Commit graph

17925 commits

Author SHA1 Message Date
Jen Herting
fd3dbb2493
New package: py-torchfile (#19481)
* [py-torchfile] created template

* [py-torchfile] set python versions

* [py-torchfile] depends on py-numpy

* [py-torchfile] fixed url format

* [py-torchfile] added homepage and description. removed fixmes

* [py-torchfile] fixed url format
2020-10-22 16:36:34 -05:00
Massimiliano Culpo
4ec404dfc0
Add scratch module roots to test configuration (#19477)
fixes #19476

Module file content is written to file in a
temporary location and read back to be analyzed
by unit tests.

The approach to patch "open" and write to a
StringIO in memory has been abandoned, since
over time other operations insisting on the
filesystem have been added to the module file
generator.
2020-10-22 13:59:39 -07:00
Jen Herting
d6f19eeed2
[py-pyarrow] cuda and orc support (#19445)
* [py-pyarrow] telling setup.py that we want cuda support

* [py-pyarrow] added orc variant

* [py-pyarrow] passing the orc variant down the line

* [py-pyarrow] added variant description
2020-10-22 15:19:16 -05:00
Jen Herting
0baaeec58d
Arrow: add orc support (#19442)
* [arrow] added orc support variant

* [arrow] depends on orc

* [arrow] added explicit disable of features for variants
2020-10-22 15:18:54 -05:00
daichi-nishi
5407a74f2b
modified:var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py (#19459) 2020-10-22 15:03:09 -05:00
daichi-nishi
680c0ac06d
modified : var/spack/repos/builtin/packages/ppopen-appl-bem/package.py (#19460) 2020-10-22 15:02:41 -05:00
daichi-nishi
fb82810d50
ppopen-appl-dem-util:change download site to github. (#19461)
* modified:var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py

* modified:var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py:deleted whitespace
2020-10-22 15:02:11 -05:00
lorddavidiii
6a82b2260f
Add opencl-headers and use ocl-icd as OpenCL provider (#19463)
* ocl-icd: fix build problems

* New package: opencl-c-headers

* New package: opencl-clhpp

* New bundled package: opencl-headers

- bundle C and C++ header files

* ocl-icd: Add +headers variant to use this as opencl provider

* ocl-icd: add new upstream release 2.2.13

* ocl-icd: add asciidoc-py3 and xmlto dependency needed for manpage generation

* ocl-icd and opencl-headers provides OpenCL 3.0

- also add more explicit version providing for older ocl-icd versions

* opencl-headers: add maximum of supported opencl versions for all versions

* opencl-headers: there aren't final releases with OpenCL 3.0
2020-10-22 15:00:40 -05:00
daichi-nishi
7c78d15e74
modified:var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py (#19464) 2020-10-22 14:57:37 -05:00
dunatotatos
61a7900573
Restrict Python version for Strelka to Python 2. (#19466)
Fix #19465
2020-10-22 14:56:54 -05:00
Jen Herting
32a68fbbd4
New Package: py-fastrlock (#19467)
* [py-fastrlock] created template

* [py-fastrlock] added dependencies and setting --with-cython

* [py-fastrlock] added homepage and description. removed fixmes
2020-10-22 14:55:14 -05:00
Andrew W Elble
e4ce123ddf
hercules (#19434) 2020-10-22 15:20:30 -04:00
darmac
0d46531791
Add new package: py-cantoolz (#18812)
* Add new package: py-cantoolz

* refine depends
2020-10-22 14:11:06 -05:00
Jen Herting
e1e0bbb4cb
New package: orc (#19441)
* [orc] created template

* [orc] depends on maven

* [orc] building with -fPIC

* [orc] fixed name of c flags option

* [orc] depends on openssl

* [orc] added dependencies and disableing installing vendored libs

* [orc] disabling hdfs

* [orc] depending on specific versions of dependencies

* [orc] no building of third party libs

* [orc] helping cmake find the dependencies

* [orc] disabling features that would require static protobuf libraries

* [orc] dependency versions are ranges

* [orc] added homepage and description. removed fixmes

* [orc] flake8

* [orc] switching to compilier indipendent code
2020-10-22 14:05:18 -05:00
Jen Herting
bd0b53f4fb
[treelite] added python and protobuf support (#19444)
* [treelite] added protobuf variant

* [treelite] adding python support

* [treelite] disable protobuf by default

* [treelite] flake8

* [treelite] reordered phases
2020-10-22 14:03:05 -05:00
Justin S
121a8a5cd9
transrate: new package at 1.0.3 (#19295)
* transrate: new package at 1.0.3

* transrate: add macOS binary distribution

* transrate: fix platform switching
2020-10-22 14:01:49 -05:00
Justin S
db167897f4
py-tomlkit: new package at 0.7.0 (#19450)
* py-tomlkit: new package at 0.7.0

* py-tomlkit: add dependencies
2020-10-22 14:01:14 -05:00
Andrew W Elble
f4049a71c2
New package: py-labours (#19433)
* py-labours

* fix dep version constraints
2020-10-22 14:14:57 -04:00
Andrew W Elble
b77279e9cc
py-seriate (#19432) 2020-10-22 12:36:12 -04:00
Andrew W Elble
745875b008
New package: py-or-tools (#19431)
* py-or-tools

* python is, of course, a runtime dep

* more dependency fixes, use extends.

* protobuf is >= 3.12.2
2020-10-22 11:59:48 -04:00
darmac
646af81263
r-sf: fix build error (#19386)
* r-sf: fix build error

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-22 10:57:28 -05:00
iarspider
601636b755
Add herwig3 (#19406)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add herwig3

* Prepare fixes based on MR (needs checking)

* Set all dependencies (except python) as build-type

* OK now

* Move import to the top of the file

* Fix dependency name

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-22 10:56:53 -05:00
Andrew W Elble
019205ec7a
cbc (#19419) 2020-10-22 11:20:19 -04:00
Andrew W Elble
7935ec501f
cgl (#19420) 2020-10-22 10:47:23 -04:00
Andrew W Elble
caab89b9c9
New package: py-lifelines (#19429)
* py-lifelines

* also carry the newer version of lifelines

* 0.25.5 needs python >= 3.6
2020-10-21 22:33:02 -05:00
Andrew W Elble
e800b6029f
clp (#19418) 2020-10-21 22:32:44 -05:00
iarspider
74e93aff41
Add Gosam (#19401)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add gosam

* Flake-8

* Flake-8

* Delete gosam-1.2.4.patch

Remove patch

* Remove patch from recipe

* Changes from MR

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 22:32:29 -05:00
Todd Gamblin
8060cca494
tests: increase tolerance of termios tests (#19456)
Synchronization on GitHub macOS runners seems to be very slow, and
frequently the foreground/background tests fail due to the race this
causes. This increases the tolerance for slowness a bit more, to allow up
to 4 spurious output lines in the tests.

This should hopefully result in no more false negatives on these tests
for macOS on GitHub.
2020-10-21 18:12:48 -07:00
Tamara Dahlgren
e78764caa1
Added _poll_lock exception tests (#19446) 2020-10-21 17:32:04 -07:00
Tom Payerle
94221fa225
new package: py-tinyarray (#19454) 2020-10-21 19:28:34 -05:00
Andrew W Elble
ec068f8070
New package: py-autograd-gamma (#19426)
* py-autograd-gamma

* missing dependencies
2020-10-21 19:19:46 -05:00
iarspider
27211ba90b
Add Njet (#19399)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add NJet

* flake-8

* Flake-8

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 19:16:29 -05:00
iarspider
399ca3b671
Add qgraf (#19404)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add qgraf

* Update package.py

Changes from review

* Changes from MR

* Fix for URLs containing @ symbol

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-21 19:16:11 -05:00
Andrew W Elble
5a0303860d
osi (#19424) 2020-10-21 19:15:34 -05:00
Todd Gamblin
16e75ecac0
shell support: make which spack output intelligible (#19256)
Zsh and newer versions of bash have a builtin `which` function that will
show you if a command is actually an alias or a function. For functions,
the entire function is printed, and our `spack()` function is quite long.
Instead of printing out all that, make the `spack()` function a wrapper
around `_spack_shell_wrapper()`, and include some no-ops in the
definition so that users can see where it was created and where Spack is
installed.

Here's what the new output looks like in zsh:

```console
$ which spack
spack () {
	: this is a shell function from: /Users/gamblin2/src/spack/share/spack/setup-env.sh
	: the real spack script is here: /Users/gamblin2/src/spack/bin/spack
	_spack "$@"
	return $?
}
```

Note that `:` is a no-op in Bourne shell; it just discards anything after
it on the line. We use it here to embed paths in the function definition
(as comments are stripped).
2020-10-21 17:04:42 -07:00
Todd Gamblin
93e7267dcc
unzip: fix build for XCode 12 on macosx (#19453)
- [x] `build_targets` should use `macosx` on macOS, `generic` on other systems
- [x] enable `LARGE_FILE_SUPPORT` by default
2020-10-21 15:31:29 -07:00
iarspider
a1278bfba0
Add Madgraph 2.8.1 (#19400)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Update madgraph to 2.8.1

* Changes from MR

* Changes from MR

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 17:13:00 -05:00
Andrew W Elble
935aa06838
New package: py-fastdtw (#19427)
* py-fastdtw

* cython is buildtime dep
2020-10-21 17:09:41 -05:00
G-Ragghianti
d61c236db4
Lapackpp package update (#19447)
* Updated blaspp package

* Modified lapackpp for newest release

* Formatting

* Updates to lapackpp package for new version

* Added dependency on cblas

* Removed cblas dependency

* updated to lapackpp

* Added new version for blaspp and lapackpp

* Removed debugging output

* Converted version matching logic for for loop
2020-10-21 17:09:25 -05:00
Justin S
05df3c3225
py-drmaa: new package at 0.7.9 (#19451) 2020-10-21 17:09:08 -05:00
Justin S
2b3ead0b72
py-sqlalchemy-utils: new package at 0.36.8 (#19449) 2020-10-21 16:52:37 -05:00
Justin S
bbc9c5533e
py-jsonref: new package at 0.2 (#19448) 2020-10-21 16:51:39 -05:00
Simon Frasch
44a81bf914
spla: Add version 1.2.1 (#19436) 2020-10-21 16:50:44 -05:00
Massimiliano Culpo
c696518efd
Skip malformed spec strings when searching for externals (#19438)
fixes #19266

fzf search method has also been updated

Co-authored-by: Tom Scogland <tom.scogland@gmail.com>
2020-10-21 21:35:02 +02:00
Sajid Ali
2bb775496e
mpich : add python build-only dependency (#19403)
* mpich: yaksa configure fix

	modified:   var/spack/repos/builtin/packages/mpich/package.py

* typo

* python is not needed when building from preconfigured tarballs

* add maintainers
2020-10-21 13:38:09 -05:00
Andrew W Elble
b616dbc56b
New package: py-autograd (#19425)
* py-autograd

* add missing dependencies
2020-10-21 13:37:05 -05:00
Lígia Diana Amorim
947ba7e8bf
Added FFLAGS for apple-clang:11 (#17935)
* Added FFLAGS for apple-clang:11

* Added issue #

* Update var/spack/repos/builtin/packages/mpich/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-21 12:34:45 -05:00
Massimiliano Culpo
bd178ead14
gromacs: fix SIMD argument for ppc64le (#19435)
fixes #19414
2020-10-21 11:33:51 -05:00
Chuck Atkins
fdf0cde5b9
veloc: Add missing openssl dependency (#19437) 2020-10-21 12:32:35 -04:00
Andrew W Elble
d4a6efd021
scipoptsuite (#19430) 2020-10-21 10:56:16 -05:00