Propka

Changes
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* Add more static typing and associated tests (177)
* Refactor deprecated `pkg_resources` usage (176)
* Increase number of valence electrons for ligand atoms (169 170)

Fixes
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* Fix topping up from all conformations, not just first (167)

Changes
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* Remove support for Python 3.6 and 3.7; add support for up to Python 3.11 ([154](https://github.com/jensengroup/propka/issues/154) and [#150](https://github.com/jensengroup/propka/pull/150))
* Add context manager for `open_file_for_reading` ([133](https://github.com/jensengroup/propka/pull/133))

Fixes
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* Fix precision of `MolecularContainer.get_pi()` ([148](https://github.com/jensengroup/propka/pull/148))
* Rename vanadium from `Va` to `V` ([141](https://github.com/jensengroup/propka/pull/141>))
* Fix rounding issues in folding profile reporting ([124](https://github.com/jensengroup/propka/pull/124))
* Fix malfunctioning `-g -w` command line options ([124](https://github.com/jensengroup/propka/pull/124))

Changes
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* Removed PROPKA input support and argument `--generate-propka-input` (99).
* Add Python 3.9 support to continuous integration (101).
* Removed logging abstraction from code to facilitate debugging and reduce code bloat (108).

Fixes
-----

* Fixed bug that raised exception when missing amide nitrogen or oxygen (17).
* `propka --version` now shows the program version and exits (89). Previously this option took a version argument to specify the sub-version of propka. However, this was non-functional at least since 2012.
* Fix pI reporting in last line of `.pka` file (91).
* Report correct version in `.pka` file header (92).
* Fix handling of multi-model PDB without MODEL 1 entry (96).
* Fixed bug and sped up algorithm for identifying bonds via bounding boxes (97, 110).
* Fixed bug in `propka --display-coupled-residues` that crashed the program (105).

This release contains bug fixes, new features, and API changes that are _backwards compatible_ to release 3.2.0.

* `run.single()` works again as documented (issue 82)
* support for using streams as input PDB file was added back (issue 83 and see also 57) with a new and improved API

From this release onwards, PROPKA will follow [semantic versioning](https://semver.org/).

This version of PROPKA contains refactoring and API changes that may affect external dependencies. This release does not include major new features nor does it include significant changes to user experience.