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2024-08-19perl-bio-bigfile: new package (#44505)Teague Sterling1-0/+80
* Adding the perl-bio-db-bigfile package * Update package.py * Update package.py * Update package.py * Updating dependent package handling Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Updating dependent package handling Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Reverting variants Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Rename package.py to package.py * Update package.py * Removing unneeded dependencies Signed-off-by: Teague Sterling <teaguesterling@gmail.com> --------- Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
2024-08-19apfel: add v3.1.1 (now CMakePackage) (#45661)Wouter Deconinck1-9/+29
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com> Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2024-08-19salmon: add v1.10.3 (#45695)snehring2-11/+37
Signed-off-by: Shane Nehring <snehring@iastate.edu>
2024-08-19WRF: add -fpermissive when using gcc@14: (#45438)Luke Robison1-0/+6
2024-08-19activeharmony: replace dead links (#45704)Wouter Deconinck1-4/+4
2024-08-19mlpack: add through v4.4.0 (#45707)Wouter Deconinck1-1/+8
2024-08-19py-keras: add v3.5 (#45711)Adam J. Stewart1-13/+20
2024-08-19py-brain-indexer: new package (#44718)Matthias Wolf3-0/+75
2024-08-19py-pyyaml: add v6.0.2 (#45716)Matt Thompson1-2/+19
2024-08-19magic-enum: fix minimum compiler versions conflicts (#45705)Pranav Sivaraman1-7/+7
2024-08-19librsvg: depends_on cairo +png (#45729)Wouter Deconinck1-3/+3
2024-08-19liftoff: add new package (#45726)snehring3-2/+73
Signed-off-by: Shane Nehring <snehring@iastate.edu>
2024-08-19bind9: add v9.18.28, v9.20.0 (#45728)Wouter Deconinck2-12/+40
2024-08-19gradle: add through v8.9 (#45731)Wouter Deconinck1-1/+10
2024-08-19maven: add v3.8.8, v3.9.8 (#45732)Wouter Deconinck1-1/+5
2024-08-19mlc-llm: new package and dependency (#44726)Alex Leute2-0/+125
2024-08-19CP2K: add 2024.2, fix dbcsr+g2g+plumed (#45614)Rocco Meli3-2/+11
2024-08-19hadoop: add v3.3.3 -> v3.4.0 (#45735)Wouter Deconinck1-3/+8
2024-08-19armpl-gcc - finish enabling debian12 (#45744)dslarm1-10/+4
2024-08-19openssh: add v9.8p1 (#45736)Wouter Deconinck1-1/+8
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2024-08-19shared-mime-info: fix url for certificate name mismatch (#45779)Wouter Deconinck1-1/+1
2024-08-19ghostscript: add v10.01.2, v10.02.1, v10.03.1 (#45780)Wouter Deconinck1-12/+21
2024-08-19graphviz: add v8.1.0 -> v12.1.0 (#45675)Wouter Deconinck1-3/+9
2024-08-19xorg-server: add variants dri and glx (#45787)Wouter Deconinck1-13/+32
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2024-08-19dbcsr: avoid using a set in a message (#45804)Massimiliano Culpo1-2/+2
2024-08-18WarpX: Python on pyAMReX (#45251)Axel Huebl5-112/+464
* WarpX: Python on pyAMReX Long overdue update for WarpX: in 2024, we updated our Python bindings to rely on the new pyAMReX package. This deprecates the old `py-warpx` package and adds a new dependency and variant to WarpX. Also deprecates old versions that we will not continue to support. * Update Cloud/E4S Pipelines for WarpX `py-warpx` is replaced by `warpx +python` oneAPI does not support IPO/LTO: diable for `py-amrex` even though pybind11 strongly encourages it.
2024-08-18Scotch: Fix sha256 for some older versions. (#44494)Rémi Lacroix1-6/+6
Most likely caused by a change in Inria's Gitlab.
2024-08-18py-torch-nvidia-apex: Add 24.04.01 and variants from the readme (#45019)Auriane R.1-14/+133
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2024-08-17py-torchaudio: upperbound on cuda (#45773)Harmen Stoppels1-0/+3
* py-torchaudio: upperbound on cuda * actually get bound right * make adam happy
2024-08-17xorgproto: new package (#45569)Teague Sterling1-0/+21
* xorgproto: new package Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * adding providers for xorgprotos Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Update var/spack/repos/builtin/packages/xorgproto/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update etc/spack/defaults/packages.yaml Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update etc/spack/defaults/packages.yaml Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update var/spack/repos/builtin/packages/xorgproto/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update var/spack/repos/builtin/packages/xorgproto/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update var/spack/repos/builtin/packages/xorgproto/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * Update var/spack/repos/builtin/packages/xorgproto/package.py Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * [@spackbot] updating style on behalf of teaguesterling * xorgproto: depends_on meson type build --------- Signed-off-by: Teague Sterling <teaguesterling@gmail.com> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-08-17libEnsemble: add v1.4.2 (#45760)Stephen Hudson1-1/+2
2024-08-16esmf package: add (optional) Python bindings (#45504)Chris Marsh1-18/+64
* Add `+python` variant * `esmf` package installs Python bindings when `+python` is set Note: this does not inherit `PythonPackage`, which force an either/or choice between the Makefile and Pip builder: it instantiates a `PythonPipBuilder` as needed (when `+python` is set).
2024-08-16GDAL: add v3.9.2 (#45794)Adam J. Stewart1-0/+1
2024-08-16py-lxml: add v5.2.2 (#45785)Paul R. C. Kent1-0/+5
* add v5.2.2 * py-lxml dependency improvements Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2024-08-16harfbuzz: enable freetype in MesonBuilder (#45654)bk1-1/+3
* harfbuzz: enable freetype in MesonBuilder to facilitate depends_on("freetype") * spack style fix * freetype is defined as a depends_on(), so set as enabled in MesonBuilder rather than an option/flag/variant * add back depends_on($lang) lines for new test api * keep original order
2024-08-16*: avoid js redirect for homepages on sourceforge (#45783)Wouter Deconinck12-12/+12
2024-08-15rccl: new test API (#45241)AcriusWinter1-5/+4
* rccl: new test API * rccl: stand-alone test docstring tweak --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2024-08-15hypre: get rid of use of deprecated run_test method (#45762)AcriusWinter1-2/+2
* hypre: get rid of depreciated run_test method * hypre: use mkdirp directly * hypre: use install() for ij for addition of permissions fix --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2024-08-15parsec: old to new test API (#45122)AcriusWinter1-11/+23
* parsec: old to new test API * parsec: restore stand-alone test subparts; preliminary test build fixes --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2024-08-15n2p2: convert from old to new test API (#45141)AcriusWinter1-26/+42
* n2p2: convert from old to new test API * n2p2: Enhance stand-alone testing checks to reduce unnecessary processing --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2024-08-15Open3d: Reinstate re-use of stand-alone test method (#45755)AcriusWinter1-8/+8
* open3d: Reinstate re-use of stand-alone test method * open3d: ignore test_open3d_import when ~python --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2024-08-15seacas: new version (#45777)Greg Sjaardema1-3/+6
Update fmt dependency to support fmt@11: Use an adios2 release instead of master New release of seacas
2024-08-15Cache extra test sources update (#45493)AcriusWinter39-50/+53
* stand-alone test API update: self.cache_extra_test_sources(...) -> cache_extra_test_sources(self, ...) * superlu: switch to new cache_extra_test_sources API --------- Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2024-08-15libmesh: explicitly disable metis in ~metis case (#45781)Richard Berger1-0/+2
2024-08-15pika: add 0.27.0 (#45772)Mikael Simberg1-0/+1
2024-08-15hwloc: add v2.11.1 (#45767)Derek Ryan Strong1-8/+4
* Add hwloc v2.11.1
2024-08-15limit patch range (#45756)David Gardner1-1/+1
2024-08-14g2: add 3.5.0 and 3.5.1 (#45750)Alex Richert1-0/+2
2024-08-15Add options for sparse checkout in GitFetcher (#45473)psakievich1-0/+17
* Add options for sparse checkout in GitFetcher Newer versions of git have a beta feature called sparse checkout that allow users to check out a portion of a large repo. This feature will be ideal for monolithic repo projects that want to model their infrastructure via spack. This PR implements an addition to the GitFetcher that allows users to add a `git_sparse_paths` attribute to package classes or versions which will then use sparse checkout on those directories/files for the package. * Style * Split git clone into multiple functions * Add sparse-checkout impl * Internalize src clone functions * Docs * Adding sparse clone test * Add test for partial clone * [@spackbot] updating style on behalf of psakievich * Small fixes * Restore default branch status * Fix attributes for package * Update lib/spack/docs/packaging_guide.rst Co-authored-by: Matthew Mosby <44072882+mdmosby@users.noreply.github.com> * Extend unit test to multiple git versions * style --------- Co-authored-by: psakievich <psakievich@users.noreply.github.com> Co-authored-by: Matthew Mosby <44072882+mdmosby@users.noreply.github.com>
2024-08-14py-fortranformat: update to version 2.0.0 (#45748)Evan Parker1-2/+5
* Feature update py-fortranformat Add more recent versions of py-fortranformat. The currently included release (0.2.5) is from 2014. I've added the latest point release of each of the major versions from the last 4 years. * update homepage
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