* scons: add a new version

* scons: address @adamjstewart review

Too much copypasta

* Update versions 2.5.0.0 and 2.5.0.1

* Applying review changes

* Updating incorrect checksum for v2.4.0.0

* Add for loop to define depends_on for preCICE versions and bindings versions

* Formatting

* Missing comma

* Add pyprecice v2.5.0.2

ref. #35400

* py-ipdb: updating versions

Signed-off-by: Loïc Pottier <[email protected]>

* py-ipdb: fixing versions problem and deleting 10.1 which is too old for Python > 3.6

Signed-off-by: Loïc Pottier <[email protected]>

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

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

* py-ipdb: removed useless dependencies

Signed-off-by: Loïc Pottier <[email protected]>

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

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

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

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

* py-ipdb: missing @

Signed-off-by: Loïc Pottier <[email protected]>

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

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

---------

Signed-off-by: Loïc Pottier <[email protected]>
Co-authored-by: Adam J. Stewart <[email protected]>

* snakemake: added versions 7.19.0-7.22.0

* snakemake: corrected +reports dependencies

Update `spack.util.environment` to remove legacy idioms.
* Remove kwargs from method signature and use a class for traces
* Uppercase a few global variables
* spack.util.environment: add type-hints
* Improve docstrings
* Fixed most style issues reported by pylint

…ng (#35376)

* Start using paths found in extra_rpaths in compilers.yaml when building

* running black and changing maintainer list

* changing import order to pass isort

---------

Co-authored-by: Matthew Lieber <[email protected]>

* add 2.14.2 py-astroid version

* add py-pylint 2.26.2

* fix black

* fix py-dill depends_on

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

* fix py-astroid minor versionning

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

* modify typing_extensions depends_on

---------

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

`mypy` only understands `sys.platform == "win32"`, not indirect assignments of that
value to things like `is_windows`. If we don't use the accepted platform checks, `mypy`
registers many Windows-only symbols as not present on Linux, when it should skip the
checks for platform-specific code.

…2-36227 (#35826)

* curl: add v7.88.1 and deprecate previous versions due to CVEs

* Add self as a maintainer to curl

* py-elasticsearch: new versions

Also add py-elastic-transport as a new dependency

* py-elasticsearch: py-urllib3 is no longer a dependency

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

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

---------

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

Currently, if two compilers with the same spec differ on the flags, the concretizer will:

1. mix both sets of flags for the spec in the ASP program
2. error noting that the set of flags from the compiler (both of them) doesn't match the set from the lower priority compiler

This PR fixes both -- only flags from the highest priority compiler with a given spec are considered.

* update proj

* re-add autotools support

* style

* Setup env in builders

* Drop direct windows conflict for older versions

* Default to CMake

Add new style class definiton

* Proj: setup_run_environment in package not builder

* Proj: move run env changes to pkg, rm cmake arg

* Set PROJ_LIB during build

* Style

* Rm redundant configure arg

* update mda dependencies

* apply black

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

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

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

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

* remove numpy upper bound

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

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

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

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

---------

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

* httpie: add v3.2.1

* Add additional 3.2.1 dependencies to httpie

* Add version condition to dependency

* Reorder dependencies for efficiency

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

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

---------

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

Two fixes:

1. `-Wl,a,b,c,d` is a comma separated list of linker arguments, we
   incorrectly assume key/value pairs, which runs into issues with for
   example `-Wl,--enable-new-dtags,-rpath,/x`
2. `-Xlinker,xxx` is not a think, so it shouldn't be parsed.

…#35803)

The Cray fortran compiler names fortran modules in uppercase by
default. Compile with the "-ef" flag to produce the lowercase
name that singularity-eos is expecting.

* Update/fix py-meldmd; update openmm

* Restrict filter_file based on openmm version

* Updates based on Adam's feedback

* [@spackbot] updating style on behalf of meyersbs

* Break up long filter_file

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

---------

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

* New package: py-imbalanced-learn

* Fix typo

* [@spackbot] updating style on behalf of meyersbs

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

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

---------

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

This commit formalizes `satisfies(lhs, rhs, strict=True/False)`
and splits it into two functions: `satisfies(lhs, rhs)` and
`intersects(lhs, rhs)`.

- `satisfies(lhs, rhs)` means: all concrete specs matching the
   left hand side also match the right hand side
- `intersects(lhs, rhs)` means: there exist concrete specs
   matching both lhs and rhs.

`intersects` now has the property that it's commutative,
which previously was not guaranteed.

For abstract specs, `intersects(lhs, rhs)` implies that
`constrain(lhs, rhs)` works.

What's *not* done in this PR is ensuring that
`intersects(concrete, abstract)` returns false when the
abstract spec has additional properties not present in the
concrete spec, but `constrain(concrete, abstract)` will
raise an error.

To accomplish this, some semantics have changed, as well
as bugfixes to ArchSpec:
- GitVersion is now interpreted as a more constrained
  version
- Compiler flags are interpreted as strings since their
  order is important
- Abstract specs respect variant type (bool / multivalued)

* py-openmesh: new package

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

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

---------

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

* "new py-thop package"

* [@spackbot] updating style on behalf of Sangu-Mbekelu

* Update package.py

modified the url and dependencies

---------

Co-authored-by: Sangu Mbekelu <[email protected]>

Currently `spack buildcache create` creates compressed tarballs that
differ between each invocation, thanks to:

1. The gzip header containing mtime set to time.time()
2. The generated buildinfo file which has a different mtime every time.

To avoid this, you have to explicitly construct GZipFile yourself, since
the Python API doesn't expose the mtime arg, and we have to manually
create the tarinfo object for the buildinfo metadata file.

Normalize mode: regular files & hardlinks executable by user, dirs, symlinks: set 0o755 permissions in tarfile; other files use 0o644