* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler
* Update packages so they do not obliterate flags
* Added append to EnvironmentModifications class
* changed EnvironmentModifications to have append_flags method
* changed flag_val to be a tuple
* Increased test coverage
* added documentation of flag handling
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* added tags and other minor changes.
* removed tags from description.
* new package: CLAMR
* changed from bool variants to single value variants and corresponding logic in build_type and cmake_args
* lowercase variant values
* updated conditionals for variants
* adjusted url and docstring
* new package to be added: NuT
* removed cmake_args() and made other changes as suggested
* Added setup_environment()
* PEP8 compliant
* edited version name, build_targets, and files/directories to install
* corrected executable directory
* compiler dependencies based on version
* Change path to CMakeLists.txt to be relative to root, not pwd
* Changes requested during code review
* Revert back to old naming of root_cmakelists_dir
* Make relative directory more clear in docs
* Revert change causing build_type AttributeError
* Fix forgotten abs_path var
* Update CLHEP with new relative path
* Update more packages with new root_cmakelists_dir syntax
somatic-sniper installs its own copy of samtools, which needs curses.
I'm not sure why I didn't stumble on this in my dev environment, but I
just stumbled over it in a standalone build.
The 4.X branches are now on the homepage, so we take the GitHub release
artifact (careful: take their upload, not the automatic tarball).
Adds a development version of ZeroMQ.
Requires a autogen run, as for all their unreleased versions,
and the pkg-config fix in #4736
Always sets the `pkg-config` environment hint for
autotools.
Required dependency for `autoreconf` of ZeroMQ when
build from source (e.g. v4.2.2) via autotools in `autogen.sh`
step for `autoreconf`.
* Add package for r-ada, update r-rpart version
Adds a package for r-ada.
Update the version for r-rpart because the previous version is
no longer at that URL. The previous version *is* in the Archive,
but list_url does not seem to be able to find it.
* Clean up FIXMEs (blush)
* savanna: Runtime framework for online workflow management from the ECP CODAR project
* savanna: added version 0.5
* savanna: Copying the package contents to prefix as part of installation
* savanna: Doing submodules=true for git checkout of develop version
* savanna: removed dependency on adios@develop. depends on adios
* Savanna: Converted package to MakefilePackage
* New Package: Pathfinder
* Added index for String format
* Changed to make Makefile edit more specific
* Make Flake8 Happy
* Removed unneeded conversion
* Add package for Sniffles
* Wire up a manual install step
The cmake infra doesn't install anything, so do it by hand.
The binaries land in a location that embeds the version...
* hybpiper: new package and spades dependency
* hybpiper: making flkae8 happy
* hybpiper: fixing dependency errors
* fixing python dep type
* removing cmake from spade dependencies
* libwebsockets: new versions
both new versions fix a nasty bug leading to a hanging
connection on connect.
* ISAAC Server: Fix libwebsockets
ISAAC server did hang in docker containers due to a bug
in libwebsockets.
* Add two python packages for editing mach-O headers. Much faster than calling otool and install_name_tool directly
* remove non-overriding function
* autopep8
* Adding OpenMP variant to Trilinos. Also building NetCDF with PNetCDF in Trilinos when necessary.
* Adding runtime error for PNetCDF variant in Trilinos when necessary. Omitting unnecessary openmp variant for Trilinos in Nalu.
* Changing variant checks to conflicts statements.
* Adding comments to Trilinos package.
Adds the `gearshifft` package, a benchmark suite for heterogeneous implementations of FFTs.
Adds clFFT, a software library containing FFT functions written in OpenCL.
see: https://github.com/clMathLibraries/clFFT
The vcftools package was installing its Perl libraries into a
directory in the staging directory named 'lib', instead of installing
them into `prefix.lib` where they should have been because the value
passed to the configure script was wrong.
The result was that any attempt to run one of the scripts in the
package failed with something like:
> Can't locate VcfStats.pm in @INC (you may need to install the
> VcfStats module) [...]
This fix provides the correct information in `configure_args`.
Tested lightly on CentOS 7.
* Dataspaces spack package, hard-wired for ubuntu VM
* Initial commit of dataspaces spack package
* Made changes and additions necessary to install on Cori and Titan
* Added temp 1.6.2.1 for testing
* Updated tar file for 1.6.2
* Fixed formatting
* Set the type of build dependencies
* Changed the way autogen.sh is called for compatibility
* Use append instead of extend to add configure flags
* Various syntax fixes
* Switched string checking to method for compatibility
Now using the six library for Python 3 compatibility. Thanks @adamjstewart
* Made MPI variant default
- renamed develop version from 'plus' to 'develop'
- patches now prefixed by corresponding OpenFOAM version number.
This makes it easier to sort and see what old/junk exists.
- remove MPI_BUFFER_SIZEk env variable (for all openfoam variants).
The OpenFOAM shell setup addresses this and there is no reason
to pollute the module environment at this stage.
* sabre initial commit, works but test does not
* removing test until I have time to fix it
* sabre: fixing flake8 errors
* sabre: changing to MakefilePackage
* mpifileutils: update to v0.7
* mpifileutils: disable --enable-experimental in v0.6 and earlier
* mpifileutils: list newest version first, avoid experimental switch unless at v0.7 or later
* * add mpii* wrappers for use with intel compilers
* in mumps package, scotch is compiled without metis option when
ptscotch variant is selected. This removes confusion over which
metis.h to use
* for intel mkl, add SPACK_COMPILER_EXTRA_RPATHS ending in 'intel64'
* scotch lib requires libz when compression is turned on. This
caused a link issue on some Ubuntu distributions (not
redhat). Change Scotch package to add -lz when needed
* * intel-mkl append to SPACK_COMPILER_EXTRA_RPATHS rather than setting
* use more concise method to obtain libz libraries for scotch
* remove changes to intel mpi
* remove commented out depends_on
* fix flake8 errors
* Add package for primer3
Built and mildly tested on CentOS 7.
* Convert to MakefilePackage
I always forget about this...
* Set build_directory the easy way
Life's not always complicated. Don't go out of my way
to make it so....
* Fix Flake8 issue
* added perl-star-fusion and perl-intervaltree
* added perl-star-fusion and all dependencies
* changes
* made changes as requested to perl-star-fusion dependencies
* changed perl-intervaltree dependency
* changes to star fusion
* now using perl properly
- Thanks to pointer from @adamjstewart - can avoid this either by
avoiding an external mxml dependency, or by making certain that they
both use consistent code generation.
The adios package uses '-fPIC' for python linkage and this seems to
require the same for mxml too. If the adios-internal version of mxml
is used, it has the same flags for both.
- The buggy flex-2.6.2 was blacklisted in the corresponding flex
package, but now also removed the md5sum to avoid suggesting that
this version should be revived.
The 2.6.3 has similar problems (at least for scotch), but 2.6.4
seems to work.
- Rejig flex restriction for scotch to exclude 2.6.2-2.6.3 only. Since
flex-2.6.4 appears to be okay again, we can remove the flex version
restriction that trickled through into the openfoam packages as a
consequent of an spack spec bug.
- Make flex a build dependency for the openfoam packages
(seems to have been an earlier oversight).
* Remove unneeded patch lines which fail for the most recent CNTK version on the head of the git repo
* Really check for NVML/GDK
* Fix some violations
* gtkplus: set XDG_DATA_DIRS
* shared-mime-info: database of common MIME types
* gtkplus: needs shared-mime-info for correct handling of stock icons
* shared-mime-info: builds with newer intltool than provided by some platforms
* atk: set XDG_DATA_DIRS at run-time
* gdk-pixbuf: set XDG_DATA_DIRS at run-time
* gtkplus: set XDG_DATA_DIRS at run-time
* pango: set XDG_DATA_DIRS at run-time
* shared-mime-info: set XDG_DATA_DIRS at run-time
