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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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Revert "MAINT, API: Remove "key" and "name" parameters (#84)"
#86
nawtrey
closed
5 days ago
1
CI: Add codecov token to yaml
#85
nawtrey
closed
1 month ago
2
ENH, API: Remove "key" and "name" parameters
#84
nawtrey
closed
1 month ago
3
WIP, API: Add simple API for KDA
#83
nawtrey
opened
3 months ago
3
MAINT: Pin `mpmath` to version 1.3.0
#82
nawtrey
closed
4 months ago
1
BUG, MAINT: Fix undirected graph params
#81
nawtrey
closed
10 months ago
1
BUG, MAINT: Fix `arrows=True` parameter for `nx.draw_networkx_edges` in `plotting.draw_diagrams()`
#80
nawtrey
closed
3 months ago
1
MAINT, ENH: Make figure objects accessible
#79
nawtrey
closed
10 months ago
1
CI, TST, MAINT: Fix HealthCheck error, update CI Python versions
#78
nawtrey
closed
10 months ago
1
CI: Update CI Python versions
#77
nawtrey
closed
10 months ago
0
MAINT, TST: hypothesis FailedHealthCheck error due to multiple executors
#76
nawtrey
closed
10 months ago
0
TST: Add test which verifies number of spanning trees using Kirchhoff's Matrix-Tree Theorem
#75
nawtrey
opened
10 months ago
2
MAINT: Fix future deprecation warning
#74
nawtrey
closed
10 months ago
0
Fix test cases in `test_get_ordered_cycle_all_node_cycles ` (issue #71)
#73
nawtrey
closed
10 months ago
3
Replace deprecated `np.product()` function calls
#72
nawtrey
closed
10 months ago
1
CI, BUG: Tests Failing on Python 3.9
#71
nawtrey
closed
10 months ago
1
make a release
#70
orbeckst
closed
4 months ago
10
ENH: Add thermodynamic consistency checker
#69
nawtrey
opened
11 months ago
0
ENH: Improve KDA API
#68
nawtrey
opened
11 months ago
0
TST: Add test for transition/cycle/operational flux relations
#67
nawtrey
opened
1 year ago
2
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
opened
2 years ago
0
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
opened
2 years ago
1
ENH: Improve cycle direction labeling strategy
#57
nawtrey
opened
2 years ago
2
ENH: Change graphs to store rates as edge weights instead of attributes
#56
nawtrey
closed
1 month ago
1
DOC: Purge "directional partial" from function docstrings
#55
nawtrey
opened
2 years 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
opened
2 years ago
0
MAINT: Change plotting function `label`/`path` behavior
#51
nawtrey
opened
2 years ago
0
DOC: Add examples to public plotting functions
#50
nawtrey
opened
2 years ago
0
TST: Add unit tests for plotting helper functions
#49
nawtrey
opened
2 years ago
2
MAINT: Write a general plotting function to handle cycle and diagram plotting
#48
nawtrey
opened
2 years ago
1
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
2 years ago
2
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