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2018-07-25core: differentiate package-level fetch URLs by args to `version()`Todd Gamblin3-2/+96
- packagers can specify two top-level fetch URLs if one is `url` - e.g., `url` and `git` or `url` and `svn` - allow only one VCS fetcher so we can differentiate between URL and VCS. - also clean up fetcher logic and class structure
2018-07-25core: fixes and tests for handling of fetcher attributes in packagesTodd Gamblin6-0/+215
- Packages can remove the top-level `url` attribute and still work - These are now legal: - Packages with *only* version-specific URLs (even with gaps) - Packages with a top-level git/hg/svn attribute and `version` directives for that. - If a package has both a top-level hg/git/svn attribute AND a top-level url attribute, the url attribute takes precedence.
2018-07-25hypre: 'master' is branch - not a tagSatish Balay1-1/+1
2018-07-26Added latest version of charliecloud (#8792)sknigh1-0/+1
2018-07-23packages: do not use generic checksum= in version() directivesTodd Gamblin2-4/+4
- This is very old usage -- preparing to deprecate this in favor of being explicit about checksums.
2018-07-23core: use sha256 instead of md5 for `spack checksum` and `spack create`Todd Gamblin1-7/+7
- This changes `get_checksums_for_versions` to generate code that uses an explicit `sha256` argument instead if the bare `md5` hash we used to generate. - also use a generic digest parameter for the `version` directive, rather than a specific `md5` parameter.
2018-07-22Trinity plugins (#8516)Levi Baber1-3/+8
* trinity: fix plugin installation * trinity: flake8 * trinity: more specific types for dependencies
2018-07-22beast1: add libbeagle support (#8525)Levi Baber1-0/+3
2018-07-22libbeagle: add java dependency so jni hooks get built (#8524)Levi Baber1-0/+5
* libbeagle: add java dependency so jni hooks get built * libbeagle: set BEAST_LIB instead of LD_LIBRARY_PATH * libbeagle: use BEAST_LIB
2018-07-22Augustus updated to version 3.3.1 (#8588)Roberto Villegas-Díaz1-5/+5
* Augustus updated to version 3.3.1 * Augustus - Version-specific URLs replaced by list_url * Augustus - Adding tool versions back
2018-07-22fix to build libmatheval with guile@2.0: (#8680)g-mathias3-0/+224
* 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)
2018-07-22Ncl update (#8747)Nasr S. Hassanein1-6/+6
* fix ncl url and hash * adding ncl version 6.5.0 * remove 6.5.0 * using github archive url
2018-07-22Make read only source file writeable in perl before patch to avoid failures ↵Jon Rood1-0/+12
on lustre filesystem. (#8764)
2018-07-22add necessary dependence on lapacak, and fix ld_flags for blas (#8776)Lukasz1-1/+3
2018-07-22add MoFEM packages (#8700)Lukasz6-0/+456
* 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
2018-07-21votca: add more deps (#8771)Christoph Junghans2-0/+7
* votca: add more deps * Update package.py
2018-07-19Add kealib 1.4.10 (#8769)Adam J. Stewart1-4/+5
2018-07-19r-qorts: Create new package. (#8744)lingnanyuan2-0/+74
* r-qorts: Create new package. * Change dependency to java, change package name. * Remove some join_path.
2018-07-19Packaged iperf2 (#8765)sknigh1-0/+36
2018-07-19Packaged iperf3 (#8762)sknigh1-0/+36
2018-07-19Py-lark-parser: new package (#8761)Matthias Diener1-0/+36
2018-07-19pycparser: add version 2.18 (#8760)Matthias Diener1-0/+1
2018-07-19nwchem: add link type to python dep (#8759)Levi Baber1-1/+1
2018-07-19votca*: update dependencies (#8757)Christoph Junghans4-4/+61
2018-07-19New package: Verrou, a floating point error checker (#8738)Hadrien G1-0/+107
* 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
2018-07-19style: bring packages in compliance with pep8-namingTodd Gamblin27-319/+315
2018-07-19style: make core comply with pep8-namingTodd Gamblin4-9/+9
2018-07-19add py-pep8-naming packageTodd Gamblin2-0/+82
2018-07-18py-pytest: Added dependency on py-setuptools-scm, as well as py-setup… (#8750)Neil Flood1-0/+1
* 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'
2018-07-18py-snuggs: Added depends_on py-parsing. The build uses setuptools, which ↵Neil Flood1-0/+1
would otherwise silently try to install pyparsing itself, presumably into the python home dir (obviously not ideal). (#8748)
2018-07-18py-pkgconfig: Made nose dependency type=build,test instead of just ↵Neil Flood1-1/+1
type=test, to prevent setuptools from silently installing its own copy of nose (#8749)
2018-07-18openmpi: add c++ exceptions cfg option variant (#8743)Cyrus Harrison1-0/+5
* openmpi: add c++ exceptions cfg option variant * address review comments
2018-07-17Cmake: add version 3.12.0 (#8731)Matthias Diener1-0/+1
2018-07-17py-pyqi: new package (#8726)Levi Baber1-0/+38
* py-pyqi: new package * py-pyqi: cleanup
2018-07-17Confine the xlf_seacas.patch for trilinos to version 12.12.1 (#8725)Jon Rood1-3/+3
* 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.
2018-07-17Packages must be added to DB to be considered installed (#8038)Massimiliano Culpo1-0/+1
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.
2018-07-17lammps: added v20180629 (#8695)Christoph Junghans1-4/+16
2018-07-17fftw: version bump (#8723)Christoph Junghans1-0/+3
* fftw: version bump * fftw: add gcc-8 conflict for v3.3.7
2018-07-17fix link to blas libs (#8721)Lukasz1-0/+2
2018-07-17Add fix for bug causing MACSio build failure when hdf5 or typhonio enabled ↵James Dickson2-2/+2
(#8722) * Add fix for bug causing build failure when hdf5 enabled * Added correct hdf5 dependency to typhonio
2018-07-16r: add memory profiling variant (#8717)Levi Baber1-0/+5
* r: add memory profiling variant * r: change memory_profiling to underscores
2018-07-16aspera-cli: a new package. (#8715)健美猞猁1-0/+53
* aspera-cli: a new package. * flak8.
2018-07-15Charm: set default backend to netlrts (#8714)Matthias Diener1-1/+1
This allows building MPI applications on top of charm/AMPI without to specify another backend.
2018-07-15Charm: more info about build targets (#8713)Matthias Diener1-0/+1
* Charm: more info about build targets * fix whitespace
2018-07-15Scotch: update package (#8711)Matthias Diener1-0/+1
2018-07-15yasm: add develop version (#8712)Matthias Diener1-0/+6
2018-07-15charm: provide MPI (#8647)Matthias Diener1-0/+19
* Charm: provide MPI * add mpicc wrappers * clarify MPI comment
2018-07-14Fixing error in amrvis package. (#8710)Jon Rood1-4/+4
2018-07-14Py-opentuner: new package (#8707)Matthias Diener1-0/+44
2018-07-13Unset F90 and F90FLAGS in mvapich2 (#8698)Jon Rood1-0/+3
* Unset F90 in mvapich2 when using intel compilers. * Fixing typo. * Unset F90 and F90FLAGS for mvapich2 at all times. * Adding comment.
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