Commit graph

13317 commits

Author SHA1 Message Date
Adam J. Stewart
51432aa92e
Add latest version of py-jinja2 (#13311) 2019-10-20 11:15:16 -05:00
Adam J. Stewart
d61b5125c5
Add latest version of py-itsdangerous (#13312) 2019-10-20 11:15:01 -05:00
Adam J. Stewart
e05d165f92
Add latest version of py-idna (#13313) 2019-10-20 11:14:46 -05:00
Adam J. Stewart
ac0fee0f34
Add latest version of py-hypothesis (#13314) 2019-10-20 11:14:32 -05:00
Adam J. Stewart
5aea70e733
Add latest version of py-httpbin (#13315) 2019-10-20 11:14:17 -05:00
Adam J. Stewart
db8f83d333
Add latest version of py-flask (#13316) 2019-10-20 11:13:55 -05:00
Adam J. Stewart
de6d53b626
Add latest version of py-torchvision (#13289) 2019-10-20 11:12:43 -05:00
Adam J. Stewart
5995c3f85b
Add latest version of py-typing-extensions (#13288) 2019-10-20 11:12:27 -05:00
Adam J. Stewart
4e2cce2c9f
Add latest version of py-urllib3 (#13286) 2019-10-20 11:11:41 -05:00
Adam J. Stewart
d2202f6d98
Add latest version of py-virtualenv (#13285) 2019-10-20 11:11:23 -05:00
Adam J. Stewart
78942c7840
Add latest version of py-werkzeug (#13284) 2019-10-20 11:11:06 -05:00
Adam J. Stewart
0443581a20
Add py-mypy-extensions package (#13283) 2019-10-20 11:10:40 -05:00
Adam J. Stewart
92a359e4ba
Add py-mypy package (#13282) 2019-10-20 11:10:22 -05:00
Adam J. Stewart
9ac7e098d9
Add py-pytest-forked package (#13281) 2019-10-20 11:10:04 -05:00
Adam J. Stewart
1dc99765e9
Add py-raven package (#13280) 2019-10-20 11:09:44 -05:00
Adam J. Stewart
a6bc0c7ee0
Add py-flake8-import-order package (#13273) 2019-10-20 11:09:23 -05:00
Adam J. Stewart
00f766b248
Add py-sphinxcontrib-devhelp package (#13278) 2019-10-20 11:09:04 -05:00
Adam J. Stewart
c8285da8e7
Add py-sphinxcontrib-applehelp package (#13279) 2019-10-20 11:08:51 -05:00
Adam J. Stewart
d37c95b80b
Add py-sphinxcontrib-htmlhelp package (#13277) 2019-10-20 11:08:34 -05:00
Adam J. Stewart
7bda2fe292
Add py-sphinxcontrib-jsmath package (#13276) 2019-10-20 11:08:16 -05:00
Adam J. Stewart
d4ac57f3a3
Add py-sphinxcontrib-qthelp package (#13275) 2019-10-20 11:07:54 -05:00
Adam J. Stewart
f35bcaf83b
Add py-sphinxcontrib-serializinghtml package (#13274) 2019-10-20 11:07:31 -05:00
Adam J. Stewart
3e18e664fc
Add py-typed-ast package (#13272) 2019-10-20 11:07:01 -05:00
Adam J. Stewart
95b7f31112
Add py-docutils-stubs package (#13271) 2019-10-20 11:06:38 -05:00
Adam J. Stewart
4f56bcc790
Add py-brotlipy package (#13270) 2019-10-20 11:06:18 -05:00
Adam J. Stewart
596f3f1d61
spack create: http -> https (#13269) 2019-10-20 11:05:54 -05:00
Todd Gamblin
20bb6fd733
shebangs: don't warn when patching long shebangs (#13266)
We've been doing this for quite a while now, and it does not seem to
cause issues.

- [x] Switch the noisy warning to a debug to make Spack a bit quieter
  while building.
2019-10-19 14:09:25 -07:00
Massimiliano Culpo
41fb0395a6 Microarchitecture specific optimizations for LLVM (#13250)
* Added architecture specific optimization flags for Clang / LLVM
* Disallow compiler optimizations for mixed toolchains
    * We emit a warning when building for a mixed toolchain
* Fixed issues with suffixed versions of compilers; Apple's Clang will, 
    for the time being, fall back on x86-64 for every compilation.
2019-10-19 13:19:29 -07:00
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
Peter Scheibel
fd88f8fefa satisfaction checks on dependencies should be strict when the parent check is strict (#13243) 2019-10-17 11:02:14 -07:00
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
Todd Gamblin
cf9de058aa
multimethods: avoid calling caller_locals() in Python 3 (#13238)
Python 3 metaclasses have a `__prepare__` method that lets us save the
class's dictionary before it is constructed.  In Python 2 we had to walk
up the stack using our `caller_locals()` method to get at this.  Using
`__prepare__` is much faster as it doesn't require us to use `inspect`.

This makes multimethods use the faster `__prepare__` method in Python3,
while still using `caller_locals()` in Python 2.  We try to reduce the
use of caller locals using caching to speed up Python 2 a little bit.
2019-10-17 06:40:23 -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
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