* new package: py-dateparser
* take setup.py dependencies into account
* fixup help->description
* reorder dependencies
* drop version constraints not enforced in setup.py
netcdf-fortran@4.5: will error if netcdf-c has been built with MPI
support:
```
configure: error:
-----------------------------------------------------------------------
The NetCDF C library is built with parallel I/O feature enabled, but
the Fortran compiler '.../lib/spack/env/gcc/gfortran' supplied in this configure command
does not support MPI-IO. Please use one that does. If parallel I/O
feature is not desired, please use a NetCDF C library with parallel
I/O feature disabled. Abort.
-----------------------------------------------------------------------
```
Copy logic from netcdf-c to add an `mpi` variant.
* pybind11: test get_include path
Helper for non-CMake downstream projects to find the pybind11
header location.
* pybind11: return proper get_include()
use our prefix instead of letting pybind11 trying to self-determine
it from given conda/virtualenv/global rules.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-ics
* drop 0.5 and move to tar-ball
* Update var/spack/repos/builtin/packages/py-ics/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-ics/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* mpi4py 3.0.3
Adds support for Python 3.8 with new Cython files.
I tried to build 3.0.0 with Python 3.8 and this builds as well,
therefor I added no conflict.
* mpi4py: update dependency version ranges
* update py-jupyter-notebook
* add setuptools dependency for newer version
the whole jupyter collection seems to use setuptools in case of
certain setup.py-arguments from the very beginning. However the latest
ones actually require it, otherwise the build will fail
* add newly introduced dependencies
* dependency constraints
* drop terminal variant and update python dep
* added relion 3.0.8 [latest stable version in 3.0 branch] as well as 3.1_beta
* relion 3.1 beta compiles without Benchmarking build type see https://github.com/3dem/relion/issues/533
* relion 3.0.X - 3.1 now supports latest cmake@3
* flux: add `url_for_version` to support their C4 repo model
Flux uses a fork of ZeroMQ's Collective Code Construction Contract
(https://github.com/flux-framework/rfc/blob/master/spec_1.adoc).
This model requires a repository fork for every stable release that has
patch releases. For example, 0.8.0 and 0.9.0 are both tags within the
main repository, but 0.8.1 and 0.9.5 would be releases on the v0.8 and
v0.9 forks, respectively.
* flux: add latest versions
* flux: remove master from `when=@0.X:,master` statements
Now that #1983 has been merged, master > 0.X.0.
* flux-core: remove extraneous `99` patch version in `when` range
Replace `when=@:0.11.99` with `when=@:0.11` since the intention is to
include all patch versions of `0.11`.
* flux-core: fix `setup_build_environment` after changes in #13411
In #13411, `setup_environment` was split into `setup_build_environment`
and `setup_run_environment`, with the `spack_env` and `run_env`
arguments being changed to `env`. Somehow the flux package was the only
one to not have its `spack_env` references in the function changed to
`env`.
* flux: add runtime environment variables that Flux checks
with older versions of Flux (i.e, 0.0:0.13), FLUX_CONNECTOR_PATH must be
set by spack to prevent failures in certain
scenarios (https://github.com/flux-framework/flux-core/issues/2456).
the flux binary also sets some other environment variables, which can be
listed by running `flux -v start`. I added a few of those just to be
sure that the Spack-installed paths are used, rather than
system-installed ones.
* flux: add optional testing dependencies to maximize test coverage
Install optional dependencies to ensure that only spack-installed
software is detected and that all tests are run when `spack install
--test` is used.
Flux's test suite will test for the existance of valgrind, jq, and any
MPI installation. If it detects them (even if they are system-installed
and outside the spack environment), it will run optional tests against
them. I noticed on my machine that the valgrind tests were running
against the system-install valgrind.
* flux-sched: switch to new `setup_run_environment` API
* r-gstat: new package at 2.0-3
* Update var/spack/repos/builtin/packages/r-gstat/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/r-gstat/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Improvements of saga-gis package
* Added explicit version ranges for old saga-gis version
* Update var/spack/repos/builtin/packages/saga-gis/package.py
Creative usage of redefinition of getter method
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/saga-gis/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/saga-gis/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Adding flecsph package
* Correcting header
* Boost version update
* Correcting Flake8 errors
* Correcting headers
* Develop preferred in FleCSI
* Removing FleCSPH branch of FleCSI
* MeshToolKit package
* formatting
* Formatting
* Correcting MSTK package
* Format
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
* Format
* Format
* Correcting package behavior
* Correcting format
* Corrections
* Update var/spack/repos/builtin/packages/mstk/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Multiline
* r-dada2: new package at 1.14
* r-dada2: add gmake dependency
* Update var/spack/repos/builtin/packages/r-dada2/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-scs
* rename
* flake8
* Update var/spack/repos/builtin/packages/py-scs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update the module files for cbtf-krell and openspeedshop adding man paths and needed papi and libmonitor paths.
* Update module files for new API.
* Use the same python for both develop and release branches.
* add support for static (via ~shared) and use vtk-m 1.2
* updating vtkh package to output cmake configure file and pinning it to vtkm 1.2
* trying a different cmake for vtkh
* removing problematic b
* making conduit respect ~python
* fixing ascent python logic
* update ascent package
* consistant cmake usage
* conditionally add tbb in ascent if vtkh
* applying becker fix
* adding vtkh tag
* fixing vtkh tagged version
* updating ascent and conduit for static builds
* enabling openmp
* reverting files that should not have been changed
* ascent updates
* more robust handling of variants
* fixing ascent package typo
* ascent: add optional support for mfem
* enable mfem conduit support for ascent
* add optional adios dep to conduit
* remove ver req from conduit
* ascent: remove confusing comment
* tweaks to conduit and ascent pkg recipes
* fix typo in conduit package
* pref conduit master
* fixing mfem typo for ascent
* reverting files
* adding mirror for bzip
* changing mfem to depend on conduit@master to get updated relay
* restore use of conduit 0.3.1 or greater for mfem
* set master as prefered conduit version
* allow mfem to use conduit master
* adding rover package and editing ascent
* updating vtkm cmake dep
* updates from axom
* guard ascent python support on +shared
* removing rover to simply ascent package
* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified
* fix fortran compiler check so it can work on cray systems
* working towards cuda fix for vtkm lagrange filter
* update ascent package with more variants, and patch to avoid nvcc issue
* hdf5 flags fix for BGQ
* flake8
* extra guards for cuda patch
* conduit and ascent fortran fix
* fix patch for non cuda case
* add test variant to conduit, tweak ascent pkg
* change min ver of cmake used for ascent
* h5z-zfp package: unset FC when ~fortran
* conform to expected upstream solution
* pinning vtkm
* going back to vtkm master
* add back vtk-m variant for shared libs
* update ascent and vtkh packages
* wire up option to run tests during install
* add post install test
* add testing to ascent
* tweak for blueos xl
* add ctest output on error for run_tests
* enable ctest output on error for run_tests
* add testing of the using-with-make example
* update using-with-make examples
* typo in ascent using-with-cmake test
* fix ascent using test exe names
* more fixes, less sleep
* more fixes, less sleep ...
* remove unwired up version
* improvments suggested on review
* adding new cmake
* Update package.py
* Update package.py
* changes post cori os update
* fix cray hack
* Update package.py
Fixing 'fix'. Inconsistent variable names in conduit package
* type in spack recipes
* add zfp support to conduit
* fix indent error in conduit pkg
* move to use build phases, add sphinx rtd as dep, fix ex names in tests
* add conduit 0.5.0 release
* flake8
* remove old cray hack
* incorp feedback from review
* fix to use proper build env sig
* Fix gcc recipe for RHEL7.
+ It appears that macOS related changes to the gcc recipe broke gcc on RHEL7.
This bug manifests as `libstdc++.so: undefined reference to libiconv` when gcc
is used.
+ Fixes#13452 by moving
`--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix)` into the darwin
OS section of the configuration.
+ Change qualification of `depends_on(libiconv)` to limit dependency to macOS.
* Replace deprecated 'setup_environment' with 'setup_run_environment'.
* Fix cut and paste error.
* Rename 'run_env' to just 'env'.
* Add versinos 1.13.3, 1.13.2, 1.12.12, and 1.12.11
* Replace setup_environment/setup_dependent_environment with
setup_build_environment and setup_dependent_{build, run}_environment
according to 9ddc98e
* Add dependency and patch perl-dbfile
There are two problems for the building of `perl-dbfile`:
1) this package depends on the package `berkeley-db`
2) fix the building using a patch, which locates the position of `berkeley-db` and modify the configuration file for the building
* Update and reformat the script package.py
* Simplify the patch
* Update package.py
* Update package.py
* This filter_file was difficult to maintain and is no longer needed.
* Clarify lack of support for HDF5 in serial QE.
* Update QE and HDF5 conflicts based on user feedback.
* Add Lizard (LZ5)
Add a new package for Lizard, formerly LZ5, a very fast compressor
and decompressor library.
* c-blosc2: use external lizard
Use an external Lizard (LZ5) dependency and add missing
"when="s for other compressor dependents.
* Fixes for libbeagle
This PR fixes a couple of issues with the libbeagle package.
- Use args.append('--with-cuda=%s' % self.spec['cuda'].prefix)
- Disable the default of compiling with -march=native as Spack now
inserts architecture specific flags
- Set BEAST_LIB in the beast1 package not in libbeagle.
* Use new setup_run_environment method
