v2.0.0

What's Changed

• fix(deps): update dependency sphinx-rtd-theme to >=3,<3.2 by @renovate[bot] in #245
• fix(deps): update dependency sphinx to v9 by @renovate[bot] in #232
• Update issue templates by @harryswift01 in #247
• Adopt Principal Axes for Translational and Rotational Coordinates at All Levels by @skfegan in #246
• Enable Issue Template Picker by Adding Templates and Adding Configuration File by @harryswift01 in #249
• Introduce Table for GitHub Badges by @harryswift01 in #252
• Add Parallel Build for Coveralls in CI by @harryswift01 in #255
• Update GitHub Issues to Include HTML Friendly Comments by @harryswift01 in #253
• Isolate CI Testing Strategies for pre-commit, docs and testing by @harryswift01 in #257
• Bump peter-evans/create-pull-request from 8.0.0 to 8.1.0 by @dependabot[bot] in #258
• Update dependency pandas to v3 by @renovate[bot] in #260
• Bump actions/setup-python from 6.1.0 to 6.2.0 by @dependabot[bot] in #259
• Remove dependabot from repository workflow by @harryswift01 in #262
• Include Zenodo DOI within README.md by @harryswift01 in #264
• Update DOI badge link in README.md by @harryswift01 in #266
• Update CI matrix and documentation for supported Python versions by @harryswift01 in #269
• Align CodeEntropy with entropy methods used in 2019 paper by @jkalayan in #267
• Improve Getting Started documentation clarity and workflow by @harryswift01 in #271
• Use MDAnalysis principal_axes() for single-UA molecules to prevent complex axes by @jkalayan in #274
• Refactor workflow to DAG architecture with expanded testing, CI modernisation, and validated numerical equivalence by @harryswift01 in #281
• Regenerate API documentation and standardise Google-style docstrings by @harryswift01 in #283
• Update Logo File Path Location by @harryswift01 in #286
• Add automated Conda publishing to release workflow by @harryswift01 in #287
• Update to version 1.1.0 by @github-actions[bot] in #288
• Fix Conda recipe version update in release workflow by @harryswift01 in #290
• Update to version 2.0.0 by @github-actions[bot] in #291

Full Changelog: 1.0.7...2.0.0

v1.0.7

What's Changed

• chore(deps): update dependency pylint to v4.0.4 by @renovate[bot] in #223
• chore(deps): update softprops/action-gh-release action to v2.5.0 by @renovate[bot] in #224
• Update Renovate to include PEP 621 support and replace-based dependency ranges by @harryswift01 in #227
• Update dependency specification to version ranges for Renovate compatibility by @harryswift01 in #230
• fix(deps): update dependency sphinx-rtd-theme to v3 by @renovate[bot] in #233
• Remove lockFileMaintenance configuration from renovate.json by @harryswift01 in #237
• Bump actions/checkout from 6.0.0 to 6.0.1 by @dependabot[bot] in #234
• Bump peter-evans/create-pull-request from 7.0.9 to 7.0.11 by @dependabot[bot] in #238
• Bump peter-evans/create-pull-request from 7.0.11 to 8.0.0 by @dependabot[bot] in #239
• Automate yearly copyright update in license file by @harryswift01 in #241
• Update license copyright year(s) by @github-actions[bot] in #242
• fix(deps): update dependency waterentropy to v2 by @renovate[bot] in #243
• Update to version 1.0.7 by @github-actions[bot] in #244

Full Changelog: 1.0.6...1.0.7

v1.0.6

What's Changed

• Fix Renovate workflow to correctly detect repository by @harryswift01 in #199
• Bump actions/checkout from 5 to 6 by @dependabot[bot] in #202
• Migrate to official Renovate GitHub App and remove self-hosted workflow by @harryswift01 in #210
• Update waterEntropy dependency to v1.2.3 by @harryswift01 in #212
• Update peter-evans/create-pull-request action to v7.0.9 by @renovate[bot] in #207
• Bump actions/setup-python from 6.0.0 to 6.1.0 by @dependabot[bot] in #213
• Pin dependencies by @renovate[bot] in #206
• Update dependency pre-commit to v4.5.0 by @harryswift01 in #203
• Update dependency markupsafe to v3 by @harryswift01 in #201
• Update Averaging over Groups of Molecules for Conformational Entropy by @skfegan in #200
• Switch GitHub Workflows to Standard Cron Schedule by @harryswift01 in #215
• Ensure Workflow uses Renovate Approved Cron Schedule by @harryswift01 in #217
• chore(deps): pin dependency markupsafe to ==3.0.3 by @renovate[bot] in #218
• chore(deps): update peter-evans/create-pull-request action to v7.0.9 by @renovate[bot] in #219
• chore(deps): update actions/setup-python action to v6.1.0 by @renovate[bot] in #220
• Update to version 1.0.6 by @github-actions[bot] in #221

New Contributors

• @renovate[bot] made their first contribution in #207

Full Changelog: 1.0.5...1.0.6

v1.0.5

What's Changed

• Fix invalid YAML in CI failure issue template by @harryswift01 in #180
• Separate MDAnalysis Compatibility Workflow, Add OS Matrix, and Pin MDAnalysis Version by @harryswift01 in #182
• Remove conditional MDAnalysis install logic by @harryswift01 in #184
• Add Renovate and Pin Dependencies for Stable CI and Automated Updates by @harryswift01 in #186
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #187
• Bump renovatebot/github-action from 40.1.4 to 44.0.3 by @dependabot[bot] in #188
• Bump coverallsapp/github-action from 2.3.6 to 2.3.7 by @dependabot[bot] in #189
• Update Dependency Management using Renovate Best Practices by @harryswift01 in #191
• Force partitioning by @ioanaapapa in #193
• Update to version 1.0.5 by @github-actions[bot] in #194

Full Changelog: 1.0.4...1.0.5

v1.0.4

What's Changed

• Bump softprops/action-gh-release from 2.3.3 to 2.3.4 by @dependabot[bot] in #164
• Bump softprops/action-gh-release from 2.3.4 to 2.4.0 by @dependabot[bot] in #165
• Bump softprops/action-gh-release from 2.4.0 to 2.4.1 by @dependabot[bot] in #168
• Change Light Atom Selection Criteria From Name To Mass by @skfegan in #167
• Update Community Documentation Post v1.0.0 by @harryswift01 in #174
• Bump softprops/action-gh-release from 2.4.1 to 2.4.2 by @dependabot[bot] in #176
• Add Python v3.14 Support for CodeEntropy by @harryswift01 in #170
• Add Support for Calculating Entropy When Forces and Coordinates Are Within Seperate Files by @skfegan in #175
• Update to version 1.0.4 by @github-actions[bot] in #177

Full Changelog: 1.0.3...1.0.4

v1.0.3

What's Changed

• Bump actions/setup-python from 5.6.0 to 6.0.0 by @dependabot[bot] in #155
• Bump softprops/action-gh-release from 2.3.2 to 2.3.3 by @dependabot[bot] in #156
• Fix broken release CI pipeline by @jimboid in #157
• Expand CI pipeline to support Windows and macOS by @harryswift01 in #160
• Fix Averaging and Conformational Analysis for Protein Multimers by @skfegan in #162
• Update to version 1.0.3 by @github-actions[bot] in #163

Full Changelog: 1.0.2...1.0.3

v1.0.2

What's Changed

• Update to version 1.0.1 by @github-actions[bot] in #153
• Update to version 1.0.2 by @github-actions[bot] in #154

Full Changelog: 1.0.1...1.0.2

v1.0.0

What's Changed

• Added documentation and dask example by @DonaldChung-HK in #2
• prints the cummulative entropy by @chabi-fin in #10
• updated to psutil 5.9.5 by @ioanaapapa in #11
• axis selection by @skfegan in #12
• Md analysis update by @ioanaapapa in #13
• Migrate to pyproject.toml and Refactor Execution Structure by @harryswift01 in #44
• Implement CI pipeline pre-commit hooks by @harryswift01 in #45
• Updated python dependencies as these are no longer used in CodeEntropy: by @harryswift01 in #51
• Add error handling for NaN and invalid values in calculations: by @harryswift01 in #53
• Upgrading the verions of MDAnalysis and NumPy to the latest versions: by @harryswift01 in #57
• Removal of poseidon from CodeEntropy: by @harryswift01 in #59
• Removal of tests/data/assert.py as this is no longer required: by @harryswift01 in #61
• fix for exec not working with pyproject.toml by @jimboid in #62
• Weighted Torque Bug by @harryswift01 in #64
• Introduction of a YAML configuration file for CodeEntropy: by @harryswift01 in #65
• Updated and cleaner version of the README.md by @harryswift01 in #67
• Resolve issue #68 where there was a mismatch in the args naming convention by @harryswift01 in #69
• Removed all instances of # End Method comments by @harryswift01 in #70
• Removal of Endian Sensitive Math by @harryswift01 in #71
• Issue 63- Conformational Entropy Calculation by @ioanaapapa in #72
• Implement Python Logging by @harryswift01 in #73
• Fix YAML input for top_traj_file: by @harryswift01 in #75
• Fix Argument Precedence by @harryswift01 in #77
• Additional Test Cases for Input Configuration by @harryswift01 in #79
• Resolve issue #80 fixing indexing issue for start parameter affecting timesteps by @skfegan in #82
• Ensure verbose flag in YAML sets logging to DEBUG mode correctly by @harryswift01 in #84
• Fixing an off by one indexing error when slicing trajectories. by @skfegan in #87
• Object-oriented programming Refactor for CodeEntropy by @harryswift01 in #88
• Refinements made to the logging outputs as mentioned in issue #89: by @harryswift01 in #91
• Additional Test Cases for run.py by @harryswift01 in #96
• Extention to CI capabilities with comparisions between CodeEntropy and MDAnalysis by @harryswift01 in #92
• Introduce Dependabot to auto update dependencies by @harryswift01 in #99
• Fix Coveralls CI failure on Dependabot PRs by using GITHUB_TOKEN by @harryswift01 in #103
• Bump actions/setup-python from 2 to 5 by @dependabot[bot] in #101
• Bump actions/checkout from 2 to 4 by @dependabot[bot] in #100
• CodeEntropy logo added to README by @jkalayan in #106
• Integration of waterEntropy into CodeEntropy by @harryswift01 in #107
• Improve Test Coverage for entropy.py by @harryswift01 in #108
• Improve Test Coverage for levels.py by @harryswift01 in #109
• Improve Test Coverage for main.py by @harryswift01 in #111
• Update waterEntropy dependency to v1.1.0 by @harryswift01 in #113
• Sanity Checks for Input Parameters by @harryswift01 in #115
• MDAnalysis File Location Bug by @harryswift01 in #117
• Enforcing MDAnalysis versions 2.9 and Above by @harryswift01 in #119
• Introduction of a CITATION.cff file by @harryswift01 in #121
• Updated CITATION.cff File by @harryswift01 in #123
• Refactor entropy calculations: switch to per-timestep computation with molecule-type grouping by @harryswift01 in #126
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #128
• Add parallelism and temperature to water entropy method call. by @jimboid in #129
• Refactor Entropy Calculations with Averaging Over Timesteps, Robust State Handling, and Enhanced Eigenvalue Filtering by @harryswift01 in #130
• add new CI for releases by @jimboid in #132
• Update CI versions for consistency by @jimboid in #134
• Remove static config.yaml and implement dynamic config loading by @harryswift01 in #135
• Introduce Splash Screen with Metadata and Refactor Water Entropy Handling by @harryswift01 in #136
• Update Documentation for v1.0 Release Candidate of CodeEntropy by @skfegan in #137
• Update to version 1.0.0 by @github-actions[bot] in #140

New Contributors

• @chabi-fin made their first contribution in #10
• @ioanaapapa made their first contribution in #11
• @harryswift01 made their first contribution in #44
• @jimboid made their first contribution in #62
• @dependabot[bot] made their first contribution in #101
• @jkalayan made their first contribution in #106
• @github-actions[bot] made their first contribution in #140

Full Changelog: 0.3.9...1.0.0

v0.3.6

Initial public release