Fixes#5189
When working with non-normalized paths containing ".." on some
file systems, Spack was found to encounter a permission error when
writing to the path. This normalizes a path written by the
intel-parallel-studio package and also normalizes all paths
written by the license install hook (for all packages) to avoid
this issue for intel-parallel-studio.
Following the discussion with Todd and Adam, find has been modified to
accept glob expressions. This should not affect performance as every
glob implementation I inspected has 3 cases (no wildcard, wildcard but
no directories involved, wildcard and directories involved) and uses
fnmatch underneath.
Mixins have been changed to do by default a non-recursive search (but
a recursive search can still be triggered using the recursive keyword).
Following a comment from Todd, the search path for the files listed in
`filter_compiler_wrappers` can now be narrowed. Anyhow, the function
implementation still makes use of `find`, the rationale being that we
have already seen packages that install artifacts in e.g. architecture
dependent folders. The possibility to have a relative search path might
be a good compromise between the previous approach and the one suggested
in the review.
Also: 'ignore_absent' and 'backup' keyword arguments can be optionally
forwarded to `filter_file`.
Following comments from Todd:
- the call to tty.debug has been moved deeper, to log the filtering of each file
- the shadowing on the name "kwargs" is avoided
Implemented a declarative syntax for the additional behavior that can
get attached to classes. Implemented a function to filter compiler
wrappers that uses the mechanism above.
- command reference now includes usage for all Spack commands as output
by `spack help`. Each command usage links to any related section in
the docs.
- added `spack commands` command which can list command names,
subcommands, and generate RST docs for commands.
- added `llnl.util.argparsewriter`, which analyzes an argparse parser and
calls hooks for description, usage, options, and subcommands
- Shorten Spack command usage for short options. Short options are now
shown as [-abc] instead of as [-a] [-b] [-c]
- fix bug that mixed long and short options for top-level `spack help`
- Add proper help for `spack buildcache` subcommands
- Reorganize the help categories of Spack commands so that buildcache is
in packaging and diy and setup are now in build.
- previously commands with this argument showed a long list of choices
that were platform specific.
- use a better metavar: {defaults,system,site,user}[/PLATFORM]
Fixes#7159
When activating extensions in external views, the --ignore-conflicts
option was being ignored. In this particular issue the conflict was
for the duplicate __init__ file for multiple python packages in the
same namespace, but in general any conflict for extensions would
cause an error whether or not --ignore-conflicts was set.
This also renames the 'force' option of do_activate to
'with_dependencies' and updates views to call do_activate with this
set to False (since it traverses the dependency dag anyway). This
isn't strictly required, it just avoids redundant calls.
This reorganizes most sections and rewords a significant portion of
the content (including all introductions) but keeps all the examples.
* Remove section 'What happens at subscript time' from tutorial:
it is too detailed for a tutorial
* Move the 'Extra query parameters' and 'Attach attributes to other
packages' sections into a separate grouping 'Other packaging topics'
* move the 'Set variables at build time yourself' section after
'Set environment variables in dependents' section since the latter
is more motivating
* start the 'set environment variables at build-time for yourself'
section with qt as an example
* renamed section 'specs build interface' to 'retrieving library
information' and updated section introduction
* renamed section 'a motivating example' to 'accessing library
dependencies'; split out the material which deals with implementing
.libs for netlib-lapack into a separate section called 'providing
libraries to dependents'. consolidated in material from the section
'single package providing multiple virtual specs' since
netlib-lapack is an example of this (this removes the material
about intel-parallel studio)
* Allow dashes in command names and fix command name handling
- Command should allow dashes in their names like the reest of spack,
e.g. `spack log-parse`
- It might be too late for `spack build-cache` (since it is already
called `spack buildcache`), but we should try a bit to avoid
inconsistencies in naming conventions
- The code was inconsistent about where commands should be called by
their python module name (e.g. `log_parse`) and where the actual
command name should be used (e.g. `log-parse`).
- This made it hard to make a command with a dash in the name, and it
made `SpackCommand` fail to recognize commands with dashes.
- The code now uses the user-facing name with dashes for function
parameters, then converts that the module name when needed.
* Improve performance of log parsing
- A number of regular expressions from ctest_log_parser have really poor
performance, most due to untethered expressions with * or + (i.e., they
don't start with ^, so the repetition has to be checked for every
position in the string with Python's backtracking regex implementation)
- I can't verify that CTest's regexes work with an added ^, so I don't
really want to touch them. I tried adding this and found that it
caused some tests to break.
- Instead of using only "efficient" regular expressions, Added a
prefilter() class that allows the parser to quickly check a
precondition before evaluating any of the expensive regexes.
- Preconditions do things like check whether the string contains "error"
or "warning" (linear time things) before evaluating regexes that would
require them. It's sad that Python doesn't use Thompson string
matching (see https://swtch.com/~rsc/regexp/regexp1.html)
- Even with Python's slow implementation, this makes the parser ~200x
faster on the input we tried it on.
* Add `spack log-parse` command and improve the display of parsed logs
- Add better coloring and line wrapping to the log parse output. This
makes nasty build output look better with the line numbers.
- `spack log-parse` allows the log parsing logic used at the end of
builds to be executed on arbitrary files, which is handy even outside
of spack.
- Also provides a profile option -- we can profile arbitrary files and
show which regular expressions in the magic CTest parser take the most
time.
* Parallelize log parsing
- Log parsing now uses multiple threads for long logs
- Lines from logs are divided into chnks and farmed out to <ncpus>
- Add -j option to `spack log-parse`
* Marking database tests as slow
* Marking url command tests as slow
* Marking every test that uses database as slow
* Marking tests that import files as slow
* Marking gpg tests as slow
* Marking all versions and one list tests as slow
* Added more markers to unit tests + cli option to skip slow tests
Following a discussion with Axel, the generic 'slowtest' marker has been
split into 'db', 'network' and 'maybeslow'. A brief description of the
meaning of each marker has been added to pytest.ini.
A command line option to run only fast tests has been added to
'spack test'
* Don't use classes to group tests together
Reverted grouping tests under a class, as required in the review
* Minor style changes
This attempts to address one of the complaints at #5996 (comment):
> Repo currently caches package instances by Spec, and those Package instances have a Spec.
> This is unnecessary and causes confusion. I think I thought that we'd need to cache instances
> after loading package classes, but really just caching the classes is fine.
With this update, Repo's package cache is removed and Specs cache the package reference themselves. One consequence is that Specs which compare as equal will store separate instances of a Package class (not doing this creates issues for #4595 (comment)).
There were several references to Spec.package that could be replaced with Spec.package_class without any additional modifications. There are still a couple remaining references to Spec.package in Spec that would require adding functionality before replacing (e.g. calling Package.provides and Package.installed).
Note this makes it difficult to mock fetchers for tests which invokes code that reconstructs specs. test_packaging was one example of this where the updates caused a failure (in that case the error was avoided by not making an unnecessary call).
Details:
* Replace instances of spec.package with spec.package_class where a class method is being called
* Remove instances of Repo.get where Spec.package_class can be used in its place
* remove Repo.get caching instances of Package class for specs
* remove redundant check (which is also incorrect now that each spec stores its own copy of its package)
* avoid creating mirror with specs because it copies specs and those copies dont refer to the mocked fetcher (and it is also not required for the test)
* remove checks that are no longer necessary since repo doesn't cache specs
* Cleaned up JUnit report generation on install
The generation of a JUnit report was previously part of the install
command. This commit factors the logic into its own module, and uses
a template for the generation of the report.
It also improves report generation, that now can deal with multiple
specs installed at once. Finally, extending the list of supported
formats is much easier than before, as it entails just writing a
new template.
* Polished report generation + added tests for failures and errors
The generation of a JUnit report has been polished, so that the
stacktrace is correctly displayed with Jenkins JUnit plugin. Standard
error is still not used.
Added unit tests to cover for installation failures and installation
errors.
Avoid adding an "outside" (local home's) python user site directory
during python package installs.
Implements #6611
Fixes packages with auto-find side effects such as `py-setuptools`
that cause `py-matplotlib` to fail to build #6558
The flag_handlers method was being set as a bound method, but when
reset in the package.py file it was being set as an unbound method
(all python2 issues). This gets the underlying function information,
which is the same in either case.
The bug was uncovered for parmetis in #6858. This is a partial fix.
Included are changes to the parmetis package.py file to make use of
flag_handlers.
The feature added in #4611 is currently broken. This commit fixes the
behavior of the command and adds unit tests to ensure the basic semantic
is maintained.
It also changes slightly the behavior of Spec.concretized to avoid
copying caches before the concretization (as this may result in a
wrong hash computation for the DAG).
- Generating the HTML from for >2300 packages from RST in Sphinx seems to
take forever.
- Add an option to `spack list` to generate straight HTML instead.
- This reduces the doc build time to about a minute (from 5 minutes on a mac laptop).
* Vendor ordereddict for python2.6 only
This commit substitutes the custom module 'ordereddict_backport' with
the more known 'ordereddict' and vendors it only for python 2.6. Other
supported versions of python will use 'collections.OrderedDict'.
* Use absolute imports also for python 2.6
See PEP-328 for more information on the subject
* Added provenance of vendored ordereddict
See #6794
This fixes cases where test-only dependencies were omitted from
consideration when modifying the environment at build time. This
includes an update to the python package definition to add
testing-related python extensions to its specialized environment
setup.
This updates the conflict-checking logic to require that the conflict
spec matches exactly and that all fields mentioned in the conflict
spec are present in the concretized spec in order to report a
conflict. This will automatically skip all conflict checks for
dependencies of externals (since externals strip dependencies). This
will not affect non-external packages since all fields and
dependencies are fully specified for such packages.
* Keep track of source and versions for external libraries
* Note source of more obscure libraries
* We aren't upgrading jsonschema after all
* Add note on modifications made to pytest
* add OctavePackage
1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix
* use setup_environment
