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Becksteinlab
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kda
Python package used for the analysis of biochemical kinetic diagrams.
GNU General Public License v3.0
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ENH: Improve KDA API
#68
nawtrey
closed
2 weeks 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
1 week 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
2 weeks 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
2 months ago
1
DOC: Purge "directional partial" from function docstrings
#55
nawtrey
closed
3 weeks 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
2 weeks 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
2 weeks 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 weeks ago
0
Replace assertion in `diagrams.enumerate_partial_diagrams()` with specific error
#30
nawtrey
closed
2 weeks 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
2 weeks 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
2 weeks ago
1
ENH: Update KDA partial and directional diagram generation algorithm
#22
nawtrey
closed
6 days 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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