fixes#2215fixes#2570fixes#6676fixes#7281closes#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.
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.
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.
'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).
- 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`
- 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- It was repetitive and out of date, and the docs at spack.readthedocs.io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- Remove the outdated specifics, and leave the minimal useful set of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`.
- 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.
- Add command-line scope option to Spack
- Rework structure of main to allow configuration system to raise
errors more naturally
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
- Fixes a bug in `llnl.util.lock`
- Locks in the current directory would fail because the parent directory
was the empty string.
- Fix this and return '.' for the parent of locks in the current
directory.
Replace regex-based target detection for Makefiles with a preliminary "make -q"
to check if a target exists. This does not work for NetBSD make; additional work
is required to detect if NetBSD make is present and to use a regex in that case.
The affected makefile target checks are only performed when the "--test" flag is
added to a "spack install" invocation.
Fixes#8036
Before this PR Package.installed was returning True if the spec prefix
existed, without checking the DB. This is wrong for external packages,
whose prefix exists before being registered into the DB. Now the property
checks for both the prefix and a DB entry.
Spack provides a number of classes based on commonly-used build systems
that users can extend when writing packages; the classes provide functionality
to perform the actions relevant to the build system (e.g. running "configure" for
an Autotools-based package). This adds documentation for classes supporting the
following build systems:
* Makefile
* Autotools
* CMake
* QMake
* SCons
* Waf
This includes build systems for managing extensions of the following packages:
* Perl
* Python
* R
* Octave
This also adds documentation on implementing packages that use a custom build
system (e.g. Perl/CMake).
Spack also provides extendable classes which aggregate functionality for related
sets of packages, e.g. those using CUDA. Documentation is added for
CudaPackage.
- The setup-env.sh script currently makes two calls to spack, but it
should only need to make one.
- Add a fast-path shell setup routine in `main.py` to allow the shell
setup to happen in a single, fast call that doesn't load more than it
needs to.
- This simplifies setup code, as it has to eval what Spack prints
- TODO: consider eventually making the whole setup script the output of a
spack command
* update help of `clean --all` to include `-p`
* remove old orphaned `.pyc` removal
* restrict removal or orphaned pyc files to `lib/spack` and `var/spack`
- Clean up error messages for when a lock can't be created, or when an
exclusive (write) lock can't be taken on a file.
- Add a number of subclasses of LockError to distinguish timeouts from
permission issues.
- Add an explicit check to prevent the user from taking a write lock on a
read-only file.
- We had a check for this for when we try to *upgrade* a lock on an RO
file, but not for an initial write lock attempt.
- Add more tests for different lock permission scenarios.
- write locks previously wrote information about the lock holder (host
and pid), and read locks woudl read this in.
- This is really only for debugging, so only enable it then
- add some tests that target debug info, and improve multiproc lock test
output
When a user specifies a URL for a specific version of a package, Spack originally
would use that URL for all newer versions of the package. This behavior has
proven to be generally more harmful than useful, so this PR removes the feature
such that a version-specific URL override affects only that version.
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available
ccache executable when compiling c/c++ code. This feature is disabled by default
(i.e. "ccache: false") and the documentation is updated with how to enable
ccache support
Functional updates:
- `python` now creates a copy of the `python` binaries when it is added
to a view
- Python extensions (packages which subclass `PythonPackage`) rewrite
their shebang lines to refer to python in the view
- Python packages in the same namespace will not generate conflicts if
both have `...lib/site-packages/namespace-example/__init__.py`
- These `__init__` files will also remain when removing any package in
the namespace until the last package in the namespace is removed
Generally (Updated 2/16):
- Any package can define `add_files_to_view` to customize how it is added
to a view (and at the moment custom definitions are included for
`python` and `PythonPackage`)
- Likewise any package can define `remove_files_from_view` to customize
which files are removed (e.g. you don't always want to remove the
namespace `__init__`)
- Any package can define `view_file_conflicts` to customize what it
considers a merge conflict
- Global activations are handled like views (where the view root is the
spec prefix of the extendee)
- Benefit: filesystem-management aspects of activating extensions are
now placed in views (e.g. now one can hardlink a global activation)
- Benefit: overriding `Package.activate` is more straightforward (see
`Python.activate`)
- Complication: extension packages which have special-purpose logic
*only* when activated outside of the extendee prefix must check for
this in their `add_files_to_view` method (see `PythonPackage`)
- `LinkTree` is refactored to have separate methods for copying a
directory structure and for copying files (since it was found that
generally packages may want to alter how files are copied but still
wanted to copy directories in the same way)
TODOs (updated 2/20):
- [x] additional testing (there is some unit testing added at this point
but more would be useful)
- [x] refactor or reorganize `LinkTree` methods: currently there is a
separate set of methods for replicating just the directory structure
without the files, and a set for replicating everything
- [x] Right now external views (i.e. those not used for global
activations) call `view.add_extension`, but global activations do not
to avoid some extra work that goes into maintaining external views. I'm
not sure if addressing that needs to be done here but I'd like to
clarify it in the comments (UPDATE: for now I have added a TODO and in
my opinion this can be merged now and the refactor handled later)
- [x] Several method descriptions (e.g. for `Package.activate`) are out
of date and reference a distinction between global activations and
views, they need to be updated
- [x] Update aspell package activations
- Spack was assuming that a group with gid == current uid would always exist.
- This was breaking the travis build for macos.
- also fix issue with the DB tarball test finding coverage filesx
- pytest was not reporing the correct version from pytest.__version__.
It reported 'unknown'
- this fixes issues on some systems where system-installed pytest plugins
would try to use the version and convert it to an int
