* new package: py-kb-python + dependencies
- py-loompy
- py-ngs-tools
- py-numpy-groupies
* Update var/spack/repos/builtin/packages/py-kb-python/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-shortuuid: add version 1.0.11
* Update var/spack/repos/builtin/packages/py-shortuuid/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update packages config to indicate that MSVC is the preferred compiler
* Update packages config to indicate that msmpi is the preferred MPI provider
* Fix msmpi external detection
Spack imports `pytest`, which *can* import `numpy`. Recent versions of `numpy` require
Python 3.8 or higher, and they use 3.8 type annotations in their type stubs (`.pyi`
files). At the same time, we tell `mypy` to target Python 3.7, as we still support older
versions of Python.
What all this means is that if you run `mypy` on `spack`, `mypy` will follow all the
static import statements, and it ends up giving you this error when it finds numpy stuff
that is newer than the target Python version:
```
==> Running mypy checks
src/spack/var/spack/environments/default/.spack-env/._view/4g7jd4ibkg4gopv4rosq3kn2vsxrxm2f/lib/python3.11/site-packages/numpy/__init__.pyi:638: error: Positional-only parameters are only supported in Python 3.8 and greater [syntax]
Found 1 error in 1 file (errors prevented further checking)
mypy found errors
```
We can fix this by telling `mypy` to skip all imports of `numpy` in `pyproject.toml`:
```toml
[[tool.mypy.overrides]]
module = 'numpy'
follow_imports = 'skip'
follow_imports_for_stubs = true
```
- [x] don't follow imports from `numpy` in `mypy`
- [x] get rid of old rule not to follow `jinja2` imports, as we now require Python 3
The code in Spack to generate install and test reports currently suffers from unneeded complexity. For
instance, we have classes in Spack core packages, like `spack.reporters.CDash`, that need an
`argparse.Namespace` to be initialized and have "hard-coded" string literals on which they branch to
change their behavior:
```python
if do_fn.__name__ == "do_test" and skip_externals:
package["result"] = "skipped"
else:
package["result"] = "success"
package["stdout"] = fetch_log(pkg, do_fn, self.dir)
package["installed_from_binary_cache"] = pkg.installed_from_binary_cache
if do_fn.__name__ == "_install_task" and installed_already:
return
```
This PR attempt to polish the major issues encountered in both `spack.report` and `spack.reporters`.
Details:
- [x] `spack.reporters` is now a package that contains both the base class `Reporter` and all
the derived classes (`JUnit` and `CDash`)
- [x] Classes derived from `spack.reporters.Reporter` don't take an `argparse.Namespace` anymore
as argument to `__init__`. The rationale is that code for commands should be built upon Spack
core classes, not vice-versa.
- [x] An `argparse.Action` has been coded to create the correct `Reporter` object based on command
line arguments
- [x] The context managers to generate reports from either `spack install` or from `spack test` have
been greatly simplified, and have been made less "dynamic" in nature. In particular, the `collect_info`
class has been deleted in favor of two more specific context managers. This allows for a simpler
structure of the code, and less knowledge required to client code (in particular on which method to patch)
- [x] The `InfoCollector` class has been turned into a simple hierarchy, so to avoid conditional statements
within methods that assume a knowledge of the context in which the method is called.
On systems with remote groups, the primary user group may be remote and may not exist on
the local system (i.e., it might just be a number). On the CLI, it looks like this:
```console
> touch foo
> l foo
-rw-r--r-- 1 gamblin2 57095 0 Dec 29 22:24 foo
> chmod 2000 foo
chmod: changing permissions of 'foo': Operation not permitted
```
Here, the local machine doesn't know about per-user groups, so they appear as gids in
`ls` output. `57095` is also `gamblin2`'s uid, but the local machine doesn't know that
`gamblin2` is in the `57095` group.
Unfortunately, it seems that Python's `os.chmod()` just fails silently, setting
permissions to `0o0000` instead of `0o2000`. We can avoid this by ensuring that the file
has a group the user is known to be a member of.
- [x] Add `ensure_known_group()` in the permissions tests.
- [x] Call `ensure_known_group()` on tempfile in `test_chmod_real_entries_ignores_suid_sgid`.
There are a number of places in our docstrings where we write "list of X" as the type, even though napoleon doesn't actually support this. It ends up causing warnings when generating docs.
Now that we require Python 3, we don't have to rely on type hints in docs -- we can just use Python type hints and omit the types of args and return values from docstrings.
We should probably do this for all types in docstrings eventually, but this PR focuses on the ones that generate warnings during doc builds.
Some `mypy` annoyances we should consider in the future:
1. Adding some of these type annotations gets you:
```
note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked]
```
because they are in unannotated functions (like constructors where we don't really need any annotations).
You can silence these with `disable_error_code = "annotation-unchecked"` in `pyproject.toml`
2. Right now we support running `mypy` in Python `3.6`. That means we have to support `mypy` `.971`, which does not support `disable_error_code = "annotation-unchecked"`, so I just filter `[annotation-unchecked]` lines out in `spack style`.
3. I would rather just turn on `check_untyped_defs` and get more `mypy` coverage everywhere, but that will require about 1,000 fixes. We should probably do that eventually.
4. We could also consider only running `mypy` on newer python versions. This is not easy to do while supporting `3.6`, because you have to use `if TYPE_CHECKING` for a lot of things to ensure that 3.6 still parses correctly. If we only supported `3.7` and above we could use [`from __future__ import annotations`](https://mypy.readthedocs.io/en/stable/runtime_troubles.html#future-annotations-import-pep-563), but we have to support 3.6 for now. Sigh.
- [x] Convert a number of docstring types to Python type hints
- [x] Get rid of "list of" wherever it appears
