* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* dealii: Added 'threads' variant that controls the TBB dependency (#13931)
* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB
* Update var/spack/repos/builtin/packages/dealii/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* amber: Adding missing flex and bison dependencies
* Removed cray variant; flex and bison now build only
* amber: Improved package.py and added version 18
- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()
* amber: Adding missing flex and bison dependencies
* Removed cray variant; flex and bison now build only
* dealii: Fixed flake8 issues
* amber: corrected typo
* amber: Removed unused variant python
Add a line to .gitattributes so that `git grep -p` shows function names
properly for `*.py` files. Without this, the class name is shown instead
of the function for python files.
This also causes diff output to use proper functions as hunk headers in
`diff` output.
Here's an example with `git grep -p`.
Before:
$ git grep -p spack_cc var/spack/repos/builtin/packages/athena
var/spack/repos/builtin/packages/athena/package.py=class Athena(AutotoolsPackage):
var/spack/repos/builtin/packages/athena/package.py: env.set('CC', spack_cc)
var/spack/repos/builtin/packages/athena/package.py: env.set('LDR', spack_cc)
After:
$ git grep -p spack_cc var/spack/repos/builtin/packages/athena
var/spack/repos/builtin/packages/athena/package.py= def setup_build_environment(self, env):
var/spack/repos/builtin/packages/athena/package.py: env.set('CC', spack_cc)
var/spack/repos/builtin/packages/athena/package.py: env.set('LDR', spack_cc)
Here's an example with `diff`.
Before:
$ git show c5da94eb58
[...]
@@ -28,6 +29,7 @@ print(u'\\xc3')
# make it executable
fs.set_executable(script_name)
+ filter_shebangs_in_directory('.', [script_name])
# read the unicode back in and see whether things work
script = ex.Executable('./%s' % script_name)
After:
$ git show c5da94eb58
[...]
@@ -28,6 +29,7 @@ def test_read_unicode(tmpdir):
# make it executable
fs.set_executable(script_name)
+ filter_shebangs_in_directory('.', [script_name])
# read the unicode back in and see whether things work
script = ex.Executable('./%s' % script_name)
* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB
* Update var/spack/repos/builtin/packages/dealii/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Created an initial recipe for Sensei
* Cleanup syntax
* Small fixes for the Sensei recipe
* Cosmetic fixes to comply with PEP8
* More cosmetic fixes before PR
* Added more documentation before PR
* Fixed flake8 errors
* Fixes following PR review
* Fixes to pass Flake8 passes
* Some changes following PR review and support for SENSEI 3
* Update var/spack/repos/builtin/packages/sensei/package.py
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Fixed Flake8 errors
Commit 78724357 added versions 2019.5 to 2019.8 but failed to update
the patches for these versions.
1. gcc_generic-pedantic patch -- include this up through 2019.5. This
was fixed in the TBB source tree in 2019.6.
2. tbb_cmakeConfig patch -- this needs to be modified (different file)
for 2019.5 and later.
3. tbb_gcc_rtm_key patch -- replace this with filter_file. This is
simpler and eliminates the need to update the patch whenever the
surrounding context changes.
* dont add perl bin directory to PATH when setting up env (this is already handled by spack core in a way that omits system dirs); also consolidate repeated logic between build/run env setup.
* the bin/ dir of each dependency is already added to PATH in Spack core, so there is no need to do this in the Perl package
* BLD: enforce C++11 std for boost + xl_r
* the spack `cxxstd` variant is not sufficient to enforce
`-std=c++11` usage in boost compile lines when `xl_r` compiler
spec is in use; while it would be nice if this were fixed
in a boost config file somewhere, for now this patch
allows boost to build on POWER9 with
an %xl_r compiler spec if the user specifies i.e.,:
`spack install boost@1.70.0+mpi cxxstd=11 %xl_r@16.1.1.5`
* Update var/spack/repos/builtin/packages/boost/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
The documentation states that Spack builds R without the recommmened
packages, with Spack handling the build of those packages to satisfy
dependencies. From the docs:
> Spack explicitly adds the --without-recommended-packages flag to
> prevent the installation of these packages. Due to the way Spack
> handles package activation (symlinking packages to the R installation
> directory), pre-existing recommended packages will cause conflicts for
> already-existing files. We could either not include these recommended
> packages in Spack and require them to be installed through
> --with-recommended-packages, or we could not install them with R and
> let users choose the version of the package they want to install. We
> chose the latter.
However, this is not what Spack is actually doing. The
`--without-recommended` configure option is not passed to R and
therefore those packages are built. This prevents R extension activation
from working as files in the recommended packages installed with R will
block linking of file from the respective `r-` packages.
This PR adds the `--without-recommended` flag to the configure options
of the R package. This will then have the Spack R build match what is
documented.
* Replace git-based Bioconductor R packages
The current collection of bioconductor packages tend to have scattered
dependencies and missing versions. This commit replaces git-based
packages with tool-generated Spack package recipes with correct
dependencies and descriptions in place.
* Fix some broken package names, add periods to title docstrings
* r-clue: new package at 0.3-57
* r-genomeinfodbdata: add 1.2.1
* r-gofuncr: new package at 1.4.0
* r-pfam-db: add 3.8.2
* Add missed package r-genelendatabase
* update r-goseq package
* update r-glimma package
* update r-rots package
* r-org-hs-eg-db: add 3.8.2
* r-vgam: fix incorrect R version
* r-rnaseqmap: new package at 2.42.0
* r-rhdf5lib: new package at 1.6.0
* r-scrime: new package at 1.3.5
* r-delayedmatrixstats: new package at 1.6.0
* r-hdf5array: new package at 1.12.1
* r-biocfilecache: new package at 1.8.0
* r-ctc: add new versions, dependencies
* r-genemeta: new package at 1.56.0
* r-scrime: fix flake8
* r-ensembldb: add missing dependencies
* Added missing dependencies to packages with certain DESCRIPTIONS
* r-mapplots: new package at 1.5.1
* r-beachmat: new package at 2.0.0
* r-beeswarm: new package at 0.2.3
* r-biocneighbors: new package at 1.2.0
* r-biocsingular: new package at 1.0.0
* r-ecp: new package at 3.1.1
* r-enrichplot: new package at 1.4.0
* r-europepmc: new package at 0.3
* r-ggbeeswarm: new package at 0.6.0
* r-ggplotify: new package at 0.0.3
* r-ggraph: new package at 1.0.2
* r-gridgraphics: new package at 0.4-1
* r-rcppannoy: new package at 0.0.12
* r-rcpphnsw: new package at 0.1.0
* r-rsvd: new package at 1.0.1
* r-scater: new package at 1.12.2
* r-singlecellexperiment: new package at 1.6.0
* r-tximport: new package at 1.12.3
* r-upsetr: new package at 1.4.0
* r-vioplot: new package at 0.3.2
* r-readr: add 1.3.1
* r-matrixstats: add 0.54.0
* r-ecp: flake8 fix
* r-biocmanager: new package at 1.30.4
* update bioconductor packages requiring BiocManager, new versions
* r-lambda-r: add 1.2.3
* r-vegan: add 2.5-5
* r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF
* r-chemometrics: flake8 fixes
* r-vgam: flake8 fixes
* CRAN packages: use cloud.r-project.org
* Use DESCRIPTION for R version constraints over bioconductor releases
* Update missed packages ABAData, acde, affydata
* Update remaining missed packages
* bio: Drop 'when' clause from first checksummed versions
* bio: improve package description generation logic
* r-genomeinfodbdata: use explicit sha256 sums
* r-pfam-db: update dependencies, add 3.10.0
* update r-org-hs-eg-db
* r-dirichletmultinomial: re-add gsl
* r-polyclip: new package at 1.10-0
* r-farver: new package at 1.1.0
* r-tweenr: new package at 1.0.1
* r-ggforce: new package at 0.3.1
* r-ggforce: remove redundant dep
* r-ggraph: add missing deps
* r-rcpphnsw: remove redundant depends_on
* r-reportingtools: re-add r-r-utils dep
* r-rhdf5: add gmake dep
* r-rhtslib: add system dependencies
* r-rsamtools: add gmake dep
* r-farver: remove redundant dep
* r-tweenr: remove redundant dep
* r-variantannotation: add gmake dep
* r-rgraphviz: add graphviz dep
* r-vsn: correct r-hexbin constraint
* r-scater: fix obsolete deps
* r-variantannotation: fix gmake dep type
* r-scater: tighten R version constraints
* r-rsamtools: fix gmake dep type
* r-rhtslib: fix gmake dep type
* r-rhtslib: use xz over lzma
* r-rhdf5: fix gmake dep type
* r-farver: replace with newer recipe for 2.0.1
* r-mzr: remove old dependency
* r-reportingtools: remove builtin dependency
* r-mzr: add gmake dep
* r-rhtslib: make system libraries link deps
* r-genomeinfodbdata: fix R version constraints
* r-geoquery: remove old deps from new versions
* r-genomicfeatures: tighten r-rmysql dep
* r-ensembldb: tighten r-annotationhub dep
* r-complexheatmap: fix r-dendextend dep
* r-cner: fix utils dep name
* r-clusterprofiler: fix r-gosemsim version req
* r-biostrings: fix r-iranges version reqs
* r-rhdf5lib: add gmake dep
* r-oligoclasses: fix r-biocinstaller dep range
* r-organismdbi: fix r-biocinstaller dep range
* r-hdf5array: add gmake dep
* r-gtrellis: tighten r-circlize version req
* r-gostats: fix r-graph version req
* r-glimma: fix old dependency ranges
* r-biostrings: syntax fix
* r-organismdbi: syntax fix
* r-dose: fix r-igraph dep
* r-dose: fix r-scales, r-rvcheck deps
* r-affy: fix r-biocinstaller dep
* r-ampliqueso: fix homepage
* r-aneufinder: fix r-biocgenerics dep
* r-beachmat: fix changed deps
* r-biocneighbors: fix old R constraint
* r-biocmanager: rewrite recipe for 1.30.10
* Update var/spack/repos/builtin/packages/r-biocinstaller/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/r-oligoclasses/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update cartopy version and fix recipe
Cartopy 0.17.0 works fine with proj 6
* Update cartopy version and fix recipe
Cartopy 0.17.0 works fine with proj 6
* Set ACCEPT_USE_OF_DEPRECATED_PROJ_API_H flag when building extension
* Add variants to py-cartopy recipe as suggested
* Fix proj dependency
* Split dependency
* Fix PEP-8; remove extra dependency
* Bump up QE version number to 6.4.1.
* Fix QMCPACK conflicts.
* HDF5 dependencies where over specified which could cause unnecessary installs of HDF5.
* Update QMCPACK testing option.
* Remove support for serial QE 6.4.1 converter. Add support for parallel QE 6.4.1. converter with serial HDF5.
* Switch to setup_run_environment.
* Fix setup_run_environment call arguements.
* Fix typo.
* switch run_env to env
* package py-cheroot
* package py-cheroot
* autopep8, docutils cleanup
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* missing deps
* flake8
* license bits
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-cheroot/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* python dep
* flake8
Note to spack people: these are expected to be end of line releases for both the 3.1.5 an 3.0.5 releases
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
* metabat: add versions 2.14 and 2.13
* update build environment
* Update var/spack/repos/builtin/packages/metabat/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/metabat/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* update py-nbconvert
* add setuptools dependency, like all the other jupyter packages
it seems to be using setuptools for some commands all the time
but requires it for the newest version
* added dependencies, not necessarily only needed for the latest one
* depends on new packages (defusedxml, pandocfilters, testpath)
* should also be moved to pypi sources?
* '@5:@5:' is a valid spec -> intended?
* make dependencies optional
* Update dependencies and add description
* relax py-mistune dependency restriction
* Update var/spack/repos/builtin/packages/py-nbconvert/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-arrow
* actually use dependencies from 0.14.7 not from current HEAD
* drop dependencies that dont appear in the source
* readd sphinx as doc dependency
* update dependencies
* drop doc-only dependencies
