CHANGELOG.rst
Versioning
==========
This project follows strictly `Semantic Versioning 2.0 <https://semver.org/#semantic-versioning-200>`_ for version control.
Upon release of version 1.0.0, all additions to the ``master`` branch are done by PR followed by its respective version increment and release on `PyPI <https://pypi.org/project/taurenmd/>`_.
Upon version 0.8, and before version 1, SV2 major version increments are reflected in the *minor* version number, and minor and patch increments are reflected together in the *patch* version number. Everything else follows SV2 rules, in this way users can track backwards incompatibilities if they happen.
Changelog
=========
v0.11.2 (2022-07-14)
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* Add output dir option to `fext` #66
v0.11.1 (2022-07-14)
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* Update badges after 0.11 #65
v0.11.0 (2022-07-13)
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* Dropped `python-bioplottemplates`
* updated export statements
* Added plots to `taurenmd rotations`
* Added plots to `taurenmd dist`
* Added plots to `taurenmd rmsf`
* Added plots to `taurenmd rmsd`
* `taurenmd dist` now can take multiple `--sel2`, and all are plotted
* `ParamsToDict` now uses `ast.literal_eval`
* trajectory slice now accepts timesteps (10ns, for example)
v0.10.4 (2022-01-14)
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* update logo link in README #63
v0.10.3 (2021-12-11)
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* Improved documentation for `cli_rotations`
* Added illustration explaining the roll, pitch, and yaw angles
v0.10.2 (2021-12-03)
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* Add frame timestep and whole trajectory duration to `report` (#61)
v0.10.1 (2021-11-24)
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* Add support for CIF topologies in libmda using openmm.app.pdbxfile
* removes the install*.yml gitactions
v0.10.0 (2021-11-24)
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* Updates MDAnalysis to version 2.0.0
* Defines versions for all other dependencies
* Updates CI
v0.9.9 (2021-11-22)
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* Corrects taking/passing of `insort` argument in some clients.
v0.9.8 (2021-11-22)
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* Upgraded roll, pitch, and yaw angle calculations with torsion angle strategy
* Removed usage of PyQuaternion
v0.9.7 (2021-11-20)
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* improved trajectory report (#54)
v0.9.6 (2021-02-22)
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* Remove README badge for build: not needed.
* Added some comments in the workflow files.
* no changes in code, only CI.
v0.9.5 (2021-02-17)
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* Upgraded CI to Github Actions according to: https://github.com/joaomcteixeira/python-project-skeleton
* Updated README badges
0.9.4 (2020-06-02)
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* Updates documentation with JOSS citation (PR #49)
0.9.3 (2020-05-25)
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* Improves CONTRIBUTION.rst guidelines (PR #46)
0.9.2 (2020-05-17)
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* Client progression is now represented by a progress bar (PR #44)
0.9.1 (2020-05-15)
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* Improves log in `.taurenmd.cmd` (PR #43)
0.9.0 (2020-05-15)
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* Adds `-i` to every `CLI` interface (PR #42)
* `major` version change because `cli_imagemol` lost backwards compatibility
0.8.14 (2020-05-12)
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* Updates `tox.ini` file for Continuous Integration (PR #40)
0.8.13 (2020-05-12)
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* Added support for sequence of trajectories in CLIs that use `MDTraj` (PR #39)
0.8.12 (2020-05-04)
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* PR: #37
* Installs taurenmd directly with Conda env
0.8.11 (2020-04-03)
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* PR: #33
* Corrected command representation in .taurenmd.cwd adding quotes when needed
0.8.10 (2020-04-02)
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* PR: #32
* Corrects incorrect usage of MDAnalysis.analysis.alignto function in ``trajedit``.
0.8.9 (2020-03-03)
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* Changed logos, PR #28
0.8.8 (2020-02-03)
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* PRs: #25 #26 #27
* Added taurenmd logo for readthedocs
* Added tauranmd logo in README
* Added taurenmd repository banner
* Improved details in the documentation
* Removed ``.ci`` folder, unnecessary
0.8.7 (2020-02-02)
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* PR #24
* Added PyPI downloads badge
* Improved installation instructions
* Improved and clarified contributing instructions
0.8.6 (2020-01-20)
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* Restructured pip deps: install_requires only takes bioplottemplates and pyquaternion
* two extras_require: `sup` and `md` and `all` which consider both
0.8.5 (2020-01-20)
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* PR #22
* organized dependencies for PyPI
* PyPI only dependencies are referred as install_requires
* MDAnalysis and MDTraj referred in extras_require
* OpenMM left out from pip, only available in Anaconda
0.8.4 (2020-01-19)
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* PR #15
* Added simtk lib import check for controlled failure
* added error message output for user
0.8.3 (2020-01-19)
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* PR #16 and #19
* corrected argparse autodoc in ReadTheDocs (mock strategy)
* improved tox configuration with better env separation
* #19 reports a communication error between TravisCI and coverage servers
0.8.2 (2020-01-17)
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* Improved CI workflow
* Dropped COVERALLS
* Dropped Codacy
* Setup test-coverage in CodeClimate
* created `.codeclimate.yml` with explicit configuration
* updated badges
0.8.1 (2020-01-15)
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* PR #14
* Corrected version display in documentation
0.8.0 (2020-01-15)
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* PR #13
* Code architecture improvements
* Complete project main documentation
* Complete library documentation
* command line documented
* Code clean
0.7.2 (2019-12-25)
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* bridged from 0.7.1
* Dropped Appveyor and EXPLICIT Windows support because of #1.
* restructured project GitHub layout. Deprecated develop branch.
* Readthedocs documentation improvements in structure and content.
0.7.0 (2019-12-23)
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* implemented :code:`cli_rotations`, calculates roll, pitch and yaw
rotation angles of selection.
0.6.0 (2019-12-15)
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* implemented :code:`cli_rmsf` to calculate RMSFs.
0.5.1 (skipped to 0.6.0)
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* added sort numbered trajs to :code:`cli_trajedit`
* added sort numbered trajectory paths in lib
* improved :code:`cli_imagemol` readability
* added selection in :code:`cli_noSol`
0.5.0 (2019-11-24)
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* created :code:`cli_angle`. Calculates angles between a plane along the trajectory. Plane is given by the three centre_of_geometries of three selections.
* args to plot passed as list are transformed to tuple
* added distance calc and plot interface :code:`cli_distances`
* :code:`trajedit` now saves topology unwrapped
0.4.1 (2019-11-21)
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* renumbered version to 0.4.1. from 0.3.1
* RMSD Cli now calculates for several selections
* Parse plot vars now registers floats
* corrected fext cli entry point
* added align option to trajedit
* topology model writen from first frame of time slicing
* added unwrap() molecule method from MDAnalysis in :code:`trajedit` with respective options
* topology output now defaults to traj name + :code:`frame0.pdb`
* added .myparents() to Path in :code:`__init__`
0.3.0 (2019-11-06)
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* Created *develop* branch
* Created client for frame extraction: :code:`cli_fext`
* Added option to disable export of frame0 topology in trajedit
0.2.1 (2019-10-26)
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* dropped py35
* separated lib MDAnalysis from MDTraj
* :code:`libio` concerns only general functions
* improved :code:`imagemol` I/O
0.2.0 (2019-10-26)
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* added :code:`cli_report`
0.1.1 (2019-10-26)
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* corrected libio
* trajectory loads based on MDAnalysis now read and concatenate multiple trajectories.
0.1.0 (2019-10-26)
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* added interfaces:
* :code:`trajedit`
* :code:`noSol`
* :code:`imagemol`
* :code:`rmsd`
* :code:`cli template`
0.0.0 (2019-10-15)
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* First release on PyPI.