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2019-11-06new package: py-jdatetime (#13569)Andreas Baumbach1-0/+15
* new package: py-jdatetime * Update var/spack/repos/builtin/packages/py-jdatetime/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-06ncview: Fix dependency check (#13615)Michael Kuhn1-1/+1
netcdf has been renamed to netcdf-c.
2019-11-06gromacs: add v2019.4 and others (#13617)Christoph Junghans1-1/+4
* gromacs: add v2019.4 and others * gromacs: fix patch applying
2019-11-06new package: py-dateparser (#13574)Andreas Baumbach1-0/+33
* new package: py-dateparser * take setup.py dependencies into account * fixup help->description * reorder dependencies * drop version constraints not enforced in setup.py
2019-11-06new package: py-nodeenv (#13594)Andreas Baumbach1-0/+17
* new package: py-nodeenv * drop python version requirements, not enforced by setup.py
2019-11-06py-tatsu: new package (#13566)Andreas Baumbach1-0/+27
* py-tatsu: new package * drop unnecessary dependencies * drop kanji, add variant, and restrict to future releases
2019-11-06netcdf-fortran: Fix parallel builds (#13612)Michael Kuhn1-1/+18
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.
2019-11-06cdo: Fix with_or_without calls (#13614)Michael Kuhn1-3/+6
netcdf has been renamed to netcdf-c and udunits2 has been renamed to udunits.
2019-11-06new package: py-pymeeus (#13572)Andreas Baumbach1-0/+17
* new package: py-pymeeus * drop unnecessary dependencies
2019-11-06new package: py-pre-commit (#13570)Andreas Baumbach1-0/+30
* new package: py-pre-commit * update missing dependencies * add python version restriction
2019-11-06new package: py-aspy-yaml (#13591)Andreas Baumbach1-0/+19
* new package: py-aspy-yaml * add python version dependency
2019-11-06go: Add 1.13.4 and 1.12.13 (#13609)Michael Kuhn1-0/+2
2019-11-06pybind11: correct get_include path (#13605)Axel Huebl1-0/+20
* 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>
2019-11-05new package: py-ics (#13576)Andreas Baumbach1-0/+39
* 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>
2019-11-05add charliecloud 0.12 (#13599)Jordan Ogas1-0/+1
* add charliecloud 0.12 * fix typo Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-05Add GDAL 3.0.2 (#13603)Adam J. Stewart1-1/+2
2019-11-05mpi4py 3.0.3 (#13601)Axel Huebl1-3/+4
* 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
2019-11-05netcdf: fix headers in v4.7.2 (#13600)Christoph Junghans1-0/+3
2019-11-05elpa: add v 2019.05.002 (#13602)Christoph Junghans1-0/+1
2019-11-05PyTorch: avoid use of third party vendored deps (#13588)Adam J. Stewart1-5/+16
* PyTorch: avoid use of third party vendored deps * Flake8 fix
2019-11-05add depends_on(python) to PythonPackage stub (#13595)Andreas Baumbach1-0/+1
2019-11-05new package: py-nose-cov (#13571)Andreas Baumbach1-0/+19
* new package: py-nose-cov * add missing dependencies
2019-11-05update py-notebook (#13423)Andreas Baumbach1-6/+16
* 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
2019-11-05new package py-cfgv (#13592)Andreas Baumbach1-0/+19
2019-11-05new package: py-identify (#13593)Andreas Baumbach1-0/+21
2019-11-05added relion 3.0.8 [latest stable version in 3.0 branch] as well as 3.1_beta ↵Douglas Duckworth1-6/+12
(#13539) * 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
2019-11-05bugfix: uninstall should find concrete specs by DAG hash (#13598)Todd Gamblin1-1/+9
This fixes a regression introduced in #10792. `spack uninstall` in an environment would not match concrete query specs properly after the index hash of enviroments changed. - [x] Search by DAG hash for specs to remove instead of by build hash
2019-11-05`spack find` now displays variants and other spec constraints (#13596)Todd Gamblin3-4/+23
If you do this in a spack environment: spack add hdf5+hl hdf5+hl will be the root added to the `spack.yaml` file, and you should really expect `hdf5+hl` to display as a root in the environment. - [x] Add decoration to roots so that you can see the details about what is required to build. - [x] Add a test.
2019-11-04new package py-testpath (#13417)Andreas Baumbach1-0/+16
* new package py-testpath dependency of py-nbconvert * py-testpath: fix flake8 * Remove the unnecessary pip dependency
2019-11-04update py-pyzmq (#13420)Andreas Baumbach1-0/+4
* update py-zmq * update dependencies
2019-11-04update py-jupyter-client and new setuptools dependency (#13425)Andreas Baumbach1-1/+6
* update py-jupyter-client and new setuptools dependency * update dependencies
2019-11-04Mothur update (#13580)xfzhao1-0/+5
* add +vserach option * fixes #967
2019-11-04added archer 2.0.0 and package build fixes (#13577)Gregory Lee1-2/+9
2019-11-04portage: fix lapack/blas linkage (#13558)Christoph Junghans1-0/+5
2019-11-04py-colorama: new version 0.4.1 (#13562)Andreas Baumbach1-0/+2
* py-colorama: new version 0.4.1 * add python dependency
2019-11-04py-regex: new version 2019.11.1, w/o setuptools (#13563)Andreas Baumbach1-1/+2
2019-11-04py-dataclasses: new package (#13564)Andreas Baumbach1-0/+18
2019-11-04py-tzlocal: add new version 2.0.0 (#13565)Andreas Baumbach1-0/+1
2019-11-04new package: py-chai (#13567)Andreas Baumbach1-0/+17
2019-11-04new package: py-umalqurra (#13568)Andreas Baumbach1-0/+16
2019-11-04Add ACTS v0.10.5 (#13556)Hadrien G1-0/+1
2019-11-04py-astor: specify py-setuptools versions as build fail with latest version ↵Sinan1-1/+3
(#13533) * specify py-setuptools dependency as build fail with latest version * explain * py-astor builds with setuptools@41.3
2019-11-04Flux v0.11.1 - v0.11.3 (#13199)Stephen Herbein2-21/+87
* 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
2019-11-04Add latest version of py-pybind11 (#13552)Adam J. Stewart1-3/+6
* Add latest version of py-pybind11 * setup_environment -> setup_build_environment
2019-11-03bugfix: fetch prefers to fetch local mirrors over remote resources (#13545)Omar Padron3-8/+11
- [x] insert at beginning of list so fetch grabs local mirrors before remote resources - [x] update the S3FetchStrategy so that it throws a SpackError if the fetch fails. Before, it was throwing URLError, which was not being caught in stage.py. - [x] move error handling out of S3FetchStrategy and into web_util.read_from_url() - [x] pass string instead of URLError to SpackWebError
2019-11-03Add py-voluptuous (#13457)Simon Pintarelli1-0/+16
Data validation library
2019-11-03r-gstat: new package at 2.0-3 (#13131)Justin S1-0/+24
* 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>
2019-11-03environments: only write when necessary (#13546)Greg Becker4-25/+66
This changes Spack environments so that the YAML file associated with the environment is *only* written when necessary (i.e., if it is changed *by spack*). The lockfile is still written out as before. There is a larger question here of which part of Spack should be responsible for setting defaults in config files, and how we can get rid of empty lists and data structures currently cluttering files like `compilers.yaml`. But that probably requires a rework of the default-setting validator in `spack.config`, as well as the code that uses `spack.config`. This will at least help for `spack.yaml`.
2019-11-03Polymake: new version and more dependencies (#13399)Ricardo Silva4-3/+45
* New package: perl-term-readline-gnu * polymake dependency * perl-term-readline-gnu: flake8 * New package: perl-xml-libxslt * polymake dependency * ppl: new version 1.2 Conflicts: var/spack/repos/builtin/packages/ppl/package.py * polymake: new version and dependencies Conflicts: var/spack/repos/builtin/packages/polymake/package.py * perl-xml-libxslt: missing dependency
2019-11-03New package py-wradlib with new dependencies (#13459)Jannek Squar5-3/+109
* New package py-wradlib with new dependencies py-deprecation, py-semver, py-xmltodict * Adjusted package source source * Adjusted xarray package to use pypi-source * Added dependencies * Added explicit gdal+python dependency * Concretised dependency versions * Removed strict version range
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