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Author SHA1 Message Date
Satish Balay
25d63aa44c petsc: add version 3.12.1 [and variant: batch] (#13390) 
* petsc: add version 3.12.1 [and variant: batch]

* fix test_prs_update_old_api errors
 2019-10-23 09:29:28 -05:00
Greg Becker
95a48b27ec env activation: use package defined env setup methods (#13249) 
This PR ensures that environment activation sets all environment variables set by the equivalent `module load` operations, except that the spec prefixes are "rebased" to the view associated with the environment.

Currently, Spack blindly adds paths relative to the environment view root to the user environment on activation. Issue #12731 points out ways in which this behavior is insufficient.

This PR changes that behavior to use the `setup_run_environment` logic for each package to augment the prefix inspections (as in Spack's modulefile generation logic) to ensure that all necessary variables are set to make use of the packages in the environment.

See #12731 for details on the previous problems in behavior.

This PR also updates the `ViewDescriptor` object in `spack.environment` to have a `__contains__` method. This allows for checks like `if spec in self.default_view`. The `__contains__` operator for `ViewDescriptor` objects checks whether the spec satisfies the filters of the View descriptor, not whether the spec is already linked into the underlying `FilesystemView` object.
 2019-10-22 23:27:40 -07:00
Benjamin Fovet
7338730528 gmsh: add version 4.4.1 (#13366) 2019-10-22 18:18:19 -05:00
Frédéric Simonis
ab5135db1c Boost package: Fix iostream autodetect libraries (#12440) 
Boost iostream autodetects the compression libraries libzstd and
liblzma outside of the Spack environment.

This commit disables mentioned libraries. In the future if the
Spack zstd/lzma packages were added as dependencies of the Spack
Boost package, additional work could be done to build Boost with
the Spack-built versions of these libraries.
 2019-10-22 14:25:03 -07:00
Axel Huebl
0f931cfc87 ADIOS2: Document endian_reverse variant (#13226) 
Update the documentation of the `endian_reverse` variant in ADIOS2.
The short description caused some confusion (for me) :-)
 2019-10-22 11:06:06 -05:00
Ruben Di Battista
49291d5a40 git-lfs: Add new version (#13356) 
PS: The old versions do not work: it's likely that they changed git
history on submodules
 2019-10-22 10:45:45 -05:00
Adam J. Stewart
526ee113ea
Default to Python 3.7 (#10319) 
* Default to Python 3

* Fix build with Intel compilers
 2019-10-22 10:22:32 -05:00
Adam J. Stewart
48e8029fb1
Add latest version of py-scikit-learn (#13295) 
* Add latest version of py-scikit-learn

* setup_environment -> setup_build_environment
 2019-10-22 09:16:58 -05:00
Adam J. Stewart
09070b0c9b
Add latest version of npth (#13353) 2019-10-22 09:16:33 -05:00
Adam J. Stewart
2de807d4cb
Add latest version of py-macs2 (#13358) 2019-10-22 09:16:07 -05:00
Adam J. Stewart
e0c310bfd3
Add latest version of py-sphinxcontrib-programoutput (#13359) 2019-10-22 09:15:39 -05:00
Adam J. Stewart
809733c7e6
Restrict parallel build of py-astropy to Python 3 (#13360) 2019-10-22 09:15:11 -05:00
Adam J. Stewart
6cb972a9d2
Add dependency version constraint to libgcrypt (#13351) 2019-10-22 00:43:44 -05:00
Adam J. Stewart
2aa51697c5
Fix configure arg to libassuan (#13350) 2019-10-22 00:43:29 -05:00
Adam J. Stewart
598274a278
Fix configure arg to libksba (#13352) 2019-10-22 00:43:11 -05:00
Adam J. Stewart
fb219cd91c
Add latest version of gnupg (#13349) 2019-10-22 00:42:56 -05:00
Adam J. Stewart
326db657da
Add latest version of patchelf (#13348) 2019-10-22 00:42:40 -05:00
Adam J. Stewart
5e6dc7ab4b
Add latest version of zstd (#13340) 
* Add latest version of zstd

* setup_environment -> setup_build_environment
 2019-10-21 21:45:48 -05:00
Toyohisa Kameyama
98c0d59a0c sniffles: fix zlib header lookup directory. (#13063) 
* sniffles: fix zlib header lookup directory.

* use bamtools and zlib to spack installed package.

* remove unneeded patch.
 2019-10-21 18:38:05 -05:00
noguchi-k
7b62b64b03 elsi:add CMAKE Fortran MODDIR FLAG for Fujitsu compiler (#13244) 
* add CMAKE Fortran MODDIR FLAG for Fujitsu compiler

* elsi:remove extra fix
 2019-10-21 18:28:38 -05:00
t-karatsu
0e3e1836ff arpack-ng: Fixed error that is not compatible with isnan. (#13246) 2019-10-21 18:27:39 -05:00
t-karatsu
26141ad489 bpp-core: Clarify 'isnan' function's namespace. (#13260) 2019-10-21 18:24:10 -05:00
Michael Kuhn
edf56d8ac4 qt: Fix build for newer versions (#13262) 
For some reason, newer versions of qt fail to build because they cannot
find certain system libraries such as libatomic and libdl.

Leaving the qmake compiler set to gcc seems to fix the problem.

Fixes #13221
 2019-10-21 18:23:03 -05:00
健美猞猁
26687988eb New package: Fl (#12877) 2019-10-21 12:04:00 -07:00
Adam J. Stewart
4ab63c17d5
Fix Python 3.8 build on macOS (#13338) 2019-10-21 11:21:47 -05:00
Adam J. Stewart
4d99663ef9
Add latest version of py-cffi (#13322) 
* Add latest version of py-cffi

* setup_environment -> setup_build_environment
 2019-10-21 11:19:48 -05:00
Adam J. Stewart
038f7b1b66
Add latest version of py-numpy (#13307) 
* Add latest version of py-numpy

* setup_environment -> setup_build_environment
 2019-10-21 11:19:05 -05:00
Adam J. Stewart
72177b6e97
Add latest version of py-tables (#13291) 
* Add latest version of py-tables

* setup_environment -> setup_build_environment
 2019-10-21 11:17:52 -05:00
Adam J. Stewart
5090071693
Add latest version of py-torch (#13290) 
* Add latest version of py-torch

* setup_environment -> setup_build_environment
 2019-10-21 11:17:15 -05:00
Adam J. Stewart
f2d91f7e3c
Use specific version of googletest for uriparser (#13339) 2019-10-20 19:08:23 -05:00
Adam J. Stewart
01e64886ac
Tut cannot be built with Python 3.7+ (#13341) 2019-10-20 19:08:04 -05:00
Adam J. Stewart
7f2aacfffc
Add latest version of proj (#13337) 2019-10-20 17:56:37 -05:00
Adam J. Stewart
030b2f8657
Add missing zlib dependency to openjpeg (#13336) 2019-10-20 17:06:43 -05:00
Adam J. Stewart
0cfc88c7d7
openblas: http -> https (#13335) 2019-10-20 17:06:30 -05:00
Adam J. Stewart
785d5d9ca3
mapserver: http -> https (#13334) 2019-10-20 16:31:55 -05:00
Adam J. Stewart
4789ac956c
liblas: http -> https (#13331) 2019-10-20 15:51:35 -05:00
Adam J. Stewart
529d1246f6
libtiff: http -> https (#13332) 2019-10-20 15:51:23 -05:00
Adam J. Stewart
b56e46ece8
libgeotiff: http -> https (#13330) 2019-10-20 15:51:08 -05:00
Adam J. Stewart
f1e595cb61
Add latest version of libyaml (#13333) 2019-10-20 15:50:48 -05:00
Adam J. Stewart
04e999162d
Add latest version of libgcrypt (#13329) 2019-10-20 14:45:00 -05:00
Adam J. Stewart
73c5a9c736
Add latest version of googletest (#13328) 2019-10-20 14:44:43 -05:00
Adam J. Stewart
1673dc5aeb
GEOS: http -> https (#13327) 2019-10-20 14:44:28 -05:00
Adam J. Stewart
c767444f88
Add missing test dependency to py-alabaster (#13325) 2019-10-20 14:44:14 -05:00
Adam J. Stewart
a602ed873d
Add latest version of py-typing (#13287) 2019-10-20 13:18:02 -05:00
Adam J. Stewart
d462749b59
Add missing dependencies to py-apipkg (#13324) 2019-10-20 13:17:44 -05:00
Adam J. Stewart
32879df9d0
Add latest version of py-babel (#13323) 2019-10-20 13:17:28 -05:00
Adam J. Stewart
ea90d2b88a
Add latest version of py-chardet (#13321) 2019-10-20 11:44:12 -05:00
Adam J. Stewart
d2744a072b
Add latest version of py-click (#13320) 2019-10-20 11:43:56 -05:00
Adam J. Stewart
41126d457f
Add latest version of py-execnet (#13317) 2019-10-20 11:21:59 -05:00
Adam J. Stewart
1007a0f7e5
Add latest version of py-decorator (#13318) 2019-10-20 11:21:46 -05:00
Adam J. Stewart
47831a95e1
Add latest version of py-coverage (#13319) 2019-10-20 11:21:32 -05:00
Adam J. Stewart
b421c97110
Add latest version of py-sphinxcontrib-websupport (#13292) 2019-10-20 11:21:03 -05:00
Adam J. Stewart
21d14a19f6
Add latest version of py-sphinx (#13293) 2019-10-20 11:20:46 -05:00
Adam J. Stewart
2268dd9e8f
Add latest version of py-snowballstemmer (#13294) 2019-10-20 11:20:21 -05:00
Adam J. Stewart
a2e7f0e9d2
Add latest version of py-requests (#13296) 2019-10-20 11:19:51 -05:00
Adam J. Stewart
35362adb97
Add latest version of py-pyyaml (#13297) 2019-10-20 11:19:29 -05:00
Adam J. Stewart
b76f1687fb
Add latest version of py-pytest-xdist (#13298) 2019-10-20 11:19:11 -05:00
Adam J. Stewart
f832f12ca6
Add latest version of py-pytest-runner (#13299) 2019-10-20 11:18:55 -05:00
Adam J. Stewart
3a2eeedf20
Add latest version of py-pytest-mock (#13300) 2019-10-20 11:18:39 -05:00
Adam J. Stewart
4d7226e561
Add latest version of py-pytest-httpbin (#13301) 2019-10-20 11:18:04 -05:00
Adam J. Stewart
63dd97f84e
Add latest version of py-pytest-cov (#13302) 2019-10-20 11:17:47 -05:00
Adam J. Stewart
03b1af0d96
Add latest version of py-pysocks (#13303) 2019-10-20 11:17:27 -05:00
Adam J. Stewart
10065b325d
Add latest version of py-pycparser (#13304) 2019-10-20 11:17:11 -05:00
Adam J. Stewart
d4f409ea51
Add latest version of py-psutil (#13305) 2019-10-20 11:16:53 -05:00
Adam J. Stewart
04af812e03
Add latest version of py-pip (#13306) 2019-10-20 11:16:36 -05:00
Adam J. Stewart
c130a2980f
Add latest version of py-mock (#13308) 2019-10-20 11:16:07 -05:00
Adam J. Stewart
0d189e779a
Add latest version of py-markupsafe (#13309) 2019-10-20 11:15:51 -05:00
Adam J. Stewart
30fdff4ff9
Add latest version of py-lxml (#13310) 2019-10-20 11:15:32 -05:00
Adam J. Stewart
51432aa92e
Add latest version of py-jinja2 (#13311) 2019-10-20 11:15:16 -05:00
Adam J. Stewart
d61b5125c5
Add latest version of py-itsdangerous (#13312) 2019-10-20 11:15:01 -05:00
Adam J. Stewart
e05d165f92
Add latest version of py-idna (#13313) 2019-10-20 11:14:46 -05:00
Adam J. Stewart
ac0fee0f34
Add latest version of py-hypothesis (#13314) 2019-10-20 11:14:32 -05:00
Adam J. Stewart
5aea70e733
Add latest version of py-httpbin (#13315) 2019-10-20 11:14:17 -05:00
Adam J. Stewart
db8f83d333
Add latest version of py-flask (#13316) 2019-10-20 11:13:55 -05:00
Adam J. Stewart
de6d53b626
Add latest version of py-torchvision (#13289) 2019-10-20 11:12:43 -05:00
Adam J. Stewart
5995c3f85b
Add latest version of py-typing-extensions (#13288) 2019-10-20 11:12:27 -05:00
Adam J. Stewart
4e2cce2c9f
Add latest version of py-urllib3 (#13286) 2019-10-20 11:11:41 -05:00
Adam J. Stewart
d2202f6d98
Add latest version of py-virtualenv (#13285) 2019-10-20 11:11:23 -05:00
Adam J. Stewart
78942c7840
Add latest version of py-werkzeug (#13284) 2019-10-20 11:11:06 -05:00
Adam J. Stewart
0443581a20
Add py-mypy-extensions package (#13283) 2019-10-20 11:10:40 -05:00
Adam J. Stewart
92a359e4ba
Add py-mypy package (#13282) 2019-10-20 11:10:22 -05:00
Adam J. Stewart
9ac7e098d9
Add py-pytest-forked package (#13281) 2019-10-20 11:10:04 -05:00
Adam J. Stewart
1dc99765e9
Add py-raven package (#13280) 2019-10-20 11:09:44 -05:00
Adam J. Stewart
a6bc0c7ee0
Add py-flake8-import-order package (#13273) 2019-10-20 11:09:23 -05:00
Adam J. Stewart
00f766b248
Add py-sphinxcontrib-devhelp package (#13278) 2019-10-20 11:09:04 -05:00
Adam J. Stewart
c8285da8e7
Add py-sphinxcontrib-applehelp package (#13279) 2019-10-20 11:08:51 -05:00
Adam J. Stewart
d37c95b80b
Add py-sphinxcontrib-htmlhelp package (#13277) 2019-10-20 11:08:34 -05:00
Adam J. Stewart
7bda2fe292
Add py-sphinxcontrib-jsmath package (#13276) 2019-10-20 11:08:16 -05:00
Adam J. Stewart
d4ac57f3a3
Add py-sphinxcontrib-qthelp package (#13275) 2019-10-20 11:07:54 -05:00
Adam J. Stewart
f35bcaf83b
Add py-sphinxcontrib-serializinghtml package (#13274) 2019-10-20 11:07:31 -05:00
Adam J. Stewart
3e18e664fc
Add py-typed-ast package (#13272) 2019-10-20 11:07:01 -05:00
Adam J. Stewart
95b7f31112
Add py-docutils-stubs package (#13271) 2019-10-20 11:06:38 -05:00
Adam J. Stewart
4f56bcc790
Add py-brotlipy package (#13270) 2019-10-20 11:06:18 -05:00
Adam J. Stewart
0fb563f3d9
GCC: fix build on macOS Catalina (#13202) 
* GCC: speed up build

* Add back 3-stage bootstrapping
 2019-10-19 12:18:31 -05:00
Adam J. Stewart
306346356c
brotli: fix darwin install name (#13258) 2019-10-19 12:18:06 -05:00
Axel Huebl
327a7368e9
ADIOS2: Dataspaces, libffi, libfabric (#13230) 
* DataSpaces: 1.8.0

Add a newer release of DataSpaces for ADIOS2.
Also add missing `-fPIC` flags since this is a static library.

* ADIOS2: Dataspaces, libffi, libfabric

Add missing dependencies to ADIOS2. Without explicit control,
those dependencies might get picked up from the system environment
and will cause unstable builds.

* Hide transitive SST dependencies

* ADIOS2: Simplify SST CMake Flags

As proposed by Chuck
 2019-10-18 13:26:56 -07:00
wspear
f9e7bf295c Updated to latest version. Removed dependency on node-js (#13055) 
* Updated to latest version. Removed dependency on node-js

* Refined dependencies

* Added dependencies, including version-specific ones. Re-added 0.9.4.

* Updated py-jupyterhub requirements. Enabled version 0.9.4 and 1.0.0
 2019-10-18 12:53:47 -05:00
Christoph Junghans
b4383825be
fftw: altivec only works for float (#13242) 2019-10-18 10:36:40 -06:00
wspear
40a11c6bf6 Added package py-python-oauth2, a dependency of py-jupyterhub@0.9.4. … (#13140) 
* Added package py-python-oauth2, a dependency of py-jupyterhub@0.9.4. Depends on #13132, #13133 and #13134

* Remove optional dependencies
 2019-10-18 11:29:26 -05:00
Justin S
af3c238c31 interproscan: add 5.38-76.0 (#13253) 2019-10-17 20:52:54 -05:00
Massimiliano Culpo
9ddc98e46a Separate setting build environment and run environment in packages (#11115) 
* Methods setting the environment now do it separately for build and run

Before this commit the `*_environment` methods were setting
modifications to both the build-time and run-time environment
simultaneously. This might cause issues as the two environments
inherently rely on different preconditions:

1. The build-time environment is set before building a package, thus
the package prefix doesn't exist and can't be inspected

2. The run-time environment instead is set assuming the target package
has been already installed

Here we split each of these functions into two: one setting the
build-time environment, one the run-time.

We also adopt a fallback strategy that inspects for old methods and
executes them as before, but prints a deprecation warning to tty. This
permits to port packages to use the new methods in a distributed way,
rather than having to modify all the packages at once.

* Added a test that fails if any package uses the old API

Marked the test xfail for now as we have a lot of packages in that
state.

* Added a test to check that a package modified by a PR is up to date

This test can be used any time we deprecate a method call to ensure
that during the first modification of the package we update also
the deprecated calls.

* Updated documentation
 2019-10-17 10:17:21 -07:00
wspear
93c34039e4 python-editor: added new package at v1.0.4 (#13126) 2019-10-17 08:46:34 +02:00
Christoph Junghans
6cd997e743
eospac: avoid conflict with linux's getopt (#13241) 
* eospac: avoid conflict with linux's getopt

* Update package.py
 2019-10-16 18:46:26 -07:00
Jeffrey Salmond
e17df2e8f5 add python version 3.8.0 (#13218) 2019-10-16 14:42:36 -07:00
Christoph Junghans
b0543005b2
expat: don't pick up external docbook (#13228) 2019-10-16 05:59:51 -07:00
Jeffrey Salmond
f08f4201c7 add latest version of vim (#13203) 2019-10-15 20:43:03 -07:00
Satish Balay
5ea0eed287 hypre: add version 2.18.1 (#13224) 2019-10-15 13:05:51 -07:00
Axel Huebl
dc3a9618a0 ADIOS2: Default no Python (#13220) 
Turn off the python variant by default.
 2019-10-15 14:55:45 -04:00
Andrey Prokopenko
41e7e5693e arborx: update v0.8-beta to v0.8-beta2 (#13143) 
- Require Kokkos with c++14
- Update the case of CMake options
 2019-10-15 11:19:16 +02:00
Andrey Prokopenko
ce5333c1fd kokkos: add cxxstd variant (#13142) 2019-10-15 11:14:37 +02:00
Tim Haines
27a339eeb2 Add version 0.177 of elfutils (#13129) 
* Add version 0.177

* Fix spacing
 2019-10-14 22:22:11 -07:00
t-karatsu
8f69c9d334 ntpoly: Define module directry when compiling with Fujitsu compiler. (#13120) 
* ntpoly: Define module directry when compiling with Fujitsu compiler.

* Delete quotes.
 2019-10-14 22:20:52 -07:00
Massimiliano Culpo
5cd28847e8 filter_file uses "surrogateescape" error handling (#12765) 
From Python docs:
--
'surrogateescape' will represent any incorrect bytes as code points in
the Unicode Private Use Area ranging from U+DC80 to U+DCFF. These
private code points will then be turned back into the same bytes when
the surrogateescape error handler is used when writing data. This is
useful for processing files in an unknown encoding.
--

This will allow us to process files with unknown encodings.

To accommodate the case of self-extracting bash scripts, filter_file
can now stop filtering text input if a certain marker is found. The
marker must be passed at call time via the "stop_at" function argument.
At that point the file will be reopened in binary mode and copied
verbatim.

* use "surrogateescape" error handling to ignore unknown chars
* permit to stop filtering if a marker is found
* add unit tests for non-ASCII and mixed text/binary files
 2019-10-14 20:35:14 -07:00
Greg Becker
3f46f03c83
bugfix: install --only dependencies works in env (#13090) 
* bugfix: install --only dependents works in env

includes regression testing
 2019-10-14 17:50:38 -07:00
Satish Balay
a63e64f1c4
py-petsc4py: add version 3.12.0 (#13209) 
* py-petsc4py: add version 3.12.0

* fix typo wrt maintainer
 2019-10-14 15:27:28 -05:00
William F Godoy
dafee9df31 Complete cleanup of the adios2 package configuration (#13107) 
Provide up to date specs for build options
Remove non-production versions
Format using autopep8 and flake8
Separate cmake options in adios2 2.4.0 version
Keep default as True as much as possible
Support for Python 2 and 3 for adios2 versions <= 2.4.0
Starting v2.5.0 only Python 3 is supported
Addressing review suggestions
 2019-10-14 12:47:55 -07:00
Hadrien G
be8f8856ce New ACTS versions (#12484) 
* Add new ACTS releases

* Update ACTS dependency requirements

* We can actually be more specific here

* The material plugin is gone as of ACTS v0.10.0

* Add 0.10.4 release

* Remove material mapping plugin

It was merged into core as of 0.10.x, and given ACTS' youth it is unlikely to have actual users at this point in time.
 2019-10-14 14:01:53 -05:00
wspear
48b7370265 py-pymongo: added new package at version 3.9.0 (#13132) 2019-10-14 20:57:54 +02:00
wspear
8a1e5f68f4 py-alembic: fixed missing dependencies. (#13127) 2019-10-14 10:53:01 +02:00
Jeffrey Salmond
2bb1bae2ae dialign: added new package at version 2.2.1 (#13130) 
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
 2019-10-14 10:49:31 +02:00
Justin S
c851cfd122 py-smart-open: new package at 1.8.4 (#13135) 2019-10-14 10:42:49 +02:00
wspear
bdcf9ba5cd py-python-memcached: added new package at version 1.59 (#13133) 
* Added package py-python-memcached, a dependency of python-oauth2

* Fixed line lengths
 2019-10-14 10:35:41 +02:00
wspear
04af0eb5a2 py-redis: added new package at version 3.3.8 (#13134) 2019-10-14 10:34:37 +02:00
Adam J. Stewart
27ad28e51a
Add py-kiwisolver 1.1.0 (#13170) 2019-10-13 22:26:49 -07:00
Satish Balay
846daa0404 amrex: add version 19.10 (#13206) 2019-10-13 19:57:11 -05:00
Satish Balay
20c2fa62aa slepc: use spack specified python in configure (#13207) 2019-10-13 19:56:27 -05:00
Satish Balay
1f29785b88 omega-h: add version 9.29.0 (#13208) 2019-10-13 19:54:41 -05:00
Adam J. Stewart
ce6bf5fba1
Add apr-util 1.6.1 (#13145) 2019-10-13 19:52:58 -05:00
Adam J. Stewart
c121ddb300
Add apr 1.7.0 (#13146) 2019-10-13 19:52:40 -05:00
Adam J. Stewart
7b21ac3188
Add bison 3.4.2 (#13147) 2019-10-13 19:52:10 -05:00
Adam J. Stewart
30c5f88255
Add freetype 2.10.1 (#13149) 2019-10-13 19:51:53 -05:00
Adam J. Stewart
518a7c5bb9
Add libpng 1.6.37 (#13153) 2019-10-13 19:51:04 -05:00
Adam J. Stewart
b3fcfc1cb2
Add lz4 1.9.2 (#13155) 2019-10-13 19:50:44 -05:00
Adam J. Stewart
48cd455cc1
Add mercurial 5.1.2 (#13156) 2019-10-13 19:50:19 -05:00
Adam J. Stewart
e5d1810bec
Add subversion 1.12.2 (#13158) 2019-10-13 19:49:53 -05:00
Adam J. Stewart
143afbd3a0
Add py-attrs 19.2.0 (#13163) 2019-10-13 19:49:29 -05:00
Adam J. Stewart
4b2b548981
Add py-cython 0.29.13 (#13166) 2019-10-13 19:49:07 -05:00
Adam J. Stewart
2884a862e8
Add py-docutils 0.15.2 (#13167) 2019-10-13 19:47:25 -05:00
Adam J. Stewart
83a96755ef
Add py-joblib 0.14.0 (#13169) 2019-10-13 19:47:07 -05:00
Adam J. Stewart
e72c20bc47
Add py-more-itertools 7.2.0 (#13171) 2019-10-13 19:46:13 -05:00
Adam J. Stewart
d61743561b
Add py-pillow 6.2.0 (#13175) 
* Add py-pillow 6.2.0

* Flake8 fix
 2019-10-13 19:45:23 -05:00
Adam J. Stewart
ec3b891714
Add py-py 1.8.0 (#13177) 2019-10-13 19:44:08 -05:00
Adam J. Stewart
f7b3524765
Add py-pyflakes 2.1.1 (#13178) 2019-10-13 19:43:50 -05:00
Adam J. Stewart
1276a182b6
Add py-pygments 2.4.2 (#13179) 2019-10-13 19:43:34 -05:00
Adam J. Stewart
8c2096aac5
Add py-pyparsing 2.4.2 (#13180) 2019-10-13 19:43:14 -05:00
Adam J. Stewart
d6f6c41d58
Add py-pytz 2019.3 (#13182) 2019-10-13 19:42:55 -05:00
Adam J. Stewart
2835e9bf17
Add py-setuptools-scm 3.3.3 (#13183) 2019-10-13 19:42:35 -05:00
Adam J. Stewart
ea4f9ebbde
gmp: fix make check on catalina (#13201) 2019-10-12 20:21:45 -05:00
Adam J. Stewart
08d448bc54
mpfr: fix make check on catalina (#13200) 2019-10-12 20:21:23 -05:00
Adam J. Stewart
41e0b069d7
Fix external numpy package support (#13197) 2019-10-12 20:21:03 -05:00
Adam J. Stewart
3df6b05c04
Add py-setuptools 41.4.0 (#13184) 2019-10-12 20:20:41 -05:00
Adam J. Stewart
ebfd06d248
Add py-pytest 5.2.1 (#13181) 2019-10-12 20:18:31 -05:00
Adam J. Stewart
328583decc
Add py-pluggy 0.13.0 (#13176) 2019-10-12 20:14:12 -05:00
Adam J. Stewart
2ced690efb
Add py-pandas 0.25.1 (#13174) 2019-10-12 20:12:41 -05:00
Adam J. Stewart
50e9dc5e2e
Add py-packaging 19.2 (#13173) 2019-10-12 20:12:19 -05:00
Adam J. Stewart
101c287e7b
Add py-numexpr 2.7.0 (#13172) 2019-10-12 20:11:57 -05:00
Adam J. Stewart
db4d06f953
Add py-importlib-metadata 0.23 (#13168) 2019-10-12 20:08:33 -05:00
Adam J. Stewart
1d7eab10ac
Add py-certifi 2019.9.11 (#13165) 2019-10-12 20:05:00 -05:00
Adam J. Stewart
a59e77e374
Add missing test dependency to py-bottleneck (#13164) 2019-10-12 20:04:34 -05:00
Adam J. Stewart
1078dfb6cc
Add py-atomicwrites 1.3.0 (#13162) 2019-10-12 20:03:01 -05:00
Adam J. Stewart
b18e4ad142
Add missing libiconv dependency to wget (#13161) 2019-10-12 20:02:41 -05:00
Adam J. Stewart
7a43817205
Add missing gettext dependency to watch (#13160) 2019-10-12 20:02:24 -05:00
Adam J. Stewart
6beb5da497
Fix valgrind concretization on macOS (#13159) 2019-10-12 20:02:05 -05:00
Adam J. Stewart
22e9aafe5f
Add SCons 3.1.1 (#13157) 2019-10-12 20:00:28 -05:00
Adam J. Stewart
73b2b2a70f
Add LLVM OpenMP 9.0.0 (#13154) 2019-10-12 19:57:36 -05:00
Adam J. Stewart
94d57446c7
Add libjpeg-turbo 2.0.3 (#13152) 2019-10-12 19:55:44 -05:00
Adam J. Stewart
1e2754f0d2
Add help2man 1.47.11 (#13151) 2019-10-12 19:55:14 -05:00
Adam J. Stewart
681c5bcceb
Add graphviz 2.42.2 (#13150) 2019-10-12 19:54:46 -05:00
Adam J. Stewart
0a8be4e311
Add cmake 3.15.4 (#13148) 2019-10-12 19:52:47 -05:00
Adam J. Stewart
18ab375968
Add utf8proc package (#13144) 2019-10-12 19:40:05 -05:00
Nichols A. Romero
ebb5ce4b69 F18 Oct2019 Minor Update (#13192) 
* Minor clean-up of package information.

* Add variants, fix dependencies, and add conflicts for compilers that do not support C++17.

* Correct dependency type for CMake.
 2019-10-12 12:30:43 -05:00
Todd Gamblin
64bdc3251f checksums: enforce that all mainline packages use sha256 checksums 
- Add a test that verifies checksums on all packages

- Also add an attribute to packages that indicates whether they need a
  manual download or not, and add an exception in the tests for these
  packages until we can verify them.
 2019-10-12 07:19:43 -07:00
Todd Gamblin
8cbd349cb4 checksums: fix packages that needed new download locations 
Some packages had incorrect checksums because they needed to be
downloaded from a new place or the package needed tweaking somehow.
These packages to sha256 and the new checksums have been verified by
fetching over https.
 2019-10-12 07:19:43 -07:00
Todd Gamblin
45a9cfcdd7 packages: remove packages that are no longer fetchable 
These packages have either been retired or are no longer retrievable from
any site we can find. They also aren't needed by other packages, so we're
removing them from Spack.

- allinea-reports: is now arm performance reports
- globus-toolkit: retired, globus is now a paid service.
- uberftp: used globus-toolkit, github site is retired.
- mpiblast: site is dead; no longer fetchable.
- py-mxnet: site and github are gone
- soap2, soapindel, soapsnp: site is gone, unfetchable
- arlecore: could not verify md5 securely
 2019-10-12 07:19:43 -07:00
Todd Gamblin
00f91ab22b checksums: Remove or fix up unfetchable or unverifiable md5 versions 
This commit either removes remaining md5 checksums, or it replaces them
with sha256 checksums verified by fetching over https.
 2019-10-12 07:19:43 -07:00
Todd Gamblin
62927654dd checksums: use sha256 checksums everywhere 
We'd like to use a consistent checksum scheme everywhere so that we can:

    a) incorporate archive checksums into our specs and have a
       consistent hashing algorithm across all specs.

    b) index mirrors with a consistent type of checksum, and not one that
       is dependent on how spack packages are written.

- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
 2019-10-12 07:19:43 -07:00
Matthew LeGendre
87fa7c15fc Add adiak package, version 0.1.1 2019-10-11 21:22:33 -07:00
Massimiliano Culpo
fd97f5c491
Fixed constraints in recipes for packages that depends on fftw (#13125) 2019-10-11 07:55:15 +02:00
Nichols A. Romero
884964d551 Fix f18 install method (#13123) 
* Install method is broken and not needed. Built-in install method works fine. Just delete.

* Change version to master.
 2019-10-10 21:52:29 -05:00
Adam J. Stewart
7af8c206ac
Add patches and missing dependency to bash (#13084) 2019-10-10 12:48:49 -05:00
Adam J. Stewart
c131a725af
Add mpfr 4.0.2 (#13091) 2019-10-10 12:48:32 -05:00
Adam J. Stewart
06dffaefed
Add tar 1.32 (#13099) 2019-10-10 12:48:16 -05:00
Jannek Squar
02564ef4ab sublime-text: New version, adapt install process (#13074) 
* Added new version, reworked installation process

* Removed explicit addition to PATH
 2019-10-10 12:13:00 -05:00
Adam J. Stewart
e925dbcefe
Add expat 2.2.9 (#13085) 2019-10-10 12:10:48 -05:00
Adam J. Stewart
f940e8616c
Add gettext 0.20.1 (#13086) 2019-10-10 12:10:19 -05:00
Adam J. Stewart
4d2b300da0
Add isl 0.21 (#13087) 2019-10-10 12:10:03 -05:00
Adam J. Stewart
15d7e2efd5
Add libiconv 1.16 (#13088) 2019-10-10 12:09:46 -05:00
Adam J. Stewart
c570c09cbf
Add libsigsegv 2.12 (#13089) 2019-10-10 12:09:28 -05:00
Adam J. Stewart
db8178d99a
Add latest openssl releases (#13092) 2019-10-10 12:09:02 -05:00
Adam J. Stewart
ace11d857f
Add latest Perl releases (#13093) 2019-10-10 12:08:40 -05:00
Adam J. Stewart
f35c845330
Add pkgconf 1.6.3 (#13094) 2019-10-10 12:08:19 -05:00
Adam J. Stewart
0cf6980437
Add readline 8.0 (#13095) 2019-10-10 12:07:48 -05:00
Adam J. Stewart
4a5bdd1afd
gdbm: https -> http (#13096) 2019-10-10 12:07:24 -05:00
Adam J. Stewart
01b87259e2
ncurses: https -> http (#13097) 2019-10-10 12:07:05 -05:00
Adam J. Stewart
f904e47c4e
Add sqlite 3.30.0 (#13098) 2019-10-10 12:06:44 -05:00
Satish Balay
dd64bdc313 hypre: add compatibility patch for petsc/mfem build failures (#13116) 2019-10-10 09:11:15 -05:00
wspear
a042a7e91e Added new versions to py-tornado (#13080) 
* Added new versions to py-tornado

* Removed all but the latest new version
 2019-10-10 09:06:01 -05:00
Matthias Wolf
e69efded32 py-line-profiler: add 2.1.2, re-run cython if needed (#13102) 
* py-line-profiler: add 2.1.2, re-run cython if needed

See rkern/line_profiler#166.

* Update var/spack/repos/builtin/packages/py-line-profiler/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
 2019-10-10 11:34:50 +02:00
Rob Latham
d93cacfa5c libfabric: new upstream release 1.8.1 (#13053) 2019-10-09 22:24:17 -05:00
wspear
c8289fcd90 Added latest versions of SQLAlchemy 1.3.X, 1.2.X and 1.1.X (#13078) 
* Added latest versions of SQLAlchemy 1.3.X, 1.2.X and 1.1.X

* Added missing dependencies
 2019-10-09 22:23:55 -05:00
wspear
e7e67fdfec Added latest versions to py-traitlets (#13079) 
* Added latest versions to py-traitlets

* Added missing dependencies
 2019-10-09 22:23:33 -05:00
Francesco Di Natale
4ef64b64d1 Add new versions of py-maestrowf (#13081) 
* Addition of 1.1.3 and 1.1.4

* Addition of conditional enum-34 installation.

* Update var/spack/repos/builtin/packages/py-maestrowf/package.py

Addition of versioning for pyyaml.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Addition of enum34 back to older versions 1.1.3 and below.
 2019-10-09 22:23:19 -05:00
Michael Kuhn
2e2b1a5e02 qt: Add 5.13.1 and missing zlib flags (#13109) 2019-10-09 22:22:52 -05:00
Michael Kuhn
469bef880a mysql: Add missing dependencies (#12717) 
This also changes the default for cxxstd from 98 to 14 because (at
least) newer versions of mysql do not compile with 98 (tested with
gcc@9).
 2019-10-09 14:45:31 -05:00
Toyohisa Kameyama
b0bf528ab3 perl-perlio-gzip: add zlib dependency. (#13060) 2019-10-08 20:51:39 -05:00
Toyohisa Kameyama
529d0f3e37 psmc: add zlib dependency. (#13061) 2019-10-08 20:51:04 -05:00
Toyohisa Kameyama
f1e1693a6a seqprep: add zlib dependency. (#13062) 2019-10-08 20:50:51 -05:00
Toyohisa Kameyama
fdc91a1705 tabix: add zlib dependency. (#13064) 2019-10-08 20:48:37 -05:00
wspear
2e4bcf223c Added py-certipy package. Dependency of py-jupyterhub. (#13068) 
* Added py-certipy package. Dependency of py-jupyterhub.

* Changed url to pypi
 2019-10-08 20:48:11 -05:00
Nichols A. Romero
2794e52ddd QMCPACK Oct2019 fix buglets (#13069) 
* Support different CMake build types correctly.

* LIBXML2 variables no longer used.

* Fix E501 as part of https://github.com/spack/spack/pull/13069
 2019-10-08 20:46:15 -05:00
wspear
8de453af54 Fixed hash of version .0.5 and added latest version (.0.7.1) (#13077) 2019-10-08 20:43:44 -05:00
Mark Olesen
e3f69f8ce6 Build older openfoam (#13071) 
* adjust building of OpenFOAM 1806 and earlier

- spack now unpacks into spack-src, but earlier OpenFOAM versions
  still expect particular directory names (eg, OpenFOAM-v1806).

  Resolve by creating a symlink during patching.

* replace openfoam 1806 patch with URL version
 2019-10-08 20:42:44 -05:00
wspear
6a99b7e262 Added py-pamela package. Dependency of py-jupyterhub. (#13075) 2019-10-08 20:08:32 -05:00
George Hartzell
4377cc7066 Add headsup note re cryptsetup patch for v2.2.2 (#13076) 2019-10-08 20:07:38 -05:00
Phil Carns
66b9009a07 pmdk: added v 1.7 (#13067) 2019-10-08 09:19:27 +02:00
Oliver Breitwieser
9600eb4f5a py-apipkg: Fix mix up of checksums (#13066) 
Change-Id: Ibae329c5a6cf7e3741a879612da523e11e3b0ab9
 2019-10-07 20:55:22 -05:00
Adam J. Stewart
c8c795e7db watch: added new package (#13044) 2019-10-07 11:11:17 +02:00
Paul
7d0e7efabb Added go 1.13.1 and 1.12.10 (#12977) 2019-10-06 20:22:05 -05:00
Denis Davydov
79bd6bbd04 gnuplot: add 5.2.7 and fix qt dep (#13058) 2019-10-06 14:28:34 -05:00
Matthias Wolf
3d247d9567 freeimage: new package (#13049) 
* freeimage: new package

* Address comments.

* Whitespace
 2019-10-06 09:20:29 -05:00
Ruben Di Battista
ba72114ba2 unrar: Add package (#12908) 2019-10-06 09:16:25 -05:00
Oliver Breitwieser
f34162a5b8 Add missing py-contextlib2 (#13056) 
Change-Id: I8e0a90d4aa2c9f46230a6fe35ce5f4fa44672faf
 2019-10-06 09:15:29 -05:00
Denis Davydov
070a536e49 qt: help pick up dependencies (#11172) 
* qt: help pick up dependencies

* qt: add 5.12.5
 2019-10-05 21:13:38 -05:00
t-karatsu
c6b8d79ea6 Package/fujitsu mpi (#12807) 
* fujitsu-mpi: commit new package

* Add homepage.

* * Modified the MPI commands to a simple form.
* Unnecessary processing has been deleted.

* Add conflict for all compilers except the Fujitsu compiler.

* Fix typo.

* Delete versions.

* Delete conditions for specifying the Fujitsu compiler.
 2019-10-05 20:58:43 -05:00
Adam J. Stewart
608f732101
expect: fix darwin install name (#13042) 
* expect: fix darwin install name

* Fix expect binary as well
 2019-10-05 20:37:44 -05:00
Teodor Nikolov
e78ca66087 New package: cxxopts (#13035) 
* New package: cxxopts

* Use +unicode instead of unicode=True

- Make the unicode option more explicit

* [cxxopts] Fix white space warnings
 2019-10-05 20:36:59 -05:00
Adam J. Stewart
c45ecafd71 procps: new package (#13043) 2019-10-05 11:39:55 +02:00
Federico Ficarelli
a362cf5ff6 grpc: new package (#13054) 
* Add grpc@1.23.1

* Let version in url match actual one
 2019-10-04 18:42:09 -05:00
Andreas Baumbach
e366f6ba39 llvm: update link to the document explaining codesign (#13047) 
Change-Id: I01242cbb43b0c62a659739a5d7e9d998dd27e794
 2019-10-04 13:31:43 -07:00
Robert Maynard
b1cdf8bd57 Update the VTK-m package with better defaults and cuda corrections (#12850) 2019-10-04 15:12:58 -04:00
Cody Balos
3cb4547348 superlu-dist: add openmp variant (#13052) 2019-10-04 13:48:56 -05:00
Toyohisa Kameyama
cb89949018 migrate: add zlib dependency. (#13039) 
* migrate: add zlib dependency.

* flake8.

* autotools related tools change to build.
 2019-10-04 13:14:09 -05:00
Felix Thaler
437236781d LLVM 9.0.0 (#13050) 2019-10-04 09:56:12 -07:00
Massimiliano Culpo
2cd800306d fftw: simplify the recipe and make use of specific targets (#12889) 
* fftw: grouped precisions in a single variant

* fftw: simd options are now based on target features and not on variants

* fftw: simplified computing the selected precisions
 2019-10-03 22:32:42 -05:00
t-karatsu
46e319ecd4 boost: Use gcc toolset for bootstrap with Fujitsu compiler. (#12876) 2019-10-03 22:20:55 -05:00
Toyohisa Kameyama
938bae1ab6 graphmap: add zlib dependency. (#13031) 2019-10-03 22:20:13 -05:00
Toyohisa Kameyama
b89fa3e01a fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030) 2019-10-03 22:19:58 -05:00
Toyohisa Kameyama
4046e10b95 hapcut2: add zlib dependency. (#13032) 2019-10-03 22:19:43 -05:00
Toyohisa Kameyama
2233a7b493 liblbxutil: Add zlib dependency. (#13033) 2019-10-03 22:19:22 -05:00
Toyohisa Kameyama
bb1d0ff6fb metabat: Add zlib and ncurses dependency. (#13034) 2019-10-03 22:18:55 -05:00
Toyohisa Kameyama
58a64f69e7 muse: add zlib dependency. (#13040) 2019-10-03 22:18:27 -05:00
Toyohisa Kameyama
c97be22ff5 ngmlr: add zlib dependency. (#13041) 2019-10-03 22:18:12 -05:00
Andreas Baumbach
4e7ea627c8 fix ipykernel dependency, newer versions are python3-only (#13019) 
* fix ipykernel dependency, newer versions are python3-only

* Update var/spack/repos/builtin/packages/py-ipykernel/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-ipykernel/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
 2019-10-03 22:17:16 -05:00
George Hartzell
882843974b Update cctools to v7.0.18 (#13037) 
- add version/checksum info for v7.0.18
- update checksum for v6.1.1 to use sha256, while I have the editor
  open...
 2019-10-03 18:57:20 -05:00
Owen Solberg
bef702d0f3 updated manta checksum (#13038) 2019-10-03 18:23:47 -05:00
Adam J. Stewart
69acb024a5
Add py-flye 2.6 (#13025) 2019-10-03 10:32:00 -05:00
Adam J. Stewart
dac34147c0 Add EasyBuild 4.0.0 (#13024) 
* Add EasyBuild 4.0.0

* Update homepage, remove no longer required deps

* Replace version ranges with fixed versions
 2019-10-03 16:48:42 +02:00
Chuck Atkins
b973f038fd
Update ECP Data & Vis SDK packages (#13027) 
* ecp-io-sdk: Add faodel and sort variants

* ecp-viz-sdk: Re-enable catalyst, sort variants, turn on by default

* ecp-io-sdk and ecp-viz-sdk: Fix dependency variants
 2019-10-03 10:05:02 -04:00
Massimiliano Culpo
76b9c56110 Remove support for generating dotkit files (#11986) 
Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.

A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.

* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
 2019-10-02 22:15:01 -07:00
Miroslav Stoyanov
b11984767b added tasmanian version 7.0 to spack (#13003) 2019-10-02 18:35:49 -05:00