Becksteinlab/kda

Issues

• ENH: Update KDA partial and directional diagram generation algorithm

  #22 opened 2 months ago by nawtrey
  4

• Potential performance improvement for `kda.diagrams.generate_flux_diagrams()`

  #27 opened 2 months ago by nawtrey
  1

• DOC: Purge "directional partial" from function docstrings

  #55 opened 3 months ago by nawtrey
  0

• ENH: Change graphs to store rates as edge weights instead of attributes

  #56 opened 4 months ago by nawtrey
  1

• TST: Add test which verifies number of spanning trees using Kirchhoff's Matrix-Tree Theorem

  #75 opened a year ago by nawtrey
  2

• BUG, MAINT: Fix `arrows=True` parameter for `nx.draw_networkx_edges` in `plotting.draw_diagrams()`

  #80 opened 7 months ago by nawtrey
  1

• make a release

  #70 opened 7 months ago by orbeckst
  10

• MAINT: Pin `mpmath` to version 1.3.0

  #82 opened 7 months ago by nawtrey
  1

• ENH: Improve cycle direction labeling strategy

  #57 opened 3 years ago by nawtrey
  2

• Remove string to SymPy functions

  #14 opened 4 years ago by nawtrey
  2

• TST: Add test for transition/cycle/operational flux relations

  #67 opened 2 years ago by nawtrey
  2

• MAINT: Change plotting function `label`/`path` behavior

  #51 opened 3 years ago by nawtrey
  0

• MAINT, TST: hypothesis FailedHealthCheck error due to multiple executors

  #76 opened a year ago by nawtrey
  0

• CI: Update CI Python versions

  #77 opened a year ago by nawtrey
  0

• Replace deprecated `np.product()` function calls

  #72 opened a year ago by nawtrey
  1

• CI, BUG: Tests Failing on Python 3.9

  #71 opened a year ago by nawtrey
  1

• ENH: Add thermodynamic consistency checker

  #69 opened a year ago by nawtrey
  0

• MAINT: create `KineticDiagram` object and move relevant functions into class body

  #58 opened 3 years ago by nawtrey
  1

• ENH: Improve KDA API

  #68 opened a year ago by nawtrey
  0

• DOC: Add install instructions

  #36 opened a year ago by nawtrey
  1

• Add analysis examples

  #6 opened a year ago by nawtrey
  2

• Release 0.1.0

  #11 opened a year ago by orbeckst
  1

• TST: Add unit tests for plotting helper functions

  #49 opened 3 years ago by nawtrey
  2

• DOC: Add algorithm references to function docstrings

  #65 opened 3 years ago by nawtrey
  0

• CI: Update `codecov` configuration

  #53 opened 3 years ago by nawtrey
  1

• CI: Add Python 3.10 to CI

  #61 opened 3 years ago by nawtrey
  0

• DOC: Update documentation for functions in `plotting.py` after gh-45 merge

  #46 opened 3 years ago by nawtrey
  1

• MAINT: Write a general plotting function to handle cycle and diagram plotting

  #48 opened 3 years ago by nawtrey
  1

• MAINT: Move single cycle/diagram plotting code into new, public plotting function

  #52 opened 3 years ago by nawtrey
  0

• Cleanup `plotting.py`

  #34 opened 3 years ago by nawtrey
  2

• DOC: Add examples to public plotting functions

  #50 opened 3 years ago by nawtrey
  0

• MAINT: Refactor `plotting.draw_cycles(panel=True)`

  #47 opened 3 years ago by nawtrey
  0

• kda.diagrams.generate_directional_partial_diagrams(return_edges=False) and kda.plotting.draw_diagrams() incompatibility

  #38 opened 3 years ago by nawtrey
  0

• TST: Add test that leverages `verification.py`

  #44 opened 3 years ago by nawtrey
  0

• See if we can use `hypothesis` to in `test_kda.py` instead of iterating over specific values

  #21 opened 3 years ago by nawtrey
  1

• ENH: leverage `kda.diagrams.enumerate_partial_diagrams()` to preallocate arrays in `generate_partial_diagrams()`

  #39 opened 3 years ago by nawtrey
  0

• Move testing suite from Travis-CI to GitHub Actions

  #18 opened 3 years ago by nawtrey
  4

• Replace assertion in `diagrams.enumerate_partial_diagrams()` with specific error

  #30 opened 3 years ago by nawtrey
  0

• Create `conftest.py` for storing global pytest fixtures in `test_kda.py`

  #31 opened 3 years ago by nawtrey
  0

• Fix _combine() function showing up in kda.diagrams page of kda.readthedocs.io

  #23 opened 4 years ago by nawtrey
  1

• Add online documentation

  #10 opened 4 years ago by orbeckst
  2

• Update name of "cycle flux" functions to "net cycle flux"

  #17 opened 4 years ago by nawtrey
  0

• Update CCW - CW explanations in functions

  #16 opened 4 years ago by nawtrey
  0

• kda.calculate_pi_difference(), kda.calculate_thermo_force() are not generating the appropriate functional forms

  #15 opened 4 years ago by nawtrey
  1

• NetworkX Cycle Definition Ambiguity

  #12 opened 4 years ago by nawtrey
  1

• Split kda.generate_flux_diagrams() into two functions

  #13 opened 4 years ago by nawtrey
  3

• Flux diagram generation issues

  #9 opened 4 years ago by nawtrey
  3

• "Color by target" feature in plot_diagrams() isn't labeling appropriate cycle nodes

  #8 opened 4 years ago by nawtrey
  1

• Fix Travis package imports so tests can run

  #5 opened 4 years ago by nawtrey
  2

• Change License to GPLv3

  #7 opened 4 years ago by nawtrey
  1