:09:14 +01:00
Harmen Stoppels
e21c1c5770
set PREFIX in make() for some packages (#34773) 2023-01-04 15:08:15 +01:00
Massimiliano Culpo
310b6b9466
Remove dead code that was needed for the old parser (#34792)
The old to token definitions and spec_id_re regular
expression are not used anymore
2023-01-04 05:47:21 -08:00
Alberto Invernizzi
a869cfd95d
Fix libvterm and libtermkey packages (#34776)
* fix PREFIX for both libvterm and libtermkey

* minor: use libtool from dependency

* switch to command-line prefix instead of replacing it in Makefile
2023-01-04 10:27:21 +01:00
Glenn Johnson
ddab6c4ac3
new package: py-kb-python + dependencies (#34737)
* new package: py-kb-python + dependencies

- py-loompy
- py-ngs-tools
- py-numpy-groupies

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-03 16:35:43 -06:00
Glenn Johnson
25cff6be14
py-shortuuid: add version 1.0.11 (#34739)
* py-shortuuid: add version 1.0.11

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-03 16:35:13 -06:00
kwryankrattiger
5fe1281b14
LLVM: Update HWLOC dep version (#34780) 2023-01-03 12:42:49 -08:00
Sebastian Grabowski
43cf60814d
jube: Add versions 2.5.0 and 2.5.1 (#34783)
* jube: Add 2.5.0 and 2.5.1

* jube: Depend on py-pyyaml
2023-01-03 12:17:32 -08:00
John W. Parent
582f165871
Windows: package defaults and MPI detection (#34614)
* Update packages config to indicate that MSVC is the preferred compiler
* Update packages config to indicate that msmpi is the preferred MPI provider
* Fix msmpi external detection
2023-01-03 08:32:18 -08:00
Harmen Stoppels
bf76f1e774
scr: require spath+mpi (#34775)
It includes `spath_mpi.h` explicitly, and in some concretizations
results in a build failure. (Don't ask me why the concretizer picks
`spath~mpi`).
2023-01-03 09:53:48 -06:00
Harmen Stoppels
9cdb862856
gmake: 4.4, remove alpha release (#34709) 2023-01-02 14:07:24 -08:00
Harmen Stoppels
2e8d165120
environment view use new traversal (#34662) 2023-01-02 19:04:55 +01:00
Christoph Junghans
6984ee291a
votca: add v2022.1 (#34650) 2023-01-02 19:02:59 +01:00
Wouter Deconinck
10d506d61b
pixman: new versions 0.42.0, 0.42.2 (#34723)
This fixes, [among other things](https://lists.freedesktop.org/archives/pixman/2022-October/004993.html),
a [bug](https://issuetracker.google.com/issues/249834910) in 0.40.0 that
prevents building with oneapi.
2023-01-02 18:58:41 +01:00
Adam J. Stewart
4549312c5e
py-sphinx: add v6.0.0 (#34724) 2023-01-02 18:57:49 +01:00
Glenn Johnson
80761bdc9d
libxau: add libs property (#34288) 2023-01-02 18:47:18 +01:00
Glenn Johnson
4eb853856a
r-affyio: add zlib dependency (#34743) 2023-01-02 18:33:27 +01:00
Glenn Johnson
790929c832
r-cairo: add needed dependency on libxt (#34744) 2023-01-02 18:33:15 +01:00
Glenn Johnson
769378c959
r-hdf5array: add needed dependency on zlib (#34745) 2023-01-02 18:32:59 +01:00
Glenn Johnson
a18e2f98b3
r-rhdf5: add needed zlib dependency (#34746) 2023-01-02 18:32:44 +01:00
Glenn Johnson
8f3bdf29dc
r-rhdf5filters: add needed zlib dependency (#34747) 2023-01-02 18:32:31 +01:00
Glenn Johnson
a28bb90b93
r-rhdf5lib: add needed zlib dependency (#34748) 2023-01-02 18:32:17 +01:00
Glenn Johnson
5c9b591439
r-rjava: add needed zlib dependency (#34749) 2023-01-02 18:31:56 +01:00
Glenn Johnson
778325db42
r-rtracklayer: add zlib and openssl dependencies (#34750) 2023-01-02 18:31:37 +01:00
Glenn Johnson
f65bb62de4
r-signac: added needed zlib dependency (#34751) 2023-01-02 18:31:22 +01:00
Glenn Johnson
e4881d5465
bcftools: add version 1.15.1 (#34752) 2023-01-02 18:31:08 +01:00
Glenn Johnson
31cccdf52b
genrich: add needed zlib dependency (#34753) 2023-01-02 18:29:23 +01:00
Glenn Johnson
2c1523debe
mumax: Set NVCC_CCBIN to spack compiler wrapper (#34754) 2023-01-02 18:28:45 +01:00
Glenn Johnson
c07881c843
openscenegraph: add dependency on fontconfig (#34755) 2023-01-02 18:28:28 +01:00
Glenn Johnson
cb807594b8
rsl: add needed dependency on rpc (#34756) 2023-01-02 18:28:10 +01:00
Michael Kuhn
0227c0a98a
miniconda3: add 22.11.1 (#34761) 2023-01-02 18:22:45 +01:00
Michael Kuhn
20a1cdd95e
anaconda3: add 2022.10 (#34762) 2023-01-02 18:21:23 +01:00
Wouter Deconinck
2a779c1234
mesa: new versions up to v22.3.2 (#34760)
disable gallium-xvmc when @:22.2
2023-01-02 18:11:03 +01:00
Weiqun Zhang
3f6109404d
amrex: add v23.01 and v22.12 (#34764)
Since amrex@22.12, CUDA >= 11 is needed for C++17 support.  Since
amrex@23.01 oneAPI >= 2023 is needed for SYCL 2020.
2023-01-02 18:07:41 +01:00
Wouter Deconinck
f83d47442d
dd4hep: depends_on root +x +opengl when +utilityapps (#34765)
UtilityApps builds teveDisplay and fails when ROOT has no ROOT::Gui and ROOT::Eve targets.
2023-01-02 17:56:34 +01:00
Wouter Deconinck
08aafe180b
singularity: bugfix add space between prefix and other options (#34766)
This fixes two issues introduced in #34474: prefix got the next
option appended, and property was not resolved without the self.
2023-01-02 17:55:30 +01:00
Peter Brady
9cbbe64cf7
emacs: json variant & cleanup (#34665)
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-01-02 07:17:04 -08:00
Cyrus Harrison
2b006bb6ec
add conduit 0.8.5 release and caliper variant (#34669) 2023-01-02 16:00:44 +01:00
Alex Richert
5509392151
libpng static (#34578) 2023-01-02 15:12:41 +01:00
lorddavidiii
2001be99b3
doxygen: use tarballs instead of git checkouts and add 1.9.5 (#34654)
* doxygen: use tarballs instead of git checkouts and add 1.9.5

* Doxygen: add 1.9.6
2023-01-02 08:44:34 -05:00
Rocco Meli
dd4409b62c
libxc: add v6.0.0 (#34621) 2023-01-02 04:26:54 -08:00
Todd Gamblin
ca265ea0c2
style: fix spurious mypy errors from numpy (#34732)
Spack imports `pytest`, which *can* import `numpy`. Recent versions of `numpy` require
Python 3.8 or higher, and they use 3.8 type annotations in their type stubs (`.pyi`
files). At the same time, we tell `mypy` to target Python 3.7, as we still support older
versions of Python.

What all this means is that if you run `mypy` on `spack`, `mypy` will follow all the
static import statements, and it ends up giving you this error when it finds numpy stuff
that is newer than the target Python version:

```
==> Running mypy checks
src/spack/var/spack/environments/default/.spack-env/._view/4g7jd4ibkg4gopv4rosq3kn2vsxrxm2f/lib/python3.11/site-packages/numpy/__init__.pyi:638: error: Positional-only parameters are only supported in Python 3.8 and greater  [syntax]
Found 1 error in 1 file (errors prevented further checking)
  mypy found errors
```

We can fix this by telling `mypy` to skip all imports of `numpy` in `pyproject.toml`:

```toml
   [[tool.mypy.overrides]]
   module = 'numpy'
   follow_imports = 'skip'
   follow_imports_for_stubs = true
```

- [x] don't follow imports from `numpy` in `mypy`
- [x] get rid of old rule not to follow `jinja2` imports, as we now require Python 3
2023-01-01 01:05:17 +00:00
Glenn Johnson
7a92579480
py-fisher: add version 0.1.10 (#34738) 2022-12-31 12:48:21 -06:00
Glenn Johnson
190dfd0269
py-youtube-dl: add version 2021.12.17 (#34740) 2022-12-31 12:42:58 -06:00
Massimiliano Culpo
b549548f69
Simplify creation of test and install reports (#34712)
The code in Spack to generate install and test reports currently suffers from unneeded complexity. For
instance, we have classes in Spack core packages, like `spack.reporters.CDash`, that need an
`argparse.Namespace` to be initialized and have "hard-coded" string literals on which they branch to
change their behavior:

```python
if do_fn.__name__ == "do_test" and skip_externals:
    package["result"] = "skipped"
else:
    package["result"] = "success"
package["stdout"] = fetch_log(pkg, do_fn, self.dir)
package["installed_from_binary_cache"] = pkg.installed_from_binary_cache
if do_fn.__name__ == "_install_task" and installed_already:
    return
```
This PR attempt to polish the major issues encountered in both `spack.report` and `spack.reporters`.

Details:
- [x] `spack.reporters` is now a package that contains both the base class `Reporter` and all 
      the derived classes (`JUnit` and `CDash`)
- [x] Classes derived from `spack.reporters.Reporter` don't take an `argparse.Namespace` anymore
       as argument to `__init__`. The rationale is that code for commands should be built upon Spack
       core classes, not vice-versa.
- [x] An `argparse.Action` has been coded to create the correct `Reporter` object based on command
       line arguments
- [x] The context managers to generate reports from either `spack install` or from `spack test` have
       been greatly simplified, and have been made less "dynamic" in nature. In particular, the `collect_info`
       class has been deleted in favor of two more specific context managers. This allows for a simpler
       structure of the code, and less knowledge required to client code (in particular on which method to patch)
- [x] The `InfoCollector` class has been turned into a simple hierarchy, so to avoid conditional statements
       within methods that assume a knowledge of the context in which the method is called.
2022-12-30 10:15:38 -08:00