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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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Update `CITATION.cff` BibTeX metadata
#118
nawtrey
opened
3 months ago
2
Add citation file
#117
nawtrey
closed
3 months ago
1
ENH: Improve partial diagrams algo
#116
nawtrey
closed
3 months ago
1
CI: Add `asv check` to CI
#115
nawtrey
closed
3 months ago
0
BENCH: Add cycle flux benchmark
#114
nawtrey
closed
3 months ago
1
ENH: Improve directional diagram algo
#113
nawtrey
closed
3 months ago
4
MAINT: Clean up code in `calculations.py` module
#112
nawtrey
closed
3 months ago
0
MAINT: Deprecate `calc_*_from_diags` functions
#111
nawtrey
closed
3 months ago
0
MAINT: Refactor `calc_net_cycle_flux`
#110
nawtrey
closed
3 months ago
0
Add airspeed velocity benchmarks
#109
nawtrey
closed
3 months ago
1
CI: Add Airspeed Velocity benchmarking to CI
#108
nawtrey
closed
3 months ago
2
TST: Fix `test_calc_pi_difference_5WL` reliability
#107
nawtrey
closed
3 months ago
1
BUG, TST: Fix `test_calc_pi_difference`
#106
nawtrey
closed
3 months ago
1
DOC: Add examples to plotting function docstrings
#105
nawtrey
closed
3 months ago
0
TST: Address remaining tests-related tasks in Issue #3
#104
nawtrey
closed
3 months ago
0
MAINT: Move fixtures from `test_plotting.py`
#103
nawtrey
closed
3 months ago
1
MAINT: Fix docstrings to follow NumPy formatting
#102
nawtrey
closed
3 months ago
0
DOC: Update `ReadtheDocs` structure or theme
#101
nawtrey
opened
3 months ago
0
DOC: Update RTD pages
#100
nawtrey
closed
3 months ago
2
MAINT: Remove unnecessary `graph_utils.py` functions
#99
nawtrey
closed
3 months ago
1
DOC: Add RTD badge, 8-state example model
#98
nawtrey
closed
3 months ago
0
MAINT, DOCS: Update `requirements.txt`, fix API docs
#97
nawtrey
closed
3 months ago
1
WIP: RTD/sphinx API reference testing
#96
nawtrey
closed
3 months ago
1
DOC, BUG: API reference fails to build on remote with `sphinx`
#95
nawtrey
closed
3 months ago
2
DOCS: Update sphinx configuration, docs, citations
#94
nawtrey
closed
3 months ago
1
DOC: Fix ReadtheDocs configuration
#93
nawtrey
closed
3 months ago
0
DOC: Update KDA function documentation
#92
nawtrey
closed
3 months ago
1
DOC: Fix instances of "directional partial diagram"
#91
nawtrey
closed
3 months ago
1
TST: Add sympy expression fixtures
#90
nawtrey
closed
3 months ago
1
TST: Create conftest.py, move state prob fixtures
#89
nawtrey
closed
3 months ago
1
Changes default calculations to symbolic outputs
#88
nawtrey
closed
3 months ago
1
ENH: Optimize state probability expression parsing
#87
nawtrey
closed
3 months ago
1
Revert "MAINT, API: Remove "key" and "name" parameters (#84)"
#86
nawtrey
closed
4 months ago
1
CI: Add codecov token to yaml
#85
nawtrey
closed
5 months ago
2
ENH, API: Remove "key" and "name" parameters
#84
nawtrey
closed
5 months ago
3
WIP, API: Add simple API for KDA
#83
nawtrey
closed
3 months ago
5
MAINT: Pin `mpmath` to version 1.3.0
#82
nawtrey
closed
8 months ago
1
BUG, MAINT: Fix undirected graph params
#81
nawtrey
closed
1 year ago
1
BUG, MAINT: Fix `arrows=True` parameter for `nx.draw_networkx_edges` in `plotting.draw_diagrams()`
#80
nawtrey
closed
8 months ago
1
MAINT, ENH: Make figure objects accessible
#79
nawtrey
closed
1 year ago
1
CI, TST, MAINT: Fix HealthCheck error, update CI Python versions
#78
nawtrey
closed
1 year ago
1
CI: Update CI Python versions
#77
nawtrey
closed
1 year ago
0
MAINT, TST: hypothesis FailedHealthCheck error due to multiple executors
#76
nawtrey
closed
1 year ago
0
TST: Add test which verifies number of spanning trees using Kirchhoff's Matrix-Tree Theorem
#75
nawtrey
closed
3 months ago
3
MAINT: Fix future deprecation warning
#74
nawtrey
closed
1 year ago
0
Fix test cases in `test_get_ordered_cycle_all_node_cycles ` (issue #71)
#73
nawtrey
closed
1 year ago
3
Replace deprecated `np.product()` function calls
#72
nawtrey
closed
1 year ago
1
CI, BUG: Tests Failing on Python 3.9
#71
nawtrey
closed
1 year ago
1
make a release
#70
orbeckst
closed
8 months ago
10
ENH: Add thermodynamic consistency checker
#69
nawtrey
opened
1 year ago
0
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