Commit graph

29641 commits

Author SHA1 Message Date
Rémi Lacroix
582ee111f6
MAFFT: Add latest version 7.505 (#34855) 2023-01-09 16:09:13 -08:00
Rémi Lacroix
c55de3f5e0
pv: Add version 1.6.20 (#34854) 2023-01-09 15:07:36 -08:00
renjithravindrankannath
0bdd4c10cf
RVS 5.1.0 and later works with googletest shared variant (#34802) 2023-01-09 14:41:40 -08:00
John Parent
521cc41db0 Remove Spack external find from startup
Spack was running an external detection of Python during each invocation
of the setup script for Windows CMD/PWSH, which has dramatic performance
implications each time the script is invoked, and is completely
unneccesary. Remove this operation.
2023-01-09 09:14:17 -08:00
John Parent
c0eb2cf9e6 Update haspywin
Inform user Spack is installing pyWin32 module behind the scenes.
This is neccesary for Windows support.
2023-01-09 09:14:17 -08:00
John Parent
9f0bb4301f Support ASCI control
Windows CMD prompt does not automatically support ASCI color control
characters on the console from Python. Enable this behavior by
accessing the current console and allowing the interpreation of ASCI
control characters from Python via the win32 API.
2023-01-09 09:14:17 -08:00
Stephen Sachs
288e728144
openfoam: OneAPI is only supported from 2106 onwards (#34797)
Also, adios2 fortran bindings are not necessary. This circumvents
https://github.com/spack/spack/issues/31817

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-09 12:19:23 +01:00
Harmen Stoppels
47011f594f
Revert "Allow spec.json files to be clearsigned, use transparent compression for *.json (#34490)" (#34856)
This reverts commit 8a1b817978.
2023-01-09 10:52:07 +01:00
Marco De La Pierre
a00f692f20
adding 3rd bunch of nf-core deps from update/nextflow-tools (#34563)
* adding 2nd bunch of nf-core deps from update/nextflow-tools

* adding 3rd bunch of nf-core deps from update/nextflow-tools

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

* py-gxformat2: added comment

* py-lagom: now using github tarballs

* fix for py-lagom

* adding missing deps to py-fastapi-utils

* another fix to py-lagom

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

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

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

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

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

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

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

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

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

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

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-08 20:06:59 -08:00
Adam J. Stewart
68bffd4689
GDAL: add v3.6.2 (#34823) 2023-01-07 13:57:18 +01:00
Wouter Deconinck
5acb20f145
acts: new version 22.0.0 (#34826)
No build system changes.
2023-01-07 13:56:37 +01:00
Harmen Stoppels
8a1b817978
Allow spec.json files to be clearsigned, use transparent compression for *.json (#34490)
This commit allows (remote) spec.json files to be clearsigned and gzipped.

The idea is to reduce the number of requests and number of bytes transferred
2023-01-07 12:22:40 +01:00
Marco De La Pierre
86e346e906
Adding recipes for py-qutip and py-qutip-qip (#34835)
* added recipes for py-qutip and py-qutip-qip

* small fix

* updated qutip 2x versions

* py-qutip-qip: tarball url from github

* style fix in py-qutip-qip

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

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

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

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

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

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

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

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

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-06 17:22:03 -08:00
Marco De La Pierre
a5ef522f98
Adding py-pennylane from Xanadu (#34838)
* draft for py-pennylane recipe

* first draft for py-strawberryfields recipe

* minimal fix

* small fixes

* accounting for circular dep in py-pennylane and py-pennylane-lightning

* removing py-strawberryfields from this branch

* updated versions for py-pennylane 2x

* needs cmake

* py-pennylane-lightning using github tarball

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

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

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-06 16:02:06 -08:00
Verinder Rana
800ac7b53d
kripke: add cuda and rocm support (#34257) 2023-01-06 15:57:00 -08:00
Luke Diorio-Toth
691e8c69c4
py-instrain and py-drep: new version and added maintainer (#34581) 2023-01-06 13:26:19 -06:00
QuellynSnead
ea970c8ab8
Fix PrgEnv detection (#34845)
* Fix PrgEnv detection for Cray compiler link paths
2023-01-06 18:11:43 +00:00
Erik Schnetter
c05827e794
mpiwrapper: New version 2.10.0 (#34795) 2023-01-06 15:46:04 +01:00
Erik Schnetter
910b13000f
cni-plugins: New version 1.1.1 (#34809) 2023-01-06 15:45:25 +01:00
Erik Schnetter
9474fdf910
conmon: New version 2.1.5 (#34810) 2023-01-06 15:44:55 +01:00
Erik Schnetter
2cdac9392f
go-md2man: New version 2.0.2 (#34811) 2023-01-06 15:44:35 +01:00
Erik Schnetter
6775c10e82
go: New version 1.19.4 (#34812) 2023-01-06 15:44:12 +01:00
Erik Schnetter
ea5d5517ce
libseccomp: New version 2.5.4 (#34814) 2023-01-06 15:43:48 +01:00
Erik Schnetter
8780c718ea
slirp4netns: New version 1.2.0 (#34816) 2023-01-06 15:07:22 +01:00
Erik Schnetter
9687491568
podman: New version 4.3.1 (#34817) 2023-01-06 15:06:36 +01:00
Erik Schnetter
9c56b97aa9
mpitrampoline: New version 5.2.0 (#34796) 2023-01-06 15:04:59 +01:00
Auriane R
df10e711f7
Fix the version number for the fmt dep of pika package (#34839)
* Fix the version number for the fmt dep of pika package

* Add version constraint for fmt standard specification
2023-01-06 14:59:23 +01:00
Harmen Stoppels
6fdb5dfa0a
cabana: version ranges (#34794)
Co-authored-by: Sam Reeve <6740307+streeve@users.noreply.github.com>
2023-01-05 19:21:57 +01:00
Stephen Sachs
ada174afbd
cmake fails with icpc warning (#34774)
The Intel compiler isn't able to deal with noinline member functions of template classses defined in headers. As such it outputs
```
warning #2196: routine is both "inline" and "noinline"
```
cmake bootstrap will fail due to the word 'warning'.

See spack/var/spack/repos/builtin/packages/protobuf/intel-v2.patch for reference.

The issue does not appear with intel@2021.7.0 or later:

```
$~: compiler=/shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-12.2.0/intel-oneapi-compilers-2022.2.0-uqvb2553zy5toeapvoopacndd27x6p5m/compiler/2022.2.0/linux/bin/intel64/icpc
$~: $compiler unique.c
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
```

This is a clean version of https://github.com/spack/spack/pull/34167

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-05 18:13:26 +01:00
Massimiliano Culpo
eace2ebb08
spack.dependency: add type hints (#34807) 2023-01-05 17:48:29 +01:00
Brent Huisman
441c0a4fee
Typo in arbor/package.py: incorrect version (#34820) 2023-01-05 13:55:31 +01:00
Sinan
0a7b0c68cf
package/libproxy: fix py3 install (#34431)
* package/libproxy: fix py3 install

* improve readability

* fix bug

* also add extend

* make flake happy

* [@spackbot] updating style on behalf of Sinan81

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

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

* python dependency implied by extends const.

* disable python variant by default

* add run_env, add py conflict

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

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

* set env for macos as well

* generalize lib dir detection

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-04 15:01:13 -06:00
Massimiliano Culpo
6a44a146af Fix building docs 2023-01-04 09:43:04 -08:00
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