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- Update YAML version to support Python 3
- Python 3 support for ordereddict backport
- Exclude Python3 YAML from version tests.
- Vendor six into Spack.
- Make Python version-check tests work with Python 3
- Add ability to add version check exceptions with '# nopyqver' line
comments.
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* Run python setup.py test if --run-tests
* Attempt to import the Python module after installation
* Add testing support to numpy and scipy
* Remove duplicated comments
* Update to new run-tests callback methodology
* Remove unrelated changes for another PR
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mxml is now hosted on GitHub.
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* Add QBank package
* Install the documentation and add it to the MANPATH
* Add Perl DBI package
* Make sure setup method variables are consistent
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- for programs that don't yet work with bison 3.x
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* perl-term-readkey: add perl Term::ReadKey package
* subversion: add variant with perl bindings
* subversion: use `which('perl')` to find perl executable in package.py
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* perl: make extendable and add Module::Build package
* perl: allow 'spack create' to identify perl packages from their contents
* perl-module-build: fix indenting of package docstring
* perl: split install() method for extensions into phases
* perl: auto-detect build method (Makefile.PL vs Build.PL) and define a 'check' method
* PerlPackage: use import statements similar to those in AutotoolsPackage
* PerlModule: fix detection of Build.PL
* PerlPackageTemplate: remove extraneous lines to avoid flake8 warnings
* PerlPackageTemplate: split into separate templates for Makefile.PL and Build.PL
* PerlPackage: add cross-references to docstrings
* AutotoolsPackage: fix ambiguous cross-references to avoid errors in doc tests
* PerlbuildPackageTemplate: depend on perl-module-build if Build.PL exists
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* ENH: add package for building OpenFOAM (1612) from www.openfoam.com
- provide 'openfoam' as virtual package.
- package as openfoam-com to reflect the distribution point.
This initial spack packaging for OpenFOAM supports a number of possible
variants and should handle 64-bit labels properly now that the scotch
package has been updated accordingly.
* ENH: update package for foam-extend (extend-project.de)
- provide 'openfoam' as virtual package.
- much of the build is now aligned with how the openfoam-com package
looks, with the aim of future refactoring.
- avoid installing intermediate targets.
- contains its own environment sourcing script for the build, for more
flexibility and robustness (doesn't touch the python build environ)
* ENH: added package for building from openfoam.org
- provide 'openfoam' as a virtual package.
- this is largely a direct copy of the openfoam-com package.
It has been supplied as a courtesy for users and to ensure maximum
consistency in quality and naming between the foam-extend,
openfoam-com and openfoam-org packages.
* CONFIG: add openfoam into bash completion providers list
* ENH: have openfoam-com use spack as USERMPI
- also simplify the generation of mplib/compiler rules
* ENH: have openfoam-org use spack as SYSTEMMPI
- this setup requires more environment settings than USERMPI
(openfoam-com), but is currently the only means of integration
for openfoam-org
- simplify generation of mplib/compiler rules
* ENH: simplify generation of mplib/compiler rules (foam-extend)
- rename mpi rules from SPACK,SPACKMPI to USER,USERMPI for consistency
with openfoam-com and to generalize for any build system.
* STYLE: record spack tree as a log file (openfoam)
- can be useful for future diagnostics and general record keeping
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* add package py-spykeutils
* fixed dependency version restriction
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* libint: updated version, ported to AutotoolsPackage
* elpa: updated version, ported to AutotoolsPackage
* wannier90: updated version, ported to MakefilePackage
* pexsi: updated version, ported to MakefilePackage
* cp2k: updated version, removed wannier 90 from dependencies if cp2k@4.1
* plumed: updated version
Modifications:
* modules has been turned into a single variant, as different versions
have different modules available
* added dictionaries for patches
* netlib-scalapack: ported to CMakePackage
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* Concretization problem breaks httpie dependency
Concretization problem breaks this. Unconditional for now...
https://github.com/LLNL/spack/issues/3628
* Flake8 cleanups
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* Add package for snakemake
* Flake8 cleanups
* Add package for py-wrapt
* Address PR feedback
Switch to pypi URL.
Tighten Python3 dependency spec.
Add missing dependencies (wrapt, requests).
- add package for wrapt.
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* Add package for httpie
* Remove wayward FIXME and flake8 cleanup
* Update dependencies, address PR feedback
Fine tune dependencies (version constraints).
Add missing dependency.
Make SOCKS support a variant.
* Flake8 cleanup
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* add package py-bokeh
* remove setuptools dependency
* add missing dependencies
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* add package py-pympler
* add python@2.5: dependency
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* add package py-pynn
* fix docstring
* fix dependency mess
* add python dependency
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* add package py-mongo
* add dependencies
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* Add abipy package and dependencies
* Add first official release of py-abipy
* Ignore files from dependencies during activation
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* Add Blast+ package.
Adds support for NCBI's blast+@2.6.0. I'll be adding a few historical versions in the near future.
It's a fairly direct transliteration of the [Homebrew Science recipe][hbs].
I skipped the mysql support.
There is a problem with HDF5 support. Blast's configure script test program defines a macro 'HOST' to a string value and one of the HDF5 bits has an variable named 'HOST'. Fun things happen. I've disabled support for now.
I've run very very basic tests. I'll get this out to my users and ensure that it works and fine tune the options and etc....
[hbs]: https://github.com/Homebrew/homebrew-science/blob/master/blast.rb
* Flake8 fixes
* Update w.t.r. mamelara's PR and cleanup
Add paths to things in the --with-* config args
Add add'l config flags from #3394.
Update patch to no-op and add comment.
Add add'l dependencies after studying `configure --help`.
* Flake8 cleanup
* Add support for blast+@2.2.30
Need to work around a configure bug. See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511.
* Re-wrap comment, line length not a problem.
I'd broken a comment across to line in a fit of flake8
induced fear. Adam pointed out that it's ok.
* Remove explicit prefix config
Remove explicit prefix config, the autotools package does it for us.
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jq is a commandline JSON processor. Oniguruma is a regexp
library on which jq depends.
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Add package for the BASH Automated Testing System.
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* Add support for 2.3.1
Updated digest and added a dependency on tbb.
* Cleanup patch name and add description
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* Update samtools family to 1.4
* simple cleanup
* Make bzip depends_on for future versions too
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* Add package for ncftp
* Flake8 cleanups
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* Add package for staden-io-lib
* Flake8 cleanups
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* Add package for mummer
Blocked on https://github.com/LLNL/spack/pull/3555.
* Make "check" step optional and flake8 cleanups
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* Add package for pigz
* Whitespace
* Remove leftover instructions (oops...)
* Flake8 cleanup
* Convert to MakefilePackage
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* Add package for blat
* Whitespace cleanup
* Flake8 cleanup
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Add support for nextflow versions 0.24.1 and 0.23.3.
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* fix for #3588
* set 'build_directory' variable instead
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