Commit graph

32079 commits

Author SHA1 Message Date
Harmen Stoppels
c6465bd9bd
Add a proper deprecation warning for update-index -d (#34520) 2022-12-15 17:45:32 +01:00
Harmen Stoppels
9025caed6e
Remove warning in download_tarball (#34549) 2022-12-15 14:03:30 +00:00
Massimiliano Culpo
7056a4bffd
Forward lookup of the "run_tests" attribute (#34531)
fixes #34518

Fix an issue due to the MRO chain of the package wrapper
during build. Before this PR we were always returning
False when the builder object was created before the
run_tests method was monkey patched.
2022-12-15 09:35:33 +01:00
snehring
d2aa8466eb
metabat: adding missing build dependency (#34530) 2022-12-15 09:23:59 +01:00
Loïc Pottier
6e4684fbca
talass: fixed URLs so the package is reachable (#34387)
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2022-12-15 09:23:05 +01:00
Brian Vanderwende
fcbf617d38
ncl: add RPC lib with ncl+hdf4 (#34451) 2022-12-15 09:22:00 +01:00
downloadico
1f8b55a021
Add G'MIC package with only the "cli" target available (#34533) 2022-12-15 09:19:50 +01:00
David Gardner
b5f8ed07fb
sundials: fix typo in smoke tests (#34539) 2022-12-15 09:07:54 +01:00
Thomas Madlener
65bd9b9ac5
podio, edm4hep: add v0.7.2 and v0.16.1 respectively (#34526)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-12-15 09:02:16 +01:00
Adam J. Stewart
6250d84b41
cpuinfo: new versions, shared libs (#34544) 2022-12-15 09:00:51 +01:00
Wouter Deconinck
99056e03bd
acts: new versions 19.11.0, 21.0.0, 21.1.0 (#34540)
* acts: new versions 19.11.0, 21.0.0, 21.1.0

https://github.com/acts-project/acts/compare/v19.10.0...v19.11.0:
- python 3.8 required if ACTS_BUILD_EXAMPLES_PYTHON_BINDINGS

https://github.com/acts-project/acts/compare/v20.3.0...v21.0.0:
- python 3.8 required if ACTS_BUILD_EXAMPLES_PYTHON_BINDINGS

https://github.com/acts-project/acts/compare/v21.0.0...v21.1.0:
- no build system changes

* acts: depends_on python@3.8: when sometimes
2022-12-15 08:56:32 +01:00
Fabien Bruneval
1db849ee5f
libcint: Fix +coulomb_erf and add +pypzpx (#34524) 2022-12-15 05:31:58 +01:00
Thomas Madlener
2f82b213df
lcio: add latest version (#34527) 2022-12-15 05:06:59 +01:00
Axel Huebl
2a5f0158bc
ParaView: Add openPMD Support (#33821)
openPMD, a metadata standard on top of backends like ADIOS2 and HDF5,
is implemented in ParaView 5.9+ via a Python3 module.

Simplify Conflicts & Variant

Add to ECP Data Vis SDK
2022-12-14 20:45:27 -07:00
Manuela Kuhn
21a1f7dd97
py-traitlets: add w5.7.1 (#34525) 2022-12-14 21:34:51 -06:00
David Boehme
4b5ed94af4
caliper: add version 2.9.0 (#34538) 2022-12-15 03:52:53 +01:00
snehring
06788019a4
apptainer: add new version 1.1.4 (#34536) 2022-12-15 02:06:22 +01:00
Sam Grayson
cab8f795a7
Patch dill._dill._is_builtin_module (#34534)
* Patch dill._dill._is_builtin_module

* Fix style

* Add test
2022-12-14 16:03:03 -07:00
finkandreas
2db38bfa38
py-archspec: replace removed .build_directory with .stage.source_path (#34521) 2022-12-15 00:00:21 +01:00
Harmen Stoppels
ea029442e6
Revert "Revert "Use urllib handler for s3:// and gs://, improve url_exists through HEAD requests (#34324)"" (#34498)
This reverts commit 8035eeb36d.

And also removes logic around an additional HEAD request to prevent
a more expensive GET request on wrong content-type. Since large files
are typically an attachment and only downloaded when reading the
stream, it's not an optimization that helps much, and in fact the logic
was broken since the GET request was done unconditionally.
2022-12-14 23:47:11 +01:00
Axel Huebl
43e38d0d12
WarpX 22.11, 22.12 & PICMI-Standard (#34517)
* PICMI: 0.0.22

* WarpX: 22.11, 22.12
2022-12-14 13:59:16 -08:00
Marco De La Pierre
2522c8b754
edits to 8x existing recipes, mostly new versions, plus two dependency fixes (#34516) 2022-12-14 12:28:33 -07:00
Marco De La Pierre
f64cb29aea
Nextflow, Tower Agent, Tower CLI: updates (#34515)
* renamed tower-agent and tower-cli with prefif nf-

* new nextflow package version

* added newest versions (today) for nf-tower-agent and nf-tower-cli
2022-12-14 11:44:22 -07:00
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