Update spack-packages from spack-packages/develop 2026/06/04 by climbfuji · Pull Request #67 · JCSDA/spack-packages

climbfuji · 2026-06-09T11:52:09Z

Description

This PR pulls in the upstream spack-packages develop branch as of 2026/06/04. I had to fix dependencies for py-pybtex, see spack#5141 for the upstream PR. Packages with merge conflicts that should be examined by the reviewers (all others were straightforward):

CDO
GDAL
HARFBUZZ
HDF_EOS2
MAPL
NETCDF_C

cylc-related updates: spack#5174

Testing and Issues

See JCSDA/spack-stack#2039

…4661)

* Add PyTf2onnx package for Tensorflow to ONNX conversion * py-tf2onnx: depends on py-tensorflow

…k#4541) When building Palace with the Intel oneAPI compiler (ifx), the STRUMPACK sparse direct solver needs ifport and ifcore runtime libraries linked. This was already handled for MUMPS but missing for STRUMPACK. Tested: palace@0.16.0 %oneapi@2025.3.2 ^intel-oneapi-mkl@2025.3.1 ^intel-oneapi-mpi@2021.17.2 on Rocky 8 / Icelake.

* healpix-cxx: restrict cfitsio@3 Signed-off-by: Shane Nehring <snehring@iastate.edu> * healpix-cxx: add c,cxx deps Signed-off-by: Shane Nehring <snehring@iastate.edu> --------- Signed-off-by: Shane Nehring <snehring@iastate.edu>

* [py-openai-whisper] new package * [py-openai-whisper] style

* [py-imaug] new package * [py-imaug] dependency readability

…4340)

Add patches for GCC 13+ and Clang 15+ compatibility. Targets top level port_platform.h header which gets most of the missing includes where they need to go. The only outlier is glob.cc which gets its own filter call.

* [cosma] Add unified memory support * Fix typo Co-authored-by: Simon Pintarelli <1237199+simonpintarelli@users.noreply.github.com> --------- Co-authored-by: Mathieu Taillefumier <mathieu.taillefumier@free.fr> Co-authored-by: Simon Pintarelli <1237199+simonpintarelli@users.noreply.github.com>

@spackbot

…pack#4297) * Patch in re2 header includes Add patch method to handle missing implicit header includes for GCC 13+ and Clang 15+. This patch is necessary and sufficient for me to build this spec: - re2@2024-07-02~icu~ipo+pic~shared build_system=cmake build_type=Release generator=make platform=linux os=rhel8 target=zen3 %cxx=gcc@13.4.0 Without errors like: [e] ^gcc@8.5.0+binutils+bootstrap~graphite+libsanitizer~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages:='c,c++,fortran' platform=linux os=rhel8 target=x86_64 [+] ^gcc-runtime@8.5.0 build_system=generic platform=linux os=rhel8 target=zen ...and the 'top' of the error output: [ 73%] Building CXX object CMakeFiles/re2.dir/re2/simplify.cc.o /storage/users/wspear/bin/SPACK/gilgamesh/spack/opt/spack/linux-zen3/compiler-wrapper-1.0-r533h4sr4uzpv32pv2w4ootpawmxmmgf/libexec/spack/gcc/g++ -I/tmp/wspear/spack-stage/spack-stage-re2-2023-09-01-o2docgedch6htv5uscgaiek7ygdv6gy2/spack-src -isystem /storage/users/wspear/bin/SPACK/gilgamesh/spack/opt/spack/linux-zen3/abseil-cpp-20260107.1-t6vh5x4y757uaf4a7ho3xoa7cayf5fz2/include -O3 -DNDEBUG -std=gnu++17 -fPIC -pthread -MD -MT CMakeFiles/re2.dir/re2/simplify.cc.o -MF CMakeFiles/re2.dir/re2/simplify.cc.o.d -o CMakeFiles/re2.dir/re2/simplify.cc.o -c /tmp/wspear/spack-stage/spack-stage-re2-2023-09-01-o2docgedch6htv5uscgaiek7ygdv6gy2/spack-src/re2/simplify.cc In file included from /tmp/wspear/spack-stage/spack-stage-re2-2023-09-01-o2docgedch6htv5uscgaiek7ygdv6gy2/spack-src/re2/set.cc:14: /tmp/wspear/spack-stage/spack-stage-re2-2023-09-01-o2docgedch6htv5uscgaiek7ygdv6gy2/spack-src/re2/prog.h: In member function 'const void* re2::Prog::PrefixAccel(const void*, size_t)': /tmp/wspear/spack-stage/spack-stage-re2-2023-09-01-o2docgedch6htv5uscgaiek7ygdv6gy2/spack-src/re2/prog.h:230:14: error: 'memchr' was not declared in this scope 230 | return memchr(data, prefix_front_, size); | ^~~~~~ /tmp/wspear/spack-stage/spack-stage-re2-2023-09-01-o2docgedch6htv5uscgaiek7ygdv6gy2/spack-src/re2/prog.h:25:1: note: 'memchr' is defined in header '<cstring>'; did you forget to '#include <cstring>'? 24 | #include "re2/sparse_set.h" +++ |+#include <cstring> 25 | * [@spackbot] updating style on behalf of wspear --------- Co-authored-by: wspear <wspear@users.noreply.github.com>

* py-b2luigi: add v1.2.8; fix build system and license * py-b2luigi: fix tpyo * py-b2luigi: license checked * py-webdavclient3: add package

* xorg: add new versions, git attributes, cmake/xproto deps, remove RC Add new versions and git attributes for Xorg X11 libraries: - bdftopcf, glew, libdrm, libxext, libxfixes, libxft, libxi, libxinerama, libxmu, libxpm, libxpresent, libxrandr, libxres, libxscrnsaver, libxvmc, libxxf86dga, libxxf86vm, xcb_util_cursor, xkbcomp - glew: add cmake@3.16: dep when @2.3: (CMakeLists.txt raised minimum) - libxft: add xproto@7.0.22: dep when @2.3.3: (commit e787bf2f) - libxi: remove commented-out RC pre-release version 1.7.99.2 Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * glew: patch APIENTRY only until 2.2 * libxft: fix xproto dependency --------- Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* root: add builtin_llvm variant to allow external LLVM Add a user-settable `builtin_llvm` variant (default: true for backward compatibility). When set to false, ROOT links against an external `llvm@20.1.0:20.1 +rtti` package instead of building its own bundled copy. ROOT's patches to llvm-project only touch `clang/` (65 files, zero in `llvm/` core), so vanilla LLVM is sufficient for this case. ROOT still builds its own patched Clang from the bundled interpreter/llvm-project/clang sources (`builtin_clang=ON` is now explicitly enforced), which is required because vanilla Clang cannot be used with ROOT. External LLVM is gated to ROOT 6.36+ where the required LLVM major version (20.1.x) is known. A conflict is added to prevent `~builtin_llvm` on older ROOT versions until those LLVM-version mappings are also handled. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * root: address code review suggestions --------- Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Signed-off-by: Harmen Stoppels <me@harmenstoppels.nl>

* Allow axom +openm+rocm * Add flag for cuda warnings * Add missing mpi guard for +rocm+mpi

* sratoolkit: adding v3.4.1 Signed-off-by: Shane Nehring <snehring@iastate.edu> * sratoolkit: adding url_for_version Signed-off-by: Shane Nehring <snehring@iastate.edu> * sratoolkit: remove url from new version Signed-off-by: Shane Nehring <snehring@iastate.edu> * sratoolkit: fixing my treasonous human hands Signed-off-by: Shane Nehring <snehring@iastate.edu> * sratoolkit: using Version comparison Signed-off-by: Shane Nehring <snehring@iastate.edu> --------- Signed-off-by: Shane Nehring <snehring@iastate.edu>

In order to limit style to only the changes made in the PR, point at the merge base between the PR HEAD and the target ref. Signed-off-by: Ryan Krattiger <ryan.krattiger@kitware.com>

…spack#4825) Bumps [actions/create-github-app-token](https://github.com/actions/create-github-app-token) from 3.0.0 to 3.2.0. - [Release notes](https://github.com/actions/create-github-app-token/releases) - [Changelog](https://github.com/actions/create-github-app-token/blob/main/CHANGELOG.md) - [Commits](actions/create-github-app-token@f8d387b...bcd2ba4) --- updated-dependencies: - dependency-name: actions/create-github-app-token dependency-version: 3.2.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Signed-off-by: Alec Scott <alec@llnl.gov>

Fixes a Process.sentinel file descriptor leak Signed-off-by: Harmen Stoppels <harmenstoppels@gmail.com>

When compiling an external viskores module, the paraview build needs some special CMake targets to find the viskores libraries and set up languages. This patch fixes problems in the paraview build.

Signed-off-by: Harmen Stoppels <harmenstoppels@gmail.com>

@spackbot

* squash: python_mumps recipe * Add copyright Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * add versions and pypi repo url * add python@310: * Add pkgconfig dependency to py_python_mumps package * fix indent in mumps recipe * fix formatting * fix indent * ruff formatting * Ensure python-mumps is registered with compilation deps when building with spack Add compiler environment setup for building. * ruff formatting * add akhmerov as maintainer (package author) * [@spackbot] updating style on behalf of williampiat3 * Add license to recipe * Update repos/spack_repo/builtin/packages/py_python_mumps/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * simplify recipe * typo * [@spackbot] updating style on behalf of williampiat3 --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Greg Becker <becker33@llnl.gov>

@spackbot

* igraph: fix libxml2 for older versions (< 0.11) * py-leidenalg: new package * py-hdf5plugin: new package * py-logomaker: new package * py-memelite: new package * py-modisco: new package * py-hdf5plugin: fix license * py-leidenalg: fixup * py-modisco: style fixup * [@spackbot] updating style on behalf of Markus92 * py-leidenalg: fix f-strings * libleidenalg: fix patch link * py-hdf5plugin: remove boilerplate * Add version suggestion Co-authored-by: Greg Becker <becker33@llnl.gov> * Update repos/spack_repo/builtin/packages/py_modisco/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * libleidenalg: clarify version requirements Co-authored-by: Greg Becker <becker33@llnl.gov> * igraph: replace openblas dependency by generic blas/lapack * igraph: remove duplicate blas requirement --------- Co-authored-by: Markus92 <Markus92@users.noreply.github.com> Co-authored-by: Greg Becker <becker33@llnl.gov> Co-authored-by: Mark Janse <markus.janse@utsouthwestern.edu>

* py-apprise: add new package * py-apprise: add license

@spackbot

* cminpack: Add cxx dependency This should fix spack#5012 * [@spackbot] updating style on behalf of payerle * Update repos/spack_repo/builtin/packages/cminpack/package.py Co-authored-by: Alec Scott <hi@alecbcs.com> --------- Co-authored-by: payerle <payerle@users.noreply.github.com> Co-authored-by: Alec Scott <hi@alecbcs.com>

…ls on (spack#5052)

…o feature/upd_spst_dev_from_upstream_20260602

…ages into feature/upd_spst_dev_from_upstream_20260602

…/package.py

…update package recipe

…intainer

…aintainer

…: Versions 80 and earlier require Python 3.13 and earlier; Versions 80+ need py-jaraco-functools@4

… py_jaraco_functools: deprecated, url_for_version

ddement and others added 30 commits May 12, 2026 15:05

kynema: Fixes feature flag names to reflect upstream renaming (spack#…

95cdc47

…4661)

py-tf2onnx: add v1.17.0 (new package) (spack#4578)

0c04727

* Add PyTf2onnx package for Tensorflow to ONNX conversion * py-tf2onnx: depends on py-tensorflow

Make PDI package extend Python (spack#4461)

31fef97

healpix-cxx: restrict cfitsio@3 (spack#4430)

5303067

* healpix-cxx: restrict cfitsio@3 Signed-off-by: Shane Nehring <snehring@iastate.edu> * healpix-cxx: add c,cxx deps Signed-off-by: Shane Nehring <snehring@iastate.edu> --------- Signed-off-by: Shane Nehring <snehring@iastate.edu>

py-openai-whisper: new package (spack#4427)

0659e9a

* [py-openai-whisper] new package * [py-openai-whisper] style

py-imaug: new package (spack#4424)

741952b

* [py-imaug] new package * [py-imaug] dependency readability

OSU MicroBenchmark: Fix compilation without the NVIDIA driver (spack#…

87f0f4c

…4340)

grpc: add patch for missing includes (spack#4299)

825103c

Add patches for GCC 13+ and Clang 15+ compatibility. Targets top level port_platform.h header which gets most of the missing includes where they need to go. The only outlier is glob.cc which gets its own filter call.

py-rachis: new package (spack#4224)

45b0539

py-b2luigi: add v1.2.8; fix build system and license (spack#4197)

96a5423

* py-b2luigi: add v1.2.8; fix build system and license * py-b2luigi: fix tpyo * py-b2luigi: license checked * py-webdavclient3: add package

fleur: add v8.1 and make CMakePackage (spack#4816)

696313f

Signed-off-by: Harmen Stoppels <me@harmenstoppels.nl>

axom: Allow +openm+rocm variant combination (spack#4421)

36d4593

* Allow axom +openm+rocm * Add flag for cuda warnings * Add missing mpi guard for +rocm+mpi

lazygit: maintainer typo (spack#4824)

5240381

fzf: fix FZF_VERSION assignment to use string method (spack#4827)

99c74ee

add v4.0.2 (spack#4826)

84dccf0

rsync: add v3.4.2 (spack#4832)

132a9bd

globus-xio-popen-driver: remove placeholder maintainers (spack#4821)

27dd134

Update script for CI style check to point at merge base (spack#4833)

fa9f88f

In order to limit style to only the changes made in the PR, point at the merge base between the PR HEAD and the target ref. Signed-off-by: Ryan Krattiger <ryan.krattiger@kitware.com>

github actions: update triage bot to use client id (spack#4834)

c1bb64b

Signed-off-by: Alec Scott <alec@llnl.gov>

ci: bump spack (spack#4837)

b3c2820

Fixes a Process.sentinel file descriptor leak Signed-off-by: Harmen Stoppels <harmenstoppels@gmail.com>

paraview: Apply patch to find viskores libs (spack#3674)

91ec78f

When compiling an external viskores module, the paraview build needs some special CMake targets to find the viskores libraries and set up languages. This patch fixes problems in the paraview build.

py-pyarrow: forward compat with py-cython (spack#4836)

2bb5a4b

Signed-off-by: Harmen Stoppels <harmenstoppels@gmail.com>

sqlite: add 3.53.1 (spack#4830)

9d84b99

michaelkuhn and others added 16 commits June 1, 2026 10:33

bash: add more patches for 5.3 (spack#5039)

1d3853d

e4s_cl: Update to 1.0.8 (spack#5030)

661ecf6

r-ggplot2: add v4.0.3 and fix dependencies (spack#5043)

0debcbd

py-mypy: add v2.1.0 and py-ast-serialize: add new package (spack#5044)

7e33048

py-apprise: add new package (spack#4967)

ed6903f

* py-apprise: add new package * py-apprise: add license

kokkos: remove test code (spack#5048)

ed21363

yosys: add v0.65 ad v0.66 (spack#5051)

29213a4

removing conflicts statement so that we can get a rocm build with too…

2ecbb0f

…ls on (spack#5052)

Merge branch 'develop' of https://github.com/spack/spack-packages int…

d5f3353

…o feature/upd_spst_dev_from_upstream_20260602

Merge branch 'spack-stack-dev' of https://github.com/jcsda/spack-pack…

336fecf

…ages into feature/upd_spst_dev_from_upstream_20260602

Fix patch order in repos/spack_repo/builtin/packages/netcdf_c/package.py

9505b92

Update dependencies for py-pybtex

a78997c

Merge branch 'spack-stack-dev' of https://github.com/jcsda/spack-pack…

a79c653

…ages into feature/upd_spst_dev_from_upstream_20260602

climbfuji self-assigned this Jun 9, 2026

climbfuji added this to spack-stack-2.2.x (2026 Q?) Jun 9, 2026

github-project-automation Bot moved this to Todo in spack-stack-2.2.x (2026 Q?) Jun 9, 2026

climbfuji moved this from Todo to In Progress in spack-stack-2.2.x (2026 Q?) Jun 9, 2026

climbfuji added 10 commits June 9, 2026 05:54

Fix package dependency in repos/spack_repo/builtin/packages/py_pybtex…

8635bd9

…/package.py

Add py-cylc-flow versions 8.6.4 and 8.5.4, deprecate older versions, …

efa90b2

…update package recipe

py-cylc-rose: deprecate older versions, update package recipe

33200c4

Ad graphene@3.4.3, update package recipe, add climbfuji as maintainer

c8eaae7

Add py-graphql-core@3.2.7, update package recipe, add climbfuji as ma…

367c8d1

…intainer

Add py-graphql-relay@3.2.0, update package recipe, add climbfuji as m…

ffc89ef

…aintainer

Reintroduce py-cylc-uiserver

e5b1258

Add py-jaraco-functools@4.1.0

bd23f89

Bug fix in repos/spack_repo/builtin/packages/py_setuptools/package.py…

f7e64f1

…: Versions 80 and earlier require Python 3.13 and earlier; Versions 80+ need py-jaraco-functools@4

Update py_cylc_flow, py_cylc_rose, py_cylc_uiserver, py_graphql_core,…

e3eaf3b

… py_jaraco_functools: deprecated, url_for_version

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Update spack-packages from spack-packages/develop 2026/06/04#67

Update spack-packages from spack-packages/develop 2026/06/04#67
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climbfuji commented Jun 9, 2026 •

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climbfuji commented Jun 9, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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climbfuji commented Jun 9, 2026 •

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