152 lines
5.2 KiB
ReStructuredText
152 lines
5.2 KiB
ReStructuredText
*********
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Changelog
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*********
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Current version
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===============
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Changes
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-------
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* Remove support for Python 3.6 and 3.7; add support for up to Python 3.11
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(`#154 <https://github.com/jensengroup/propka/issues/154>`_ and
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`#150 <https://github.com/jensengroup/propka/pull/150>`_)
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* Add context manager for ``open_file_for_reading``
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(`#133 <https://github.com/jensengroup/propka/pull/133>`_)
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Fixes
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-----
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* Fix precision of ``MolecularContainer.get_pi()``
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(`#148 <https://github.com/jensengroup/propka/pull/148>`_)
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* Rename vanadium from ``Va`` to ``V``
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(`#141 <https://github.com/jensengroup/propka/pull/141>`_)
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* Fix rounding issues
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(`#124 <https://github.com/jensengroup/propka/pull/124>`_)
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* Fix malfunctioning ``-g -w`` command line options
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(`#124 <https://github.com/jensengroup/propka/pull/124>`_)
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v3.4.0 (2020-12-19)
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===================
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Changes
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-------
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* Removed PROPKA input support and argument ``--generate-propka-input``
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(`#99 <https://github.com/jensengroup/propka/issues/99>`_)
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* Add Python 3.9 support to continuous integration.
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(`#101 <https://github.com/jensengroup/propka/issues/101>`_)
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* Removed logging abstraction from code to facilitate debugging and reduce code bloat.
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(`#108 <https://github.com/jensengroup/propka/issues/108>`_)
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Fixes
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-----
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* Fixed bug that raised exception when missing amide nitrogen or oxygen.
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(`#17 <https://github.com/jensengroup/propka/issues/17>`_)
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* ``propka --version`` now shows the program version and exits. Previously this option took a version argument to specify the sub-version of propka.
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However, this was non-functional at least since 2012.
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(`#89 <https://github.com/jensengroup/propka/issues/89>`_)
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* Fix pI reporting in last line of :file:`.pka` file.
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(`<https://github.com/jensengroup/propka/pull/91>`_)
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* Report correct version in :file:`.pka` file header.
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(`<https://github.com/jensengroup/propka/pull/92>`_)
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* Fix handling of multi-model PDB without MODEL 1 entry.
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(`<https://github.com/jensengroup/propka/issues/96>`_)
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* Fixed bug and sped up algorithm for identifying bonds via bounding boxes.
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(`#97 <https://github.com/jensengroup/propka/issues/97>`_, `#110 <https://github.com/jensengroup/propka/pull/110>`_)
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* Fixed bug in ``propka --display-coupled-residues`` that crashed the program.
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(`#105 <https://github.com/jensengroup/propka/issues/105>`_)
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v3.3.0 (2020-07-18)
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===================
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Additions
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---------
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* Add Sphinx documentation on `readthedocs.io <https://propka.readthedocs.io>`_
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(`#69 <https://github.com/jensengroup/propka/issues/69>`_, `#76 <https://github.com/jensengroup/propka/pull/76>`_, `#79 <https://github.com/jensengroup/propka/pull/79>`_)
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Changes
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-------
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* Updated :func:`read_molecule_file` to accept file-like objects.
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(`#83 <https://github.com/jensengroup/propka/issues/83>`_)
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* Use `versioneer <https://github.com/python-versioneer/python-versioneer>`_ for version management.
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(`#87 <https://github.com/jensengroup/propka/issues/87>`_)
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* Add `code coverage <http://codecov.io>`_ to continuous integration pipeline.
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(`#62 <https://github.com/jensengroup/propka/pull/62>`_, `#71 <https://github.com/jensengroup/propka/pull/71>`_, `#76 <https://github.com/jensengroup/propka/pull/76>`_)
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Fixes
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-----
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* Bundle required JSON files with package.
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(`#48 <https://github.com/jensengroup/propka/issues/48>`_)
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* Fixed :class:`KeyError` bug in :func:`read_parameter_file`.
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(`#65 <https://github.com/jensengroup/propka/pull/65>`_)
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* Update links to web server.
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(`#80 <https://github.com/jensengroup/propka/pull/80>`_)
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* Fixed PDB reading for PROPKA "single" runs.
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(`#82 <https://github.com/jensengroup/propka/issues/82>`_)
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v3.2.0 (2020-06-19)
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===================
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Additions
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---------
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* Significantly expanded testing framework.
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(`#30 <https://github.com/jensengroup/propka/pull/30>`_, `#36 <https://github.com/jensengroup/propka/pull/36>`_, `#37 <https://github.com/jensengroup/propka/pull/37>`_)
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Changes
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-------
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* Improved ability to use PROPKA as a module in other Python scripts.
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(`#8 <https://github.com/jensengroup/propka/pull/8>`_)
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* Improved output via :mod:`logging`.
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(`#11 <https://github.com/jensengroup/propka/pull/11>`_, `#12 <https://github.com/jensengroup/propka/pull/12>`_)
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* Replaced data/parameter pickle file with human-readable JSON.
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(`#29 <https://github.com/jensengroup/propka/pull/29>`_)
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* Significant delinting and formatting standardization against PEP8.
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(`#33 <https://github.com/jensengroup/propka/pull/33>`_, `#40 <https://github.com/jensengroup/propka/pull/40>`_)
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* Improved package documentation.
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(`#41 <https://github.com/jensengroup/propka/pull/41>`_, `#61 <https://github.com/jensengroup/propka/pull/61>`_)
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* Significant package refactoring.
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(`#46 <https://github.com/jensengroup/propka/issues/46>`_, `#47 <https://github.com/jensengroup/propka/pull/47>`_, `#59 <https://github.com/jensengroup/propka/pull/59>`_)
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* Simplify module import structure.
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(`#49 <https://github.com/jensengroup/propka/issues/49>`_, `#61 <https://github.com/jensengroup/propka/pull/61>`_)
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* Improved tempfile handling.
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(`#61 <https://github.com/jensengroup/propka/pull/61>`_)
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v3.1.0
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======
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*Archaeologists wanted* to help us document the history of the code in versions 3.1.0 and earlier. |