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* libbeagle: add java dependency so jni hooks get built
* libbeagle: set BEAST_LIB instead of LD_LIBRARY_PATH
* libbeagle: use BEAST_LIB
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* Augustus updated to version 3.3.1
* Augustus - Version-specific URLs replaced by list_url
* Augustus - Adding tool versions back
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* fix to build libmatheval with guile@2.0:
* fixed formatting issues
* fixed formatting issues2
* fixed check for autoreconf and renaming of configure.in
* fixed force_autoreconf
* now patching configure, which is hopefully more robust
* minimal patches for guile 2.0 and 2.2 (disabeling unit testing for libmatheval)
* minimal patches for guile 2.0 and 2.2 (disabeling unit testing for libmatheval)
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* fix ncl url and hash
* adding ncl version 6.5.0
* remove 6.5.0
* using github archive url
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on lustre filesystem. (#8764)
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* add mofem-cephas package
* add mofem fracture module
* add user modules build and fracture modyle
* add minimal surface module
* add slepc variant
* bump mofem core lib version
* bump mofem core lib version
* bump version
* fix bug
* set upper bound to petsc version and other chanes
* fix indentation
* add minimal med file installation
* chcekc with flake8 and installation with spack packages
* add variants to med package
* upper bound to adol-c and remove obsolete internal package install
* fix basic module install
* module install from external source in extended prefix
* remove obsolte code and reverse to variant doxygen
* fix git adress
* improve packaging for mofem users modules
* fix flake8
* move dependencies after variants
* move root_cmakelists_dir right before cmake_args
* remove unused variants
* use append for single element
* replace root_cmakelists_dir
* use install_tree instead copy tree
* simplify code
* remove phase and mkdirp
* add run tests
* instal ext modules to ext_users_modules directory
* move version below url
* simplify directory name
* use underscore in variant name
* remove unused variable
* fix link to blas libs
* add missing boost dependence
* fix problem with copying module source code
* change variant name form doxygen to docs
* add expanded description
* make installation consistent with spack
* fix flake8
* make extensions installed
* code comments and minor corrections
* make slepc variant false by default
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- two stage tests weren't properly using the mutable_config fixture.
- this caused running `spack test` to modify the user's config.yaml
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* votca: add more deps
* Update package.py
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Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
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- Add command-line scope option to Spack
- Rework structure of main to allow configuration system to raise
errors more naturally
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
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- Fixes a bug in `llnl.util.lock`
- Locks in the current directory would fail because the parent directory
was the empty string.
- Fix this and return '.' for the parent of locks in the current
directory.
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* r-qorts: Create new package.
* Change dependency to java, change package name.
* Remove some join_path.
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* New package: Verrou, a floating point error checker
* Clean up usage of patch
* Account for future patches in version ranges
* Manual call to autogen is not needed anymore, but extra dependencies are needed
* Use trick from automake to evade shebang length limit
* Use a glob instead of an explicit file list
* Turns out conflict() does not do what I want...
* Suggestions from @citibeth reviews
- Use 'develop' convention for the master branch
- Prefer tarballs over git repositories
- Increase robustness against default configuration
* Drop a couple of older releases with a different patching procedure
* Playing coding style golf
* Various bug squashing
- Missed master -> develop substitution
- Turns out manually calling autogen.sh is needed after all
- Missed + in spec
* More style golfing to fit in 80 columns
* Remove unnecessary mention of the develop branch
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Enforce PEP8 naming conventions for things like variables, methods,
classes, etc.
See the table here:
https://pypi.org/project/pep8-naming/
...for error codes emitted, in case some should be added as
exceptions in the flake8 configuration files.
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* py-pytest: Added dependency on py-setuptools-scm, as well as py-setuptools, to prevent the build from silently installing its own copy of setuptools-scm
* py-pytest: Dependency on setuptools-scm only needs to be 'build'
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would otherwise silently try to install pyparsing itself, presumably into the python home dir (obviously not ideal). (#8748)
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type=test, to prevent setuptools from silently installing its own copy of nose (#8749)
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* openmpi: add c++ exceptions cfg option variant
* address review comments
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Replace regex-based target detection for Makefiles with a preliminary "make -q"
to check if a target exists. This does not work for NetBSD make; additional work
is required to detect if NetBSD make is present and to use a regex in that case.
The affected makefile target checks are only performed when the "--test" flag is
added to a "spack install" invocation.
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* py-pyqi: new package
* py-pyqi: cleanup
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* The xlf_seacas.patch fails on the latest trilinos develop branch so confine it up to version 12.12.1.
* Fixing likely mistak in seacas patch version range.
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Fixes #8036
Before this PR Package.installed was returning True if the spec prefix
existed, without checking the DB. This is wrong for external packages,
whose prefix exists before being registered into the DB. Now the property
checks for both the prefix and a DB entry.
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Spack provides a number of classes based on commonly-used build systems
that users can extend when writing packages; the classes provide functionality
to perform the actions relevant to the build system (e.g. running "configure" for
an Autotools-based package). This adds documentation for classes supporting the
following build systems:
* Makefile
* Autotools
* CMake
* QMake
* SCons
* Waf
This includes build systems for managing extensions of the following packages:
* Perl
* Python
* R
* Octave
This also adds documentation on implementing packages that use a custom build
system (e.g. Perl/CMake).
Spack also provides extendable classes which aggregate functionality for related
sets of packages, e.g. those using CUDA. Documentation is added for
CudaPackage.
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* fftw: version bump
* fftw: add gcc-8 conflict for v3.3.7
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(#8722)
* Add fix for bug causing build failure when hdf5 enabled
* Added correct hdf5 dependency to typhonio
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* r: add memory profiling variant
* r: change memory_profiling to underscores
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- The setup-env.sh script currently makes two calls to spack, but it
should only need to make one.
- Add a fast-path shell setup routine in `main.py` to allow the shell
setup to happen in a single, fast call that doesn't load more than it
needs to.
- This simplifies setup code, as it has to eval what Spack prints
- TODO: consider eventually making the whole setup script the output of a
spack command
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* aspera-cli: a new package.
* flak8.
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This allows building MPI applications on top of charm/AMPI without
to specify another backend.
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* Charm: more info about build targets
* fix whitespace
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