Becksteinlab kda issues

Becksteinlab / kda

Python package used for the analysis of biochemical kinetic diagrams.

GNU General Public License v3.0

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issues

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ENH: Improve KDA API

#68 nawtrey closed 3 months ago
1
TST: Add test for transition/cycle/operational flux relations

#67 nawtrey opened 1 year ago
3
BUG, TST: Fix flux diagram `cbt=True` panel, add test for "color by target" attribute

#66 nawtrey closed 2 years ago
1
DOC: Add algorithm references to function docstrings

#65 nawtrey closed 3 months ago
2
CI: Update pytest command

#64 nawtrey closed 2 years ago
0
CI: Update `codecov` configuration

#63 nawtrey closed 2 years ago
1
CI: Add Python 3.10 to CI

#62 nawtrey closed 2 years ago
1
CI: Add Python 3.10 to CI

#61 nawtrey closed 2 years ago
0
MAINT, TST, ENH: Simplify flux diagram generation algo, update directional diagram algo to leverage `nx.all_simple_edge_paths()`

#60 nawtrey closed 2 years ago
4
TST: Add test for counting flux diagrams for known models

#59 nawtrey closed 2 years ago
2
MAINT: create `KineticDiagram` object and move relevant functions into class body

#58 nawtrey closed 3 months ago
2
ENH: Add `KineticModel` method for calculating net cycle fluxes

#57 nawtrey opened 2 years ago
4
ENH: Change graphs to store rates as edge weights instead of attributes

#56 nawtrey closed 5 months ago
1
DOC: Purge "directional partial" from function docstrings

#55 nawtrey closed 3 months ago
0
DOC, MAINT: Update `plotting.py` documentaion

#54 nawtrey closed 2 years ago
4
CI: Update `codecov` configuration

#53 nawtrey closed 2 years ago
1
MAINT: Move single cycle/diagram plotting code into new, public plotting function

#52 nawtrey closed 3 months ago
1
MAINT: Change plotting function `label`/`path` behavior

#51 nawtrey opened 2 years ago
1
DOC: Add examples to public plotting functions

#50 nawtrey closed 3 months ago
1
TST: Add unit tests for plotting helper functions

#49 nawtrey opened 2 years ago
2
API: Add a `KineticModel` method to handle cycle and diagram plotting

#48 nawtrey opened 2 years ago
2
MAINT: Refactor `plotting.draw_cycles(panel=True)`

#47 nawtrey opened 2 years ago
0
DOC: Update documentation for functions in `plotting.py` after gh-45 merge

#46 nawtrey closed 2 years ago
1
MAINT: Simplify plotting module

#45 nawtrey closed 2 years ago
4
TST: Add test that leverages `verification.py`

#44 nawtrey opened 2 years ago
0
MAINT: Refactor `test_plotting.py`

#43 nawtrey closed 2 years ago
2
DOC: Update documentation in `diagrams.py`

#42 nawtrey closed 2 years ago
2
MAINT: Simplify `generate_directional_partial_diagrams()` and change to "directional diagrams"

#41 nawtrey closed 2 years ago
3
ENH: Optimize partial diagram generation

#40 nawtrey closed 2 years ago
3
ENH: leverage `kda.diagrams.enumerate_partial_diagrams()` to preallocate arrays in `generate_partial_diagrams()`

#39 nawtrey closed 2 years ago
0
kda.diagrams.generate_directional_partial_diagrams(return_edges=False) and kda.plotting.draw_diagrams() incompatibility

#38 nawtrey closed 2 years ago
0
BUG: Fix plt.close() calls and incorrect imports

#37 nawtrey closed 3 years ago
2
DOC: Add install instructions

#36 nawtrey closed 1 year ago
1
TST: Migrates CI from Travis to GitHub Actions

#35 nawtrey closed 3 years ago
5
Cleanup `plotting.py`

#34 nawtrey closed 2 years ago
2
ENH, TST: Cleans up `plotting.py` and adds new tests for `graph_utils.py`

#33 nawtrey closed 3 years ago
4
MAINT: Fixes SVD-related issues in `rmsd.py` and `timing.py`

#32 nawtrey closed 3 years ago
3
Create `conftest.py` for storing global pytest fixtures in `test_kda.py`

#31 nawtrey closed 3 months ago
0
Replace assertion in `diagrams.enumerate_partial_diagrams()` with specific error

#30 nawtrey closed 3 months ago
1
ENH, TST: Misc changes to ODE and matrix solvers

#29 nawtrey closed 3 years ago
3
ENH: Adds code that assures generated rate values stay between 1e-7 and 1e7 for `verification.py`

#28 nawtrey closed 3 years ago
1
Potential performance improvement for `kda.diagrams.generate_flux_diagrams()`

#27 nawtrey closed 3 months ago
1
TST: Refactors `test_kda.py`

#26 nawtrey closed 3 years ago
3
ENH: Changes diagram generation and probability calculations to work in terms of lists of edges instead of NetworkX diagrams

#25 nawtrey closed 3 years ago
10
Misc updates to verification scripts

#24 nawtrey closed 3 years ago
4
Fix _combine() function showing up in kda.diagrams page of kda.readthedocs.io

#23 nawtrey closed 3 months ago
1
ENH: Update KDA partial and directional diagram generation algorithm

#22 nawtrey closed 3 months ago
4
See if we can use `hypothesis` to in `test_kda.py` instead of iterating over specific values

#21 nawtrey closed 2 years ago
1
Splits `kda.core` into multiple modules and updates documentation

#20 nawtrey closed 3 years ago
2
Changes names of cycle flux functions to net cycle flux

#19 nawtrey closed 3 years ago
2

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