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2018-07-21config: allow user to add configuration scopes on the command line.Elizabeth Fischer4-72/+194
- 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>
2018-07-21locks: fix bug when creating lockfiles in the current directory.Todd Gamblin2-0/+25
- 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.
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 Gamblin35-104/+106
2018-07-19style: Add pep8-naming plugin to flake8Scott Wittenburg1-0/+1
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.
2018-07-19add py-pep8-naming packageTodd Gamblin3-5/+92
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
2018-07-18Better Makefile target detection (#8223)Adam J. Stewart1-21/+46
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.
2018-07-18shell: Add spack to PATH before calling spack in setup-env.csh (#8740)Adam J. Stewart1-1/+1
2018-07-17shell: fixed a typo in spack --print-shell-vars (#8732)Massimiliano Culpo2-6/+6
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 Culpo4-6/+64
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.
2018-07-17Add documentation on build systems (#5015)Adam J. Stewart17-0/+3941
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.
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
2018-07-16add `spack --print-shell-vars` to speed up `setup-env.[c]sh` (#8101)Todd Gamblin4-21/+128
- 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
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
2018-07-14clean up of spack clean (#8610)Andreas Baumbach2-37/+15
* update help of `clean --all` to include `-p` * remove old orphaned `.pyc` removal * restrict removal or orphaned pyc files to `lib/spack` and `var/spack`
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.
2018-07-13py-fn: new package (#8705)Matthias Diener1-0/+37
2018-07-13mothur: mpi not used (#8706)Levi Baber1-3/+0
2018-07-13Scotch: fix compilation of 6.0.5a (#8704)Matthias Diener2-0/+12
Prevent this error: metis_graph_part.c:301:7: error: non-void function 'METIS_PartGraphVKway' should return a value [-Wreturn-type]
2018-07-13update version for numexpr (#8702)Sajid Ali1-1/+2
* modified: package.py * deleted: var/spack/repos/builtin/packages/py-numexpr/numexpr-2.6.5.tar.gz
2018-07-13Add py-backcall (#8701)Sajid Ali1-0/+34
* new file: var/spack/repos/builtin/packages/py-backcall/package.py * Update package.py * Update package.py * Update package.py * Update package.py
2018-07-12flang: add support for llvm-6 (#8073)Christoph Junghans2-8/+65
* flang: add support for llvm-6 * flang: review changes * pgmath: make flake8 happy
2018-07-12locks: improve errors and permission checkingTodd Gamblin2-52/+145
- Clean up error messages for when a lock can't be created, or when an exclusive (write) lock can't be taken on a file. - Add a number of subclasses of LockError to distinguish timeouts from permission issues. - Add an explicit check to prevent the user from taking a write lock on a read-only file. - We had a check for this for when we try to *upgrade* a lock on an RO file, but not for an initial write lock attempt. - Add more tests for different lock permission scenarios.