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2020-04-12py-setuptools-rust: add new package (#16008)Adam J. Stewart1-0/+18
2020-04-11tau: added new variants (#16005)Carson Woods1-0/+20
* Add more tau variants * Add more tau variants
2020-04-11new package: openmm (#16002)Andrew W Elble1-0/+48
* new package: openmm * dependency adjustments * 1. modify dependencies 2. openmm dynamically compiles cuda kernels during runtime, attempt to set up an environment that will work. * Update var/spack/repos/builtin/packages/openmm/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-10[py-jupyter-core] added version 4.6.3 (#15991)Jennifer Herting1-0/+3
* [py-jupyter-core] added version 4.6.3 * [py-jupyter-core] updated python version requirement
2020-04-10votca-tools: add mkl support (#15997)Christoph Junghans1-0/+8
* votca-tools: add mkl support * Update package.py
2020-04-10votca-*: add v1.6_rc2 (#15999)Christoph Junghans6-10/+15
* votca-*: add v1.6_rc2 * votca-*: develop -> master
2020-04-10Add Go versions 1.14.2 and 1.13.10 (#16000)Paul1-0/+2
2020-04-10gromacs: install header files (#15996)Christoph Junghans1-0/+3
2020-04-10gdal: Patch to support hdf linked against libtirpc (#15995)Tom Payerle1-0/+7
If hdf was built with +libtirpc, we need to add -ltirpc to our link flags.
2020-04-10hdf: Add option to link against libtirpc package (#15993)Tom Payerle1-0/+7
This adds a boolean 'libtirpc' variant to the hdf package. Default is false, which will reproduce previous behavior (which was to rely either on system xdr headers/library, or have hdf use it's builtin xdr lib/headers (which are only for 32 bit)) If true, a dependency is added on 'libtirpc', and the LIBS and CPPFLAGS are updated in the configure command to find the libtirpc library and xdr.h header. This is needed as RHEL8 (and presumably other distros have or will be) removed xdr.h from glib-headers package,which was breaking the previous behavior of using system xdr headers.
2020-04-10new package: py-torchsummary (#15990)Andrew W Elble1-0/+21
* new package: py-torchsummary * add numpy
2020-04-10new package: py-torchaudio (#15989)Andrew W Elble1-0/+26
2020-04-10opencv: assorted fixes (#15971)Andrew W Elble1-1/+30
* opencv: assorted fixes 1. depends on blas when +lapack 2. set cuda nvcc flags for cuda_arch 3. let cuda/contrib builds work 4. depends on hdf5 when cuda/contrib 5. depends on ant when +java 6. allow protobuf version to be different 7. let opencv recompile it's protoc files. * ant is a build-time dependency * register +cuda~contrib as impossible.
2020-04-10fujitsu compiler: Delete custom environment function. (#15988)Tomoki, Karatsu1-4/+0
2020-04-10New package: tensorboardX (#15955)Andrew W Elble1-0/+24
* New package: tensorboardX * prune back to just what's in setup.py for now
2020-04-10Add new version of py-hypothesis (#15942)iarspider1-0/+3
* Add new version of py-hypothesis * Update package.py * Update package.py
2020-04-10Update yaml-cpp package to enable for build of old api (#15983)Jacob Merson1-1/+9
The old api is found in version 0.3.0 which uses a different release name, so the url function was updated to properly find the older releases. Also, this removes the boost constraint on the 0.3.0 version which does not need it.
2020-04-09update URL and sha256 for aws-parallelcluster 2.6.1 (#15980)tilne1-1/+2
Signed-off-by: Tim Lane <tilne@amazon.com>
2020-04-09py-clint: new package at 0.5.1 (#15905)Justin S1-0/+18
* py-clint: new package at 0.5.1 * py-clint: update py-setuptools dep type
2020-04-09meson: Add 0.54.0 (#15952)Michael Kuhn4-16/+45
* meson: Add 0.54.0 This change also improves the rpath patch we are using. Instead of never removing the rpath, we now only keep it if running within Spack to guarantee consistent behavior of Meson. * meson: Make ninja a hard dependency
2020-04-09[py-pygdal] added version 3.0.4.6 (#15973)Jennifer Herting1-0/+2
2020-04-09aperture-photometry: add new version (#15967)noguchi-k1-1/+1
2020-04-09Update doxygen package (#15969)Ryan Pepper1-0/+6
* Update doxygen package * Add new version releases 1.8.16 and 1.8.17 * Add mscgen as an optional dependency. * Update doxygen package.py Fix typo in mscgen dependency specification * Remove whitespace for flake8
2020-04-09primer3: move to github, add 2.5.0, fix 2.3.7 (#15958)George Hartzell1-3/+15
* primer3: move to github, add 2.5.0, fix 2.3.7 - The Primer3 project moved to GitHub. - update the URL - compare the tarballs 2.3.7 from Sourceforge and github, no significant differences (e.g. the Sourceforge tarball contained a couple of "tmp" files). - update the signature for the 2.3.7 tarball. - @2.3.7 doesn't build with gcc@8.4.0, there's a dubious pointer/int comparison that causes an error. It was fixed upstream in newer versions, apply simple patch to this version so that it continues to be build-able with newer compilers. See: - https://github.com/primer3-org/primer3/issues/2 - https://github.com/primer3-org/primer3/issues/3 - Add info for @2.5.0, which builds cleanly. * Flake8 cleanup
2020-04-09NetCDF packages: switch to the official FTP server. (#15641)Sergey Kosukhin3-7/+11
2020-04-09New package: gtk-doc (#15768)Jennifer Herting1-0/+41
* [gtk-doc] created template * [gtk-doc] using custom url to standardize on dotted version * [gtk-doc] added description and homepage * [gtk-doc] added dependencies and added pdf variant * [gtk-doc] commented out pdf variant * [gtk-doc] cleaned up leftover fixmes * [gtk-doc] flake8 * [gtk-doc] readded url * [gtk-doc] python packages are build and run dependencies
2020-04-09papi: check existence of a fortran compiler (#15968)Massimiliano Culpo1-4/+8
fixes #5029
2020-04-09[podio] add recipe for podio (#15726)vvolkl1-0/+58
2020-04-09py-torch: Fix v1.4.0 by adding v1.4.1 (#15761)Andrew W Elble1-1/+6
* py-torch: Fix v1.4.0 by adding v1.4.1 version/tag hack so that 1.4.0 is still workable. see pytorch/pytorch#35149 * delete/disable fbgemm support in 1.4.0 * moved conflict
2020-04-09NAG compiler fix: skip implicit RPATH detection (#15902)Peter Scheibel1-2/+6
* Skip collection of compiler link paths if compiler does not define a verbose flag * modules config bug: allow user to configure a compiler without an explicit entry for loaded modules
2020-04-09uchardet: added package at v0.6.0 (#15937)darmac1-0/+29
2020-04-09Papi packge: refactored to inherit from AutotoolsPackage (#15962)G-Ragghianti1-43/+44
2020-04-08elasticsearch: change depends on from jdk to java (#15964)darmac1-1/+1
2020-04-08glib: Add new stable versions (#15947)Michael Kuhn2-6/+118
Newer versions of glib require Meson, so this PR adds support for that using a hybrid approach. glib@5.28: will be built using Meson, older versions still make use of Autotools.
2020-04-08py-gpaw: Add libvdwxc as variant (#15948)T.Tian1-0/+7
* Add libvdwxc as variant * py-gpaw: add missing line for libvdwxc conditions
2020-04-08- Fixes build issues. (#15951)Aniruddha Marathe1-3/+10
- Updates Kripke URL to its Github repository. - Adds previous Kripke versions. - Adds 'caliper' variant.
2020-04-08py-tensorflow-estimator: fix build (#15953)Andrew W Elble1-11/+34
Change the build to work again, and be more in line with the other tensorflow packages. Add version 2.1.
2020-04-08Fixed bad expand option for openjdk versions. (#15956)Paul Ferrell1-1/+1
The most recent change to the openjdk package set expand=False for all versions of the package. This means only the unexpanded archive will be installed, which is not correct.
2020-04-08py-awesome-slugify: new package at 1.6.5 (#15907)Justin S1-0/+21
* py-awesome-slugify: new package at 1.6.5 * py-awesome-slugify: fix typo in version range * py-awesome-slugify: update dependencies
2020-04-08F18 update April 2020 (#15930)Nichols A. Romero1-1/+24
* Update dependencies and support variant for Fortran Intermediate Representation. * Add Cmake flags that toggle Fortran Intermediate Representation on/off. Exclude Flang tests for now. * f18+fir variant needs next release of llvm or master. * Only build tests if you are pass in --test to spack install
2020-04-08New package: py-tensorboard (#15829)Andrew W Elble1-0/+67
* New package: py-tensorboard * some basic dependencies based on requirements.txt remove the older version that doesn't build * requested changes * add additional dependencies * more dependency changes
2020-04-08py-onnx: only use py-typing if python < 3.5 (#15931)Andrew W Elble1-2/+3
* py-onnx: only use py-typing if python < 3.5 avoids a 'Callable has no attribute __abc_registry' error. See onnx/onnx#2199 and python/typing#573 * add version 1.6.0 while we're here.
2020-04-08MariaDB: added v10.4.12 (#15943)iarspider1-0/+1
2020-04-08pytest: added v4.6.9 (#15944)iarspider1-1/+2
2020-04-08http-parser: added package at v2.9.4 (#15936)darmac1-0/+21
2020-04-08environment-modules: add version 4.5.0 (#15938)Xavier Delaruelle1-2/+3
Add new version 4.5.0 and update quarantine variable list to also include LD_PRELOAD in addition to LD_LIBRARY_PATH (to avoid side-effect when the first depends on the latter).
2020-04-07Update hugo version and add extended variant (#15933)George Hartzell1-1/+8
- Add info for version 0.68.3 - Add variant to package that enables the "extended" features. It works with both of the existing versions (not sure how far back it goes, but confirmed that it's valid fro 0.53). Tested on OS X with go@1.14.1.
2020-04-07Add new package: open-isns (#15914)darmac1-0/+29
* Add new package: open-isns * refine args
2020-04-07py-cyvcf2: new package at 0.11.7 (#15908)Justin S1-0/+25
* py-cyvcf2: new package at 0.11.7 * py-cyvcf2: update dependencies
2020-04-07py-yahmm: new package at 1.1.3 (#15909)Justin S1-0/+22
* py-yahmm: new package at 1.1.3 * py-yahmm: update dependencies
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