Commit graph

12652 commits

Author SHA1 Message Date
Owen Solberg
4468ee2437 py-dnaio: new package need by py-cutadapt (#12743)
* add new package py-dnaio

* provide git url with https, not ssh, protocol

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08 10:37:49 -05:00
Todd Gamblin
a2220f3150 flake8: make entire repository pass spack flake8 -a
- Fix trailing whitespace missed by the bug described in #12755.

- Fix other style issues that have crept in over time (this can happen
  when flake8 adds new checks with new versions)
2019-09-07 23:59:10 -07:00
Todd Gamblin
0ec80e8f16
flake8: only add E501 exemptions when absolutely necessary (#12755)
E501 (line too long) exemptions are probably our most common ones -- we
add them for directives, URLs, hashes, etc. in packages.  But we
currently add them even when a line *doesn't* need them, which can mask
trailing whitespace errors.

This changes `spack flake8` so that it will only add E501 exemptions if
the line is *actually* too long.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-07 23:58:12 -07:00
Owen Solberg
48c3c833e8 patch boost version 1.54-1.55 when being built with ANY gcc version after 5.0 (#12718) 2019-09-07 22:45:53 -05:00
Kevin Huck
35221c127e Updating TAU package. Fixing compiler specification for OSX (#12720)
and making Fortran an option that can be disabled.  Also added
support for the POSIX I/O wrapper and OMPT for OpenMP.
2019-09-07 22:44:40 -05:00
Howard Pritchard
1a38285be9 mesa: disable use of libunwind for arm arch (#12735)
There are problems with libunwind for arm and trying to use it with mesa.
See for example:

https://github.com/grate-driver/mesa/issues/6

disabling use of libunwind for arm, allows the package to be built

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2019-09-07 22:33:30 -05:00
Jonas Lippuner
c3a2528022 add mpi variant to p4est package to allow turning off MPI (#12739) 2019-09-07 22:29:53 -05:00
Axel Huebl
331e4e32be ncurses: improve build time (#12621)
Apply configure options to skip manpage generation
and test builds for both wide and non-wide builts.
2019-09-07 22:27:07 -05:00
Ruben Di Battista
ac7a17754f luarocks: Use make command instead of install (#12703)
This way luarocks does not attempt to pull stuff from the internet.

Fix #3909
2019-09-07 21:06:52 -05:00
Adam J. Stewart
faa3d6a2a5
Add py-numpy 1.17.2 (#12753) 2019-09-07 20:44:46 -05:00
Piotr Luszczek
bbdb033e5f Add patches to work around CMake versions (#12744)
- Use of symbol testing macro requires explicit include()
- CMake policies are not version-portable and the support has to queried
  based on CMake version
2019-09-07 19:04:20 -05:00
Owen Solberg
c4da66be4c font-util 1.3.2 (#12728) 2019-09-07 18:57:22 -05:00
Adam J. Stewart
a4aa1b5a05
Update docs on module loads command (#12702) 2019-09-07 18:32:02 -05:00
Sinan
754ce972a3 new package: py-pygdal (#12747) 2019-09-07 18:23:38 -05:00
Vanessasaurus
25bbc27716 adding shadow-uidmap (#12750)
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
2019-09-07 17:36:45 -05:00
Mathias Jacquelin
696e12da98 upcxx: new package
Adding a UPC++ spack package pointing to the default 2019.3.2 UPC++
version, and allowing to build UPC++ with the experimental CUDA variant.
2019-09-06 16:04:33 -07:00
Toyohisa Kameyama
5def1dd39d openspeedshop: fixed build on arm. (#11861)
* openspeedshop: fixed build on arm.

* remove patch comment.
2019-09-06 13:26:24 -07:00
Geoffrey Oxberry
8fe5405e1b libpeas@1.22.0: new package (#12385)
* libpeas@1.22.0: new package

* libpeas: note more build dependencies

Build and link dependencies were obtained through a combination of
examining the `config.log` file from `configure` and looking at the
pkg-config files of `libpeas`.

* libpeas: add search path for GIR/typelib files
2019-09-06 12:53:12 -05:00
Geoffrey Oxberry
071fb3dd6a iso-codes: new package (#12389) 2019-09-06 12:48:08 -05:00
Greg Becker
3f1c78128e
make env view loading unconditional (#12719) 2019-09-05 18:15:36 -07:00
Toyohisa Kameyama
34647913be fftw: change default value of simd variant for other than x86_64 (#11627)
* Use spec.architecture.target insted of platform.

* remove default in simd variant value.
simd variant change to archtecture independent values.

* Add check simd values.

* rewrite check simd values.

* * flake8
* change aarch64 to arm (neon support only 32 bit arm.)
2019-09-05 11:42:04 -07:00
Matthieu Dorier
1dbf3c208b FIX Catalyst: corrected catalyst package for aarch64 targets (#12707)
* corrected catalyst package for aarch64 targets

* corrected syntax

* corrected undefined variable
2019-09-05 12:44:38 -05:00
Ruben Di Battista
6ef95481ef Add pixz package (#12698) 2019-09-05 09:40:29 -05:00
Jennifer Herting
ca8db06e37 [jemalloc] added version 5.2.1 (#12706) 2019-09-05 09:39:42 -05:00
Hironori-Yamaji
ed6a2f0ef9 textparser: new package (#12713)
* textparser: new package

* textparser: use 'parallel = False'
2019-09-05 09:37:21 -05:00
Michael Kuhn
ad93f47c8f mariadb: Add missing dependencies (#12715)
Found while building mariadb in a minimal build environment.
2019-09-05 09:34:44 -05:00
Janne Blomqvist
30756a643b py-ase: New version 3.18 (#12697)
* py-ase: New version 3.18

Add ASE version 3.18. ASE 3.18 has dropped support for python 2.x,
hence add a dependency on python@3.5: for it.

* Add more ASE dependencies

Address review comments, add dependencies on py-scipy, py-matplotlib,
py-flask, and also add type=('build', 'run') dependency specifiers.
2019-09-05 09:09:37 -05:00
Toyohisa Kameyama
e50dbe6f76 cctools: fixed to build on ARM. (#11862) 2019-09-04 16:45:41 -07:00
Paul Bryant
cb2d18c1e6 Add Go 1.13 2019-09-04 15:04:51 -07:00
t-karatsu
e08f527004 openblas: Add route to f_check for Fujitsu compiler. (#11804) 2019-09-04 15:01:58 -07:00
Chris Green
7f8fe11e4d Improve mock_archive versatility; Remove unwanted ALLOWED_ARCHIVE_TYPES. (#12513)
mock_archive can now take multiple extension / tar option pairs (default matches old behavior).

url_fetch.test_fetch tests more archive types.

compression.EXTS split into EXTS and NOTAR_EXTS to avoid unwanted, non-meaningful combinatoric extensions such as .tar.tbz2.
2019-09-04 13:49:00 -05:00
asmaahassan90
00b02fd234 Add gams recipe (#12700)
* Add gams recipe

* Break down lines to pass lint
2019-09-04 10:13:58 -05:00
t-karatsu
fc9e17289a boost: add -c option to C/C++ compile commands for clang. (#12694) 2019-09-04 10:07:31 -05:00
Mario Melara
407834fffa cppflags point to ncurses headers (#12691)
While debugging this package on our Cray machine, tmux was throwing an
error involving the ncurses headers. Tmux would look for headers in
system locations rather than where spack installed ncurses. Tested only
on a Cray.
2019-09-04 10:06:35 -05:00
asmaahassan90
5953336c3e Add tecplot recipe (#12688)
* Add tecplot recipe

* break down description to pass lint

* fix format to match python 2.6 requiremnets

* importing os
2019-09-04 09:25:43 -05:00
Matthieu Dorier
3181021c11 Boost: fixed problem when requesting ~signals for boost >= 1.69 (#12627)
* fixed problem when requesting ~signals for boost >= 1.69

* added checks for all libs in with_libs
2019-09-04 09:25:00 -05:00
Sinan
d7ef97392c new package: liblas (#12619)
* new package: liblas

* explicitly disable build options

* fix indentation
2019-09-04 09:20:38 -05:00
Todd Gamblin
6b619daef3 specs: better lookup by hash; allow references to missing dependency hashes
- previously spec parsing didn't allow you to look up missing (but still
  known) specs by hash

- This allows you to reference and potentially reinstall
  force-uninstalled dependencies

- add testing for force uninstall and for reference by spec

- cmd/install tests now use mutable_database
2019-09-04 00:25:36 -07:00
Tamara Dahlgren
c141e99e06 Use spack/user-specific stage root by default; stage cleaning (#12516)
* When cleaning the stage root, only remove directories that appear
  to be used for staging Spack packages. Previously Spack was clearing
  all directories in the stage root, which could remove content not
  related to Spack if the user chose a staging root which contains
  files/directories not managed by Spack.
* The documentation is updated with warnings about choosing a stage
  directory that is only managed by Spack (although generally the
  check added in this PR for "spack clean" should avoid removing
  content that was not created by Spack)
* The default stage directory (in config.yaml) is now
  $tempdir/$user/spack-stage and the logic is updated to omit the
  $user portion of this path if $tempdir already contains a $user
  directory.
* When creating stage root assign user read/write permissions to all
  directories in the path under $user. Previously Spack was assigning
  the permissions of the first existing parent directory
2019-09-03 16:31:27 -07:00
Peter Scheibel
868f7869e0
py-chardet package: add py-pytest-runner dependency (#12692)
This required dependency was missing
2019-09-03 14:56:53 -07:00
Sinan
c14b7379f9 new package: protobuf-c (#12634)
* new package: protobuf-c

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-03 16:16:50 -05:00
Todd Gamblin
d79f85d763 perf: spack find -p now does only one DB transaction
`spec.prefix` reads from Spack's database, and if you do this with
multiple consecutive read transactions, it can take a long time.  Or, at
least, you can see the paths get written out one by one.

This uses an outer read transaction to ensure that actual disk locks are
acquired only once for the whole `spack find` operation, and that each
transaction inside `spec.prefix` is an in-memory operation. This speeds
up `spack find -p` a lot.
2019-09-03 07:41:38 -07:00
t-karatsu
ae41ef9146 Boost/Change the method for analysis version (#12676)
* boost:Change the method for analysis version when using Fujitsu compiler.

* Change version to apply patch for Fujitsu.

* fix typo
2019-09-03 09:27:48 -05:00
Hironori-Yamaji
9e1800d81c pmlib: new package (#12625)
* pmlib: new package

* pmlib: fix options and add patch

* pmlib: fix the patch file
2019-09-03 09:26:47 -05:00
Hironori-Yamaji
6ea27cabd6 ccs-qcd: new package (#12681)
* ccs-qcd: new package

* ccs-qcd: fix variant and replacement string
2019-09-03 09:15:34 -05:00
Todd Gamblin
da7fed86a8 tests: add tests for spack extensions command
- add tests for `spack extensions`
- refactor `test_activations` test to use real extensions.
2019-09-02 19:24:48 -07:00
Todd Gamblin
1b877e8e0f tests and completions for spack find --json and spack find --format 2019-09-02 19:24:48 -07:00
Todd Gamblin
2dc7467760 tests: remove extraneous print statement 2019-09-02 19:24:48 -07:00
Todd Gamblin
d4bad06202 refactor: clean up spack find, make spack find -dp work properly
Refactor `spack.cmd.display_specs()` and `spack find` so that any options
can be used together with -d. This cleans up the display logic
considerably, as there are no longer multiple "modes".
2019-09-02 19:24:48 -07:00
Todd Gamblin
987d8cbaaa docs: add docs for spack find --format and spack find --json
- add docs for `spack find --format`
- add docs for `spack find --json`
- update references to Spec.format() docs and add links
2019-09-02 19:24:48 -07:00