- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
I lost my mind a bit after getting the completion stuff working and
decided to get Mypy working for spack as well. This adds a
`.mypy.ini` that checks all of the spack and llnl modules, though
not yet packages, and fixes all of the identified missing types and
type issues for the spack library.
In addition to these changes, this includes:
* rename `spack flake8` to `spack style`
Aliases flake8 to style, and just runs flake8 as before, but with
a warning. The style command runs both `flake8` and `mypy`,
in sequence. Added --no-<tool> options to turn off one or the
other, they are on by default. Fixed two issues caught by the tools.
* stub typing module for python2.x
We don't support typing in Spack for python 2.x. To allow 2.x to
support `import typing` and `from typing import ...` without a
try/except dance to support old versions, this adds a stub module
*just* for python 2.x. Doing it this way means we can only reliably
use all type hints in python3.7+, and mypi.ini has been updated to
reflect that.
* add non-default black check to spack style
This is a first step to requiring black. It doesn't enforce it by
default, but it will check it if requested. Currently enforcing the
line length of 79 since that's what flake8 requires, but it's a bit odd
for a black formatted project to be quite that narrow. All settings are
in the style command since spack has no pyproject.toml and I don't
want to add one until more discussion happens. Also re-format
`style.py` since it no longer passed the black style check
with the new length.
* use style check in github action
Update the style and docs action to use `spack style`, adding in mypy
and black to the action even if it isn't running black right now.
Users can add test() methods to their packages to run smoke tests on
installations with the new `spack test` command (the old `spack test` is
now `spack unit-test`). spack test is environment-aware, so you can
`spack install` an environment and then run `spack test run` to run smoke
tests on all of its packages. Historical test logs can be perused with
`spack test results`. Generic smoke tests for MPI implementations, C,
C++, and Fortran compilers as well as specific smoke tests for 18
packages.
Inside the test method, individual tests can be run separately (and
continue to run best-effort after a test failure) using the `run_test`
method. The `run_test` method encapsulates finding test executables,
running and checking return codes, checking output, and error handling.
This handles the following trickier aspects of testing with direct
support in Spack's package API:
- [x] Caching source or intermediate build files at build time for
use at test time.
- [x] Test dependencies,
- [x] packages that require a compiler for testing (such as library only
packages).
See the packaging guide for more details on using Spack testing support.
Included is support for package.py files for virtual packages. This does
not change the Spack interface, but is a major change in internals.
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Co-authored-by: wspear <wjspear@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
If the Python used by Spack does not include Setuptools, then
'spack test' will fail because Spack's vendored pytest dependency
imports and uses Setuptools in some of its functions. It turns out
that Spack doesn't use the functionality those methods enable, so
this PR removes those functions and thereby allows 'spack test' to
run without Setuptools.
* Buildcache: Install into non-default directory layouts
Store a dictionary mapping of original dependency prefixes to dependency hashes
Use the loaded spec to grab the new dependency prefixes in the new directory layout.
Map the original dependency prefixes to the new dependency prefixes using the dependency hashes.
Use the dependency prefixes map to replace original rpaths with new rpaths preserving the order.
For mach-o binaries, use the dependency prefixes map to replace the dependency library entires for libraries and executables and the replace the library id for libraries.
On Linux, patchelf is used to replace the rpaths of elf binaries.
On macOS, install_name_tool is used to replace the rpaths and dependency libraries of mach-o binaries and the id of mach-o libraries.
On Linux, macholib is used to replace the dependency libraries of mach-o binaries and the id of mach-o libraries.
Binary text with padding replacement is attempted for all binaries for the following paths:
spack layout root
spack prefix
sbang script location
dependency prefixes
package prefix
Text replacement is attempted for all text files using the paths above.
Symbolic links to the absolute path of the package install prefix are replaced, all others produce warnings.
This commit removes the `python_version.py` unit test module
and the vendored dependencies `pyqver2.py` and `pyqver3.py`.
It substitutes them with an equivalent check done using
`vermin` that is run as a separate workflow via Github Actions.
This allows us to delete 2 vendored dependencies that are unmaintained
and substitutes them with a maintained tool.
Also, updates the list of vendored dependencies.
Spack doesn't need `requests`, and neither does `jsonschema`, but
`jsonschema` tries to import it, and it'll succeed if `requests` is on
your machine (which is likely, given how popular it is). This commit
removes the import to improve Spack's startup time a bit.
On a mac with SSD, the import of requests is ~28% of Spack's startup time
when run as `spack --print-shell-vars sh,modules` (.069 / .25 seconds),
which is what `setup-env.sh` runs.
On a Linux cluster where Python is mounted from NFS, this reduces
`setup-env.sh` source time from ~1s to .75s.
Note: This issue will be eliminated if we upgrade to a newer `jsonschema`
(we'd need to drop Python 2.6 for that). See
https://github.com/Julian/jsonschema/pull/388.
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
- 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
- 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`
* 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`
* 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
* 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
- This steals the magic regular expressions that CTest uses to parse log
files and addds them to Spack. See here:
https://github.com/Kitware/CMake/blob/master/Source/CTest/cmCTestBuildHandler.cxx
These are BSD licensed, so the port is in `externa/ctest_log_parser.py`
- We currently use these to do better filtering of errors from build
output. Plan is to use them to generate good CDash output.
* Module files now are generated using a template engine refers #2902#3173
jinja2 has been hooked into Spack.
The python module `modules.py` has been splitted into several modules
under the python package `spack/modules`. Unit tests stressing module
file generation have been refactored accordingly.
The module file generator for Lmod has been extended to multi-providers
and deeper hierarchies.
* Improved the support for templates in module files.
Added an entry in `config.yaml` (`template_dirs`) to list all the
directories where Spack could find templates for `jinja2`.
Module file generators have a simple override mechanism to override
template selection ('modules.yaml' beats 'package.py' beats 'default').
* Added jinja2 and MarkupSafe to vendored packages.
* Spec.concretize() sets mutual spec-package references
The correct place to set the mutual references between spec and package
objects at the end of concretization. After a call to concretize we
should now be ensured that spec is the same object as spec.package.spec.
Code in `build_environment.py` that was performing the same operation
has been turned into an assertion to be defensive on the new behavior.
* Improved code and data layout for modules and related tests.
Common fixtures related to module file generation have been extracted
in `conftest.py`. All the mock configurations for module files have been
extracted from python code and have been put into their own yaml file.
Added a `context_property` decorator for the template engine, to make
it easy to define dictionaries out of properties.
The default for `verbose` in `modules.yaml` is now False instead of True.
* Extendable module file contexts + short description from docstring
The contexts that are used in conjunction with `jinja2` templates to
generate module files can now be extended from package.py and
modules.yaml.
Module files generators now infer the short description from package.py
docstring (and as you may expect it's the first paragraph)
* 'module refresh' regenerates all modules by default
`module refresh` without `--module-type` specified tries to
regenerate all known module types. The same holds true for `module rm`
Configure options used at build time are extracted and written into the
module files where possible.
* Fixed python3 compatibility, tests for Lmod and Tcl.
Added test for exceptional paths of execution when generating Lmod
module files.
Fixed a few compatibility issues with python3.
Fixed a bug in Tcl with naming_scheme and autoload + unit tests
* Updated module file tutorial docs. Fixed a few typos in docstrings.
The reference section for module files has been reorganized. The idea is
to have only three topics at the highest level:
- shell support + spack load/unload use/unuse
- module file generation (a.k.a. APIs + modules.yaml)
- module file maintenance (spack module refresh/rm)
Module file generation will cover the entries in modules.yaml
Also:
- Licenses have been updated to include NOTICE and extended to 2017
- docstrings have been reformatted according to Google style
* Removed redundant arguments to RPackage and WafPackage.
All the callbacks in `RPackage` and `WafPackage` that are not build
phases have been modified not to accept a `spec` and a `prefix`
argument. This permits to leverage the common `configure_args` signature
to insert by default the configuration arguments into the generated
module files. I think it's preferable to handling those packages
differently than `AutotoolsPackage`. Besides only one package seems
to override one of these methods.
* Fixed broken indentation + improved resiliency of refresh
Fixed broken indentation in `spack module refresh` (probably a rebase
gone silently wrong?). Filter the writers for blacklisted specs before
searching for name clashes. An error with a single writer will not
stop regeneration, but instead will print a warning and continue
the command.
- Get rid of pkgsort() usage for preferred variants.
- Concretization is now entirely based on key-based sorting.
- Remove PreferredPackages class and various spec cmp() methods.
- Replace with PackagePrefs class that implements a key function for
sorting according to packages.yaml.
- Clear package pref caches on config test.
- Explicit compare methods instead of total_ordering in Version.
- Our total_ordering backport wasn't making Python 3 happy for some
reason.
- Python 3's functools.total_ordering and spelling the operators out
fixes the problem.
- Fix unicode issues with spec hashes, json, & YAML
- Try to use str everywhere and avoid unicode objects in python 2.
- Update YAML version to support Python 3
- Python 3 support for ordereddict backport
- Exclude Python3 YAML from version tests.
- Vendor six into Spack.
- Make Python version-check tests work with Python 3
- Add ability to add version check exceptions with '# nopyqver' line
comments.
* Removing the nobuild, nolink, and alldeps dependency types in favor of being explicit.
* This will help with maintenance going forward, as adding more dependency types won't affect existing declared dependencies in weird ways.
* default deptype is still `('build', 'link')`
* Porting: substitute nose with ytest
This huge commit substitutes nose with pytest as a testing system. Things done here:
* deleted external/nose as it is no longer used
* moved mock resources in their own directory 'test/mock/'
* ported two tests (cmd/find, build_system) to pytest native syntax as an example
* build_environment, log: used monkeypatch instead of try/catch
* moved global mocking of fetch_cache to an auto-used fixture
* moved global mocking from test/__init__.py to conftest.py
* made `spack test` a wrapper around pytest
* run-unit-tests: avoid running python 2.6 tests under coverage to speed them up
* use `pytest --cov` instead of coverage run to cut down testing time
* mock/packages_test: moved mock yaml configuration to files instead of leaving it in the code as string literals
* concretize.py: ported tests to native pytest, reverted multiprocessing in pytest.ini as it was creating the wrong report for coveralls
* conftest.py, fixtures: added docstrings
* concretize_preferences.py: uses fixtures instead of subclassing MockPackagesTest
* directory_layout.py: uses fixtures instead of subclassing MockPackagesTest
* install.py: uses fixtures instead of subclassing MockPackagesTest
* optional_deps.py: uses fixtures instead of subclassing MockPackagesTest
optional_deps.py: uses fixtures instead of subclassing MockPackagesTest
* packages.py: uses fixtures instead of subclassing MockPackagesTest
* provider_index.py: uses fixtures instead of subclassing MockPackagesTest
* spec_yaml.py: uses fixtures instead of subclassing MockPackagesTest
* multimethod.py: uses fixtures instead of subclassing MockPackagesTest
* install.py: now uses mock_archive_url
* git_fetch.py: uses fixtures instead of subclassing MockPackagesTest
* hg_fetch.py: uses fixtures instead of subclassing MockPackagesTest
* svn_fetch.py, mirror.py: uses fixtures instead of subclassing MockPackagesTest
repo.py: deleted
* test_compiler_cmd.py: uses fixtures instead of subclassing MockPackagesTest
* cmd/module.py, cmd/uninstall.py: uses fixtures instead of subclassing MockDatabase
* database.py: uses fixtures instead of subclassing MockDatabase, removed mock/database
* pytest: uncluttering fixture implementations
* database: changing the scope to 'module'
* config.py: uses fixtures instead of subclassing MockPackagesTest
* spec_dag.py, spec_semantics.py: uses fixtures instead of subclassing MockPackagesTest
* stage.py: uses fixtures instead of subclassing MockPackagesTest. Removed mock directory
* pytest: added docstrings to all the fixtures
* pytest: final cleanup
* build_system_guess.py: fixed naming and docstrings as suggested by @scheibelp
* spec_syntax.py: added expected failure on parsing multiple specs closes#1976
* Add pytest and pytest-cov to Spack externals.
* Make `spack flake8` ignore externals.
* run-unit-tests runs spack test and not pytest.
* Remove all the special stuff for `spack test`
- Remove `conftest.py` magic and all the special case stuff in `bin/spack`
- Spack commands can optionally take unknown arguments, if they want to
handle them.
- `spack test` is now a command like the others.
- `spack test` now just delegates its arguments to `pytest`, but it does
it by receiving unknown arguments and NOT taking an explicit
help argument.
* Fix error in fixtures.
* Improve `spack test` command a bit.
- Now supports an approximation of the old simple interface
- Also supports full pytest options if you want them.
* Use external coverage instead of pytest-cov
* Make coverage use parallel-mode.
* change __init__.py docs to include pytest
* Ensure that every package has a license
Also fixes URLs with http://http:// doubled.
This is a continuation of #2656.
* Add license to every file in Spack
* Make sure Todd is the author of all packages
* Fix flake8 tests
* Don't license external Sphinx docs
* Don't display licenses in tutorial example packages
Also fixes typos and converts command-line examples
from tcsh to bash, which is more common
