Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / gemdat-repos/gemdat issues and pull requests

#334 - Update README.md

Pull Request - State: closed - Opened by stefsmeets about 2 months ago

#333 - example notebooks broken - plots backend option

Issue - State: closed - Opened by tfamprikis about 2 months ago - 6 comments

#332 - Fix coverage badge

Pull Request - State: closed - Opened by stefsmeets 2 months ago

#331 - Fix shaded rendering for msd plot

Pull Request - State: closed - Opened by stefsmeets 2 months ago

#330 - Add GROMACS support

Pull Request - State: closed - Opened by AstyLavrinenko 2 months ago - 1 comment

#329 - MSD plot

Issue - State: closed - Opened by AstyLavrinenko 2 months ago - 11 comments

#327 - Add LAMMPS trajectory reader

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#326 - Add option to switch between plotting backends

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#325 - Add method to create a graph from jumps

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

#324 - Add plotly plot for shape

Pull Request - State: closed - Opened by SCiarella 4 months ago - 3 comments

#323 - Add warning for multiple paths

Pull Request - State: closed - Opened by SCiarella 4 months ago

#322 - Approach to percolation with networkx graphs

Issue - State: closed - Opened by SCiarella 4 months ago - 1 comment

#321 - Fix ruff config

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#320 - Fix rdf plotly test

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#319 - Make backend for plots user configurable

Issue - State: closed - Opened by stefsmeets 4 months ago

#318 - Add shortcut for calculating and plotting RDFs

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#317 - Move to ruff for autoformatting

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#316 - Move legacy.py out of main library

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#315 - Add plotly plot for shape analysis

Issue - State: closed - Opened by stefsmeets 4 months ago

#314 - Move legacy.py to scipts

Issue - State: closed - Opened by stefsmeets 4 months ago

#313 - Add plotly plots

Pull Request - State: closed - Opened by stefsmeets 4 months ago - 2 comments

#312 - Tests are failing

Issue - State: closed - Opened by stefsmeets 4 months ago - 2 comments

#311 - Replace yapf and nbqa by ruff for formatting

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#310 - Housekeeping

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#309 - Add option to show shaded area for std

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#308 - Update captions for plots

Pull Request - State: closed - Opened by stefsmeets 4 months ago

#307 - Orientational sites

Pull Request - State: open - Opened by SCiarella 5 months ago - 1 comment

#306 - Return molecule trajectory from Orientations

Issue - State: open - Opened by stefsmeets 5 months ago

#305 - Refactor Pathway class

Pull Request - State: closed - Opened by stefsmeets 5 months ago - 2 comments

#304 - Add zenodo link and how to cite

Pull Request - State: closed - Opened by stefsmeets 5 months ago

#303 - Update Orientations api

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

#302 - More plotly plots

Issue - State: closed - Opened by stefsmeets 5 months ago - 1 comment

#301 - Tweak method names and update default dimensions

Pull Request - State: closed - Opened by stefsmeets 5 months ago

#300 - Revise shaded areas for plots

Issue - State: closed - Opened by stefsmeets 5 months ago

#299 - Update captions to all plots

Issue - State: closed - Opened by stefsmeets 5 months ago - 2 comments

#298 - Add citation / zenodo link to readme

Issue - State: closed - Opened by stefsmeets 5 months ago

#296 - Streamline Orientations api

Issue - State: closed - Opened by stefsmeets 5 months ago - 1 comment

#295 - Fix broken publish action

Pull Request - State: closed - Opened by stefsmeets 5 months ago

#294 - Update actions versions

Pull Request - State: closed - Opened by stefsmeets 5 months ago

#293 - Fix Orientations IO

Pull Request - State: closed - Opened by SCiarella 6 months ago - 2 comments

#292 - Orientations should return Trajectories instead of np.ndarrays

Issue - State: closed - Opened by SCiarella 6 months ago - 2 comments

#291 - Add option to select MSD algorithm

Pull Request - State: closed - Opened by SCiarella 6 months ago - 6 comments

#290 - autocorrelation should use unit vectors

Issue - State: closed - Opened by tfamprikis 6 months ago

#289 - orientations function to return non-normalized cartesian vectors

Issue - State: closed - Opened by tfamprikis 6 months ago - 1 comment

#288 - orientations.get_conventional_coordinates()

Issue - State: closed - Opened by tfamprikis 6 months ago - 2 comments

#286 - rectilinear plot

Issue - State: closed - Opened by tfamprikis 6 months ago - 2 comments

#285 - accelerate MSD calc.

Issue - State: closed - Opened by tfamprikis 6 months ago - 4 comments

#284 - Refactor 3d plots module

Pull Request - State: closed - Opened by stefsmeets 6 months ago

#283 - Implement Haven ratio

Pull Request - State: closed - Opened by stefsmeets 6 months ago - 3 comments

#282 - Refactor Volume class to support multiple data types

Pull Request - State: closed - Opened by stefsmeets 7 months ago - 5 comments

#281 - Vesta add energy landscape to data file

Issue - State: closed - Opened by stefsmeets 7 months ago - 1 comment

#280 - rename all displacement_per_site to displacement_per_atom

Pull Request - State: closed - Opened by v1kko 7 months ago

#279 - fix periodic jumps of matplotlib jumps_3d plot

Pull Request - State: closed - Opened by v1kko 7 months ago - 1 comment

#278 - Added some plotly plots

Pull Request - State: closed - Opened by v1kko 7 months ago - 1 comment

#277 - Update notebooks in documentation build

Issue - State: closed - Opened by stefsmeets 7 months ago - 2 comments

#276 - VESTA plots

Issue - State: closed - Opened by SCiarella 7 months ago - 5 comments

#275 - Path enhancements

Issue - State: closed - Opened by SCiarella 7 months ago - 5 comments

#274 - MSD enhancements

Issue - State: closed - Opened by SCiarella 7 months ago

#273 - Fix displacement plot labels

Issue - State: closed - Opened by SCiarella 7 months ago - 3 comments
Labels: documentation

#272 - Percolation analysis through jump graph

Issue - State: open - Opened by v9lgraf 7 months ago - 9 comments

#271 - Finding neighbours and common neighbors for supercells

Issue - State: open - Opened by v9lgraf 7 months ago - 3 comments

#270 - Plotly output for notebooks might be broken (this is how to fix it)

Issue - State: closed - Opened by v1kko 7 months ago - 3 comments
Labels: documentation

#269 - Calculate the Haven's Ratio

Issue - State: closed - Opened by v1kko 7 months ago - 2 comments

#268 - Create a plot with activation energy and jumps plot as shown by victor

Issue - State: closed - Opened by v1kko 7 months ago - 1 comment

#267 - Advanced jumps/percolation analysis

Issue - State: closed - Opened by v1kko 7 months ago - 1 comment

#266 - Allow loading of cache file without vasprun.xml file

Issue - State: closed - Opened by v1kko 7 months ago - 4 comments

#265 - Calculate transitions with custom radii per site type

Pull Request - State: closed - Opened by stefsmeets 7 months ago - 10 comments

#264 - Make api more accessible, part 2

Pull Request - State: closed - Opened by stefsmeets 7 months ago - 1 comment

#263 - Include new notebooks in documentation

Issue - State: closed - Opened by SCiarella 7 months ago - 2 comments

#262 - Add straight path as method on `optimal_path()`

Issue - State: closed - Opened by stefsmeets 7 months ago - 2 comments

#261 - Fix docs build

Pull Request - State: closed - Opened by stefsmeets 7 months ago

#260 - Add more plotly plots

Issue - State: closed - Opened by stefsmeets 7 months ago - 1 comment

#259 - Make user api more intuitive

Pull Request - State: closed - Opened by stefsmeets 7 months ago

#258 - Multiple paths

Pull Request - State: closed - Opened by SCiarella 7 months ago - 1 comment

#257 - Fix documentation build

Pull Request - State: closed - Opened by stefsmeets 7 months ago

#256 - Small tweaks to Transitions

Pull Request - State: closed - Opened by stefsmeets 7 months ago

#255 - Fix RDF test

Pull Request - State: closed - Opened by stefsmeets 8 months ago - 1 comment

#254 - Problem importing trajectory with newest gemdat version

Issue - State: closed - Opened by v9lgraf 8 months ago - 3 comments

#253 - Fix wrong `n_floating` bug

Pull Request - State: closed - Opened by stefsmeets 8 months ago

#252 - `.n_floating` returns the wrong number

Issue - State: closed - Opened by stefsmeets 8 months ago

#251 - Refactor sites methods/attrs into other classes

Pull Request - State: closed - Opened by stefsmeets 8 months ago - 2 comments

#250 - Turn Jumps.rates and Jumps.activation energies into dataframes

Pull Request - State: closed - Opened by stefsmeets 8 months ago

#249 - Use dataframes where possible

Issue - State: closed - Opened by stefsmeets 8 months ago

#248 - Improve MSD calculation

Pull Request - State: closed - Opened by SCiarella 8 months ago

#246 - Return structure with occupancy set as Composition

Pull Request - State: closed - Opened by stefsmeets 8 months ago - 1 comment

#245 - Split time / distance constraint for jump definition

Issue - State: closed - Opened by stefsmeets 8 months ago

#244 - Change return type for occupancy

Issue - State: closed - Opened by stefsmeets 8 months ago

#243 - Check 3d jumps plot

Issue - State: closed - Opened by v1kko 8 months ago - 1 comment
Labels: bug

#242 - Add method to extend trajectory

Pull Request - State: closed - Opened by stefsmeets 8 months ago - 5 comments

#241 - b65577 breaks rdf plot 1, investigate

Issue - State: closed - Opened by v1kko 8 months ago - 4 comments
Labels: validation

#240 - SitesData contains data and functions that do not belong there

Issue - State: closed - Opened by v1kko 8 months ago - 2 comments

#239 - Add multiple pathfinding options

Pull Request - State: closed - Opened by SCiarella 8 months ago

#238 - Fix number of sites by type

Pull Request - State: closed - Opened by AstyLavrinenko 8 months ago

#237 - Use multiple starting point to compute the MSD

Issue - State: open - Opened by SCiarella 8 months ago - 2 comments

#237 - Use multiple starting point to compute the MSD

Issue - State: closed - Opened by SCiarella 8 months ago - 4 comments

#236 - Merge consecutive trajectories

Issue - State: closed - Opened by SCiarella 8 months ago