Irfan Alibay
Irfan Alibay
## Expected behavior ## The contents of `charges` is always expected to contain partial charges. ## Actual behavior ## For mmtf, formal charges are fed into `charges`, which a) leads...
As of writing, the MDAnalysis docs have `-dev0` entries for 1.0.1, 1.0.2 (which never existed), 2.0.0, 2.1.0, 2.2.0, and 2.3.0. Ideally the `dev` version should be limited to unreleased versions...
Just trying to work out why: 1) we have two coveragerc files 2) codecov is still reporting legacy and due.py Changes made in this Pull Request: - PR Checklist ------------...
H5PY 3.4.0 causes H5MD writer tests fail with PermissionError on Windows (investigate temporary pin)
## Expected behavior ## All tests pass. ## Actual behavior ## For the Windows runners TestH5MDWriterWithRealTrajectory.test_write_with_drivers[core] fails due to a permission error in writing the H5MD file. ## Code to...
## Expected behavior ## For readers which can derive their own `dt` values, passing a value for `dt` to the reader should yield the same behaviour across all readers. ##...
Follow up from #3685 - in order to fix copying of readers we have a rather cumbersome decorator in place. As @lilyminium mentioned it _might_ be possible to get this...
## Expected behavior ## Either creating a universe via `in_memory=True` or using :meth:`transfer_to_memory` should allow me to pass optional kwargs through to the `MemoryReader` creation (they aren't super useful, but...
Github pages is leaving behind quite a lot of artifacts (31 since April) For full list see: ``` curl \ -H "Accept: application/vnd.github.v3+json" \ https://api.github.com/repos/MDAnalysis/mdanalysis/actions/artifacts ``` They have a retention...
As discussed in this thread: https://github.com/MDAnalysis/mdanalysis/pull/2778#discussion_r443195698 the `analysis.__init__` docstring doesn't seem to be used anywhere and is somewhat superseded by `analysis_modules.rst`, thoughts on what to do with this text? Furthermore,...
**Describe the bug** Passing a PDB with residues with insertion codes such as what is demonstrated below leads to a squashed residue rather than two individual ones: ``` ATOM 2601...