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2022-12-15Add a proper deprecation warning for update-index -d (#34520)Harmen Stoppels4-5/+38
2022-12-15Remove warning in download_tarball (#34549)Harmen Stoppels1-4/+0
2022-12-15Forward lookup of the "run_tests" attribute (#34531)Massimiliano Culpo2-1/+20
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.
2022-12-15metabat: adding missing build dependency (#34530)snehring1-0/+1
2022-12-15talass: fixed URLs so the package is reachable (#34387)Loïc Pottier1-2/+5
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2022-12-15ncl: add RPC lib with ncl+hdf4 (#34451)Brian Vanderwende1-1/+12
2022-12-15Add G'MIC package with only the "cli" target available (#34533)downloadico1-0/+41
2022-12-15sundials: fix typo in smoke tests (#34539)David Gardner1-1/+1
2022-12-15podio, edm4hep: add v0.7.2 and v0.16.1 respectively (#34526)Thomas Madlener2-0/+7
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-12-15cpuinfo: new versions, shared libs (#34544)Adam J. Stewart1-29/+9
2022-12-15acts: new versions 19.11.0, 21.0.0, 21.1.0 (#34540)Wouter Deconinck1-0/+5
* 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
2022-12-15libcint: Fix +coulomb_erf and add +pypzpx (#34524)Fabien Bruneval1-1/+7
2022-12-15lcio: add latest version (#34527)Thomas Madlener1-0/+1
2022-12-14ParaView: Add openPMD Support (#33821)Axel Huebl2-1/+13
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
2022-12-14py-traitlets: add w5.7.1 (#34525)Manuela Kuhn1-0/+3
2022-12-15caliper: add version 2.9.0 (#34538)David Boehme1-2/+3
2022-12-15apptainer: add new version 1.1.4 (#34536)snehring1-0/+1
2022-12-14Patch dill._dill._is_builtin_module (#34534)Sam Grayson2-0/+39
* Patch dill._dill._is_builtin_module * Fix style * Add test
2022-12-15py-archspec: replace removed .build_directory with .stage.source_path (#34521)finkandreas1-1/+1
2022-12-14Revert "Revert "Use `urllib` handler for `s3://` and `gs://`, improve ↵Harmen Stoppels4-159/+92
`url_exists` through HEAD requests (#34324)"" (#34498) This reverts commit 8035eeb36d5068fcbae613e51dd13cb1ae9f4888. 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.
2022-12-14WarpX 22.11, 22.12 & PICMI-Standard (#34517)Axel Huebl3-2/+10
* PICMI: 0.0.22 * WarpX: 22.11, 22.12
2022-12-14edits to 8x existing recipes, mostly new versions, plus two dependency fixes ↵Marco De La Pierre8-4/+14
(#34516)
2022-12-14Nextflow, Tower Agent, Tower CLI: updates (#34515)Marco De La Pierre5-1/+150
* 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
2022-12-14New neuroscience packages: py-bmtk, py-neurotools (#34464)Erik Heeren3-0/+75
* 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>
2022-12-14bufr: add v11.6, 11.7, 11.7.1 (#34509)eugeneswalker1-0/+3
2022-12-14fms: add v2019.01.03 (#34511)eugeneswalker1-0/+3
2022-12-14Use update-index --mirror-url <url> instead of -d <url> (#34519)Harmen Stoppels3-3/+3
2022-12-14justbuild: add v1.0.0 (#34467)Alberto Sartori1-0/+1
2022-12-13r-rgdal: adding new version 1.6-2 (#34502)snehring1-0/+1
2022-12-13Use file paths/urls correctly (#34452)Harmen Stoppels29-472/+260
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.
2022-12-13py-submitit: add 1.4.5 (#34460)Matthias Wolf1-1/+3
2022-12-13py-tifffile: add 2022.10.10 (#34499)Manuela Kuhn1-2/+7
2022-12-13py-sphinxcontrib-qthelp: add 1.0.3 (#34495)Manuela Kuhn1-1/+3
2022-12-13py-sqlalchemy: add 1.4.45 (#34497)Manuela Kuhn1-25/+2
2022-12-13trilinos: extend range of Teuchos patch (#34504)Paul Kuberry1-1/+1
2022-12-13Update pFunit, add gFTL, gFTL-Shared, fArgParse, pFlogger, yaFyaml (#34476)Matthew Thompson6-14/+296
* 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>
2022-12-13py-tensorboard-data-server: build needs rust+rustfmt (#34465)Bernhard Kaindl1-1/+1
2022-12-13pcre2: add new versions and update URL (#34477)Mosè Giordano1-1/+4
2022-12-13gromacs: enable linking with acfl FFT (#34494)Annop Wongwathanarat1-0/+5
2022-12-13Don't fetch to order mirrors (#34359)Harmen Stoppels2-11/+15
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.
2022-12-13build(deps): bump actions/checkout from 3.1.0 to 3.2.0 (#34480)dependabot[bot]7-25/+25
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](https://github.com/actions/checkout/compare/93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8...755da8c3cf115ac066823e79a1e1788f8940201b) --- 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>
2022-12-13py-cartopy: add v0.21.1 (#34482)Adam J. Stewart1-2/+4
2022-12-13libicd: macOS now supported (#34483)Adam J. Stewart1-3/+0
2022-12-13Fix markdown links in rst files (#34488)Aidan Heerdegen1-4/+6
2022-12-13spack/package.py: improve editor support for some +/- static props (#34319)Harmen Stoppels2-20/+20
2022-12-13scons: fix signature for `install_args` (#34481)Massimiliano Culpo1-4/+4
2022-12-13py-shapely: add v2.0.0 (#34475)Adam J. Stewart2-13/+31
2022-12-13Be strict on the markers used in unit tests (#33884)Massimiliano Culpo1-1/+1
2022-12-12py-pyld: add with dependency (#34472)Erik Heeren2-0/+41
* py-pyld: add with dependency * py-pyld and py-frozendict: update copyright expiration * [@spackbot] updating style on behalf of heerener
2022-12-12py-sh: new versions (#34458)Matthias Wolf1-0/+2
* py-sh: new versions * style