* `py-dm-tree`: add v0.1.8

* Update dependencies

* Fix hash

…230710

* py-networkx: add 3.1 (spack#38377)

* py-networkx: add 3.1

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

Co-authored-by: Adam J. Stewart <[email protected]>

* Add default variant

---------

Co-authored-by: Adam J. Stewart <[email protected]>

* py-pyproj: add v3.6.0 (spack#38399)

* hpx: Add conflict with some GCC versions and `+rocm` due to `valarray` bug (spack#38297)

* hpx: Add conflict with some GCC versions and +rocm due to valarray bug

https://gcc.gnu.org/bugzilla/show_bug.cgi?id=103022

* remove conflict for %[email protected] since there is none

---------

Co-authored-by: eugeneswalker <[email protected]>

* qt: new version 5.15.10 (spack#38489)

No changes to the build system, no changes to `package.py` needed.

Changelog: qt/qtbase@v5.15.9-lts-lgpl...v5.15.10-lts-lgpl

Main change taking up space:
- bundled 3rdparty/pcre2 updated from 10.39 to 10.40 (spack now includes 10.42, and we don't put specific version requirements in `package.py`)

* py-patsy: add 0.5.3 (spack#38433)

* py-prompt-toolkit: add 3.0.38 (spack#38472)

* py-platformdirs: add 3.5.3 (spack#38435)

* py-platformdirs: add 3.5.3

* py-typing-extensions: add 4.6.3

* open turns: Add libxml2 dependency and increase version to v1.20 (spack#38038)

* Add libxml2 dependency and increase version to v1.20

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

Co-authored-by: Alec Scott <[email protected]>

* Add v19

* Add libxml2 variant

* Fix variant specification

---------

Co-authored-by: Marc Schouler <[email protected]>
Co-authored-by: Alec Scott <[email protected]>

* py-numexpr: add 2.8.4 (spack#38416)

* Add LFortran (spack#30901)

It installs the LFortran runtime library and
LFortran can compile codes to binaries. The interactive mode does not
work yet with LLVM > 11, that has to be fixed upstream.

Co-authored-by: Wileam Y. Phan <[email protected]>

* py-notebook: add 6.5.4 (spack#38415)

* py-notebook: add 6.5.4

* [@spackbot] updating style on behalf of manuelakuhn

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

Co-authored-by: Adam J. Stewart <[email protected]>

* Fix version of py-nbclassic dependency

---------

Co-authored-by: Adam J. Stewart <[email protected]>

* freefem: add missing dependencies (spack#38290)

Also remove the custom `autoreconf` method as it does not seem to be
necessary and potentially hides useful output provided by the default.

* VASP package: Zen4 Support (spack#36800)

* zen4 support for vasp
* encourage openmp support in fftw/blas when +openmp
* enable gamma and non-collinear builds

* py-packaging: add 23.1 (spack#38417)

* rust: Add v1.70.0 and simplify package bootstrap (spack#38311)

* Add rust v1.70.0 and simplify package logic by moving bootstrap to dedicated package

* Fix formatting of rust-bootstrap package file

* Re-enable Rust as extendable

* Add nightly version to rust and rust-bootstrap

* Manually inject openssl certs into environment

* Add master and beta versions to rust

* Add additional documentation for using rust development releases

* Remove @AndrewGaspar as maintainer

* Emblmygff3 (spack#38515)

* py-bcbio-gff: adding new version 0.7.0

* emblmygff3: adding new package

* emblmygff3: adding py-setuptools dep

* Add 1606 (spack#38511)

* py-python-gitlab: add 3.15.0 (spack#38524)

* py-qmtest: add patch for the removed bdist_wininst class (spack#38253)

Co-authored-by: jmcarcell <[email protected]>

* py-pytz: add 2023.3 (spack#38525)

* spack buildcache sync (--manifest-glob <glob> | <src> <dest>) are mutually exclusive (spack#38533)

* Add numa variant in ucx package (spack#38423)

* zlib-ng: add latest, default to drop in replacement of zlib (spack#37370)

* fix version dependency logic (spack#38535)

* Added version 0.33 (spack#38534)

* Add recipe for iterative-stats (spack#38039)

* Add recipe for iterative-stats

* Fix branch name and remove comment

* Add git link

* Add package maintainer

* Enforce multiple requested changes

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

Co-authored-by: Adam J. Stewart <[email protected]>

* Update checksum

* Fix openturns dependency specification

* Add python variant spec to openturns

---------

Co-authored-by: Marc Schouler <[email protected]>
Co-authored-by: Adam J. Stewart <[email protected]>

* py-pytest: add 7.3.2 (spack#38522)

* py-pytest: add 7.3.2

* [@spackbot] updating style on behalf of manuelakuhn

* Swap py-importlib-metadata dependency order

* Restrict python version for older versions

* libEnsemble: add v0.10.0 (spack#37954)

* libEnsemble: add v0.10.0

* Make new deps required

* Fixes to deps

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

Co-authored-by: Adam J. Stewart <[email protected]>

* Fix build, run

* Reorder required deps

---------

Co-authored-by: Adam J. Stewart <[email protected]>

* range-v3: remove overbroad boost dependence (spack#38539)

Co-authored-by: greenc-FNAL <[email protected]>

* Fixes openmpi configure args for multinode execution on slurm (spack#38403)

Remove `--enable-mca-no-build=btl-uct` check for ucx spec
as it is already fixed in the openmpi open-mpi/ompi#6666

* lammps: new verisons (spack#38532)

* DMTCP: add v3.0.0. (spack#38307)

* pfunit: fix the max_array_rank variant definition (spack#38528)

* libzmq: Fix static assertion failure with gcc-13 (spack#38391)

* Fix syntax to set default target in aws-pcluster pipelines (spack#38048)


Co-authored-by: Massimiliano Culpo <[email protected]>

* GSI-ncdiag: add v1.1.0 and v1.1.1. (spack#38196)


Co-authored-by: [David Huber] <[[email protected]]>

* clp and osi depend on pkgconfig (spack#31505)

Co-authored-by: Massimiliano Culpo <[email protected]>
Co-authored-by: Harmen Stoppels <[email protected]>

* hpctoolkit: convert to new stand-alone test process (spack#35752)

* gaudi: new versions 36.[11-14] (spack#38498)

* etsf-io: convert to new stand-alone test process (spack#35746)

* apptainer: add squashfuse dep (spack#38499)

* circe2: add new package (spack#38491)

* gmap-gsnap: updating to 2023-06-01 (spack#38428)

Co-authored-by: LMS Bioinformatics <[email protected]>

* ascent: add optional occa dep (spack#38426)

Co-authored-by: cyrush <[email protected]>

* libxml2: convert to new stand-alone test process (spack#37694)

* bzip2: add pkg-config file (spack#38355)

Co-authored-by: HongZhi He <[email protected]>

* MOLGW: add new package (spack#37878)

* py-scipy: add v1.11.0 (spack#38546)


Co-authored-by: adamjstewart <[email protected]>

* acts: ensure Python_EXECUTABLE uses ^python when +python (spack#38540)

By default, `find_package(Python)` searches from highest version to lowest version, identifying the highest version that satisfies the requirements. This means that `/usr/bin/python3.11` will be found before `$(spack location -i python)/bin/python3.10`, even when other packages have been built with the `python` in spack.

This ensures that the `python` dependency is explicitly the `python` version that is used.

* Add raw attribute to env.set command (spack#38465)

Update `env.set` command and underlying `SetEnv` object to add the `raw`
boolean attribute. `raw` is optional and set to False by default. When
set to True, value format is skipped for object when generating
environment modifications.

With this change it is now possible to define environment variable
whose value contains variable reference syntax (like `{foo}` or `{}`)
that should be set as-is.

Fixes spack#29578

* tests/*mpi*: convert to new stand-alone test process (spack#35802)

* spectre: add v2023.06.19 (spack#38474)

Co-authored-by: sxs-bot <[email protected]>

* demuxlet: add new package (spack#38425)

* py-python-lzo: add 1.15 (spack#38418)

* py-python-lzo: add 1.15

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <[email protected]>

* armpl-gcc: remove version 23.04 (spack#38362)

* acfl: remove version 23.04 (spack#38363)

* ginkgo: add version 1.6.0 (spack#38439)

* scotch: add new variants + bison version min.  (spack#37958)

* mmseqs2: patching to support building with %gcc@13: (spack#38296)

Co-authored-by: LMS Bioinformatics <[email protected]>

* netcdf-c: apply patches (spack#38324)

* netcdf-c: fix building on macOS

* netcdf-c: add patch fixing multi-threaded HDF5 calls

* netcdf-c: update patch url

* cromwell: add v85 (spack#38427)

Co-authored-by: LMS Bioinformatics <[email protected]>

* tests/heffte/tasmanian: convert to new stand-alone test process (spack#35750)

* ufs-utils: update urls, versions, and dependencies (spack#37255)

* llvm: fix build against libstdc++ 13 (spack#38329)

llvm @13-15 is required for ispc, but fails to build with GCC 13.
14.0.6 and 15.0.7 built successfully with upstream patch, 13.0.1
still fails. Thus upstream patch is applied to 14 and 15 only.

* Openfoam: replace two boolean variants with multi-valued variant for precision option (spack#37736)

* Adds new Qthreads package version (spack#38421)

* Add new versions of Qthreads
* Add version URLs explicitly as it has recently changed
* Use function to extrapolate version URL for older versions
* Fix url formatter

* modules: ignore more Modules variables in from_sourcing_file (spack#38455)

Update list of excluded variables in `from_sourcing_file` function to
cover all variables specific to Environment Modules or Lmod. Add
specifically variables relative to the definition of `module()`, `ml()`
and `_module_raw()` Bash functions.

Fixes spack#13504

* krb5: add missing findutils dependency (spack#38440)


Co-authored-by: Massimiliano Culpo <[email protected]>

* Updates to symlinking for Windows (spack#34701)

* Support hardlinks/junctions on Windows systems without developer
  mode enabled
  * Generally, use of llnl.util.symlink.symlink is preferred over
    os.symlink since it handles this automatically
* Generally an error is now reported if a user attempts to create a
  symlink to a file that does not exist (this was previously allowed
  on Linux/Mac).
  * One exception to this: when Spack installs files from the source
    into their final prefix, dangling symlinks are allowed (on
    Linux/Mac - Windows does not allow this in any circumstance).
    The intent behind this is to avoid generating failures for
    installations on Linux/Mac that were succeeding before.
* Because Windows is strict about forbidding dangling symlinks,
  `traverse_tree` has been updated to skip creating symlinks if they
  would point to a file that is ignored. This check is not
  transitive (i.e., a symlink to a symlink to an ignored file would
  not be caught appropriately)
* Relocate function: resolve_link_target_relative_to_the_link
  (this is not otherwise modified)

Co-authored-by: jamessmillie <[email protected]>

* py-numpy: add v1.24.4 (spack#38555)

* CachedCMakePackage: set build type (spack#38502)

Fixed the cached CMake package so that the build_type field is saved
in the cached configuration file.

* Revert "Updates to symlinking for Windows (spack#34701)" (spack#38578)

This reverts commit 66f7540.

* py-bx-python: add 0.9.0 (spack#38419)

* py-bx-python: add 0.9.0

* remove dependency

* Remove python upper bound

* Clarify dependency requirements

---------

Co-authored-by: LMS Bioinformatics <[email protected]>

* cargs: add new package (spack#38548)

* fairmq: add v1.7.0 (spack#38550)

* Adjust cc90 to require at least CUDA 12 (spack#38572)

* tests/py-genshi: convert to new stand-alone test process (spack#38345)

* py-genshi: convert to new stand-alone test process

* py-genshi: add run as py-setuptools deptype; remove test_testsuite comment

* Update superlu home page (spack#38562)

* superlu-dist: convert to new stand-alone test process (spack#38188)

* Kokkos Kernels: adding release 3.7.1 and 4.0.0 (spack#36655)

Co-authored-by: eugeneswalker <[email protected]>

* ci: remove compiler bootstrapping code (spack#38543)

* py-lightning: add v2.0.4, drop +extra (spack#38531)

* py-lightning: add v2.0.4, drop +extra

* Update dependencies

* kokkos-kernels: require kokkos+cuda_lambda (spack#38568)

(when +cuda, and on version 4.0.00 and up)

* py-rfc3986: add 2.0.0 (spack#38570)

* py-rich: add 13.4.2, py-markdown-it-py: add 3.0.0, py-mdurl: new (spack#38573)

* py-rich: add 13.4.2, py-markdown-it-py: add 3.0.0, py-mdurl: add new package

* Fix style

* py-rst2pdf: add 0.100 (spack#38581)

* py-setupmeta: add 3.4.0 (spack#38589)

* py-reportlab: add 4.0.4 (spack#38561)

* HDF5: is_enabled helper (ON) (spack#35705)

* HDF5: is_enabled helper (ON)
  Slightly generalize the `is_enabled` helper in the HDF5 package.
  `ON` is the most typical CMake bool option passed, besides many
  other possible `true` values, and should be included as a possible
  check to the config.
* Simplify
---------

Co-authored-by: Tamara Dahlgren <[email protected]>

* py-lightly: add v1.4.10 (spack#38594)

* py-ruamel-yaml: add 0.17.32 and py-ruamel-yaml-clib: add 0.2.7 (spack#38585)

* py-ruamel-yaml: add 0.17.32 and py-ruamel-yaml-clib: add 0.2.7

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

Co-authored-by: Adam J. Stewart <[email protected]>

* Fix style

* Fix python dependency

---------

Co-authored-by: Adam J. Stewart <[email protected]>

* intel-oneapi-mkl: handle external mkl with external mpi (spack#38263)

* mindthegap: adding new version 2.3.0 (spack#38596)

* geos: add v3.12.0 (spack#38595)

* environment-modules: add version 5.3.1 (spack#38597)

* Windows: Add PowerShell env support (spack#37951)

PowerShell requires explicit shell and env support in Spack.
This is due to the distinct differences in shell interactions between
cmd and pwsh. Add a doskey in pwsh piping 'spack' commands to a
powershell script similar to the sh function 'spack'. Add
support for PowerShell-specific shell interactions from Spack
(set/unset shell variables).

* celeritas: add patch when using geant4@10 (spack#38592)

* e4s ci: add hdf5-vol-daos (spack#37887)

* e4s ci: add hdf5-vol-daos

* hdf5-vol-daos: comment with failure notes

* [intel-tbb] support for building 2020.3 with icx (for dyninst) (spack#38610)

* pruners-ninja: patch in upstream fix for spack issue spack#32112 (spack#38613)

* openblas: do not build tests when installing (spack#38591)

* openblas: do not build tests when installing
* Add note about building tests

* py-pykerberos: needs krb5 for build to determine link and cflags via krb5-config binary (spack#38623)

* py-rasterio: add v1.3.8 (spack#38621)

* relion: use patch from github for relion 4.0 (spack#38432)

* numaprof: New package (version : 1.1.4) (spack#35271)

* numaprof: New package (version : 1.1.4)
* numaprof: Improve the deps description by adding 'type'
* numaprof: Fix maintainer semantic

* py-pandas: add v2.0.3 (spack#38636)

* CI: Disable building VisIt in CI (spack#38642)

VisIt requires a deprecated version of Python (3.7) due to a VTK 8
dependency. Spack CI does not support building deprecated versions.

* py-scipy: add v1.11.1 (spack#38635)

* `py-nvidia-dali`: add v1.27.0 (spack#38605)

* `py-nvidia-dali`: add v1.27.0

* Style

* py-iterative-stats: Change maintainer, add new version (spack#38609)

* Change maintainer, add new version and deprecate old one

* Fix style issue

* Revert deprecation

---------

Co-authored-by: Marc Schouler <[email protected]>

* Py-shroud: add version 0.12.2 (spack#38643)

* add py-shroud version

* change version number based on advice of adamjstewart

* tests/pythons: convert to new stand-alone test process (spack#38340)

* gitlab ci: reorganize when we check for specs on mirrors (spack#38626)

Move the logic checking which mirrors have the specs we need closer
to where that information is needed.  Also update the staging summary
to contain a brief description of why we scheduled or pruned each
job.  If a spec was found on any mirrors, regardless of whether
we scheduled a job for it, print those mirrors.

* XZ package (Windows): install .dll files in bin (spack#35888)

Windows runtime library loading searches PATH, and therefore bin/ is
the appropriate place to put .dll files. Prior to this change, XZ was
installing both .dll and .lib files to the lib/ directory.

* Python: add new versions (spack#38620)

* Remove deprecated versions and packages (spack#37895)

This PR removes deprecated versions for all packages that I'm maintaining. In future Spack releases, I'm planning to do this on a much larger scale, but we can hold off until we have better reproducibility.

I'm hoping that this will improve the maintainability of these packages. If any other maintainers of these recipes would like to retain any of these deprecated versions, or add new versions, speak now or forever hold your peace 😄 

---------

Co-authored-by: adamjstewart <[email protected]>

* tests/slepc: convert to new stand-alone test process (spack#38653)

* tests/petsc: convert to new stand-alone test process (spack#38652)

* Add Caliper variant in hypre package (spack#38651)

* [py-onnx-runtime] Remove package superseded by py-onnxruntime (spack#37392)

* New package: pipx (spack#38658)

* py-userpath: new package

* pipx: new package

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

Co-authored-by: Adam J. Stewart <[email protected]>

* pipx: Remove incorrect dependency on py-platformdirs

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

Co-authored-by: Adam J. Stewart <[email protected]>

* py-userpath: Remove version requirements to match upstream

---------

Co-authored-by: Adam J. Stewart <[email protected]>

* [intel-oneapi-mkl] add openmpi support for +cluster (spack#38554)

* mercurial: add 6.x, fix python bounds (spack#38668)

* mercurial: add 6.x, fix python bounds

* remove python@2 versions, cause package audits is complaining

* icarus: add v11_0 and v12_0 (spack#38666)

* openrasmol: convert to new stand-alone test process (spack#38630)

* build(deps): bump docker/setup-buildx-action from 2.7.0 to 2.8.0 (spack#38625)

Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.7.0 to 2.8.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](docker/setup-buildx-action@ecf9528...16c0bc4)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Revert "openblas: do not build tests when installing (spack#38591)" (spack#38662)

This reverts commit 51c75c6.

* SIPPackage: documentation fix (spack#38672)

* Deprecate Python 3.7 (spack#38619)

* Deprecated Python 3.7

* Add Python 3.7.17 because why not

* Add libfabric 1.18.1 release (spack#38669)

* Add support to Paraview for TBB (spack#38582)

Co-authored-by: Jean Favre <[email protected]>

* xmlto: fix missing dependency on util-linux (spack#38678)

* Deprecate conda for Python 2 (spack#38681)

* bash: adam now uses fish (spack#38684)

* qt-base: disable accessibility by default (spack#38680)

* dbus: AutotoolsPackage, optional documentation build (spack#38679)

Co-authored-by: Harmen Stoppels <[email protected]>

* guile: fix %oneapi fast math madness (spack#38691)

* add support for oneapi compiler to wrf 4.4 (spack#38607)

Signed-off-by: Andrey Parfenov <[email protected]>

* python: require xz libs=shared when +lzma (spack#38593)

* Drop requirement of [email protected] since it's deprecated (spack#38692)

* add ascent 0.9.2 release (spack#38661)

* Add hash for octopusV13 (spack#38655)

* py-pillow: add v10.0.0 (spack#38670)

* hdf5-vol-log: depends on mpi (spack#38693)

From the configure.ac file:

> H5VL_log is built on top of MPI. Configure option --without-mpi or
> --with-mpi=no should not be used. Abort.

This currently fails to build in the oneAPI pipeline on `develop`

* `ffmpeg`: patch build failure (spack#38656)

* `ffmpeg`: patch build failure

* [@spackbot] updating style on behalf of thomas-bouvier

---------

Co-authored-by: thomas-bouvier <[email protected]>

* Add NCCL v2.18.3-1 release to recipe (spack#38647)

* py-ruff: add 0.0.276 (spack#38702)

* py-numpydoc: add 1.5.0 (spack#38701)

* Remove from __future__ imports (spack#38703)

* spack make-installer: deterministic choice order (spack#38706)

* plink2: add new package @2.00a4.3 (spack#38469)

Co-authored-by: LMS Bioinformatics <[email protected]>

* util-linux: add v2.39.1, fix macOS build (spack#38677)

* Fix DYLD_* propagation to Python process from fish shell (spack#38615)

* macos sip: apply on macos only, dont store LD_LIBRARY_PATH (spack#38687)

* Temporarily disable aws-pcluster pipelines (spack#38708)

* wrf: add ARM compiler support (spack#38695)

* nvtx: add new package (spack#38430)

Co-authored-by: thomas-bouvier <[email protected]>

* Added Python Prometheus client as dependency (spack#38700)

* conduit: remove no longer needed blueos logic (spack#38698)

* quantum-espresso:  change in maintainers (spack#38688)

* gpi-space: add new versions (spack#38709)


Co-authored-by: Massimiliano Culpo <[email protected]>

* py-requests: add 2.31.0 (spack#38563)

* remove another Python 3.7 requirement & preference, since it was deprecated (spack#38710)

* spack commands: add type hints and docstrings (spack#38705)

* py-pymatgen: add 2022.9.8 (spack#38714)

* intel-oneapi-mkl: support for cray mpich (spack#38725)

* py-lightly: add v1.4.11 (spack#38717)

* amrex: add v23.07 (spack#38676)

* py-pyqt4: stricter dependency versions (spack#38673)

* hcoll: ucx version requirements (spack#38665)

* Installations: don't set group permissions when they match what is desired (spack#38036)

* When installing a package Spack will attempt to set group permissions on
the install prefix even when the configuration does not specify a group.

Co-authored-by: David Gomez <[email protected]>

* xrootd: add _STAT_VER patch (spack#38547)



Co-authored-by: jmcarcell <[email protected]>

* git-annex: add latest version 10.20230408 (spack#38728)

* Build NAMD with Tcl by default (spack#38645)

NAMD users expect the Tcl scripting interface to be enabled as it is used in many examples and tutorials in addition to being required for features such as multi-copy algorithms.

* tests/papyrus: convert to new stand-alone test process (spack#38627)

* tests/qthreads: convert to new stand-alone test process (spack#38600)

* ip: add v4.1.0, and additional variants (spack#38526)

* tk: convert to new stand-alone test process (spack#38575)

* Add version 1.8.23 that fixes a compilation bug on clang-15. (spack#38541)

* damask: fix build of alpha release (spack#38457)

* Update cosma and a few related recipes (spack#35615)

* Add maintainers 

* Updated cosma archive checksum and costa version

- updated cosma version (in the cosma build system)
- updated costa version
- use the default generic url for downloading packages
- do not build tiled-mm when the cpu only version is needed


Signed-off-by: Dr. Mathieu Taillefumier <[email protected]>
Co-authored-by: Rocco Meli <[email protected]>
Co-authored-by: Harmen Stoppels <[email protected]>

* plumed: deprecate non-buildable versions, patch Python makefile only when supported (spack#38713)

* salmon: patching to build with %gcc@13: (spack#38553)


Co-authored-by: LMS Bioinformatics <[email protected]>

* Drop Python 2 object subclassing (spack#38720)

* Drop Python 2 super syntax (spack#38718)

* acts: new variant cxxstd (spack#38682)

* acts: allow ^root cxxstd=20

* acts: new variant cxxstd, pass through to root

* acts: always args.append CMAKE_CXX_STANDARD from variant

* acts: remove unused import

* acts: fix self.define_from_variant

* py-spglib: add 2.0.2 (spack#38715)

* py-spglib: add 2.0.2

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

Co-authored-by: Adam J. Stewart <[email protected]>

* Remove py-setuptools as run dependency

---------

Co-authored-by: Adam J. Stewart <[email protected]>

* perl: add 5.38.0, 5.36.1; prefer all even minor versions over development versions (spack#38690)

* perl: add 5.38.0, 5.36.1; prefer all even minor versions over development versions

* fix libxcrypt build with new perl

* fix libxcrypt with a patch

* py-pip: add 23.1.2 (spack#38608)

* py-pip: add 23.1.2

* Restrict py-pip version for py-protobuf

* Restrict py-pip version for straightforward packages

* Restrict py-pip version for nrm

* Fix --install-option name in comments

* Simplify py-pip restriction for py-scs

* nrm: fix wrong comment

* `py-horovod`: update to v0.28.1 (spack#38732)

* `py-dm-tree`: add v0.1.8 (spack#38606)

* `py-dm-tree`: add v0.1.8

* Update dependencies

* Fix hash

* [py-cymem] added version 2.0.7 (spack#38267)

* [py-cymem] added version 2.0.3

* [py-cymem] added restriction to py-wheel limitation

* py-abipy: add 0.9.3 (spack#38716)

* py-abipy: add 0.9.3

* Remove py-cython dependency

* Remove dep version restrictions for new release

* namd: add maintainer (spack#38740)

* [py-blis] added versions 0.7.9 and 0.9.1 (spack#38269)

* [py-blis] added version 0.7.9

* [py-blis] added version 0.9.1

* [py-blis]

- removed type run for dependency py-cython

* openfoam.org: add a maintainer(spack#37280) (spack#37697)

Co-authored-by: Dom Heinzeller <[email protected]>

* py-scikit-learn: add v1.3.0 (spack#38660)

* `py-torch`: fix build (spack#38730)

* Disable fortran in openblas for darwin ci, fix variant default value (spack#38752)

* Add new version 5.0.0 of PyAMG (spack#38674)

* Added v5.0.0 of PyAMG.  This required v7.1.0 of setuptools_scm due to a bug in 7.0.5.

* Added comment about version requirement.

* Loosened dependency based on build experiments.

* Updated tomli deps.

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

Dependence for 7.0 only.

Co-authored-by: Adam J. Stewart <[email protected]>

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

Co-authored-by: Adam J. Stewart <[email protected]>

* Swapped lines.

---------

Co-authored-by: Adam J. Stewart <[email protected]>

* Curl Package: Fixup bugs preventing build on Win (spack#38757)

* mlpack: new package (spack#38277)

* mlpack: new package

mlpack is an intuitive, fast, and flexible header-only C++ machine learning library with bindings to other languages. It is meant to be a machine learning analog to LAPACK, and aims to implement a wide array of machine learning methods and functions as a "swiss army knife" for machine learning researchers.

* mlpack: upstream merged patch to allow python installation in spack

* freesurfer: add 7.4.1, 7.4.0, 7.3.2 (spack#38544)

* add cgns 4.4.0 (spack#38530)

* add info about spack env from spack-configs for oneAPI build tools (spack#38751)

Signed-off-by: Andrey Parfenov <[email protected]>

* Prevent "spack external find" to error out on wrong permissions (spack#38755)

fixes spack#38733

* Fix multiple quadratic complexity issues in environments (spack#38771)

1. Fix O(n^2) iteration in `_get_overwrite_specs`
2. Early exit `get_by_hash` on full hash
3. Fix O(n^2) double lookup in `all_matching_specs` with hashes
4. Fix some legibility issues

* Remove "node_compiler" from the list of unknown atoms (spack#38753)

* py-astropy: fix import tests and restrict py-pip version (spack#38731)

* py-astropy: fix import tests and restrict py-pip version

* Fix --install-option name in comments

* Rename variant and fix variant dependencies

* Remove parquet variant from py-pyarrow

* New package: py-nanobind (spack#38327)

* initial commit of nanobind package

* style fixes

* Update package.py

Typo

* addressed PR comments

* add v1.4.0

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

Co-authored-by: Adam J. Stewart <[email protected]>

---------

Co-authored-by: Matthew Archer <[email protected]>
Co-authored-by: Adam J. Stewart <[email protected]>

* py-matplotlib: add v3.7.2 (spack#38745)

* py-matplotlib: add v3.7.2

* Update dep versions

* py-pyarrow: disable dataset variant by default (spack#38775)

* py-pyarrow: enable parquet variant by default

* Disable parquet variant by default

* Add conflict to enable parquet when dataset is active

* Disable dataset variant by default

* PyNVTX: added new package (spack#38763)

* qt-* (Qt6 pkgs): new versions 6.5.0, 6.5.1 (spack#36705)

* qt-base: new version 6.5.0

* qt-declarative: new version 6.5.0

* qt-quick3d: new version 6.5.0

* qt-quicktimeline: new version 6.5.0

* qt-shadertools: new version 6.5.0

* qt-*: new version 6.5.1

* qt-base: new version 6.5.1

* gcc: add 10.5.0 (spack#38784)

* pkgconf: Update to new upstream URL (spack#38800)

See pkgconf/pkgconf@437c2a3

* Don’t call spec.format in Database._get_matching_spec_key (spack#38792)

`"%s" % spec` formats the spec with deps included, which produces sometimes KBs
of data and is slow to run in pure Python. It can delay otherwise very short-lived
read/write locks on the database.

Discovered in spack#38762 where profile output showed about 2 seconds is spent in
`spec.format`, which is significant overhead when using multiprocessing to install
from binary cache in parallel (installation often takes <5s for small packages). With
this change, `spec.format` no longer shows up in profile output.

(This line hasn't changed since Spack v0.9 ;p)

* move format() call to custom NoSuchSpecError exception
* add a comment saying why, so we can eventually change `Spec.__str__`

* Automated deployment to update package flux-core 2023-07-08 (spack#38790)

Co-authored-by: github-actions <[email protected]>

* ci: Fix broken SPACK_CHECKOUT_VERSION (spack#38778)

* openssl: prefer 3.x (spack#36729)

* openssl: prefer 3.x

This PR is not intended to be merged immediately, but it would be good
to see what packages fail to build in CI so that we can get proper
version constraints on openssl (before all packages update and support
both openssl 1 and 3)

* Disable assembly for 3.x %oneapi

* cmake: depend on spack curl, to deal with curl - openssl compat

* also make zlib external

* remove overly strict & unsafe requirement on py-cryptographty patch version number

* update openssl compat bounds in py-cryptography

* smaller diff

* Make libssh2 an autotools/cmake package

* fix weird upperbound in libssh2 as there is not openssl v2

* libssh2: pc file lists plain -lssl -lcrypto w/o leading -L flag, confusing libgit2 parsing of pkg-config output

* Actually fix the issue in libssh2: its pc file looks broken

* py-triangle: restrict Python version (spack#38808)

* Added package py-bitstruct (spack#38761)

* Added packages bitstruct, callmonitor, and PYnvtx

* Revert "Added packages bitstruct, callmonitor, and PYnvtx"

This reverts commit 76d25aa.

* py-bitstruct: This module is intended to have a similar interface as the python struct module, but working on bits instead of primitive data types (char, int, …)

* Update package.py

To pass the style prechecks

* PyNVTX: new package

* Delete package.py

Accidentally added this package.

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

Co-authored-by: Adam J. Stewart <[email protected]>

---------

Co-authored-by: eugeneswalker <[email protected]>
Co-authored-by: Adam J. Stewart <[email protected]>

* find: add `--hashes` shortcut for piping to other commands (spack#38663)

People frequently ask us how to pipe `spack find` output to other commands, and we tell
them to do things like this:

```console
$ spack find --format "/{hash}" | spack uninstall -ay
```

Sometimes users don't know about hash references and come up with potentially ambiguous
formulations like this:

```console
spack find --format {name}@{version}%{compiler} | spack uninstall -ay
```

Since this is a common enough thing to want to do, and to make it more obvious how, this
PR adds a `-H` / `--hashes` as a shortcut, so you can now just do:

```console
spack find -H | spack uninstall -ay
```

* Removing inactive maintainer (spack#38773)

* Update cp2k recipe to use cmake or the current build system (spack#35718)

* Update cp2k recipe to use cmake or the current build system

Offers the possibility to build cp2k with the new cmake build system. commands like this are now supported

spack install cp2k@master build_system=cmake +.....

the recipe supports the following optional functionalities

- superlu, cosma, sirius, spglib, metis, spglib, libxc, libint, cuda/rocm, mkl/openblas/sci (and others), mpi, openmp, dbcsr
- dbcsr is built separately using the currently available recipe.

Two PRs need to be merged to be fully functional (cosma update in spack + one PR in cp2k github).

* Fix indentation

* Fix indentation

* Update libvori

* More typos

* Simplify BLAS/LAPACK

* Simplify BLAS/LAPACK

* Add A100 gpu value

* Fix typo

* Add the enable_regtests option

if -DCP2K_ENABLE_REGTESTS=ON (+enable_regtests with spack) then the location of the binary executables will be in the cp2k root directory under exe/build-cmake-*. This option is needed to run the regtests afterwards.

* Minor update

* more fixes

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Mikael Simberg <[email protected]>

* small changes

* Remove any reference to nvidia architecture in the rocm list

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <[email protected]>

* Update var/spack/repos/builtin/packages/cp2k/package.py

Co-authored-by: Alberto Invernizzi <[email protected]>

* Final reformating

* Update py-fypp

---------

Co-authored-by: Mikael Simberg <[email protected]>
Co-authored-by: Alberto Invernizzi <[email protected]>

* Fix style errors

* Fix flake8 errors

* More unit test failures

* Remove guard for untested code from lib/spack/spack/test/modules/lmod.py

* Replace path with manifest_dir in lib/jcsda-emc/spack-stack/stack/stack_env.py, remove init_file

* Fix style errors in lib/jcsda-emc/spack-stack/stack/stack_env.py

* Update call to Environment class in lib/jcsda-emc/spack-stack/tests/test_setup_meta_modules.py

* Fix more style errors

* More style errors in lib/jcsda-emc/spack-stack/stack/stack_env.py

* Update bufr package to use CMakeBuilder and CustomPythonPipBuilder

* Fix style errors in var/spack/repos/builtin/packages/bufr/package.py

* Add in missing bufr build steps

* Revert bufr and add -march=native

* Fix style errors in var/spack/repos/builtin/packages/bufr/package.py

* Update var/spack/repos/builtin/packages/bufr/package.py: Add dependency on py-wheel, apply patch to fix Python version in install dir, remove extra py install step

* Fix unused import in var/spack/repos/builtin/packages/bufr/package.py

* Bug fix in lib/jcsda-emc/spack-stack/stack/meta_modules.py: on macOS, recent spack versions use compiler version format @=x.y.z

* Black-format lib/jcsda-emc/spack-stack/stack/meta_modules.py

* Update static logic from var/spack/repos/builtin/packages/cmake/package.py, openssl is no longer a dependency for make

* Update cray_backend.py

* add python path fix to bufr

* import os in bufr

---------

Signed-off-by: dependabot[bot] <[email protected]>
Signed-off-by: Andrey Parfenov <[email protected]>
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* `py-dm-tree`: add v0.1.8

* Update dependencies

* Fix hash