Pdb2pqr

Changes

* Updated Python versions to 3.11-3.13 (https://github.com/Electrostatics/pdb2pqr/issues/414)
* Linting/formatting changes (https://github.com/Electrostatics/pdb2pqr/issues/409, https://github.com/Electrostatics/pdb2pqr/issues/411, https://github.com/Electrostatics/pdb2pqr/issues/412)
* Simplified Python build system and test matrix (https://github.com/Electrostatics/pdb2pqr/issues/404, https://github.com/Electrostatics/pdb2pqr/issues/420)
* Improved test suite (https://github.com/Electrostatics/pdb2pqr/pull/379, https://github.com/Electrostatics/pdb2pqr/pull/382, https://github.com/Electrostatics/pdb2pqr/pull/410, https://github.com/Electrostatics/pdb2pqr/pull/414)
* Updated Sphinx versions (https://github.com/Electrostatics/pdb2pqr/issues/384)

Fixes

* Removed unnecessary binary (https://github.com/Electrostatics/pdb2pqr/pull/418)
* Fix module shadowing (https://github.com/Electrostatics/pdb2pqr/pull/402)
* Fixed editable installs (https://github.com/Electrostatics/pdb2pqr/pull/372)
* Documentation updates (https://github.com/Electrostatics/pdb2pqr/pull/364, https://github.com/Electrostatics/pdb2pqr/pull/366)

Changes
=======

* Added warnings about ignored PROPKA options (365)

Fixes
=====

* Fixed problem locating files with editable installations (6)
* Fixed broken links in documentation (363)

Known issues
============

* There is a confirmed issue with naming using the CHARMM force field for uncommon protonation states (358)
* There is a potential problem adding hydrogens to non-experimental computer-generated structures (365)

Fixes
=====

* Fixed problems with documentation build (348)

Fixes
=====

* Fix problems with protonated terminal residue naming (301)
* Fix problem with terminal histidine protonation (301)

Changes
=======

* Rename `pdb2pqr30` to `pdb2pqr`. The old `pdb2pqr30` executable is still available but will be deprecated in a future release.
* Update Python version support for compatibility with PROPKA (342); minimal supported Python is 3.8, highest tested is 3.11
* Eliminate need for extra temporary file (315)
* Add support for cyclic peptides (307)

Fixes
===

* Fixes problems with XML parsing of large files (293)

Changes
=======

* Add support for integer-only residue names (291).
* Remove temporary files created by PDB2PQR (286).