Commit graph

11712 commits

Author SHA1 Message Date
mic84
61aa1831e3 AMReX: update package.py (#8697) 2018-07-26 13:29:03 -05:00
Hadrien G
8b718e7cd6 Templight package (#8782)
* First draft of a templight recipe

* Let's be explicit for now, we can be clever later on

* The clang6 version does not work, drop it

* Reorder FIXMEs more logically

* Add patch for current templight develop branch

* Create an artificial stable release of templight

* Take some additional inspiration from llvm package

* Added the templight supporting tools

* Remove old notes from the no-url branch

* Avoid unnecessary join_path
2018-07-26 11:19:14 -05:00
Simon Flood
80741bc427 hmmer: added version 3.2.1 & updated URL (#8787)
Add HMMER 3.2.1 and updated URL then removed url_for_version function as no longer required - all HMMER downloads available from updated URL.
2018-07-26 10:07:55 -05:00
Michael Kuhn
643a4fbb59 papi: Update to 5.6.0 and fix build with %gcc@8 (#8796) 2018-07-26 10:02:07 -05:00
Mario Melara
cb410b3003 Add package DMTCP (#8808) 2018-07-26 09:47:55 -05:00
Satish Balay
d5957f147b mfem: mfem-3.3-3.4-petsc-3.9.patch is not needed for latest develop version (#8809) 2018-07-26 09:47:28 -05:00
Todd Gamblin
ab1cd6577c readme: add our @spackpm Twitter handle (#8810) 2018-07-26 09:45:32 -05:00
Mark W. Krentel
af60f962cd intel-tbb: Add tm variant to disable transactional memory. (#8799)
* intel-tbb: Add variant `tm` to disable transactional memory.

Some AMD or very old Intel systems don't support transactional memory. This commit adds a variant `tm` that defaults to `True`, but can be switched off to allow running on those systems.
2018-07-25 23:14:17 -07:00
Adam J. Stewart
7902f3eb49 Add docs on new top-level VCS attributes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
5d07042f23 Unit test fixes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
68c2bdfaf6 Further improvements to version parsing 2018-07-25 23:10:10 -07:00
Adam J. Stewart
e948a54d8e All git URLs end in .git 2018-07-25 23:10:10 -07:00
Adam J. Stewart
31417bf66c Replace git=git with explicit branch names 2018-07-25 23:10:10 -07:00
Adam J. Stewart
3f18c04865 Add top-level attributes for git R-Z packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
a1572bb999 Add top-level attributes for git R (Bioconductor) packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
908d2dcd4d Add top-level attributes for git M-P packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
4c6aca533a Add top-level attributes for hg, svn, and git A-L packages 2018-07-25 23:10:10 -07:00
Todd Gamblin
5f00056490 tests: convert mirror test to pytest with free functions. 2018-07-25 23:10:10 -07:00
Todd Gamblin
020c34e136 tests: add checks and tests for consistent version() arguments
- Previously, Spack didn't check the arguments you put in version()
  directives.

- So, you could do something like this, where there are arguments for a
  URL fetcher AND for a git fetcher:

  version('1.0', md5='abc123', git='https://foo.bar', commit='feda2343')

- Now, we check the arguments before constructing a fetcher, to ensure
  that each package has *only* arguments for a single type of fetcher.

- Also added `test_package_version_consistency()` to the `package_sanity`
  test, so that all builtin packages are required to have valid
  `version()` directives.
2018-07-25 23:10:10 -07:00
Todd Gamblin
6f7eaecfa0 tests: correct name of check_db to check_repo
- this test is checking the package *repository*, not the database.
2018-07-25 23:10:10 -07:00
Todd Gamblin
773cfe088f core: differentiate package-level fetch URLs by args to version()
- packagers can specify two top-level fetch URLs if one is `url`
  - e.g., `url` and `git` or `url` and `svn`

- allow only one VCS fetcher so we can differentiate between URL and VCS.

- also clean up fetcher logic and class structure
2018-07-25 23:10:10 -07:00
Todd Gamblin
04aec9d6f8 core: add check for conflicting top-level fetch attributes in packages
- ensure that packages can't have more than one of git, hg, svn, or url
2018-07-25 23:10:10 -07:00
Todd Gamblin
6837da2ad7 style: clean up exception definitions in package.py 2018-07-25 23:10:10 -07:00
Todd Gamblin
498d8cf04b core: fixes and tests for handling of fetcher attributes in packages
- Packages can remove the top-level `url` attribute and still work

- These are now legal:
  - Packages with *only* version-specific URLs (even with gaps)

  - Packages with a top-level git/hg/svn attribute and `version`
    directives for that.

- If a package has both a top-level hg/git/svn attribute AND a top-level
  url attribute, the url attribute takes precedence.
2018-07-25 23:10:10 -07:00
Adam J. Stewart
5792a805fc core: quick fix for packages without URLs
Some packages do not have a `url` and are instead downloaded via `git`,
`hg`, or `svn`. Some packages like `spectrum-mpi` cannot be downloaded at
all, and are placeholder packages for system installations. Previously,
`__init__()` in `PackageBase` crashed if a package did not have a `url`
attribute defined.

I hacked this section of code out, but I have no idea what the
repercussions of that are.
2018-07-25 23:10:10 -07:00
Satish Balay
f59666587b hypre: 'master' is branch - not a tag 2018-07-25 22:17:37 -07:00
sknigh
b0499cf45e Added latest version of charliecloud (#8792) 2018-07-26 06:54:09 +02:00
Adam J. Stewart
13c52066a5 Fix order of regexes reported by spack url summary 2018-07-24 21:02:28 -07:00
Todd Gamblin
656e935e50 core: make spack.util.crypto initialization less expensive.
- This hard-codes the hash lengths rather than computing them on import.

- Also cleans up the code in `spack.util.crypto` to make it easier to
  understand.
2018-07-24 18:35:02 -07:00
Todd Gamblin
674eb00e53
bugfix: spack module -m error message (#8794)
Fix this output error:

```
$ spack -m module loads mpileaks
==> Error: `spack module loads -m t -m c -m l ...` has been moved. Try this instead:

    $ spack module t loads mpileaks
    $ spack module c loads mpileaks
    $ spack module l loads mpileaks
```
2018-07-24 16:12:47 -07:00
Massimiliano Culpo
5b8b7a5873 The auto-completion file is now consistent with spack module 2018-07-24 11:27:17 -07:00
Massimiliano Culpo
6bb2256043 Die with a meaningful error if a deprecated command is used
In case a deprecated form of the module command is used, the program
will exit non-zero and print an informative error message suggesting
which command should be used instead.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
35cef16974 Grouped all the module commands under spack module
As requested in the review all the commands meant to manage module
files have been grouped under the `spack module` command.

Unit tests have been refactored to match the new command structure.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
7cbe1aedb7 module file tutorial: rebuilt docker image and updated the script 2018-07-24 11:27:17 -07:00
Massimiliano Culpo
576f0c98d2 Added --dependencies to the help text of spack load
fixes #6321
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
443d702971 spack load exits with 1 if module does not exist or is not installed
fixes #2215
fixes #2570
fixes #6676
fixes #7281
closes #3827

This PR reverts the use of `spack module loads` in favor of
`spack module find` when loading module files via Spack. After this PR
`spack load` will accept a single spec at a time, and will be able
to interpret correctly the `--dependencies` option.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
c0d9de240a Revert "Fix recursive module loading."
This reverts commit 732c24f603.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
7a49ba56b6 Added blacklisting of implicit modules in docs + regression tests
fixes #4400

The feature requested in #4400 was already part of the module file
configuration, but it was neither tested nor documented. This
commit takes care of adding a few lines in the documentation and a
regression test.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
ff83003eaf Renamed 'patch_configuration' fixture to 'module_configuration'
This just because the fixture has been moved one level above the one
it was originally defined. In this more general context there's more
than one configuration file that could be patched for tests.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
008f171a7e Added a unit test for 'spack lmod setdefault' 2018-07-24 11:27:17 -07:00
Massimiliano Culpo
e81c0c3e2c Updated references to spack module in the documentation. 2018-07-24 11:27:17 -07:00
Massimiliano Culpo
6ab57571c2 Added 'setdefault' subcommand to 'spack lmod'
Added a subcommand that sets the default module to be loaded, if
multiple installations of the same package are present.
2018-07-24 11:27:17 -07:00
Massimiliano Culpo
0457c1fbee Split 'spack module' into multiple commands
'spack module' has been split into multiple commands, each one tied to a
specific module type. This permits the specialization of the new
commands with features that are module type specific (e.g. set the
default module file in lmod when multiple versions of the same package
are installed at the same time).
2018-07-24 11:27:17 -07:00
Todd Gamblin
fdcaf5c4c8 bugfix: fix spack spec --yaml
- repo membership test was broken by the refactor of spack/__init__.py

- refactor singleton so that 'spec in repo' works again for `spack.repo.path`

- fix spec command and add basic tests for `spack spec` and `spack spec --yaml`
2018-07-24 11:25:34 -07:00
Massimiliano Culpo
6ba1c82858 tests: Add python 3.7 to Travis CI (#8778)
* Test Spack on Python 3.7 as part of Travis CI
* Currently using xenial to pull-in python 3.7
    * As xenial is not officially supported yet, Travis tolerates failures on it.
2018-07-23 23:07:36 -07:00
Todd Gamblin
e2e8108dc4 packages: do not use generic checksum= in version() directives
- This is very old usage -- preparing to deprecate this in favor of being
  explicit about checksums.
2018-07-23 11:57:52 -07:00
Todd Gamblin
d4c4effb5e docs: update old docs for spack.package.PackageBase
- There was a lot of documentation in `PackageBase` dating back to the
  very first versions of Spack.

- It was repetitive and out of date, and the docs at spack.readthedocs.io
  are better.

- Remove the outdated specifics, and leave the minimal useful set of
  developer docs in `package.py`.
2018-07-23 11:57:52 -07:00
Todd Gamblin
bd3ffc7b76 core: use sha256 instead of md5 for spack checksum and spack create
- This changes `get_checksums_for_versions` to generate code that uses an
  explicit `sha256` argument instead if the bare `md5` hash we used to
  generate.

- also use a generic digest parameter for the `version` directive, rather
  than a specific `md5` parameter.
2018-07-23 11:57:52 -07:00
Todd Gamblin
305c95b69f tests: move doc tests to the unit test stage
- Frequently, the documentation build will fail mysteriously in some
  spack command.

- The cause is some new bug introduced by the PR, but this is not
  apparent because the unit tests haven't run and the doc tests aren't
  targeted at code bugs.

- Users end up puzzled by doc failures when they're really code failures.

- Move the doc tests parallel with the code tests, so that we can more
  easily see bugs like this.
2018-07-23 07:27:48 -07:00
Levi Baber
0cef7b4355 Trinity plugins (#8516)
* trinity: fix plugin installation

* trinity: flake8

* trinity: more specific types for dependencies
2018-07-22 17:17:44 -05:00