Commit graph

14025 commits

Author SHA1 Message Date
Kevin Huck
f21073d231 tau: add conflicts for libelf/libdwarf variants (#11944)
Declare a conflict for TAU versions older than 2.28.1, that they
can't depend on libelf or libdwarf.  The user can still install it
by specifying tau@2.24~libelf~libdwarf.
2019-07-05 19:08:43 -07:00
Christoph Junghans
e392bf0412 cmake: add v3.14.5 2019-07-05 17:02:34 -07:00
Todd Gamblin
5686c2a544 setup-env.sh: make setup scripts work with set -u
- Add set -u to the setup-env.sh test script

- Refactor lines in setup-env.sh that tested potentially undefined
  variables to use the `[ -z ${var+x} ]` construct
2019-07-05 12:54:17 -07:00
Todd Gamblin
47e9f7aac9 tests: add tests for setup-env.sh
- tests use a shell-script harness and test all Spack commands that
  require special shell support.

- tests work in bash, zsh, and dash

- run setup-env.sh tests on macos and linux builds.
  - we run them on macos and linux
2019-07-05 12:54:17 -07:00
Todd Gamblin
e625ee3ffd setup-env.sh: now compatible with bash, zsh, and dash
- replace use of [[ with [

- replace function foo { .. } with foo() { .. }

- wrap some long lines

- add lsof and /proc/fd magic so that we can find the sourced file even in dash

- only do the complicated shell checks in one place; test $_sp_shell
  elsewhere.
2019-07-05 12:54:17 -07:00
Milton Woods
a7da5dcb19 py-stratify: vertical interpolation/stratification of atmos/ocean data (#11911)
* py-stratify: vertical interpolation/stratification of atmos/ocean data

* py-stratify: download from pypi.io
2019-07-04 10:38:48 -04:00
Milton Woods
d88c657f79 py-scikit-image: include more dependencies (#11912)
* py-scikit-image: include more dependencies

* py-scikit-image: limit some dependencies to recent versions
2019-07-04 10:38:02 -04:00
Hironori-Yamaji
cd18dadf92 jdk: Add JDK 12.0.1 (#11903) 2019-07-04 10:36:21 -04:00
Paul
1ce6490132 Added latest version, 0.7.1 (#11927) 2019-07-04 10:26:59 -04:00
Milton Woods
e7a3f703be py-antlr4-python3-runtime: new package (#11890)
* py-antlr4-python3-runtime: new package

* py-antlr4-python3-runtime: fix for flake8

* py-antlr4-python3-runtime: indent docstring

* py-antlr4-python3-runtime: clarify role of this package vs ANTLR in docstring

* py-antlr4-python3-runtime: remove whitespace at end of line
2019-07-04 10:12:54 -04:00
Glenn Johnson
54e87c8da0 Set ignore files for py-reportlab (#11928)
The py-reportlab package includes binaries for easy_install and pip.
That blocks activation if py-setuptools and/or py-pip are installed.
This PR block the binaries from py-reportlab as easy_install and pip
should be installed with their respective packages.
2019-07-03 19:15:01 -07:00
t-karatsu
adffb2bff4 libtool: execute autoreconf at ver.2.4.2 (#11913)
Version 2.4.6 did not require running autoreconf, so this only does
autoreconf for 2.4.2
2019-07-03 18:04:29 -07:00
shanedsnyder
902dcfd194 libfabric package: add version 1.8.0 (#11918) 2019-07-03 17:30:25 -07:00
Todd Gamblin
c45afb7578
coverage: remove sub-reports; only show project/patch on PRs (#11926)
- There's too much information on our PRs, and the Travis test results
  (which are arguably more important than coverage) get buried in
  coverage information

- Remove coverage sub-categories, as you can browse codecov's file view
  to see roughly the same thing

- show only project/patch on GitHub PRs.
2019-07-03 17:11:07 -07:00
Milton Woods
fae14bff21 py-cf-units: new package (#11891)
* py-cf-units: new package

* py-cf-units: download from pypi.io

* py-cf-units: include py-pytest-runner as build dep

* py-cf-units: remove empty build_args function

* py-cf-units: fix for flake8

* py-cf-units: indent docstring

* py-cf-units: remove excess spaces

* py-cf-units: list master branch ahead of numeric versions

* py-cf-units: remove extension keyword from version
2019-07-03 19:20:34 -04:00
Alberto Chiusole
f3bf89ebfe OpenMPI: add support for pbs/tm at configure. (#10620) 2019-07-03 14:07:51 -07:00
Justin M Wozniak
28949787e9 turbine: Better auto-detection of R location (#11711)
If R is provided by the system with a module (i.e. registered in
packages.yaml with a "module" entry) and has no discernible prefix,
this allows turbine to still make use of R.
2019-07-03 11:24:20 -07:00
Milton Woods
ea1df6a9b4 py-pyke: new package (#11894)
* py-pyke: automatic python program generator

* py-pyke: expand the package docstring
2019-07-02 15:58:14 -04:00
Milton Woods
48bfece55e py-pyugrid: unstructured grids in netcdf files (#11900) 2019-07-02 15:56:18 -04:00
ktsai7
229ba28ad5 Add llvm as deps when static analyzer is enabled (#11888)
* dep llvm if static analyzer
dep caliper if caliper

* fix typo

* adding variants for toggles
2019-07-02 11:45:13 -06:00
Toyohisa Kameyama
f1592e339d portcullis package: remove -m64 on aarch64. (#11905)
GCC on aarch64 dose not support -m64. This patch removes the -m64
flag if target is aarch64.
2019-07-02 10:42:06 -07:00
Phil Carns
2709f948fa opa-psm2 package: correct installation prefixes and add 11.2.77 (#11658)
This PR corrects a problem with the opa-psm2 package. It was
installing headers into <prefix>/usr/include and libraries into
<prefix>/usr/lib instead of <prefix>/include and <prefix>/lib.
The extra level of usr/ subdirectories causes dependent packages
like libfabric to fail to build.
2019-07-02 10:34:58 -07:00
Mark Olesen
5fd3b5acda openfoam: rename openfoam-com to openfoam (#11876)
The original packaging, with openfoam as a virtual and with
openfoam-com, openfoam-org and openfoam-extend as
providers, adds an obfuscation layer without any benefit.

- Rename `openfoam-com` to `openfoam`, and remove the 
  `openfoam` virtual package.
2019-07-01 22:54:36 -07:00
Todd Gamblin
515b4045e9 specs: remove parse_anonymous_spec(); use Spec() instead
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't
  support nameless specs.  We don't need it anymore because now we can
  write Spec() for a spec that will match anything, and satisfies()
  semantics work properly for anonymous specs.

- Delete `parse_anonymous_spec()` and replace its uses with simple calls
  to the Spec() constructor.

- make then handling of when='...' specs in directives more consistent.

- clean up Spec.__contains__()

- refactor directives and tests slightly to accommodate the change.
2019-07-01 18:45:44 -07:00
Todd Gamblin
12b9fad7b6 cray: use the cle-release file to determine CNL version
- CNL OS previously used the *Cray PE* version to determine the OS
  version.  Cray does not synchronize PE and CLE releases; you can run
  CLE7 with PrgEnv 6 (and NERSC currently does).

- Fix Spack's OS detection by using the cle-release file to detect the OS
  version.  This file is updated with every CLE OS release.

- Add some tests for our parsing logic
2019-07-01 18:36:02 -07:00
Milton Woods
1ad9f6268b New packages: libmo-unpack and py-mo-pack (#11895)
* libmo-unpack: package to encode and decode UM fields
* py-mo-pack: python interface for libmo-unpack
2019-07-01 18:24:45 -07:00
Justin S
781a115656 New package: r-gwmodel (starting at 2.0-9) (#11887) 2019-07-01 18:14:29 -07:00
Justin S
196886e708 New package: r-spatialreg (starting at 1.1-3) (#11886) 2019-07-01 18:13:06 -07:00
Justin S
a7cd7fdcd4 New package: r-spdata (starting at version 0.3.0) (#11883) 2019-07-01 18:11:16 -07:00
Milton Woods
711a80832a New package: py-nc-time-axis (#11898) 2019-07-01 18:07:57 -07:00
Glenn Johnson
b66c296562 py-markdown package: update dependency version range (#11908)
The python dependency specifies that 2.7 or 2.8 are allowed when in
fact it should specify a version range (anything between 2.7 and 2.8,
inclusive).
2019-07-01 17:52:41 -07:00
Sameer Shende
4d0926464c mpich: wrapperrpath variant allows disablement of RPATH usage in mpicc
Added a wrapperrpath variant to mpich that defaults to `True`.

Users can set this to `False` (e.g., spack install mpich~wrapperrpath) to
disable the wrapper RPATHs.  This makes it easier to replacing an MPICH
installation in a container with an MPICH for the host system,
e.g., Cray MPICH with Shifter on Cori, Intel MPI, MVAPICH2, etc.

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2019-07-01 15:09:40 -07:00
Toyohisa Kameyama
54de03548b planck-likelihood: remove -m64 on ARM (#11902) 2019-07-01 10:48:45 -07:00
Axel Huebl
1b3c11e793 ADIOS2: v2.4.0 (#11904)
Add the latest release of ADIOS2.
2019-07-01 13:47:31 -04:00
Milton Woods
6856972745 tk: avoid search for X headers and libraries (#11892) 2019-07-01 13:47:04 -04:00
t-karatsu
8ca5c3685a camellia: fix hdf5 dependency (#11810)
* camellia: fix hdf5 dependency

* camellia: Add comment
2019-07-01 13:40:53 -04:00
Justin S
b517be2c68 r-spacetime: new package at 1.2-2 (#11885) 2019-07-01 13:39:15 -04:00
Patrick Gartung
9bf9c0cec3
buildcache: add replace_prefix_bin function to deal with hard coded paths in libraries and executables. (#11882) 2019-07-01 10:16:23 -05:00
Milton Woods
0f703b7e81 py-netcdf4: depend on hdf5+hl (#11893) 2019-07-01 15:38:35 +02:00
Todd Gamblin
f51c4c5e77
readme: make list of links even tighter. 2019-06-30 23:15:37 -07:00
Todd Gamblin
af39390578 README: Tighten up text, mention the Code of Conduct in the README. 2019-06-30 23:08:33 -07:00
Todd Gamblin
9c37a4c948 meta: move CODE_OF_CONDUCT.md and CONTRIBUTING.md to .github
- Trying to reduce the number of top-level files in Spack.

- CODE_OF_CONDUCT.md can be referenced from the README.

- CONTRIBUTING.md is only used to display a message on pull requests, and
  it still does that when in .github.
2019-06-30 23:08:33 -07:00
Dr Owain Kenway
441401bb8b llvm: don't build CppBackend for flang versions of llvm (#11841)
The version of LLVM used by flang is new enough that CppBackend doesn't exist.  Unfortunately, `flang-xxxxxxxx` is seen as < `3.9.0` by the version check.  

* add a special case for `flang` versions.
2019-06-30 17:04:29 -07:00
Oliver Breitwieser
cf76a143a2 libtomlc99: Update version
The PR for shared libraries has been merged upstream -> add new version.
2019-06-30 16:02:08 -07:00
Todd Gamblin
4189640ee8 style: remove unnecessary NOQA exceptions 2019-06-30 16:01:23 -07:00
Todd Gamblin
600f3c1104 setup-env.sh: send cd output to /dev/null when it affects Spack
- We've seen this a few times now where users have set up `cd` to echo
  the new directory, and it screws up `setup-env.sh`

- In the past we've said this is user error.

- Here, we just fix it by sending `cd` output to /dev/null where needed.
  - this works in bash, zsh, and dash
2019-06-29 19:01:44 -07:00
Peter Scheibel
9c16b4a7f6 Allow uninstalling missing packages (#11874)
Remove package access from directory_layout; add regression test to ensure
that specs can be uninstalled without a package being known
2019-06-29 16:04:15 -07:00
Christoph Junghans
7f2e364fa1
legion: added recent releases (#11889) 2019-06-29 07:12:24 -06:00
Justin S
7f6266eef6 r-intervals: new package at 0.15.1 (#11884) 2019-06-28 19:42:55 -04:00
Mark W. Krentel
8aa8b50f91 docs: add example for an external module in packages.yaml
Add an example of a 'modules:' entry for an external package in
packages.yaml.  The 'External Packages' section of 'Build
Customization' mentions 'paths:' and 'modules:' and gives an
example of paths, but not modules.
2019-06-28 11:59:10 -07:00