* petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0
* workaround for dealii build failure [with petsc version check]
* pism: add compatibility fix to for petsc@3.18
* add in hipsolver dependency
* Add checksum for py-gitpython 3.1.27
* Update package.py
* Update var/spack/repos/builtin/packages/py-gitpython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
When a pipeline generation job is automatically failed because it
generated jobs for specs known to be broken on develop, print better
information about the broken specs that were encountered. Include
at a minimum the hash and the url of the job whose failure caused it
to be put on the broken specs list in the first place.
* new package + deps
* Update var/spack/repos/builtin/packages/py-about-time/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-alive-progress/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* removed unnecessary python version dep
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add new lua releases
* split install phase and move it into a build phase, remove hardcoded standard flag
* revert back to the original hardcoded std flag, guard patch against versions above 5.4
* py-pyopenssl: add version 22.1.0
* Update var/spack/repos/builtin/packages/py-pyopenssl/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-regex 2022.8.17
* Update var/spack/repos/builtin/packages/py-regex/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-async-lru 1.0.3
* [@spackbot] updating style on behalf of iarspider
* Update var/spack/repos/builtin/packages/py-async-lru/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* env depfile: allow deps only install
- Refactor `spack env depfile` to use a Jinja template, making it a bit
easier to follow as a human being.
- Add a layer of indirection in the generated Makefile through an
`<prefix>/.install-deps/<hash>` target, which allows one to specify
different options when installing dependencies. For example, only
verbose/debug mode on when installing some particular spec:
```
$ spack -e my_env env depfile -o Makefile --make-target-prefix example
$ make example/.install-deps/<hash> -j16
$ make example/.install/<hash> SPACK="spack -d" SPACK_INSTALL_FLAGS=--verbose -j16
```
This could be used to speed up `spack ci rebuild`:
- Parallel install of dependencies from buildcache
- Better readability of logs, e.g. reducing verbosity when installing
dependencies, and splitting logs into deps.log and current_spec.log
* Silence please!
* Add bioc attribute to r-do-db
* add version 1.38.1 to bioconductor package r-annotationforge
* add version 1.30.4 to bioconductor package r-biocparallel
* add version 2.64.1 to bioconductor package r-biostrings
* add version 4.4.4 to bioconductor package r-clusterprofiler
* add version 2.12.1 to bioconductor package r-complexheatmap
* add version 1.18.1 to bioconductor package r-delayedmatrixstats
* add version 3.22.1 to bioconductor package r-dose
* add version 3.38.4 to bioconductor package r-edger
* add version 1.16.2 to bioconductor package r-enrichplot
* add version 2.20.2 to bioconductor package r-ensembldb
* add version 1.32.4 to bioconductor package r-genomeinfodb
* add version 1.32.1 to bioconductor package r-genomicalignments
* add version 1.48.4 to bioconductor package r-genomicfeatures
* add version 1.44.1 to bioconductor package r-ggbio
* add version 3.4.4 to bioconductor package r-ggtree
* add version 1.24.2 to bioconductor package r-hdf5array
* add version 2.30.1 to bioconductor package r-iranges
* add version 1.36.3 to bioconductor package r-keggrest
* add version 3.52.4 to bioconductor package r-limma
* add version 1.8.1 to bioconductor package r-matrixgenerics
* update r-org-hs-eg-db
* add version 1.38.1 to bioconductor package r-organismdbi
* add version 1.36.1 to bioconductor package r-pathview
* add version 1.56.1 to bioconductor package r-rtracklayer
* add version 1.4.1 to bioconductor package r-scaledmatrix
* add version 1.24.1 to bioconductor package r-scran
* add version 1.6.3 to bioconductor package r-scuttle
* add version 1.18.1 to bioconductor package r-singlecellexperiment
* add version 1.20.2 to bioconductor package r-treeio
* Revert "Add bioc attribute to r-do-db"
This reverts commit 36be5c6072c98ec70bb16f9d613a6fe24407fee1.
* Fix quotes on versions
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
