Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / Becksteinlab/kda issues and pull requests
#85 - CI: Add codecov token to yaml
Pull Request -
State: closed - Opened by nawtrey about 1 month ago
- 2 comments
Labels: CI
#84 - ENH, API: Remove "key" and "name" parameters
Pull Request -
State: closed - Opened by nawtrey about 1 month ago
- 3 comments
Labels: enhancement, API
#83 - WIP, API: Add simple API for KDA
Pull Request -
State: open - Opened by nawtrey 3 months ago
- 3 comments
Labels: API
#82 - MAINT: Pin `mpmath` to version 1.3.0
Issue -
State: closed - Opened by nawtrey 4 months ago
- 1 comment
Labels: maintenance
#81 - BUG, MAINT: Fix undirected graph params
Pull Request -
State: closed - Opened by nawtrey 10 months 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 10 months ago
- 1 comment
Labels: bug, maintenance
#79 - MAINT, ENH: Make figure objects accessible
Pull Request -
State: closed - Opened by nawtrey 10 months ago
- 1 comment
Labels: enhancement, maintenance
#78 - CI, TST, MAINT: Fix HealthCheck error, update CI Python versions
Pull Request -
State: closed - Opened by nawtrey 10 months ago
- 1 comment
Labels: testing, maintenance, CI
#77 - CI: Update CI Python versions
Issue -
State: closed - Opened by nawtrey 10 months ago
Labels: good first issue, CI
#76 - MAINT, TST: hypothesis FailedHealthCheck error due to multiple executors
Issue -
State: closed - Opened by nawtrey 10 months ago
Labels: testing, maintenance
#75 - TST: Add test which verifies number of spanning trees using Kirchhoff's Matrix-Tree Theorem
Issue -
State: open - Opened by nawtrey 10 months ago
- 2 comments
Labels: enhancement, good first issue, testing
#74 - MAINT: Fix future deprecation warning
Pull Request -
State: closed - Opened by nawtrey 10 months ago
Labels: maintenance
#73 - Fix test cases in `test_get_ordered_cycle_all_node_cycles ` (issue #71)
Pull Request -
State: closed - Opened by nawtrey 10 months ago
- 3 comments
#72 - Replace deprecated `np.product()` function calls
Issue -
State: closed - Opened by nawtrey 10 months ago
- 1 comment
Labels: good first issue, maintenance
#71 - CI, BUG: Tests Failing on Python 3.9
Issue -
State: closed - Opened by nawtrey 10 months ago
- 1 comment
Labels: bug, CI
#70 - make a release
Issue -
State: closed - Opened by orbeckst 10 months ago
- 10 comments
#69 - ENH: Add thermodynamic consistency checker
Issue -
State: open - Opened by nawtrey 11 months ago
Labels: enhancement
#68 - ENH: Improve KDA API
Issue -
State: open - Opened by nawtrey 11 months ago
Labels: API
#67 - TST: Add test for transition/cycle/operational flux relations
Issue -
State: open - Opened by nawtrey over 1 year ago
- 2 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 about 2 years ago
- 1 comment
Labels: bug, testing
#65 - DOC: Add algorithm references to function docstrings
Issue -
State: open - Opened by nawtrey over 2 years ago
Labels: documentation
#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 over 2 years ago
- 2 comments
Labels: testing
#58 - MAINT: create `KineticDiagram` object and move relevant functions into class body
Issue -
State: open - Opened by nawtrey over 2 years ago
- 1 comment
Labels: API
#57 - ENH: Improve cycle direction labeling strategy
Issue -
State: open - Opened by nawtrey over 2 years ago
- 2 comments
Labels: enhancement, API
#56 - ENH: Change graphs to store rates as edge weights instead of attributes
Issue -
State: closed - Opened by nawtrey over 2 years ago
- 1 comment
Labels: enhancement, API
#55 - DOC: Purge "directional partial" from function docstrings
Issue -
State: open - Opened by nawtrey over 2 years ago
Labels: documentation
#54 - DOC, MAINT: Update `plotting.py` documentaion
Pull Request -
State: closed - Opened by nawtrey over 2 years ago
- 4 comments
Labels: documentation, maintenance
#53 - CI: Update `codecov` configuration
Issue -
State: closed - Opened by nawtrey over 2 years ago
- 1 comment
Labels: CI
#52 - MAINT: Move single cycle/diagram plotting code into new, public plotting function
Issue -
State: open - Opened by nawtrey over 2 years ago
Labels: maintenance
#51 - MAINT: Change plotting function `label`/`path` behavior
Issue -
State: open - Opened by nawtrey over 2 years ago
Labels: maintenance
#50 - DOC: Add examples to public plotting functions
Issue -
State: open - Opened by nawtrey over 2 years ago
Labels: documentation
#49 - TST: Add unit tests for plotting helper functions
Issue -
State: open - Opened by nawtrey over 2 years ago
- 2 comments
Labels: testing
#48 - MAINT: Write a general plotting function to handle cycle and diagram plotting
Issue -
State: open - Opened by nawtrey over 2 years ago
- 1 comment
Labels: maintenance
#47 - MAINT: Refactor `plotting.draw_cycles(panel=True)`
Issue -
State: open - Opened by nawtrey over 2 years ago
Labels: maintenance
#46 - DOC: Update documentation for functions in `plotting.py` after gh-45 merge
Issue -
State: closed - Opened by nawtrey over 2 years ago
- 1 comment
Labels: documentation
#45 - MAINT: Simplify plotting module
Pull Request -
State: closed - Opened by nawtrey over 2 years ago
- 4 comments
Labels: testing, maintenance
#44 - TST: Add test that leverages `verification.py`
Issue -
State: open - Opened by nawtrey over 2 years ago
Labels: testing
#43 - MAINT: Refactor `test_plotting.py`
Pull Request -
State: closed - Opened by nawtrey over 2 years ago
- 2 comments
Labels: maintenance
#42 - DOC: Update documentation in `diagrams.py`
Pull Request -
State: closed - Opened by nawtrey over 2 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 over 2 years ago
- 3 comments
Labels: maintenance
#40 - ENH: Optimize partial diagram generation
Pull Request -
State: closed - Opened by nawtrey over 2 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 over 2 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 almost 3 years ago
Labels: bug
#37 - BUG: Fix plt.close() calls and incorrect imports
Pull Request -
State: closed - Opened by nawtrey almost 3 years ago
- 2 comments
Labels: bug, maintenance
#36 - DOC: Add install instructions
Issue -
State: closed - Opened by nawtrey almost 3 years ago
- 1 comment
Labels: documentation
#35 - TST: Migrates CI from Travis to GitHub Actions
Pull Request -
State: closed - Opened by nawtrey almost 3 years ago
- 5 comments
Labels: testing
#34 - Cleanup `plotting.py`
Issue -
State: closed - Opened by nawtrey about 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 about 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 about 3 years ago
- 3 comments
Labels: maintenance
#31 - Create `conftest.py` for storing global pytest fixtures in `test_kda.py`
Issue -
State: open - Opened by nawtrey about 3 years ago
Labels: good first issue, maintenance
#30 - Replace assertion in `diagrams.enumerate_partial_diagrams()` with specific error
Issue -
State: open - Opened by nawtrey about 3 years ago
Labels: good first issue, testing
#29 - ENH, TST: Misc changes to ODE and matrix solvers
Pull Request -
State: closed - Opened by nawtrey about 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 about 3 years ago
- 1 comment
Labels: enhancement, testing
#27 - Potential performance improvement for `kda.diagrams.generate_flux_diagrams()`
Issue -
State: open - Opened by nawtrey about 3 years ago
Labels: enhancement
#26 - TST: Refactors `test_kda.py`
Pull Request -
State: closed - Opened by nawtrey about 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 about 3 years ago
- 10 comments
Labels: enhancement
#24 - Misc updates to verification scripts
Pull Request -
State: closed - Opened by nawtrey about 3 years ago
- 4 comments
Labels: enhancement, testing
#23 - Fix _combine() function showing up in kda.diagrams page of kda.readthedocs.io
Issue -
State: open - Opened by nawtrey over 3 years ago
- 1 comment
Labels: documentation
#22 - Update KDA Partial/Directional Partial diagram generation method
Issue -
State: open - Opened by nawtrey over 3 years ago
- 1 comment
Labels: enhancement
#21 - See if we can use `hypothesis` to in `test_kda.py` instead of iterating over specific values
Issue -
State: closed - Opened by nawtrey over 3 years ago
- 1 comment
Labels: testing
#20 - Splits `kda.core` into multiple modules and updates documentation
Pull Request -
State: closed - Opened by nawtrey over 3 years ago
- 2 comments
Labels: documentation
#19 - Changes names of cycle flux functions to net cycle flux
Pull Request -
State: closed - Opened by nawtrey over 3 years ago
- 2 comments
Labels: documentation
#18 - Move testing suite from Travis-CI to GitHub Actions
Issue -
State: closed - Opened by nawtrey over 3 years ago
- 4 comments
Labels: testing
#17 - Update name of "cycle flux" functions to "net cycle flux"
Issue -
State: closed - Opened by nawtrey over 3 years ago
Labels: documentation
#16 - Update CCW - CW explanations in functions
Issue -
State: open - Opened by nawtrey almost 4 years ago
Labels: documentation
#15 - kda.calculate_pi_difference(), kda.calculate_thermo_force() are not generating the appropriate functional forms
Issue -
State: closed - Opened by nawtrey almost 4 years ago
- 1 comment
Labels: bug
#14 - Remove string to SymPy functions
Issue -
State: open - Opened by nawtrey almost 4 years ago
- 2 comments
Labels: enhancement
#13 - Split kda.generate_flux_diagrams() into two functions
Issue -
State: closed - Opened by nawtrey almost 4 years ago
- 3 comments
Labels: enhancement
#12 - NetworkX Cycle Definition Ambiguity
Issue -
State: closed - Opened by nawtrey almost 4 years ago
- 1 comment
Labels: bug
#11 - Release 0.1.0
Issue -
State: closed - Opened by orbeckst about 4 years ago
- 1 comment
#10 - Add online documentation
Issue -
State: closed - Opened by orbeckst about 4 years ago
- 2 comments
Labels: documentation
#9 - Flux diagram generation issues
Issue -
State: closed - Opened by nawtrey about 4 years ago
- 3 comments
Labels: bug
#8 - "Color by target" feature in plot_diagrams() isn't labeling appropriate cycle nodes
Issue -
State: closed - Opened by nawtrey about 4 years ago
- 1 comment
Labels: bug
#7 - Change License to GPLv3
Issue -
State: closed - Opened by nawtrey about 4 years ago
- 1 comment
#6 - Add analysis examples
Issue -
State: closed - Opened by nawtrey about 4 years ago
- 2 comments
Labels: documentation
#5 - Fix Travis package imports so tests can run
Issue -
State: closed - Opened by nawtrey about 4 years ago
- 2 comments
#4 - plotting.py
Issue -
State: closed - Opened by nawtrey about 4 years ago
- 1 comment
Labels: enhancement
#3 - TST: `test_kda.py` recommendations
Issue -
State: open - Opened by nawtrey about 4 years ago
- 1 comment
Labels: testing
#2 - Code performance overhaul
Issue -
State: closed - Opened by nawtrey about 4 years ago
- 3 comments
Labels: enhancement
#1 - Analyze Hussey et al. 8/10 State Model of EmrE
Issue -
State: closed - Opened by nawtrey about 4 years ago