* py-pybedtools: Create new package
* py-pybedtools: add py-six requirement
* py-pybedtools: remove py-cython dependency for release version
* py-pybedtools: include minimum version of py-pysam
* Provide build_type variant for Metis.
+ Ideally, we would make Metis a CMakePackage, but `metis@:5` doesn't use CMake.
+ For now, provide a `build_type=` variant similar what is found in
CMakePackage.
+ There is a potential for duplicate specification of `CMAKE_BUILD_TYPE` if both
variants `+debug` and `build_type=` are specified. I am looking for advice on
how this can be resolved.
* Update metis recipe in response to flake8 and user comments.
+ Wrap comment lines that used more than 80 columns.
+ Change `+debug` variant to avoid potential for multiple `-DCMAKE_BUID_TYPE=`
arguments provided to cmake. Specifying this variant no longer appends this
configure option. However, if `+debug` is specified, require
`build_type=Debug` to maintain expected behavior.
* For metis, remove +debug variant; use build_type= instead.
+ Update recipe for metis@4 to extract `build_type=` values and set `OPTFLAGS`
accordingly.
+ For metis@5:, the behavior from the previously supported variant `+debug` can
be obtained with the options `+gdb build_type=Debug`
* Conflicts added for metis@4 when build_type != Release|Debug.
* Use spack function conflicts instead of 'raise InstallError'.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Adding NEURON package widely used in computational neuroscience community
* flake8 fixes
* Add rx3d variant
* Addressed review comments from Adam
* Addressed 2nd review comments
* Added check for +mpi on bg-q
* Filter spack compiler wrappers in NEURON scripts
Add gcc march=native flag to make front-end build robust
* Make develop as preferred version due to bug in long filename handlings in <= v7.4
* Avoid use of gcc in cross compiling environment
Use arch specific options on cray and bg-q arch
* Simplify cross compiling build:
- v7.5 added and no longer need develop as preferred version
- legacy cray related options removed
- cross compiling args reduced
- python arguments reduced as neuron finds proper libraries
* Simplify bg-q configurations
* Cleanup and unify arch options
* Make sure to add commonly available packages as dependency
* Arch path added to dependent_environment as nrniv needed at runtime
* Support for Power 8 architecture
* Fix python3 on OS X
* flake8 fix
* remove unnecessary conflcist directives
* Added a package for the MDAnalysis toolkit.
* Added a patch file to get rid of compiler warnings with intel compiler
and inlining. Added checksum values for other versions of protobuf.
* Added dependency on Intel compiler for intel patch
* added variant examples to paraview package.py
* qt: added libxt dependency
* add variant to use external hdf5, this is needed when compiling with gcc@4.8.5
* paraview: added python dependecies to PYTHONPATH
* Start adding Nek5000 package
* Add tools to install: genmap, prenek, postnek
* Address comments by @davydden
* Use install_tree (thanks @junghans) and polish
* Update url
* Fix flake formatting errors
* Change F77 and CC compilers
Apparently spack compilers can't be called outside spack and we
have an underscore test in our Nek5000/core/makenek.inc file which
calls F77 compiler.
* Add support for visit and profiling options
* Fix a typo
* Fix a typo
* Remove the C check
* Add visit variant
* Update the install of int_tp tool
* Let MAXNEL to be set during installation
* Added magma package
* Incorporated Serban's change
* Remove deleted files
* argparse.py
* Sync forked Spack repo in github
* Add spectrum-mpi lib path to LD_LIBRAY_PATH in spack_env.
As a result of supporting alternate installation directories, spectrum-mpi does
not use rpath anymore, so we need to set LD_LIBRARY_PATH in spack_env to allow
MPI programs to run during dependent package configuration.
* Fix flake8 error (blank line at EOF)
* xios: XML-IO-SERVER library for IO management of climate models
* xios: install to prefix directory
* xios: add a test case
* xios: define versions to use cache and mirror directories
* xios: use proper svn URL for version 910
* xios: package url must be defined, otherwise uninstall fails
* xios: add trunk version to allow building latest revision
* xios: enable parallel build
* xios: allow installation with mpif90 compiler wrappers
* xios: use mpi variants of dependencies
* xios: allow user to specify MPI launcher via MPIRUN environment variable
* xios: prefer spack versions of blitz and boost (needed for gcc@7)
* xios: enable builds with clang+gfortran on OSX
* xios: use numeric versions for releases, @develop for trunk
* xios: different patches required for @1.0 and @develop
* xios: patch function for clang works across revisions
* xios: link blitz library
* xios: workaround bug 17782 in llvm
* xios: whitespace adjustments for flake8
* xios: avoid bare except clause
* xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
* combine all patches for 1612 into a single file, with additional
comments to explain the rational.
* Add kahip decomposition variant.
* Add support for ARM64 architecture.
* filter instead of patching etc/config.*/settings. This eliminates
patch files for 1706, perhaps for the future as well.
* URLs at or before version 1612 have a different structure, so
provide a url_for_version implementation to handle this
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch
* renamed to develop
* added master branch properly
* add OctavePackage
1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix
* use setup_environment
* esmf: put .mod files in the spack compiler search path
* esmf: allow building with Cray mpi
* esmf: create run-path dependent libraries on osx
* esmf: link fortran interface libraries when building with mpich
