Commit graph

6894 commits

Author SHA1 Message Date
Audrey Thoma
de5111cd50 hapcut2: new package (#5238) 2017-08-30 00:57:57 -07:00
Andrey Prokopenko
c830eda0e6 Slightly better error matching when parsing spack logs (#5236) 2017-08-30 00:56:17 -07:00
alalazo
462de9847c Added unit tests for Spec.__init__ exceptional paths 2017-08-29 00:44:43 -07:00
alalazo
bf7b861554 Fixed bug in Spec._dup, updated docstring
The private method `Spec._dup` was missing a line (when setting compiler
flags the parent spec was not set to `self`). This resulted in
an inconsistent state of the duplicated Spec. This problem has been
fixed here. The docstring of `Spec._dup` has been updated.
2017-08-29 00:44:43 -07:00
Todd Gamblin
ee93993b07 Make Spec construction simpler (#5227) 2017-08-29 00:02:25 -07:00
Christoph Junghans
6036a5a113 lammps: install headers (#5226)
* lammps: install headers
* use prefix.include.lammps
2017-08-28 16:33:30 -07:00
Audrey Thoma
56f4f74b72 redundans: new package (#5217)
* redundans: new package

* fixing url for fastaindex and adding dep for pyscaf
2017-08-28 15:25:19 -05:00
Matthew Scott Krafczyk
c94933343a Add --show-full-compiler option to 'spack find'
When 'spack find' is invoked with the '--show-full-compiler' option,
the compiler flags and version are shown for each spec that is found.
2017-08-28 10:35:46 -07:00
Massimiliano Culpo
005b22aa8b Removed default value for 'dirty' function argument. (#5109)
This change is done to avoid inconsistencies during refactoring. The rationale is that functions at different levels in the call stack all define a default for the 'dirty' argument. This PR removes the default value for all the functions except the top-level one (`PackageBase.do_install`).

In this way not defining 'dirty' will result in an error, instead of the default value being used. This will reduce the risk of having an inconsistent behavior after a refactoring.
2017-08-25 20:40:37 -07:00
Michael Kuhn
91143e9db4 Fix copyright years in spack create template (#5203) 2017-08-25 20:38:56 -07:00
Michael Kuhn
92df1492f6 go: Update to 1.9 (#5216) 2017-08-25 20:29:02 -05:00
Michael Kuhn
b94711a54f Improve Ubuntu arch detection (#2649)
Ubuntu uses a YY.{04,10} release scheme, where YY.04 is not necessarily
binary-compatible with YY.10.
2017-08-25 17:30:40 -07:00
Mark C. Miller
c769e99eda Zfp shared libs (#5212) 2017-08-25 15:08:49 -07:00
scheibelp
499617897b Link extra_rpaths from compilers.yaml at build time (#5211) 2017-08-25 11:02:36 -07:00
Gregory Lee
9a1fd166aa patch config.guess for any ppc64le arch (#5215) 2017-08-25 10:55:41 -07:00
Todd Gamblin
313771c734 Improve grammar in build log error message. (#5214)
- "1 error found" instead of "1 errors found"

- don't print any build log context if no errors were found; just refer
  the user to the build log.
2017-08-25 04:07:42 -07:00
Mark C. Miller
a0f39397c1 Add contributors link to Sphinx docs (#5213) 2017-08-25 02:57:44 -07:00
Sergey Kosukhin
fda3249c8b Respect --insecure (-k) flag when fetching list_url. (#5178)
* Respect --insecure when fetching list_url.
* Ensure support for Python 2.6, and that urlopen works for python versions prior 2.7.9 and between 3.0 and 3.4.3.
2017-08-25 02:15:46 -07:00
Denis Davydov
c0d3d33b58 dealii: add nanoflann, sundials and adol-c plus fixes on macOS (#5175)
* expat: fix build on macOS

* nanoflann: add new package

* sundials: fix compilation on macOS with clang+gfortran

* adol-c: add 2.6.3

* dealii: add adol-c, nanoflann, sundials and 8.5.1

* sundials: minor cleanup
2017-08-24 20:18:06 -05:00
Michael Kuhn
61cc55985b pkgconf: New package (#5202)
pkgconf is a new pkg-config implementation with additional features and
no external dependencies.

For a detailed comparison, see: http://pkgconf.org/features.html
2017-08-24 17:54:14 -07:00
Audrey Thoma
6ff82ff5a3 ray: new package (#5200) 2017-08-24 16:31:21 -07:00
Ben Boeckel
0e7071befe test/gpg: init from the testing key directory
The old testing pattern set an attribute on the parser directly. Now
that there is a parsed flag, use it instead.
2017-08-24 16:17:35 -07:00
Ben Boeckel
f564b2abf7 gpg: add an argument for the import directory
This is hidden because it is only meant for use by the tests.
2017-08-24 16:17:35 -07:00
Sergey Kosukhin
a48b5a627c Make jpeg a virtual dependency. (#5190)
* Make jpeg a virtual dependency.

* Make 'libjpeg-turbo' the default implementation of 'jpeg'.
2017-08-24 10:30:35 +02:00
sknigh
49a9d63be7 Added options to libfabrics (#5191) 2017-08-23 15:47:28 -07:00
Massimiliano Culpo
5d7901b312 Improve Spec literals, add Spec.from_dict() (#5151)
* Simplified Spec.__init__ signature by removing the *dep_like argument.

The `*dep_like` argument of `Spec.__init__` is used only for tests. This
PR removes it from the call signature and introduces an equivalent
fixture to be used in tests.

* Refactored ``spec_from_dict`` to be a static method of ``Spec``

The fixture ``spec_from_dict`` has been refactored to be a static method
of ``Spec``. Test code has been updated accordingly. Added tests for
exceptional paths.

* Renamed argument `unique` to `normal` + added LazySpecCache class

As requested in the review the argument `unique` of `Spec.from_literal`
has been renamed to `normal`. To avoid eager evaluations of
`Spec(spec_like)` expressions a subclass of `collections.defaultdict`
has been introduced.

* Spec object can be keys of the dictionary for a spec literal.

Added back the possibility use a spec directly as a key. This permits
to build DAGs that are partially normalized.
2017-08-23 14:20:40 -07:00
Christoph Junghans
fa1d0a8a4d Add --source option to spack install (#4102)
- -- source will copy source into prefix along with the package.
- added a test for --source, as well
2017-08-23 14:08:52 -07:00
Audrey Thoma
359b21c888 pgdspider: new package (#5186)
* pgdspider: new package

* couple of fixes
2017-08-23 08:34:12 -05:00
Axel Huebl
0daa639788 Boost: develop (#5184)
Adds a development version of boost, based on their github master
repo.
Git clones the submodules forever, but installs! :)

Useful for testing since boost tends to break complex software
dependencies quite often. This helps testing it before releases.
2017-08-23 07:31:34 -05:00
healther
15186d4ae8 add test for lua and node patching in sbang (#5169)
* add test for lua and node handling in sbang patching (cf #5086)
2017-08-23 01:05:36 -07:00
Todd Gamblin
40e9171390 Add testing for new build output.
- Update handling of ChildError so that its output is capturable from a
  SpackCommand

- Update cmd/install test to make sure Python and build log output is
  being displayed properly.
2017-08-22 16:14:38 -07:00
Todd Gamblin
f51b541ef8 Make install command reusable within single Spack run
- install and probably other commands were designed to run once, but now
  we can to test them from within Spack with SpackCommand

- cmd/install.py assumed that it could modify do_install in PackageBase
  and leave it that way; this makes the decorator temporary

- package.py didn't properly initialize its stage if the same package had
  been built successfully before (and the stage removed).
  - manage stage lifecycle better and remember when Package needs to
    re-create the stage
2017-08-22 16:14:38 -07:00
Todd Gamblin
fa1faa61c4 SpackCommand uses log_output to capture command output. 2017-08-22 16:14:38 -07:00
Todd Gamblin
4f444c5f58 log_ouptut can take either a filename or a file object 2017-08-22 16:14:38 -07:00
Todd Gamblin
139d5bfa6b Display build output on ProcessError, instead of Python context.
- If a failure comes from an external command and NOT the Python code,
  display errors highlighted with some context.

- Add some rudimentary support for parsing errors out of the build log
  (not very sophisticated yet).

- Build errors in Python code will still display with Python context.
2017-08-22 16:14:38 -07:00
Todd Gamblin
d54110d208 Limit package context to 3 lines and colorize in error output. 2017-08-22 16:14:38 -07:00
Massimiliano Culpo
4600d106e2 Config scopes are now returning OrderedDicts instead of dicts. (#5183)
It seems 8f21332fec introduced a bug
in that normal dictionaries are returned from ConfigScope objects
instead of OrderedDicts. This is fixed here.
2017-08-22 14:20:19 -07:00
Audrey Thoma
79df4db8e5 tcoffee: new package (#5185) 2017-08-22 13:48:23 -05:00
Axel Huebl
61c5b5faa7 Boost: 1.65.0 (#5182)
Adds the latest boost release.
Downloads seem to be pointing to bintray from the official homepage.
2017-08-22 13:46:54 -05:00
Sergey Kosukhin
f52bdeda2a Package 'libaec': no need to specify per version urls. (#5176) 2017-08-22 09:27:03 +02:00
Sergey Kosukhin
e55efdf8ed Updates for package 'cdo'. (#5179)
* Package 'cdo': removed obsolete version 1.6.9.

* Package 'cdo': updated urls.

* Package 'cdo': added version 1.9.0.

* Package 'cdo': no need to specify per version urls.

* Package 'cdo': switched from Package to AutotoolsPackage.

* Package 'cdo': added new variant 'openmp'.

* Package 'cdo': variants 'curl' and 'magics' by default.
2017-08-22 08:42:55 +02:00
Matthew Scott Krafczyk
48bf1e276b Add environment variables to path substitution
Update documentation on config file variable substitutions and
add expansion of environment variables in config files.
2017-08-21 18:35:00 -07:00
Audrey Thoma
e0ebf44239 py-pyrad: new package (#5181) 2017-08-21 17:58:05 -05:00
Massimiliano Culpo
581f70ff6f Added custom messages for conflicts directive. fixes #4965 (#5083)
Users can now add an optional custom message to the conflicts directive.
Layout on screen has been changed to improve readability and the long
spec is shown in tree format. Two conflicts in `espresso` have been
modified to showcase the feature.
2017-08-21 09:20:07 -07:00
Axel Huebl
bd8ac0a738 Protobuf: 3.4 (#5177) 2017-08-21 07:29:47 -05:00
Todd Gamblin
10bb681b57 Unbuffer so that output from packages appears when redirecting
- Python I/O would not properly interleave (or appear) with output from
  subcommands.

- Add a flusing wrapper around sys.stdout and sys.stderr when
  redirecting, so that Python output is synchronous with that of
  subcommands.
2017-08-20 16:51:10 -07:00
Todd Gamblin
79045afada Add tests for output redirection. 2017-08-20 16:51:10 -07:00
Todd Gamblin
11196e7b69 Preserve verbosity across installs when 'v' is pressed.
- 'v' toggle was previously only good for the current install.
- subsequent installs needed user to press 'v' again.
- 'v' state is now preserved across dependency installs.
2017-08-20 16:51:10 -07:00
Todd Gamblin
48440766df Fix exit call in SpackError.die()
- Previously we would use `os._exit()` in to avoid Spack error handling
  in the parent process when build processes failed.  This isn't
  necessary anymore since build processes propagate their exceptions to
  the parent process.

- Use `sys.exit` instead of `os._exit`. This has the advantage of
  automatically flushing output streams on quit, so output from child
  processes is not lost when Spack exits.
2017-08-20 16:51:10 -07:00
Todd Gamblin
05cc6c966f Rework output redirection in Spack.
- Simplify interface to log_output. New interface requires only one
  context handler instead of two.  Before:

      with log_output('logfile.txt') as log_redirection:
           with log_redirection:
               # do things ... output will be logged

  After:

      with log_output('logfile.txt'):
          # do things ... output will be logged

  If you also want the output to be echoed to ``stdout``, use the
  `echo` parameter::

      with log_output('logfile.txt', echo=True):
          # do things ... output will be logged and printed out

  And, if you just want to echo *some* stuff from the parent, use
  ``force_echo``:

      with log_output('logfile.txt', echo=False) as logger:
          # do things ... output will be logged

          with logger.force_echo():
              # things here will be echoed *and* logged

  A key difference between this and the previous implementation is that
  *everything* in the context handler is logged.  Previously, things like
  `Executing phase 'configure'` would not be logged, only output to the
  screen, so understanding phases in the build log was difficult.

- The implementation of `log_output()` is different in two major ways:

  1. This implementation avoids race cases by using only one pipe (before
     we had a multiprocessing pipe and a unix pipe).  The logger daemon
     stops naturally when the input stream is closed, which avoids a race
     in the previous implementation where we'd miss some lines of output
     because the parent would shut the daemon down before it was done
     with all output.

  2. Instead of turning output redirection on and off, which prevented
     some things from being logged, this version uses control characters
     in the output stream to enable/disable forced echoing.  We're using
     the time-honored xon and xoff codes, which tell the daemon to echo
     anything between them AND write it to the log.  This is how
     `logger.force_echo()` works.

- Fix places where output could get stuck in buffers by flushing more
  aggressively.  This makes the output printed to the terminal the same
  as that which would be printed through a pipe to `cat` or to a file.
  Previously these could be weirdly different, and some output would be
  missing when redirecting Spack to a file or pipe.

- Simplify input and color handling in both `build_environment.fork()`
  and `llnl.util.tty.log.log_output()`.  Neither requires an input_stream
  parameter anymore; we assume stdin will be forwarded if possible.

- remove `llnl.util.lang.duplicate_stream()` and remove associated
  monkey-patching in tests, as these aren't needed if you just check
  whether stdin is a tty and has a fileno attribute.
2017-08-20 16:51:10 -07:00