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2020-02-27Improved the build error templateMassimiliano Culpo1-7/+18
2020-02-27Improved the bug report templateMassimiliano Culpo1-7/+22
2020-02-27hpcviewer: add version 2020.02Mark W. Krentel1-0/+6
2020-02-27New package: XCFun (#15199)Roberto Di Remigio1-0/+37
2020-02-27Add new timeout fetch_optionMichael Kuhn3-10/+21
This allows packages to override the global connect_timeout.
2020-02-27Generalize curl_options into fetch_optionsMichael Kuhn2-19/+22
This allows us to support higher-level concepts such as 'cookie' and 'timeout' without users having to specify curl options.
2020-02-27config: Add a new option connect_timeoutMichael Kuhn4-2/+14
connect_timeout can be used to increase the time Spack waits for the server to answer. This can be used to work around slow connections or servers. Fixes #14700
2020-02-27release sz 2.1.8.3 (#15250)Sheng Di1-0/+1
2020-02-27CudaPackage: add support for Tesla K80 and older CUDA (#15031)Adam J. Stewart1-30/+46
* CudaPackage: add support for Tesla K80 and older CUDA * Flake8 fixes * Fix cuda_arch when no arch is set * Fine-tune cuda_arch=37,50 supported CUDA versions * CUDA 6.5+ supports SM_37 * Add @svenevs as a maintainer
2020-02-27new package: py-cnvkit and py-pomegranate (#15222)Glenn Johnson2-0/+51
The py-pomegranate package is a dependency of py-cnvkit
2020-02-27new package: py-pycifrw (#15224)Glenn Johnson1-0/+18
2020-02-27new package: py-pycosat (#15225)Glenn Johnson1-0/+20
2020-02-27New packages: py-pymc3 and py-arviz (#15226)Glenn Johnson2-0/+55
This PR adds py-pymc3 and py-arviz as a dependency.
2020-02-27Added go 1.14 (#15249)Paul1-0/+1
2020-02-27Docs: "spack env" is in the meantime called "spack build-env" (#15233)TZ1-10/+10
2020-02-27arpack-ng: ILP64 support (#15103)Kai Torben Ohlhus1-1/+5
Details about ILP64 support: `INTERFACE64=1` are described on the [ARPACK-NG GitHub website](https://github.com/opencollab/arpack-ng).
2020-02-26f77-zmq: add version 4.3.2 (#15204)Anthony Scemama1-1/+3
Version 4.3.1 only works with Python3. Version 4.3.2 also works with Python2. These constraints were not listed before and are added by this commit.
2020-02-26py-git-review: add version 1.28 (#15203)Andreas Baumbach1-0/+1
2020-02-26AWS ParallelCluster: add version 2.6.0 (#15240)Luca Carrogu1-1/+2
2020-02-26h5py: add version 2.10.0 (#15205)genric1-1/+3
Also add dependency on py-cached-property
2020-02-26bugfix: Add dependents when initializing spec from yaml (#15220)Tamara Dahlgren2-11/+17
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents. - [x] populate dependents when loading from yaml
2020-02-26SQLite shouldn't be enabled by default for TAU package (#15228)Kevin Huck1-1/+5
Also Adding conflict for SQLite and ADIOS2 for older TAU releases
2020-02-26Default to +termlib for ncurses for LLVM (#15039)Seth R. Johnson1-1/+1
LLVM is the only package that explicitly sets the "termlib" variant of ncurses and it specifies +termlib. ncurses defaults to ~termlib; if a package depends on LLVM and ncurses, there is a concretizer bug that incorrectly detects a constraint conflict (see #267). Setting +termlib as the default is a stopgap measure to avoid this conflict. If other packages were to explicitly request ~termlib in the future, the same issue would come up again (and could not be resolved by adjusting the default of "termlib"). Setting +termlib on ncurses moves some symbols into a separate "libtinfo". Not all packages may be able to detect libtinfo properly so may require an update; vim, samtools, and libedit have been updated to use ncurses+termlib (in the case of libedit, the only necessary action was to add a newer version where the build system was updated to check libtinfo).
2020-02-26Uniquify suffixes added to module names (#14920)Seth R. Johnson3-1/+4
2020-02-26Basis set exchange command-line tool (#15126)Anthony Scemama1-0/+33
* Flake8 OK * Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Added missing dependencies proposed by @adamjstewart * Without py-versioneer * Added py-versioneer * Python2 for bse * Python build error * Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Removed py-versioneer, according to @adamjstewart Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-26A few edits for the Basic Usage Doc page (#15215)Glenn Johnson1-8/+16
This PR corrects a few minor things and adds a note about colorized output.
2020-02-25buildcache cmd: add explicit message with default output dir for ↵Patrick Gartung3-13/+64
buildcaches. (#15090) * Make -d directory a required option. Print messages about where buildcaches will be written. * Add mutually exclusive required options * spack commands --update-completion * Apply @opadron's patch * Update share/spack/spack-completion.bash * Incorporate @opadron's suggestions
2020-02-25add --only option to buildcache create cmd (#14921)Omar Padron3-13/+32
* add --only option to buildcache create cmd replaces the --no-deps option
2020-02-25remove catch-all exception handling in buildcache command (#15185)Omar Padron3-7/+20
* remove catch-all exception handling in buildcache command * fix test
2020-02-25Buildcache cmd: add install -o/--otherarch option for installing macOS ↵Patrick Gartung2-4/+10
buildcaches on linux (#15192) * Buildcache command: add install option -o/--otherarch This will allow matching specs from other archs, for example installing macOS buildcaches on linux hosts. * spack commands --update-completion
2020-02-25qrupdate: ILP64 support (#15104)Kai Torben Ohlhus1-6/+20
- When compiling qrupdate with `FFLAGS=-fdefault-integer-8` it can be perfectly used for larger problem dimensions. - Improved the readability of the file with the added rules.
2020-02-24Adding ADIOS2 and SQLite3 output support to TAU. Also fixing MPI include ↵Kevin Huck1-3/+17
and library paths. (#15189) Setup package to use MPI the way Spack recommends, and remove extra iowrapper option from configure Making flake happy
2020-02-24Update of OpenFOAM package.py (#15190)OliverPerks1-2/+4
2020-02-24suite-sparse: add version 5.7.1 (#15195)Kai Torben Ohlhus1-0/+1
Release notes: https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.7.1 Version 5.7.0 was an incomplete release.
2020-02-24update flecsi and legion package.py (#15159)ktsai72-19/+35
* update flecsi and legion package.py * comment out a conflict * update to use extend
2020-02-24docs: Fix tiny typo (#15181)Michael Kuhn1-1/+1
2020-02-24cmd/load: Fix usage output (#15180)Michael Kuhn1-2/+3
args.specs is a list, which results in output like this: ``` eval `spack load --sh ['libxml2', 'xz']` ``` We want this instead: ``` eval `spack load --sh libxml2 xz` ```
2020-02-24modules: store configure args during build (#11084)Michael Kuhn4-11/+41
This change stores packages' configure arguments during build and makes use of them while refreshing module files. This fixes problems such as in #10716.
2020-02-24add new package : agrep (#15165)darmac1-0/+23
* add new package : agrep * agrep: move binary to bin/
2020-02-24Added extra versions of OCaml (#15177)Anthony Scemama1-0/+11
* Aded extra versions for OCaml * Added maintainer
2020-02-24sz: update to version 2.1.8.1 (#15154)Robert Underwood1-12/+81
The newer versions of SZ now uses CMake to build.
2020-02-24Update py-bx-python package (#15175)Glenn Johnson2-4/+29
* Update py-bx-python package - add update to py-bx-python - switch to pypi downloads - set dependencies * Update var/spack/repos/builtin/packages/py-bx-python/package.py I had initially pulled version 0.8.6 and then updated that to 0.8.8 but missed the change in the python specs between those two versions. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Fix version 0.7.4 - set dependency on python2 - add dependency on py-python-lzo - add py-python-lzo package - set py-numpy dependency to correspond to latest version that works with python2 * Add constraint for py-six dependency * Update var/spack/repos/builtin/packages/py-bx-python/package.py Ah, I had that `when` clause in and then took it out as it did not seem to be needed. I guess it is always better to be more explicit. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Remove py-numpy constraint Let the concretizer catch the conflict with python2 and py-numpy versions. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-23Update py-rseqc package (#15176)Glenn Johnson1-4/+10
This PR depends on #15175 - add updated version - set depedencies
2020-02-23add new package : batctl (#15160)darmac1-0/+24
* add new package : batctl * batctl: move binary to bin/
2020-02-23add new package : bubblewrap (#15162)darmac1-0/+28
* add new package : bubblewrap * bubblewrap: remove some comment in package.py
2020-02-23Merge branch 'releases/v0.14' into developTodd Gamblin5-1/+11810
2020-02-23update CHANGELOG.md for 0.14.0v0.14.0Todd Gamblin1-0/+97
2020-02-23version bump: 0.14.0Todd Gamblin4-1/+11713
2020-02-23py-setproctitle: Add new package (#15170)Michael Kuhn1-0/+18
2020-02-23create: Mention that python dependency does not have to be added (#15173)Michael Kuhn1-1/+3
A generic python dependency is already added implicitly by the PythonPackage class.
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