* 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]>

…` 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]>

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-platformdirs: add 3.5.3

* py-typing-extensions: add 4.6.3

…ck#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]>

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

* [@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]>

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

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

* 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

* py-bcbio-gff: adding new version 0.7.0

* emblmygff3: adding new package

* emblmygff3: adding py-setuptools dep

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

…ually exclusive (spack#38533)

)

* 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

* [@spackbot] updating style on behalf of manuelakuhn

* Swap py-importlib-metadata dependency order

* Restrict python version for older versions

* 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]>

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

…38403)

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

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

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

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

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

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

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

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

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.

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

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

* py-python-lzo: add 1.15

* Update package.py

---------

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

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

* netcdf-c: fix building on macOS

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

* netcdf-c: update patch url

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

…k#35750)

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.

…precision option (spack#37736)

* 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

…8455)

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

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

* 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]>

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

This reverts commit 66f7540.

* py-bx-python: add 0.9.0

* remove dependency

* Remove python upper bound

* Clarify dependency requirements

---------

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

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

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

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

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

* Update dependencies

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

…ck#38573)

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

* Fix style

* 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]>

…#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]>

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).

* e4s ci: add hdf5-vol-daos

* hdf5-vol-daos: comment with failure notes