Document changes associated with older releases.

Fixes #117.

docs/source/changelog.rst

@@ -5,10 +5,119 @@ Changelog
 v3.4.0
 ======
 
-Backwards Incompatible Changes
-------------------------------
+Changes
+-------
 
-* ``propka --version`` now shows the program version and exits. Previously this
-  option took a version argument to specify the sub-version of propka. However,
-  this was non-functional at least since 2012.
-  (https://github.com/jensengroup/propka/issues/89)
+* Removed PROPKA input support.
+  (`#99 <https://github.com/jensengroup/propka/issues/99>`_)
+
+* Add Python 3.9 support to continuous integration.
+  (`#101 <https://github.com/jensengroup/propka/issues/101>`_)
+
+* Removed logging abstraction from code to facilitate debugging and reduce code bloat.
+  (`#108 <https://github.com/jensengroup/propka/issues/108>`_)
+
+
+Fixes
+-----
+
+* Fixed bug that raised exception when missing amide nitrogen or oxygen.
+  (`#17 <https://github.com/jensengroup/propka/issues/17>`_)
+
+* ``propka --version`` now shows the program version and exits. Previously this option took a version argument to specify the sub-version of propka.
+  However, this was non-functional at least since 2012.
+  (`#89 <https://github.com/jensengroup/propka/issues/89>`_)
+
+* Fix pI reporting in last line of :file:`.pka` file.
+  (`<https://github.com/jensengroup/propka/pull/91>`_)
+
+* Report correct version in :file:`.pka` file header.
+  (`<https://github.com/jensengroup/propka/pull/92>`_)
+
+* Fix handling of multi-model PDB without MODEL 1 entry.
+  (`<https://github.com/jensengroup/propka/issues/96>`_)
+
+* Fixed bug and sped up algorithm for identifying bonds via bounding boxes.
+  (`#97 <https://github.com/jensengroup/propka/issues/97>`_, `#110 <https://github.com/jensengroup/propka/pull/110>`_)
+
+* Fixed bug in ```propka --display-coupled-residues`` that crashed the program.
+  (`#105 <https://github.com/jensengroup/propka/issues/105>`_)
+
+
+v3.3.0
+======
+
+Additions
+---------
+
+* Add Sphinx documentation on `readthedocs.io <https://propka.readthedocs.io>`_
+  (`#69 <https://github.com/jensengroup/propka/issues/69>`_, `#76 <https://github.com/jensengroup/propka/pull/76>`_, `#79 <https://github.com/jensengroup/propka/pull/79>`_)
+
+Changes
+-------
+
+* Updated :func:`read_molecule_file` to accept file-like objects.
+  (`#83 <https://github.com/jensengroup/propka/issues/83>`_)
+
+* Use `versioneer <https://github.com/python-versioneer/python-versioneer>`_ for version management.
+  (`#87 <https://github.com/jensengroup/propka/issues/87>`_)
+
+* Add `code coverage <http://codecov.io>`_ to continuous integration pipeline.
+  (`#62 <https://github.com/jensengroup/propka/pull/62>`_, `#71 <https://github.com/jensengroup/propka/pull/71>`_, `#76 <https://github.com/jensengroup/propka/pull/76>`_)
+
+Fixes
+-----
+
+* Bundle required JSON files with package.
+  (`#48 <https://github.com/jensengroup/propka/issues/48>`_)
+
+* Fixed :class:`KeyError` bug in :func:`read_parameter_file`.
+  (`#65 <https://github.com/jensengroup/propka/pull/65>`_)
+
+* Update links to web server.
+  (`#80 <https://github.com/jensengroup/propka/pull/80>`_)
+
+* Fixed PDB reading for PROPKA "single" runs.
+  (`#82 <https://github.com/jensengroup/propka/issues/82>`_)
+
+
+v3.2.0
+======
+
+Additions
+---------
+
+* Significantly expanded testing framework.
+  (`#30 <https://github.com/jensengroup/propka/pull/30>`_, `#36 <https://github.com/jensengroup/propka/pull/36>`_, `#37 <https://github.com/jensengroup/propka/pull/37>`_)
+
+Changes
+-------
+
+* Improved ability to use PROPKA as a module in other Python scripts.
+  (`#8 <https://github.com/jensengroup/propka/pull/8>`_)
+
+* Improved output via :mod:`logging`.
+  (`#11 <https://github.com/jensengroup/propka/pull/11>`_, `#12 <https://github.com/jensengroup/propka/pull/12>`_)
+
+* Replaced data/parameter pickle file with human-readable JSON.
+  (`#29 <https://github.com/jensengroup/propka/pull/29>`_)
+
+* Significant delinting and formatting standardization against PEP8.
+  (`#33 <https://github.com/jensengroup/propka/pull/33>`_, `#40 <https://github.com/jensengroup/propka/pull/40>`_)
+
+* Improved package documentation.
+  (`#41 <https://github.com/jensengroup/propka/pull/41>`_, `#61 <https://github.com/jensengroup/propka/pull/61>`_)
+
+* Significant package refactoring.
+  (`#46 <https://github.com/jensengroup/propka/issues/46>`_, `#47 <https://github.com/jensengroup/propka/pull/47>`_, `#59 <https://github.com/jensengroup/propka/pull/59>`_)
+
+* Simplify module import structure.
+  (`#49 <https://github.com/jensengroup/propka/issues/49>`_, `#61 <https://github.com/jensengroup/propka/pull/61>`_)
+
+* Improved tempfile handling.
+  (`#61 <https://github.com/jensengroup/propka/pull/61>`_)
+
+v3.1.0
+======
+
+*Archaeologists wanted* to help us document the history of the code in versions 3.1.0 and earlier.