Thomas Holder

suppress "Separator in survey name" warning

2

Current survex allows introducing survey name "a.b" implicitly and then entering "a" and "b" one after the other without any warnings: ``` ; no warnings 1 2 1.0 0.0 0.0...

allow same name for station and survey

2

Current survex allows the same name for a station and a survex using this syntax: ``` ; no warnings 1 2 1.0 0.0 0.0 2 2.1 1.0 90.0 0.0 2.1...

Document backwards incompatible changes, like --chain -> --keep-chain

1

I just noticed that the PROPKA 2.1 `--chain` argument is now `--keep-chain` (changed in 6f733072be5ee6dfdbe841eb0a8ab7bb7c9b9d24), and `--chain` now takes an argument and has a different meaning (is handled by `PROPKA`)....

mmCIF based PQR format

17

This is a feature request. It would be great if pdb2pqr and apbs could replace the PQR format with a modified mmCIF based format which simply adds a charge (e.g....

new API to export geometry per selection

1

This is a feature request to export geometry per selection. First requested by @jaredsampson on the `pymol-users` mailing list: https://www.mail-archive.com/[email protected]/msg15640.html Input arguments: - atom selection - representation (e.g. `surface` or...

File.as_handle_and_flag

5

Follow-up on https://github.com/biopython/biopython/pull/4377 ("mypy pre-commit hook"). - New function `as_handle_and_flag` - New function `check_handle_mode` - Use `as_handle` or `as_handle_and_flag` where appropriate - Move `_PathLikeTypes`, `_IOSource` and `_TextIOSource` to `Bio.File` module...

- [X] I hereby agree to dual licence this and any previous contributions under both the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_. - [X] I have read the...

Add ruff check to CI

4

Currently checks a single rule (W605) to identitfy invalid escape sequences as reported in https://github.com/mdtraj/mdtraj/issues/1806 Same as https://github.com/mdtraj/mdtraj/pull/1807 but without the code fixes, so the pipeline is expected to fail.

Use raw strings to fix invalid escape sequences

2

Add [ruff](https://beta.ruff.rs/) check of [invalid-escape-sequence (W605)](https://beta.ruff.rs/docs/rules/invalid-escape-sequence/) linter rule to CI pipeline. Fixes https://github.com/mdtraj/mdtraj/issues/1806

DeprecationWarning: invalid escape sequence '\g'

2

I'm getting several "DeprecationWarning: invalid escape sequence". These can also be detected using a linter like `ruff` or `flake8` with the [W605](https://beta.ruff.rs/docs/rules/invalid-escape-sequence/) rule: ```sh ruff check --select W605 mdtraj ```...