Versioning¶
This project follows strictly Semantic Versioning 2.0 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.
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)¶
Add output dir option to fext #66
v0.11.1 (2022-07-14)¶
Update badges after 0.11 #65
v0.11.0 (2022-07-13)¶
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)¶
update logo link in README #63
v0.10.3 (2021-12-11)¶
Improved documentation for cli_rotations
Added illustration explaining the roll, pitch, and yaw angles
v0.10.2 (2021-12-03)¶
Add frame timestep and whole trajectory duration to report (#61)
v0.10.1 (2021-11-24)¶
Add support for CIF topologies in libmda using openmm.app.pdbxfile
removes the install*.yml gitactions
v0.10.0 (2021-11-24)¶
Updates MDAnalysis to version 2.0.0
Defines versions for all other dependencies
Updates CI
v0.9.9 (2021-11-22)¶
Corrects taking/passing of insort argument in some clients.
v0.9.8 (2021-11-22)¶
Upgraded roll, pitch, and yaw angle calculations with torsion angle strategy
Removed usage of PyQuaternion
v0.9.7 (2021-11-20)¶
improved trajectory report (#54)
v0.9.6 (2021-02-22)¶
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)¶
Upgraded CI to Github Actions according to: https://github.com/joaomcteixeira/python-project-skeleton
Updated README badges
0.9.4 (2020-06-02)¶
Updates documentation with JOSS citation (PR #49)
0.9.3 (2020-05-25)¶
Improves CONTRIBUTION.rst guidelines (PR #46)
0.9.2 (2020-05-17)¶
Client progression is now represented by a progress bar (PR #44)
0.9.1 (2020-05-15)¶
Improves log in .taurenmd.cmd (PR #43)
0.9.0 (2020-05-15)¶
Adds -i to every CLI interface (PR #42)
major version change because cli_imagemol lost backwards compatibility
0.8.14 (2020-05-12)¶
Updates tox.ini file for Continuous Integration (PR #40)
0.8.13 (2020-05-12)¶
Added support for sequence of trajectories in CLIs that use MDTraj (PR #39)
0.8.12 (2020-05-04)¶
PR: #37
Installs taurenmd directly with Conda env
0.8.11 (2020-04-03)¶
PR: #33
Corrected command representation in .taurenmd.cwd adding quotes when needed
0.8.10 (2020-04-02)¶
PR: #32
Corrects incorrect usage of MDAnalysis.analysis.alignto function in
trajedit
.
0.8.9 (2020-03-03)¶
Changed logos, PR #28
0.8.8 (2020-02-03)¶
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)¶
PR #24
Added PyPI downloads badge
Improved installation instructions
Improved and clarified contributing instructions
0.8.6 (2020-01-20)¶
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)¶
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)¶
PR #15
Added simtk lib import check for controlled failure
added error message output for user
0.8.3 (2020-01-19)¶
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)¶
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)¶
PR #14
Corrected version display in documentation
0.8.0 (2020-01-15)¶
PR #13
Code architecture improvements
Complete project main documentation
Complete library documentation
command line documented
Code clean
0.7.2 (2019-12-25)¶
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)¶
- implemented
cli_rotations
, calculates roll, pitch and yaw rotation angles of selection.
- implemented
0.6.0 (2019-12-15)¶
implemented
cli_rmsf
to calculate RMSFs.
0.5.1 (skipped to 0.6.0)¶
added sort numbered trajs to
cli_trajedit
added sort numbered trajectory paths in lib
improved
cli_imagemol
readabilityadded selection in
cli_noSol
0.5.0 (2019-11-24)¶
created
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
cli_distances
trajedit
now saves topology unwrapped
0.4.1 (2019-11-21)¶
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
trajedit
with respective optionstopology output now defaults to traj name +
frame0.pdb
added .myparents() to Path in
__init__
0.3.0 (2019-11-06)¶
Created develop branch
Created client for frame extraction:
cli_fext
Added option to disable export of frame0 topology in trajedit
0.2.1 (2019-10-26)¶
dropped py35
separated lib MDAnalysis from MDTraj
libio
concerns only general functionsimproved
imagemol
I/O
0.2.0 (2019-10-26)¶
added
cli_report
0.1.1 (2019-10-26)¶
corrected libio
trajectory loads based on MDAnalysis now read and concatenate multiple trajectories.
0.1.0 (2019-10-26)¶
added interfaces: *
trajedit
*noSol
*imagemol
*rmsd
*cli template
0.0.0 (2019-10-15)¶
First release on PyPI.