From d87afb3df55d97080756c3739af1f856d2b5a94d Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sun, 13 Dec 2020 16:49:26 -0800 Subject: [PATCH] Document changes associated with older releases. Fixes #117. --- docs/source/changelog.rst | 121 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 115 insertions(+), 6 deletions(-) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 05f7afe..1ea49bc 100644 --- a/docs/source/changelog.rst +++ b/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 `_) + +* 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. Previously this option took a version argument to specify the sub-version of propka. + However, this was non-functional at least since 2012. + (`#89 `_) + +* Fix pI reporting in last line of :file:`.pka` file. + (``_) + +* Report correct version in :file:`.pka` file header. + (``_) + +* Fix handling of multi-model PDB without MODEL 1 entry. + (``_) + +* 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 `_) + + +v3.3.0 +====== + +Additions +--------- + +* Add Sphinx documentation on `readthedocs.io `_ + (`#69 `_, `#76 `_, `#79 `_) + +Changes +------- + +* Updated :func:`read_molecule_file` to accept file-like objects. + (`#83 `_) + +* Use `versioneer `_ for version management. + (`#87 `_) + +* Add `code coverage `_ to continuous integration pipeline. + (`#62 `_, `#71 `_, `#76 `_) + +Fixes +----- + +* Bundle required JSON files with package. + (`#48 `_) + +* Fixed :class:`KeyError` bug in :func:`read_parameter_file`. + (`#65 `_) + +* Update links to web server. + (`#80 `_) + +* Fixed PDB reading for PROPKA "single" runs. + (`#82 `_) + + +v3.2.0 +====== + +Additions +--------- + +* Significantly expanded testing framework. + (`#30 `_, `#36 `_, `#37 `_) + +Changes +------- + +* Improved ability to use PROPKA as a module in other Python scripts. + (`#8 `_) + +* Improved output via :mod:`logging`. + (`#11 `_, `#12 `_) + +* Replaced data/parameter pickle file with human-readable JSON. + (`#29 `_) + +* Significant delinting and formatting standardization against PEP8. + (`#33 `_, `#40 `_) + +* Improved package documentation. + (`#41 `_, `#61 `_) + +* Significant package refactoring. + (`#46 `_, `#47 `_, `#59 `_) + +* Simplify module import structure. + (`#49 `_, `#61 `_) + +* Improved tempfile handling. + (`#61 `_) + +v3.1.0 +====== + +*Archaeologists wanted* to help us document the history of the code in versions 3.1.0 and earlier. \ No newline at end of file