Commit graph

29406 commits

Author SHA1 Message Date
Erik Heeren
80e30222e1
New neuroscience packages: py-bmtk, py-neurotools (#34464)
* Add py-bmtk and py-neurotools

* py-bmtk: version bump

* [@spackbot] updating style on behalf of heerener

* Maybe the copyright needs to be extended to 2022 for the check to pass

* Process review remarks

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-14 12:00:26 -06:00
eugeneswalker
55356e9edb
bufr: add v11.6, 11.7, 11.7.1 (#34509) 2022-12-14 06:24:26 -07:00
eugeneswalker
eec09f791d
fms: add v2019.01.03 (#34511) 2022-12-14 04:50:00 -07:00
Harmen Stoppels
9032179b34
Use update-index --mirror-url <url> instead of -d <url> (#34519) 2022-12-14 10:03:18 +01:00
Alberto Sartori
45b40115fb
justbuild: add v1.0.0 (#34467) 2022-12-14 01:17:42 -07:00
snehring
e030833129
r-rgdal: adding new version 1.6-2 (#34502) 2022-12-13 20:06:31 -07:00
Harmen Stoppels
e055dc0e64
Use file paths/urls correctly (#34452)
The main issue that's fixed is that Spack passes paths (as strings) to
functions that require urls. That wasn't an issue on unix, since there
you can simply concatenate `file://` and `path` and all is good, but on
Windows that gives invalid file urls. Also on Unix, Spack would not deal with uri encoding like x%20y for file paths. 

It also removes Spack's custom url.parse function, which had its own incorrect interpretation of file urls, taking file://x/y to mean the relative path x/y instead of hostname=x and path=/y. Also it automatically interpolated variables, which is surprising for a function that parses URLs.

Instead of all sorts of ad-hoc `if windows: fix_broken_file_url` this PR
adds two helper functions around Python's own path2url and reverse.

Also fixes a bug where some `spack buildcache` commands
used `-d` as a flag to mean `--mirror-url` requiring a URL, and others
`--directory`, requiring a path. It is now the latter consistently.
2022-12-13 23:44:13 +01:00
Matthias Wolf
c45729cba1
py-submitit: add 1.4.5 (#34460) 2022-12-13 16:11:14 -06:00
Manuela Kuhn
b02b2f0f00
py-tifffile: add 2022.10.10 (#34499) 2022-12-13 16:09:01 -06:00
Manuela Kuhn
3ded50cc8c
py-sphinxcontrib-qthelp: add 1.0.3 (#34495) 2022-12-13 16:08:06 -06:00
Manuela Kuhn
a7280cd5bb
py-sqlalchemy: add 1.4.45 (#34497) 2022-12-13 16:07:34 -06:00
Paul Kuberry
2837b47ea5
trilinos: extend range of Teuchos patch (#34504) 2022-12-13 14:49:20 -07:00
Matthew Thompson
ea2c61c683
Update pFunit, add gFTL, gFTL-Shared, fArgParse, pFlogger, yaFyaml (#34476)
* Add GFE packages, Update pFUnit
* Remove citibeth as maintainer per her request
* Version 3.3.0 is an odd duck. Needs a v

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-12-13 22:40:33 +01:00
Bernhard Kaindl
217b34825a
py-tensorboard-data-server: build needs rust+rustfmt (#34465) 2022-12-13 10:56:31 -07:00
Mosè Giordano
17d90f4cbc
pcre2: add new versions and update URL (#34477) 2022-12-13 10:48:27 -07:00
Annop Wongwathanarat
7a5bd8cac4
gromacs: enable linking with acfl FFT (#34494) 2022-12-13 09:32:42 -08:00
Harmen Stoppels
333da47dc7
Don't fetch to order mirrors (#34359)
When installing binary tarballs, Spack has to download from its
binary mirrors.

Sometimes Spack has cache available for these mirrors.

That cache helps to order mirrors to increase the likelihood of
getting a direct hit.

However, currently, when Spack can't find a spec in any local cache
of mirrors, it's very dumb:

- A while ago it used to query each mirror to see if it had a spec,
  and use that information to order the mirror again, only to go
  about and do exactly a part of what it just did: fetch the spec
  from that mirror confused
- Recently, it was changed to download a full index.json, which
  can be multiple dozens of MBs of data and may take a minute to
  process thanks to the blazing fast performance you get with
  Python.

In a typical use case of concretizing with reuse, the full index.json
is already available, and it likely that the local cache gives a perfect
mirror ordering on install. (There's typically no need to update any
caches).

However, in the use case of Gitlab CI, the build jobs don't have cache,
and it would be smart to just do direct fetches instead of all the
redundant work of (1) and/or (2).

Also, direct fetches from mirrors will soon be fast enough to
prefer these direct fetches over the excruciating slowness of
index.json files.
2022-12-13 17:07:11 +01:00
dependabot[bot]
8b68b4ae72
build(deps): bump actions/checkout from 3.1.0 to 3.2.0 (#34480)
Bumps [actions/checkout](https://github.com/actions/checkout) from 3.1.0 to 3.2.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](93ea575cb5...755da8c3cf)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-12-13 09:05:50 -07:00
Adam J. Stewart
40a3fdefa8
py-cartopy: add v0.21.1 (#34482) 2022-12-13 07:12:24 -07:00
Adam J. Stewart
a61474f2c1
libicd: macOS now supported (#34483) 2022-12-13 07:12:00 -07:00
Aidan Heerdegen
b95a75779b
Fix markdown links in rst files (#34488) 2022-12-13 14:11:38 +00:00
Harmen Stoppels
0ff6a1bd1c
spack/package.py: improve editor support for some +/- static props (#34319) 2022-12-13 13:55:32 +01:00
Massimiliano Culpo
f9cfc2f57e
scons: fix signature for install_args (#34481) 2022-12-13 12:21:44 +01:00
Adam J. Stewart
f4fb20e27e
py-shapely: add v2.0.0 (#34475) 2022-12-13 09:59:23 +01:00
Massimiliano Culpo
3ff5d49102
Be strict on the markers used in unit tests (#33884) 2022-12-13 09:21:57 +01:00
Erik Heeren
238d4f72f5
py-pyld: add with dependency (#34472)
* py-pyld: add with dependency

* py-pyld and py-frozendict: update copyright expiration

* [@spackbot] updating style on behalf of heerener
2022-12-12 20:15:43 -07:00
Matthias Wolf
c5bc469eeb
py-sh: new versions (#34458)
* py-sh: new versions

* style
2022-12-12 20:15:28 -07:00
Sam Grayson
b01e7dca9d
Update packages for running azure (#34403)
* Update packages for running azure

* Update py-msal-extensions

* Respond to comments
2022-12-12 21:10:50 -06:00
Jean Luca Bez
c62906f781
New python package: Drishti (#33316)
* include Drishti

* fix syntax

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

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

* Update package.py

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-12 19:33:50 -07:00
Sam Grayson
94bac8d6dd
Add new package: micromamba (#34195)
* Add new packages

* wip

* wip

* wip

* wip

* wip

* wip

* wip

* wip

* style

* wip

* Respond to comments

* Respond to comments

* Spack style

* Remove linkage=full_static to pass package audit

* Spack style

* Moved tl-expected version
2022-12-12 14:00:41 -06:00
Manuela Kuhn
cd9c9b47e8
py-sphinxcontrib-devhelp: add 1.0.2 (#34462)
* py-sphinxcontrib-devhelp: add 1.0.2

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-12 13:57:06 -06:00
Manuela Kuhn
8560295529
py-sphinxcontrib-applehelp: add 1.0.2 (#34461)
* py-sphinxcontrib-applehelp: add 1.0.2

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-12 13:56:48 -06:00
Adam J. Stewart
fd248ad0b8
GEOS: add v3.10-3.11 (#34473) 2022-12-12 11:50:03 -08:00
renjithravindrankannath
0578ccc0e6
ROCm 5.3.0 updates (#33320)
* ROCm 5.3.0 updates
* New patches for 5.3.0 on hip and hsakmt
* Adding additional build arguments in hip and llvm
* RVS updates for 5.3.0 release
* New patches and rocm-tensile, rocprofiler-dev, roctracer-dev recipe updates for 5.3.0
* Reverting OPENMP fix from rocm-tensile
* Removing the patch to compile without git and adding witout it
* Install library in to lib directory instead of lib64 across all platform
* Setting lib install directory to lib
* Disable gallivm coroutine for libllvm15
* Update llvm-amdgpu prefix path in hip-config.cmake.in
  Removing libllvm15 from Mesa dependency removing
* hip-config.cmake.in update required from 5.2
* hip-config.cmake.in update required from 5.2 and above
* hip-config.cmake.in update required for all 5.2 release above
* Style check correction in hip update
* ginkgo: add missing include
* Patching hsa include path for rocm 5.3
* Restricting patch for llvm-15
* Style check error correction
* PIC flag required for the new test applications
* Passing -DCMAKE_POSITION_INDEPENDENT_CODE=ON in the cmake_args instead of setting -fPIC in CFLAGS

Co-authored-by: Cordell Bloor <Cordell.Bloor@amd.com>
2022-12-12 13:46:20 -06:00
Glenn Johnson
fcc2ab8b4b
julia: have recipe explicitly use Spack compiler wrapper (#34365) 2022-12-12 19:53:26 +01:00
Vanessasaurus
76511ac039
Automated deployment to update package flux-core 2022-12-12 (#34456) 2022-12-12 11:47:36 -07:00
Jim Edwards
e4547982b3
allow esmf to use parallelio without mpi (#34182)
* allow esmf to use parallelio without mpi
* add hash for 8.4.0
* spack no longer sets arch to cray
2022-12-12 09:50:41 -08:00
Manuela Kuhn
80722fbaa3
py-snowballstemmer: add 2.2.0 (#34459) 2022-12-12 10:23:55 -06:00
Wouter Deconinck
c2fa444344
geant4: rm preference for 10.7.3 now that 11.1.0 is out (#34445) 2022-12-12 09:05:47 -07:00
Stephen Sachs
088ece1219
[texinfo] @7.0: needs c-11 syntax (#34261)
gnulib/lib/malloca.c uses single value `static_assert()` only available in c-11
syntax. `gcc` seems to be fine, but `icc` needs extra flag.

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-12-12 16:52:26 +01:00
Veselin Dobrev
fcdd275564
MFEM: fix issue with cxxflags (#34435) 2022-12-12 16:52:00 +01:00
Mikael Simberg
b6d6a1ab2c
Build tests for fmt conditionally (#34424) 2022-12-12 16:49:05 +01:00
Robert Blake
7efcb5ae73
Fixes to the silo packages for 4.11. (#34275) 2022-12-12 07:39:24 -07:00
Mikael Simberg
06e6389258
stdexec: skip build phase (#34425)
Since it's a header-only library there's nothing to build. However, the
default targets include tests and examples and there's no option to turn
them off during configuration time.
2022-12-12 07:16:40 -07:00
Simon Flood
b7f0f7879d
foam-extend: add v4.1 (released Oct 2019) (#34398) 2022-12-12 07:16:17 -07:00
Bernhard Kaindl
f7cfbe2702
hdf5: "hdf5@1.13:" needs a depends_on "cmake@3.18:" for build. (#34447) 2022-12-12 15:12:55 +01:00
Wouter Deconinck
1466f8d602
geant4-data: depends_on g4emlow@7.9.1 when @10.6 (#34444)
Per https://geant4.web.cern.ch/node/1837 the correct dependency for 10.6 is on `g4emlow@7.9.1`, not on both `g4emlow@7.9` and `g4emlow@7.9.1`.

This is a minor cosmetic fix. The concretization for 10.6 works just fine here. But this removes the duplicate entry.
2022-12-12 07:11:42 -07:00
Glenn Johnson
9fdb36585f
Fix openblas build with intel compiler (#34432)
This PR patches the f_check script to detect the ifort compiler and
ensure that F_COMPILER is iset to INTEL. This problem was introduced with
openblas-0.3.21. Without this patch, the value of F_COMPILER falls back
to G77 and icc rather than ifort is used for the linking stage. That
results in the openblas library missing libifcore, which in turn means
many Fotran programs can not be compiled with ifort.
2022-12-12 14:27:54 +01:00
Filippo Spiga
1f0a9fdc11
Adding NVIDIA HPC SDK 22.11 (#33954) 2022-12-12 14:26:39 +01:00
Jen Herting
0baba62900
arrow: dependency fixes (#33666)
+python needs more dependencies
don't look for dependency spec when it's not there
2022-12-12 14:26:02 +01:00