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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
2019-11-03Added dependencies (#13519)Jannek Squar1-1/+3
* Added dependencies * Adjusted dependency
2019-11-03Update package saga gis (#13520)Jannek Squar1-10/+38
* 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>
2019-11-03constexpr_longdouble.patch should be applied to v6 too (#13548)Daryl W. Grunau1-1/+1
2019-11-02Add latest version of protobuf (#13551)Adam J. Stewart1-10/+11
2019-11-02Add QNNPACK package (#13549)Adam J. Stewart2-1/+85
2019-11-02chgcentre: a new package. (#13500)健美猞猁1-0/+20
* chgcentre: a new package. * flake8.
2019-11-01spack create: http -> https (#13547)Adam J. Stewart1-2/+2
2019-11-01Bugfix: respect order of mirrors in mirrors.yaml (#13544)Peter Scheibel1-1/+4
Commands like "spack mirror list" were displaying mirrors in a different order than what was listed in the corresponding mirrors.yaml file. This restores commands to iterate over mirrors in the order that they appear in the config file.
2019-11-01environments: make shell modifications partially unconditional (#13523)Greg Becker2-1/+37
* environments: make shell modifications partially unconditional * flake * missing module name * add regression test * flake
2019-11-01Add py-tables 3.6.1 (#13536)Adam J. Stewart1-1/+2
2019-11-01libxc: update URL / new API (#13471)Simon Pintarelli2-36/+3
- setup_environment -> setup_build_environment - remove patch
2019-11-01allow bootstrap buildcache install of patchelf (#13430)Marc Mengel2-3/+36
* allow bootstrap buildcache install of patchelf * file not path_name on one * style * add test for relocating patchelf * blank lines..
2019-11-01bugfix: spack.util.url.join() now handles absolute paths correctly (#13488)Omar Padron3-2/+379
* fix issue where spack.util.url.join() failed to correctly handle absolute path components * add url util tests
2019-11-01sbang: use utf-8 for encoding when patching (#13490)Gregory Lee1-4/+13
This fixes a UnicodeDecodeError in the sbang patching function.
2019-11-01Specs with quoted flags containing spaces are parsed correctly (#13521)Massimiliano Culpo2-1/+22
2019-11-01targets: print a warning message before downgrading (#13513)Massimiliano Culpo2-25/+57
* Make package preferences a soft failure for targets, instead of a hard failure. * Added unit tests for preferences expressed via packages.yaml
2019-10-31hypre: add version 2.18.2 (#13527)Satish Balay1-0/+1
2019-10-31dd Open MPI v. 4.0.2 (#13257)Daniel Topa1-1/+2
Verification builds on LANL Darwin x86_64, ARM, and, Power9: x86_64: OPTANE dantopa@cn733:pr-openmpi-4.0.2.spack $ spack arch linux-centos7-skylake_avx512 $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 2m 15.65s. Build: 6m 13.17s. Total: 8m 28.82s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.0.2-jrypg7vfnk6nl5if2rnzt65wdrjelxsq NEHALEM $ spack arch linux-centos7-nehalem $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 50.48s. Build: 9m 11.45s. Total: 10m 1.93s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-centos7-nehalem/gcc-4.8.5/openmpi-4.0.2-4jz3bcwjci44taizt4jqzxqh4y75uswc ARM $ spack arch linux-rhel7-aarch64 $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 1m 10.47s. Build: 11m 41.45s. Total: 12m 51.92s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/openmpi-4.0.2-ygr77roadqzdnsdgqz3uactjqnb5nayn POWER9 $ spack arch linux-rhel7-power9le $ spack install openmpi @ 4.0.2 % gcc @ 4.8.5 ==> Warning: Using GCC 4.8 to optimize for Power 8 might not work if you are not on Red Hat Enterprise Linux 7, where a custom backport of the feature has been done. Upstream support from GCC starts in version 4.9 ... ==> Installing openmpi ... ==> Successfully installed openmpi Fetch: 23.95s. Build: 9m 7.67s. Total: 9m 31.62s. [+] /scratch/users/dantopa/new-spack/pr-openmpi-4.0.2.spack/opt/spack/linux-rhel7-power8le/gcc-4.8.5/openmpi-4.0.2-cid4wfzr2iwgz6ybhkexludwu7koi266 $ spack find -ldf openmpi ==> 4 installed packages -- linux-centos7-haswell / gcc@4.8.5 ---------------------------- jrypg7v openmpi@4.0.2%gcc lliismp hwloc@1.11.11%gcc 7dqpxas libpciaccess@0.13.5%gcc viidrh5 libxml2@2.9.9%gcc yhvj3br numactl@2.0.12%gcc pkmj6e7 zlib@1.2.11%gcc -- linux-centos7-nehalem / gcc@4.8.5 ---------------------------- 4jz3bcw openmpi@4.0.2%gcc pcauu6w hwloc@1.11.11%gcc yiqf6bj libpciaccess@0.13.5%gcc wpfgqf2 libxml2@2.9.9%gcc fd2xpnm numactl@2.0.12%gcc xguzaxf zlib@1.2.11%gcc -- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------ ygr77ro openmpi@4.0.2%gcc omy3xi2 hwloc@1.11.11%gcc 6a4he35 libpciaccess@0.13.5%gcc txqo4cc libxml2@2.9.9%gcc m5neuus numactl@2.0.12%gcc 67s2oqn zlib@1.2.11%gcc -- linux-rhel7-power8le / gcc@4.8.5 ----------------------------- cid4wfz openmpi@4.0.2%gcc zcdnwb3 hwloc@1.11.11%gcc lencfon libpciaccess@0.13.5%gcc bve4jop libxml2@2.9.9%gcc kajzqwg numactl@2.0.12%gcc tjbynt2 zlib@1.2.11%gcc Thu Oct 17 19:02:50 MDT 2019 Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-10-31Bugfix: BundlePackage staging/installation (#13524)Peter Scheibel1-0/+3
4af4487 added a mirror_id function to most FetchStrategy implementations that is used to calculate resource locations in mirrors. It left out BundleFetchStrategy which broke all packages making use of BundlePackage (e.g. xsdk). This adds a noop implementation of mirror_id to BundleFetchStrategy so that the download/installation of BundlePackages can proceed as normal.
2019-10-31Docs: unlock requirement versions (#13384)Adam J. Stewart1-3/+3
2019-10-31Travis CI: Test Python 3.8 (#13347)Adam J. Stewart4-15/+35
* Travis CI: Test Python 3.8 * Fix use of deprecated cgi.escape method * Fix version comparison * Fix flake8 F811 change in Python 3.8 * Make flake8 happy * Use Python 3.8 for all test categories
2019-10-31Bump up PGMath Library to latest version. More transparent name of the ↵Nichols A. Romero1-2/+3
branch, version name equals branch name. (#13511)
2019-10-31Add GRASS 7.8.0 (#13026)Adam J. Stewart1-49/+99
* Add GRASS 7.8.0 * Add new variants/dependencies * Remove unused dep * Filter entire libiconv line
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