Markus Gerstel

Add support for PEP 519 (file system path protocol)

3

Gemmi currently cannot deal with python path protocol objects ([PEP 519](https://www.python.org/dev/peps/pep-0519/), [PEP 428](https://www.python.org/dev/peps/pep-0428/)): ```bash $ python -c "import gemmi,pathlib; gemmi.cif.read_file(pathlib.Path('z'))" Traceback (most recent call last): File "", line 1, in...

pypi source package fundamentally broken

2

``` $ pip install --no-binary :all: cmakelang Collecting cmakelang Downloading cmakelang-0.6.13.tar.gz (123 kB) |████████████████████████████████| 123 kB 7.9 MB/s ERROR: Command errored out with exit status 1: command: python3.8 -c 'import...

```bash $ wget https://files.pythonhosted.org/packages/74/c0/75d4806cf21dcb4198e9fba02f4d2fa61c8db919b7db788862d9cd5f4433/cmakelang-0.6.13.tar.gz -O - | tar xvz cmakelang-0.6.13/ cmakelang-0.6.13/README.rst cmakelang-0.6.13/setup.cfg cmakelang-0.6.13/cmakelang/ cmakelang-0.6.13/cmakelang/annotate.py cmakelang-0.6.13/cmakelang/config_util.py cmakelang-0.6.13/cmakelang/render.py cmakelang-0.6.13/cmakelang/format/ cmakelang-0.6.13/cmakelang/format/layout_tests.py cmakelang-0.6.13/cmakelang/format/invocation_tests.py cmakelang-0.6.13/cmakelang/format/__main__.py cmakelang-0.6.13/cmakelang/format/__init__.py cmakelang-0.6.13/cmakelang/format/formatter.py cmakelang-0.6.13/cmakelang/__init__.py cmakelang-0.6.13/cmakelang/markup.py cmakelang-0.6.13/cmakelang/parse/ cmakelang-0.6.13/cmakelang/parse/statement_node.py cmakelang-0.6.13/cmakelang/parse/simple_nodes.py cmakelang-0.6.13/cmakelang/parse/printer.py cmakelang-0.6.13/cmakelang/parse/__init__.py cmakelang-0.6.13/cmakelang/parse/funs/...

Make cctbx_project version number programmatically accessible

2

Could we please have a way to programmatically determine the installed `cctbx_project` package version? I'm thinking something along the lines of ``` __version_tuple__ = (2020, 11) __version__ = ".".join(str(_n) for...

test cctbx/regression/tst_grm_modifications.py broken

5

And has been since [at least March 2019](https://github.com/dials/cctbx/commit/d0701c3608db4313ebbcc37597d2a3324aaec60c). As the test is skipped unless CCP4 is present we only notice its failure during our release process, at which point we...

Remove boost.python.injector

1

This is known to not work in Python 3 and its continued availability makes debugging harder than necessary. Any places still refering to `boost.python.injector` should use the `@boost.python.inject_into` decorator instead....

Test in #421 is failing, but libtbx testing mistakenly treats it as success and only notes the standard error output. The test is not listed in the "This-is-broken-this-is-fine" category. ```...

smtbx/refinement/restraints/tests/tst_restraints.py broken on Python 3

1

loads of tests still failing on python 3. This one is run by azure: https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=184 `libtbx.python smtbx/refinement/restraints/tests/tst_restraints.py --verbose --scatterers=5 --resolution=0.2` ``` Standard error: Traceback (most recent call last): File "/__w/1/modules/cctbx_project/smtbx/refinement/restraints/tests/tst_restraints.py",...

boost_adaptbx/tests/tst_python_streambuf.py failing on python 3

2

loads of tests still failing on python 3. This one is run by azure: https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=184 ``` Standard error: Traceback (most recent call last): File "/__w/1/modules/cctbx_project/boost_adaptbx/tests/tst_python_streambuf.py", line 7, in import StringIO...

loads of tests still failing on python 3. This one is run by azure: https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=184 ``` Standard error: Traceback (most recent call last): File "/__w/1/modules/cctbx_project/cctbx/regression/tst_xray.py", line 1465, in run() File...