MDAnalysis/solvation-analysis issues and pull requests

#107 - Try unpin scipy

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

#106 - Unpin scipy

Issue - State: closed - Opened by tsmathis 5 months ago - 4 comments

#105 - plots

Pull Request - State: closed - Opened by orionarcher 7 months ago - 2 comments

#104 - Disable Pep8Speaks

Issue - State: open - Opened by orionarcher 7 months ago

#103 - Package modernization

Pull Request - State: closed - Opened by orionarcher 7 months ago - 2 comments

#102 - RDF calculations can now ignore residue level self-self bonds, use internally

Issue - State: closed - Opened by orionarcher 7 months ago
Labels: enhancement

#101 - rdf_data not initialized properly when running solute.run()

Issue - State: open - Opened by Caboomi 8 months ago - 6 comments
Labels: bug

#100 - Add type hints

Issue - State: closed - Opened by orionarcher 8 months ago
Labels: enhancement

#99 - build with `pip install -e .` incorrectly states version number is `v0.1.5`

Issue - State: open - Opened by orionarcher 8 months ago
Labels: bug

#98 - Update CI.yaml for Py3.12 and drop Py3.8

Pull Request - State: closed - Opened by hmacdope 11 months ago - 7 comments

#97 - Check Python 3.12 compatibility with develop version of MDAnalysis

Issue - State: closed - Opened by IAlibay about 1 year ago - 1 comment

#96 - switch from conda incubator to micromamba action

Issue - State: open - Opened by IAlibay about 1 year ago - 1 comment
Labels: testing

#95 - Add action to point to the right RTD link

Issue - State: open - Opened by IAlibay about 1 year ago
Labels: documentation

#94 - pin pandas<2

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

#93 - CI broken for pandas 2.1

Issue - State: closed - Opened by IAlibay about 1 year ago - 4 comments

#92 - pin pandas<2.1 and add cron trigger to CI

Pull Request - State: closed - Opened by IAlibay about 1 year ago - 12 comments

#91 - Include statistics for `solvents` that aren't participating in solvation

Issue - State: open - Opened by orionarcher over 1 year ago
Labels: bug, enhancement

#90 - Update speciation.py to use backticks in query()

Pull Request - State: closed - Opened by orionarcher over 1 year ago - 1 comment

#89 - Allow for default cutoff radii to be set

Issue - State: closed - Opened by orionarcher over 1 year ago - 1 comment
Labels: enhancement, good first issue

#88 - remove pathlib from deps

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 2 comments

#87 - Response to JOSS feedback.

Pull Request - State: closed - Opened by orionarcher over 1 year ago - 2 comments

#86 - Add pyproject.toml

Pull Request - State: closed - Opened by hmacdope almost 2 years ago - 9 comments
Labels: enhancement

#85 - Plot updates

Pull Request - State: closed - Opened by orionarcher almost 2 years ago - 2 comments
Labels: enhancement

#84 - Release prior to JOSS paper

Issue - State: closed - Opened by hmacdope almost 2 years ago - 7 comments

#83 - Add JOSS paper draft.

Pull Request - State: closed - Opened by orionarcher almost 2 years ago - 4 comments

#82 - debugged error in residence time

Pull Request - State: closed - Opened by orionarcher almost 2 years ago

#81 - Concatenation Issue for Residence Time Calculation

Issue - State: closed - Opened by SophiaRuan almost 2 years ago - 1 comment

#80 - PEP518 compliance, add a `pyproject.toml`

Issue - State: closed - Opened by hmacdope about 2 years ago

#79 - Styling and consistency of documentation could be improved

Issue - State: open - Opened by orionarcher about 2 years ago
Labels: documentation

#78 - Doc upgrade

Pull Request - State: closed - Opened by orionarcher about 2 years ago - 2 comments
Labels: documentation

#77 - Tutorials should be written out in the documentation

Issue - State: closed - Opened by orionarcher about 2 years ago
Labels: documentation

#76 - Getting started page lacks enough information to get started

Issue - State: closed - Opened by orionarcher about 2 years ago
Labels: documentation

#75 - Support for multi atom solutes

Pull Request - State: closed - Opened by orionarcher about 2 years ago - 8 comments
Labels: enhancement, core

#74 - Revert "Support for multi-atom solutes"

Pull Request - State: closed - Opened by orionarcher about 2 years ago - 1 comment

#73 - Rename solution to solute

Pull Request - State: closed - Opened by orionarcher about 2 years ago - 1 comment

#72 - Support for multi-atom solutes

Pull Request - State: closed - Opened by orionarcher about 2 years ago - 3 comments

#71 - Replace `solvation_data_dup` data frame with only the duplicates

Issue - State: closed - Opened by orionarcher about 2 years ago - 2 comments

#70 - Enhancements to support composable Solutions and self-solvating solutes

Pull Request - State: closed - Opened by orionarcher about 2 years ago - 7 comments
Labels: enhancement, core, high-priority

#69 - Reorganize analysis library

Pull Request - State: closed - Opened by orionarcher about 2 years ago - 1 comment
Labels: core, testing

#68 - Work towards MDAKit integration

Issue - State: closed - Opened by hmacdope over 2 years ago - 6 comments

#67 - Solvation plots

Pull Request - State: closed - Opened by laurlee over 2 years ago - 1 comment

#66 - Have identical atoms as solutes in a single Solution.

Issue - State: closed - Opened by hmacdope over 2 years ago - 2 comments

#65 - New test data

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

#64 - Init kwargs fix

Pull Request - State: closed - Opened by orionarcher over 2 years ago - 3 comments
Labels: enhancement

#63 - Rdf fitting improvement

Pull Request - State: closed - Opened by orionarcher over 2 years ago - 5 comments

#62 - No dimensions while using GROMACS trr or xtc file

Issue - State: closed - Opened by sli259 over 2 years ago - 2 comments
Labels: question

#61 - Add Plots for Visualization

Pull Request - State: closed - Opened by laurlee over 2 years ago - 11 comments
Labels: enhancement

#60 - Visualization module [WIP]

Pull Request - State: closed - Opened by orionarcher over 2 years ago - 2 comments

#59 - Residence times and solute-solvent network calculations

Pull Request - State: closed - Opened by orionarcher over 2 years ago - 8 comments
Labels: enhancement

#58 - Make Solution composable to handle large solutes

Issue - State: closed - Opened by orionarcher over 2 years ago
Labels: enhancement

#57 - Create a `save_data` method for solution

Issue - State: closed - Opened by orionarcher almost 3 years ago - 1 comment

#56 - Update tutorial notebooks and add custom RDF fitting demo

Pull Request - State: closed - Opened by hmacdope almost 3 years ago - 6 comments
Labels: documentation

#55 - Should we allow custom functions for calculating solvation shells at the RDF step?

Issue - State: open - Opened by hmacdope almost 3 years ago - 5 comments
Labels: enhancement, core, discussion

#54 - Add additional notebook showing use of custom RDF parser function

Issue - State: closed - Opened by hmacdope almost 3 years ago - 3 comments
Labels: documentation, enhancement

#53 - implement basic save and load functionality

Pull Request - State: closed - Opened by orionarcher almost 3 years ago - 2 comments
Labels: enhancement

#52 - Add save() and load() method to solution.

Issue - State: open - Opened by orionarcher almost 3 years ago - 6 comments
Labels: enhancement, core

#51 - Two small bug fixs

Pull Request - State: closed - Opened by orionarcher almost 3 years ago - 1 comment

#50 - Run will fail if no trajectory dimensions are set

Issue - State: closed - Opened by orionarcher almost 3 years ago - 2 comments
Labels: bug

#49 - Solvation analysis assumes type is an int

Issue - State: closed - Opened by orionarcher almost 3 years ago - 1 comment
Labels: bug

#48 - Formalize Roadmap in Projects tab

Issue - State: closed - Opened by hmacdope about 3 years ago - 8 comments
Labels: release

#47 - Reliably handle multi-atom solutes

Issue - State: closed - Opened by orionarcher about 3 years ago - 5 comments
Labels: bug, enhancement

#46 - Feature Request: pass Solution.run() kwargs to RDF

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

#45 - Mismatched 0-indexing and 1-indexing in Solution._single_frame()

Issue - State: closed - Opened by orionarcher about 3 years ago - 4 comments
Labels: bug

#44 - change license to GNUv3

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 1 comment

#43 - Improve solvation distance kernel

Issue - State: closed - Opened by orionarcher over 3 years ago - 7 comments
Labels: enhancement

#42 - Conda release in the future.

Issue - State: closed - Opened by hmacdope over 3 years ago - 5 comments
Labels: release

#41 - Licensing and BSD-3 vs GPL3

Issue - State: closed - Opened by hmacdope over 3 years ago - 4 comments
Labels: documentation, high-priority

#40 - add visualization tutorial

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 10 comments
Labels: bug, documentation, enhancement

#39 - Add functionality to analysis classes

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 2 comments
Labels: enhancement

#38 - Tag not merged.

Issue - State: closed - Opened by hmacdope over 3 years ago - 3 comments
Labels: release

#37 - add versioneer

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 3 comments
Labels: high-priority, release

#36 - tutorials

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 12 comments
Labels: documentation, high-priority

#35 - Implement analysis tests on toy data frames

Issue - State: closed - Opened by orionarcher over 3 years ago
Labels: testing

#34 - Pip release of 0.0.1

Issue - State: closed - Opened by hmacdope over 3 years ago - 14 comments
Labels: release

#33 - Docs do not have any ReST written for API

Issue - State: closed - Opened by hmacdope over 3 years ago - 1 comment
Labels: documentation, high-priority

#32 - Investigate atomgroup based core data structure.

Issue - State: closed - Opened by hmacdope over 3 years ago - 2 comments
Labels: question, core, performance

#31 - make solute also be able to be a solvent

Issue - State: closed - Opened by orionarcher over 3 years ago - 2 comments
Labels: bug, enhancement

#30 - Add tiled rdf plots

Issue - State: closed - Opened by orionarcher over 3 years ago - 2 comments
Labels: enhancement

#29 - analysis functions

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 34 comments
Labels: core, high-priority

#28 - Decide hierarchy of analysis classes/methods

Issue - State: closed - Opened by hmacdope over 3 years ago - 11 comments
Labels: question, core, high-priority

#27 - Move large raw csv datafiles to .npz files

Issue - State: closed - Opened by hmacdope over 3 years ago - 2 comments
Labels: testing

#26 - Add Jupyter notebook for validation of visual elements of minima finding.

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

#25 - Parse RDF's and find minima

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 20 comments
Labels: core, testing, high-priority

#24 - Remove universe argument to solvation selection functions

Issue - State: closed - Opened by orionarcher over 3 years ago - 1 comment
Labels: enhancement, core

#23 - Add type hinting to solvation selection functions

Issue - State: closed - Opened by orionarcher over 3 years ago - 5 comments
Labels: enhancement

#22 - Generalize get_nearest_n_mol

Issue - State: closed - Opened by orionarcher over 3 years ago - 1 comment
Labels: enhancement, core

#21 - Make analyses subclass AnalysisBase

Issue - State: closed - Opened by hmacdope over 3 years ago - 1 comment

#20 - Update README.md, issue #18

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 1 comment
Labels: documentation

#19 - Complete get_n_shells / generalize identify solvation cutoff

Issue - State: closed - Opened by hmacdope over 3 years ago - 5 comments
Labels: enhancement, core

#18 - Add some more info to the README.

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

#17 - CI and doc changes to address issues #9 and #4

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 2 comments

#16 - Basic testing with Pytest

Pull Request - State: closed - Opened by orionarcher over 3 years ago - 17 comments
Labels: core, testing

#15 - Solvation selection framework

Issue - State: closed - Opened by hmacdope over 3 years ago - 1 comment
Labels: core

#14 - Possible enhancements to capped-distances

Issue - State: closed - Opened by hmacdope over 3 years ago - 3 comments
Labels: enhancement, upstream

#13 - Finalize and develop tutorial

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

#12 - Refine, refactor, document

Issue - State: closed - Opened by hmacdope over 3 years ago
Labels: documentation, testing

#11 - Solvation analysis framework

Issue - State: closed - Opened by hmacdope over 3 years ago
Labels: core

#10 - Set up Linting with Black

Issue - State: closed - Opened by orionarcher over 3 years ago - 1 comment
Labels: testing

#9 - Setup issue labels

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

#8 - Setup continuous integration.

Issue - State: closed - Opened by hmacdope over 3 years ago - 5 comments
Labels: testing, high-priority

GitHub / MDAnalysis/solvation-analysis issues and pull requests