* Add libpressio and dependencies; some of these packages are
maintained as forks of the original repositories and in those
cases the docstring mentions this.
* Add optional dependency in adios2 on libpressio
* cub package: set CUB_DIR environment variable for dependent
installations
* Clear R_HOME/R_ENVIRON before Spack installation (avoid sources
outside of Spack from affecting the installation in Spack)
* Rename dlib to dorian3d-dlib and update dependents; add new dlib
implementation. Pending an official policy on how to handle
packages with short names, reviewer unilaterally decided that
the rename was acceptable given that the new Spack dlib package
is referenced more widely (by orders of magnitude) than the
original
Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
* ADIOS2: ZFP<1.0
The tagged ADIOS2 releases in Spack (and develop) do not yet
work with ZFP 1.0. Express valid depedency range before someone
updates the ZFP package and triggers the incompatibility.
* Use semver
Explicitly import package utilities in all packages, and corresponding fallout.
This includes:
* rename `spack.package` to `spack.package_base`
* rename `spack.pkgkit` to `spack.package`
* update all packages in builtin, builtin_mock and tutorials to include `from spack.package import *`
* update spack style
* ensure packages include the import
* automatically add the new import and remove any/all imports of `spack` and `spack.pkgkit`
from packages when using `--fix`
* add support for type-checking packages with mypy when SPACK_MYPY_CHECK_PACKAGES
is set in the environment
* fix all type checking errors in packages in spack upstream
* update spack create to include the new imports
* update spack repo to inject the new import, injection persists to allow for a deprecation period
Original message below:
As requested @adamjstewart, update all packages to use pkgkit. I ended up using isort to do this,
so repro is easy:
```console
$ isort -a 'from spack.pkgkit import *' --rm 'spack' ./var/spack/repos/builtin/packages/*/package.py
$ spack style --fix
```
There were several line spacing fixups caused either by space manipulation in isort or by packages
that haven't been touched since we added requirements, but there are no functional changes in here.
* [x] add config to isort to make sure this is maintained going forward
The number of commit characters in patch files fetched from GitHub can change,
so we should use `full_index=1` to enforce full commit hashes (and a stable
patch `sha256`).
Similarly, URLs for branches like `master` don't give us stable patch files,
because branches are moving targets. Use specific tags or commits for those.
- [x] update all github patch URLs to use `full_index=1`
- [x] don't use `master` or other branches for patches
- [x] add an audit check and a test for `?full_index=1`
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* fix remaining flake8 errors
* imports: sort imports everywhere in Spack
We enabled import order checking in #23947, but fixing things manually drives
people crazy. This used `spack style --fix --all` from #24071 to automatically
sort everything in Spack so PR submitters won't have to deal with it.
This should go in after #24071, as it assumes we're using `isort`, not
`flake8-import-order` to order things. `isort` seems to be more flexible and
allows `llnl` mports to be in their own group before `spack` ones, so this
seems like a good switch.
Example replacement:
```
'-D(\w+)(:BOOL)?=\{0\}'\.\s*format\s*\(\s*'(ON|YES|true|TRUE)' if '\+(\w+)' in (self\.)?spec else '(OFF|NO|false|FALSE)'\)
```
with
```
self.define_from_variant('\1', '\4')
```
This will cause failures if any variants were misspelled: I have already caught two packages with nonexistent variants.
This release also includes the HDF5 VOL plugin so I've added an additional
funciton to ensure the HDF5_PLUGIN_PATH env var gets updated with the adios
install prefix
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
* ADIOS2: Version `master`
Rename branch version to supported, real development branch `master`.
The old name is legacy Spack when alternative development branch
names were not yet supported.
* ADIOS: Simplify via spec Variable
use the already defined local variable `spec` to shorten
lines
* DataSpaces: 1.8.0
Add a newer release of DataSpaces for ADIOS2.
Also add missing `-fPIC` flags since this is a static library.
* ADIOS2: Dataspaces, libffi, libfabric
Add missing dependencies to ADIOS2. Without explicit control,
those dependencies might get picked up from the system environment
and will cause unstable builds.
* Hide transitive SST dependencies
* ADIOS2: Simplify SST CMake Flags
As proposed by Chuck
Provide up to date specs for build options
Remove non-production versions
Format using autopep8 and flake8
Separate cmake options in adios2 2.4.0 version
Keep default as True as much as possible
Support for Python 2 and 3 for adios2 versions <= 2.4.0
Starting v2.5.0 only Python 3 is supported
Addressing review suggestions
* ZFP: CMake Package
ZFP is primarily build via CMake, which will have all install logic
and configuration files generated.
The 0.5.0 release did not support this yet, so we toss it.
* Patch ADIOS1: ZFP 0.5.1+ support
* ZFP: Expose all CMake variants
* ADIOS 2.4.0: Add new Deps
Version 2.4.0 of ADIOS2 added new dependencies that are not
yet listed as `depends_on` and/or disabled otherwise. Add them
now to avoid picking them up from system paths, e.g. `libpng`.
* ADIOS2: Variant Defaults Change
* Python: False by default
* ADIOS1: only used prior to 2.3.0
Update older md5 checksums to sha256. Require CMake >= 3.6.0 (updated
from 3.5.0). Remove some third-party depends_on statements (which
were commented out before).
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
