Commit graph

9102 commits

Author SHA1 Message Date
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