Commit graph

12977 commits

Author SHA1 Message Date
Todd Gamblin
e65b7f8ebf
importing: make importlib_importer recognize .pyc cache (#13239)
Our importer was always parsing from source (which is considerably
slower) because the source size recorded in the .pyc file differed from
the size of the input file.

Override path_stats in the prepending importer to fool it into thinking
that the source size is the size *with* the prepended code.
2019-10-16 17:07:18 -07:00
Michael Kuhn
ffe87ed49f filter_file: fix multiple invocations on the same file (#13234)
Since the backup file is only created on the first invocation, it will
contain the original file without any modifications. Further invocations
will then read the backup file, effectively reverting prior invocations.

This can be reproduced easily by trying to install likwid, which will
try to install into /usr/local. Work around this by creating a temporary
file to read from.
2019-10-16 15:15:24 -07:00
Tamara Dahlgren
1ef71376f2 Bugfix: stage directory permissions and cleaning (#12733)
* This updates stage names to use "spack-stage-" as a prefix.
  This avoids removing non-Spack directories in "spack clean" as
  c141e99 did (in this case so long as they don't contain the
  prefix "spack-stage-"), and also addresses a follow-up issue
  where Spack stage directories were not removed.
* Spack now does more-stringent checking of expected permissions for
  staging directories. For a given stage root that includes a user
  component, all directories before the user component that are
  created by Spack are expected to match the permissions of their
  parent; the user component and all deeper directories are expected
  to be accessible to the user (read/write/execute).
2019-10-16 14:55:37 -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
Greg Becker
94e80933f0 Feature: installed file verification (#12841)
This feature generates a verification manifest for each installed
package and provides a command, "spack verify", which can be used to
compare the current file checksums/permissions with those calculated
at installed time.

Verification includes

* Checksums of files
* File permissions
* Modification time
* File size

Packages installed before this PR will be skipped during verification.
To verify such a package you must reinstall it.

The spack verify command has three modes.

* With the -a,--all option it will check every installed package.
* With the -f,--files option, it will check some specific files,
  determine which package they belong to, and confirm that they have
  not been changed.
* With the -s,--specs option or by default, it will check some
  specific packages that no files havae changed.
2019-10-15 14:24:52 -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
Massimiliano Culpo
d33b0ffc50 lmod: module files are written in a root folder named by target family (#13121)
fixes #13005

This commit fixes an issue with the name of the root directory for
module file hierarchies. Since #3206 the root folder was named after
the microarchitecture used for the spec, which is too specific and
not backward compatible for lmod hierarchies. Here we compute the
root folder name using the target family instead of the target name
itself and we add target information in the 'whatis' portion of the
module file.
2019-10-15 11:20:49 -07:00
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
Todd Gamblin
385d2bf3fa
commands: add resource stats to spack url stats (#13205)
`spack url stats` now also looks at packages' resources when outputting
statistics.

Example:

```
$ spack url stats
==> URL stats for 3531 packages:
--------------------------------------------------------------
stat                    versions        %   resources        %
--------------------------------------------------------------
url                         8335    89.3%         339    89.0%
    schemes
        https               6489    69.5%          93    24.4%
        ftp                   32     0.3%           8     2.1%
        http                1763    18.9%         237    62.2%
        file                  51     0.5%           1     0.3%
    checksums
        md5                   26     0.3%           0     0.0%
        sha256              8306    89.0%         336    88.2%
        no checksum            3     0.0%           3     0.8%
--------------------------------------------------------------
go                             1     0.0%           0     0.0%
--------------------------------------------------------------
hg                             7     0.1%           0     0.0%
--------------------------------------------------------------
no code                        4     0.0%           0     0.0%
--------------------------------------------------------------
svn                            4     0.0%          16     4.2%
--------------------------------------------------------------
git                          981    10.5%          26     6.8%
    branch                   442     4.7%           4     1.0%
    commit                   362     3.9%          14     3.7%
    no ref                    36     0.4%           2     0.5%
    tag                      141     1.5%           6     1.6%
--------------------------------------------------------------
```
2019-10-14 08:58:01 -07:00
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
Adam J. Stewart
e1cf35a82b Fix svn tests, skip if svnadmin not found (#13137) 2019-10-14 10:40:20 +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