Commit graph

19753 commits

Author SHA1 Message Date
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
Andrew W Elble
e9eb9cdc41
py-hdbscan (#19428) 2020-10-21 10:53:43 -05:00
Andrew W Elble
c678f119ba
glog (#19423) 2020-10-21 10:48:07 -05:00
Andrew W Elble
70cfdab372
gflags (#19422) 2020-10-21 10:47:31 -05:00
Andrew W Elble
a26b744b65
coinutils (#19421) 2020-10-21 10:46:50 -05:00
albestro
f006a54db2
Update git to 2.29.0 (#19415) 2020-10-21 11:39:43 -04:00
darmac
f4ecc8bad7
update version to avoid compile error (#19363)
* update version to avoid compile error

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-21 10:39:02 -05:00
Kelly (KT) Thompson
490105ea20
Provide doxygen@1.8.20. (#19412) 2020-10-21 10:38:40 -05:00
darmac
1a57787686
py-cvxopt: refine dependency @1.1.9 and update version to @1.2.5 (#19385)
* refine dependency @1.1.9 and update version to @1.2.5

* refine depends_on() for python
2020-10-21 10:22:26 -05:00
iarspider
640d1a0034
Add FORM (#19397)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add FORM

* Update package.py

Changes from review

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 10:20:26 -05:00
iarspider
cf733b2dd2
Add QD (#19402)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add QD

* Update package.py

Changes from review

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 10:18:15 -05:00
Chris Richardson
f0712bde48
Add Allinea to cray-libsci (#19232) 2020-10-21 10:06:31 -05:00
Toyohisa Kameyama
35ad3bb0fc
quantum-espresso: fix build fail @6.6 and add conflicts a64fx. (#19383)
* quantum-espresso: fix build fail @6.6 and add conflicts a64fx.

* get patch to gitlab.

* Add +patch
2020-10-21 10:03:54 -05:00
Omri Mor
1147220b9b
CMakePackage: added 'ipo' variant (#18374)
+ipo sets CMAKE_INTERPROCEDURAL_OPTIMIZATION=ON
The option is not supported for CMake < 3.9
2020-10-21 11:09:45 +02:00
Massimiliano Culpo
bed929e7a9
Make url_fetch test independent of locale settings (#19390) 2020-10-21 09:18:50 +02:00
Greg Becker
a5faf7d27a
Change 'any' to wildcard for variants (#19381) 2020-10-21 08:05:29 +02:00
Martin Aumüller
0e6b818c52
Add new packages: ispc & embree (#19361)
* Add new package: ispc

* Add new package: embree
2020-10-20 19:00:45 -05:00
iarspider
03611f2e89
Thepeg fix (#19405)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Fixes for thepeg

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-20 16:33:17 -05:00
Josh Essman
cee5c2e755
mfem: Fix support for SUNDIALS and PETSc features (#19326)
* mfem: specify PETSC_DIR, link correct sundials libraries

* fix: only use PETSC_DIR directly for static builds

* fix: only use sundials nvecmpiplusx for MFEM 4.2+
2020-10-20 16:26:34 -05:00
eugeneswalker
fa9ad0a3da
tau unwind patch: only patch 2.29, not 2.29.1 (#19409) 2020-10-20 16:25:52 -05:00
iarspider
d9bb90d06e
Lhapdf extends python (#19398)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* LHAPDF should extend Python to get env variables correct

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-20 14:59:54 -05:00
Jean-Paul Pelteret
3a56248eba
deal.II: Add more conflicts due to symbol clashes between dependencies (#19408) 2020-10-20 14:55:22 -05:00
Massimiliano Culpo
a51702e3a2
py-archspec: added new package at v0.1.1 (#19395) 2020-10-20 18:40:31 +02:00