Becksteinlab/kda issues and pull requests

#118 - Update `CITATION.cff` BibTeX metadata

Issue - State: open - Opened by nawtrey 3 months ago - 2 comments
Labels: maintenance

#117 - Add citation file

Pull Request - State: closed - Opened by nawtrey 3 months ago - 1 comment

#116 - ENH: Improve partial diagrams algo

Pull Request - State: closed - Opened by nawtrey 3 months ago - 1 comment
Labels: enhancement, performance

#115 - CI: Add `asv check` to CI

Pull Request - State: closed - Opened by nawtrey 3 months ago
Labels: CI

#114 - BENCH: Add cycle flux benchmark

Pull Request - State: closed - Opened by nawtrey 3 months ago - 1 comment
Labels: benchmarks

#113 - ENH: Improve directional diagram algo

Pull Request - State: closed - Opened by nawtrey 4 months ago - 4 comments
Labels: enhancement, performance

#112 - MAINT: Clean up code in `calculations.py` module

Pull Request - State: closed - Opened by nawtrey 4 months ago
Labels: maintenance

#111 - MAINT: Deprecate `calc_*_from_diags` functions

Pull Request - State: closed - Opened by nawtrey 4 months ago
Labels: maintenance

#110 - MAINT: Refactor `calc_net_cycle_flux`

Pull Request - State: closed - Opened by nawtrey 4 months ago
Labels: maintenance

#109 - Add airspeed velocity benchmarks

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment

#108 - CI: Add Airspeed Velocity benchmarking to CI

Issue - State: closed - Opened by nawtrey 4 months ago - 2 comments
Labels: CI

#107 - TST: Fix `test_calc_pi_difference_5WL` reliability

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: bug, testing

#106 - BUG, TST: Fix `test_calc_pi_difference`

Issue - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: bug, testing

#105 - DOC: Add examples to plotting function docstrings

Pull Request - State: closed - Opened by nawtrey 4 months ago
Labels: documentation

#104 - TST: Address remaining tests-related tasks in Issue #3

Pull Request - State: closed - Opened by nawtrey 4 months ago
Labels: testing

#103 - MAINT: Move fixtures from `test_plotting.py`

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: maintenance

#102 - MAINT: Fix docstrings to follow NumPy formatting

Pull Request - State: closed - Opened by nawtrey 4 months ago
Labels: maintenance

#101 - DOC: Update `ReadtheDocs` structure or theme

Issue - State: open - Opened by nawtrey 4 months ago
Labels: documentation

#100 - DOC: Update RTD pages

Pull Request - State: closed - Opened by nawtrey 4 months ago - 2 comments
Labels: documentation

#99 - MAINT: Remove unnecessary `graph_utils.py` functions

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: maintenance

#98 - DOC: Add RTD badge, 8-state example model

Pull Request - State: closed - Opened by nawtrey 4 months ago
Labels: documentation

#97 - MAINT, DOCS: Update `requirements.txt`, fix API docs

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: documentation, maintenance

#96 - WIP: RTD/sphinx API reference testing

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment

#95 - DOC, BUG: API reference fails to build on remote with `sphinx`

Issue - State: closed - Opened by nawtrey 4 months ago - 2 comments
Labels: bug, documentation

#94 - DOCS: Update sphinx configuration, docs, citations

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: documentation

#93 - DOC: Fix ReadtheDocs configuration

Issue - State: closed - Opened by nawtrey 4 months ago
Labels: documentation

#92 - DOC: Update KDA function documentation

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: documentation

#91 - DOC: Fix instances of "directional partial diagram"

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: documentation, maintenance

#90 - TST: Add sympy expression fixtures

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: testing

#89 - TST: Create conftest.py, move state prob fixtures

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: testing, maintenance

#88 - Changes default calculations to symbolic outputs

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: API

#87 - ENH: Optimize state probability expression parsing

Pull Request - State: closed - Opened by nawtrey 4 months ago - 1 comment
Labels: enhancement

#86 - Revert "MAINT, API: Remove "key" and "name" parameters (#84)"

Pull Request - State: closed - Opened by nawtrey 5 months ago - 1 comment

#85 - CI: Add codecov token to yaml

Pull Request - State: closed - Opened by nawtrey 6 months ago - 2 comments
Labels: CI

#84 - ENH, API: Remove "key" and "name" parameters

Pull Request - State: closed - Opened by nawtrey 6 months ago - 3 comments
Labels: enhancement, API

#83 - WIP, API: Add simple API for KDA

Pull Request - State: closed - Opened by nawtrey 8 months ago - 5 comments
Labels: API

#82 - MAINT: Pin `mpmath` to version 1.3.0

Issue - State: closed - Opened by nawtrey 9 months ago - 1 comment
Labels: maintenance

#81 - BUG, MAINT: Fix undirected graph params

Pull Request - State: closed - Opened by nawtrey about 1 year ago - 1 comment
Labels: bug, maintenance

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

Issue - State: closed - Opened by nawtrey about 1 year ago - 1 comment
Labels: bug, maintenance

#79 - MAINT, ENH: Make figure objects accessible

Pull Request - State: closed - Opened by nawtrey about 1 year ago - 1 comment
Labels: enhancement, maintenance

#78 - CI, TST, MAINT: Fix HealthCheck error, update CI Python versions

Pull Request - State: closed - Opened by nawtrey about 1 year ago - 1 comment
Labels: testing, maintenance, CI

#77 - CI: Update CI Python versions

Issue - State: closed - Opened by nawtrey about 1 year ago
Labels: good first issue, CI

#76 - MAINT, TST: hypothesis FailedHealthCheck error due to multiple executors

Issue - State: closed - Opened by nawtrey about 1 year ago
Labels: testing, maintenance

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

Issue - State: closed - Opened by nawtrey about 1 year ago - 3 comments
Labels: good first issue, testing

#74 - MAINT: Fix future deprecation warning

Pull Request - State: closed - Opened by nawtrey about 1 year ago
Labels: maintenance

#73 - Fix test cases in `test_get_ordered_cycle_all_node_cycles ` (issue #71)

Pull Request - State: closed - Opened by nawtrey about 1 year ago - 3 comments

#72 - Replace deprecated `np.product()` function calls

Issue - State: closed - Opened by nawtrey about 1 year ago - 1 comment
Labels: good first issue, maintenance

#71 - CI, BUG: Tests Failing on Python 3.9

Issue - State: closed - Opened by nawtrey about 1 year ago - 1 comment
Labels: bug, CI

#70 - make a release

Issue - State: closed - Opened by orbeckst about 1 year ago - 10 comments

#69 - ENH: Add thermodynamic consistency checker

Issue - State: open - Opened by nawtrey over 1 year ago
Labels: enhancement

#68 - ENH: Improve KDA API

Issue - State: closed - Opened by nawtrey over 1 year ago - 1 comment
Labels: API

#67 - TST: Add test for transition/cycle/operational flux relations

Issue - State: open - Opened by nawtrey almost 2 years ago - 3 comments
Labels: testing

#66 - BUG, TST: Fix flux diagram `cbt=True` panel, add test for "color by target" attribute

Pull Request - State: closed - Opened by nawtrey over 2 years ago - 1 comment
Labels: bug, testing

#65 - DOC: Add algorithm references to function docstrings

Issue - State: closed - Opened by nawtrey over 2 years ago - 2 comments
Labels: documentation, wontfix

#64 - CI: Update pytest command

Pull Request - State: closed - Opened by nawtrey over 2 years ago
Labels: CI

#63 - CI: Update `codecov` configuration

Pull Request - State: closed - Opened by nawtrey over 2 years ago - 1 comment
Labels: CI

#62 - CI: Add Python 3.10 to CI

Pull Request - State: closed - Opened by nawtrey over 2 years ago - 1 comment
Labels: CI

#61 - CI: Add Python 3.10 to CI

Issue - State: closed - Opened by nawtrey over 2 years ago
Labels: CI

#60 - MAINT, TST, ENH: Simplify flux diagram generation algo, update directional diagram algo to leverage `nx.all_simple_edge_paths()`

Pull Request - State: closed - Opened by nawtrey over 2 years ago - 4 comments
Labels: enhancement, testing, maintenance

#59 - TST: Add test for counting flux diagrams for known models

Pull Request - State: closed - Opened by nawtrey almost 3 years ago - 2 comments
Labels: testing

#58 - MAINT: create `KineticDiagram` object and move relevant functions into class body

Issue - State: closed - Opened by nawtrey almost 3 years ago - 2 comments
Labels: API

#57 - ENH: Add `KineticModel` method for calculating net cycle fluxes

Issue - State: open - Opened by nawtrey almost 3 years ago - 4 comments
Labels: enhancement, API

#56 - ENH: Change graphs to store rates as edge weights instead of attributes

Issue - State: closed - Opened by nawtrey almost 3 years ago - 1 comment
Labels: enhancement, API

#55 - DOC: Purge "directional partial" from function docstrings

Issue - State: closed - Opened by nawtrey almost 3 years ago
Labels: documentation

#54 - DOC, MAINT: Update `plotting.py` documentaion

Pull Request - State: closed - Opened by nawtrey almost 3 years ago - 4 comments
Labels: documentation, maintenance

#53 - CI: Update `codecov` configuration

Issue - State: closed - Opened by nawtrey almost 3 years ago - 1 comment
Labels: CI

#52 - MAINT: Move single cycle/diagram plotting code into new, public plotting function

Issue - State: closed - Opened by nawtrey almost 3 years ago - 1 comment
Labels: API

#51 - MAINT: Change plotting function `label`/`path` behavior

Issue - State: open - Opened by nawtrey almost 3 years ago - 1 comment
Labels: maintenance, API

#50 - DOC: Add examples to public plotting functions

Issue - State: closed - Opened by nawtrey almost 3 years ago - 1 comment
Labels: documentation

#49 - TST: Add unit tests for plotting helper functions

Issue - State: open - Opened by nawtrey almost 3 years ago - 2 comments
Labels: testing

#48 - API: Add a `KineticModel` method to handle cycle and diagram plotting

Issue - State: open - Opened by nawtrey almost 3 years ago - 2 comments
Labels: API

#47 - MAINT: Refactor `plotting.draw_cycles(panel=True)`

Issue - State: open - Opened by nawtrey almost 3 years ago
Labels: maintenance

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

Issue - State: closed - Opened by nawtrey almost 3 years ago - 1 comment
Labels: documentation

#45 - MAINT: Simplify plotting module

Pull Request - State: closed - Opened by nawtrey almost 3 years ago - 4 comments
Labels: testing, maintenance

#44 - TST: Add test that leverages `verification.py`

Issue - State: open - Opened by nawtrey almost 3 years ago
Labels: testing

#43 - MAINT: Refactor `test_plotting.py`

Pull Request - State: closed - Opened by nawtrey almost 3 years ago - 2 comments
Labels: maintenance

#42 - DOC: Update documentation in `diagrams.py`

Pull Request - State: closed - Opened by nawtrey almost 3 years ago - 2 comments
Labels: documentation

#41 - MAINT: Simplify `generate_directional_partial_diagrams()` and change to "directional diagrams"

Pull Request - State: closed - Opened by nawtrey almost 3 years ago - 3 comments
Labels: maintenance

#40 - ENH: Optimize partial diagram generation

Pull Request - State: closed - Opened by nawtrey about 3 years ago - 3 comments
Labels: enhancement, testing

#39 - ENH: leverage `kda.diagrams.enumerate_partial_diagrams()` to preallocate arrays in `generate_partial_diagrams()`

Issue - State: closed - Opened by nawtrey about 3 years ago
Labels: enhancement

#38 - kda.diagrams.generate_directional_partial_diagrams(return_edges=False) and kda.plotting.draw_diagrams() incompatibility

Issue - State: closed - Opened by nawtrey about 3 years ago
Labels: bug

#37 - BUG: Fix plt.close() calls and incorrect imports

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 2 comments
Labels: bug, maintenance

#36 - DOC: Add install instructions

Issue - State: closed - Opened by nawtrey over 3 years ago - 1 comment
Labels: documentation

#35 - TST: Migrates CI from Travis to GitHub Actions

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 5 comments
Labels: testing

#34 - Cleanup `plotting.py`

Issue - State: closed - Opened by nawtrey over 3 years ago - 2 comments
Labels: documentation, maintenance

#33 - ENH, TST: Cleans up `plotting.py` and adds new tests for `graph_utils.py`

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 4 comments
Labels: enhancement, testing

#32 - MAINT: Fixes SVD-related issues in `rmsd.py` and `timing.py`

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 3 comments
Labels: maintenance

#31 - Create `conftest.py` for storing global pytest fixtures in `test_kda.py`

Issue - State: closed - Opened by nawtrey over 3 years ago
Labels: good first issue, maintenance

#30 - Replace assertion in `diagrams.enumerate_partial_diagrams()` with specific error

Issue - State: closed - Opened by nawtrey over 3 years ago - 1 comment
Labels: good first issue, testing

#29 - ENH, TST: Misc changes to ODE and matrix solvers

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 3 comments
Labels: enhancement, testing

#28 - ENH: Adds code that assures generated rate values stay between 1e-7 and 1e7 for `verification.py`

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 1 comment
Labels: enhancement, testing

#27 - Potential performance improvement for `kda.diagrams.generate_flux_diagrams()`

Issue - State: closed - Opened by nawtrey over 3 years ago - 1 comment
Labels: enhancement

#26 - TST: Refactors `test_kda.py`

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 3 comments
Labels: testing

#25 - ENH: Changes diagram generation and probability calculations to work in terms of lists of edges instead of NetworkX diagrams

Pull Request - State: closed - Opened by nawtrey over 3 years ago - 10 comments
Labels: enhancement

GitHub / Becksteinlab/kda issues and pull requests