diff --git a/CHANGELOG.md b/CHANGELOG.md index d1f67daf..f029e3bf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,232 +1 @@ -# Changelog -All notable changes to this project will be documented in this file. - -The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), -and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - - -## v0.3.8 -- 2024-04-11 - -### Authors -- @lilyminium -- @mattwthompson - -### Added -- Helper methods for debugging (PR #111) - -### Changed -- Moved from importlib_resources to plain importlib with 3.9+ -- Removed 3.9 compatibility for NAGL (PR #105) -- Removed pyarrow as a core dependency (PR #113) - - - -## v0.3.7 -- 2024-04-05 - -### Authors -- @lilyminium -- mattwthompson - -### Fixed -- Refactored resonance enumeration to avoid generating whole - molecules with itertools.product where possible (PR #102, Issue #101) -- Refactored NXMolGraph.in_edges to use np.where to speed code up (PR #102, Issue #101) -- Removed Binder tooling (PR #99) - - -## v0.3.6 -- 2024-03-22 - -### Authors -- @lilyminium - -### Fixed -- Fixed typing of conformer generation from RDKit (PR #97) - -## v0.3.5 -- 2024-03-21 - -### Authors - -- @Yoshanuikabundi -- @lilyminium - -### Fixed -- Fixes to docs and examples (Issue #92, PR #73) - - -## v0.3.4 -- 2024-02-15 - -### Authors - -- @lilyminium -- @mattwthompson - -### Fixed - -- Fixed CUDA launch error (Issue #81, PR #83) -- Updated versioneer (PR #86) -- Fixed batch distribution hardcoding (Issue #80, PR #82) -- Fixed node and edge typing, adding DGL 2.0 compatibility (Issue #78, PR #79) - - -## v0.3.3 - 2023-12-22 - -### Authors - -- @lilyminium -- @IAlibay - -### Fixed - -- Fixed OpenFF molecule conversion with toolkit wrappers (Issue #69, PR #71) -- Bug report templates - -## v0.3.2 - 2023-10-26 - -### Authors - -- @lilyminium - -### Changed -- Added documentation link in README (PR #66, Issue #63) -- Removed `capture_toolkit_warnings` usage in Molecule - creation as OpenFF Toolkit v0.14.4 no longer needs it, - and removed warnings filter from method (PR #65, Issue #64) - -## v0.3.1 - 2023-09-08 - -### Authors - -- @lilyminium - -### Changed - -- Guarded openff.toolkit imports (PR #61, Issue #56) - -## v0.3.0 - 2023-08-29 - -### Authors - -- @lilyminium -- @mattwthompson - -### Reviewers -- @lilyminium - -### Added -- Codecov coverage (PR #43) -- Multiple target objectives and configuratin files (PR #45) -- Support for pydantic v2 (PR #46) -- Added `ChemicalDomain` and model versioning (PR #54) - - -### Fixed - -- pytest runs (PR #44) -- documentation badge and links (PR #51, #52) - -### Changed - -- Major refactor to move to using Arrow databases (PR #45, PR #48) -- Removed importing `OFFMolecule` in favour of `Molecule` (PR #50, Issue #13) - -### Removed -- Old `_app` and `_cli` utilities that were not well tested - are not supported in refactor (PR #49) - -## v0.2.3 - 2023-07-05 - -### Authors - -- @lilyminium -- @yoshanuikabundi - -### Reviewers -- @lilyminium - -### Added -- Link to OpenFF install guide (PR #37) - -### Fixed - -- Versioneer version prefix (PR #42) - -### Changed - -- Update examples for central examples page (PR #40) - -## v0.2.2 - 2023-03-29 - -### Authors - -- @lilyminium -- @yoshanuikabundi - -### Reviewers -- @lilyminium - -### Added -- `GNNModel.load` (PR #26) -- `GNNModel.save` function (PR #29) -- General documentation (PR #21, PR #33) -- Documentation of creation of custom features (PR #36) - -### Fixed - -- Fix edge ordering in NXMol graph (Issue #28, PR #34) - -### Changed - -- Migrate away from pkg_resources to importlib_resources (PR #35) -- Expose base classes and hide metaclasses (PR #32) -- Update examples for central examples page (PR #40) - -## v0.2.1 - 2023-03-02 - -### Authors - -- @lilyminium - -### Reviewers -- @mattwthompson - -### Added -- `GNNModel.load` function (PR #26) -- `convolution_dropout` and `readout_dropout` keywords to GNNModel (PR #26) - -### Fixed - -- Versioneer `__version__` string (PR #25) - -## v0.2.0 - 2023-02-05 - -### Authors - -- @sboothroyd -- @jthorton -- @mattwthompson -- @lilyminium - -### Added - -- New toolkit wrappers (PR #14, PR #16) - -### Fixed - - -### Changed - -- Refactored code so DGL is not required for install or model inference (PR #23) - -### Deprecated - - -### Removed - +See docs/CHANGELOG.md \ No newline at end of file diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md new file mode 100644 index 00000000..3a0ee7a7 --- /dev/null +++ b/docs/CHANGELOG.md @@ -0,0 +1,239 @@ +# Changelog +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + + + +## v0.3.8 -- 2024-04-11 + +This version drops pyarrow and rich as core dependencies. It also removes Python 3.9 support. + +### Authors +- [@lilyminium] + +## What's Changed +- Switch to plain importlib (PR #109) +- Add unprocessed methods(PR #111) +- Remove dgl config (PR #110) +- Make pyarrow optional (PR #113) +- Remove rich library (PR #115) + + +## v0.3.7 -- 2024-04-05 + +### Authors +- [@lilyminium] +- [@mattwthompson] + +### Fixed +- Refactored resonance enumeration to avoid generating whole + molecules with itertools.product where possible (PR #102, Issue #101) +- Refactored NXMolGraph.in_edges to use np.where to speed code up (PR #102, Issue #101) +- Removed Binder tooling (PR #99) + + +## v0.3.6 -- 2024-03-22 + +### Authors +- [@lilyminium] + +### Fixed +- Fixed typing of conformer generation from RDKit (PR #97) + +## v0.3.5 -- 2024-03-21 + +### Authors + +- [@Yoshanuikabundi] +- [@lilyminium] + +### Fixed +- Fixes to docs and examples (Issue #92, PR #73) + + +## v0.3.4 -- 2024-02-15 + +### Authors + +- [@lilyminium] +- [@mattwthompson] + +### Fixed + +- Fixed CUDA launch error (Issue #81, PR #83) +- Updated versioneer (PR #86) +- Fixed batch distribution hardcoding (Issue #80, PR #82) +- Fixed node and edge typing, adding DGL 2.0 compatibility (Issue #78, PR #79) + + +## v0.3.3 - 2023-12-22 + +### Authors + +- [@lilyminium] +- [@IAlibay] + +### Fixed + +- Fixed OpenFF molecule conversion with toolkit wrappers (Issue #69, PR #71) +- Bug report templates + +## v0.3.2 - 2023-10-26 + +### Authors + +- [@lilyminium] + +### Changed +- Added documentation link in README (PR #66, Issue #63) +- Removed `capture_toolkit_warnings` usage in Molecule + creation as OpenFF Toolkit v0.14.4 no longer needs it, + and removed warnings filter from method (PR #65, Issue #64) + +## v0.3.1 - 2023-09-08 + +### Authors + +- [@lilyminium] + +### Changed + +- Guarded openff.toolkit imports (PR #61, Issue #56) + +## v0.3.0 - 2023-08-29 + +### Authors + +- [@lilyminium] +- [@mattwthompson] + +### Reviewers +- [@lilyminium] + +### Added +- Codecov coverage (PR #43) +- Multiple target objectives and configuratin files (PR #45) +- Support for pydantic v2 (PR #46) +- Added `ChemicalDomain` and model versioning (PR #54) + + +### Fixed + +- pytest runs (PR #44) +- documentation badge and links (PR #51, #52) + +### Changed + +- Major refactor to move to using Arrow databases (PR #45, PR #48) +- Removed importing `OFFMolecule` in favour of `Molecule` (PR #50, Issue #13) + +### Removed +- Old `_app` and `_cli` utilities that were not well tested + are not supported in refactor (PR #49) + +## v0.2.3 - 2023-07-05 + +### Authors + +- [@lilyminium] +- [@Yoshanuikabundi] + +### Reviewers +- [@lilyminium] + +### Added +- Link to OpenFF install guide (PR #37) + +### Fixed + +- Versioneer version prefix (PR #42) + +### Changed + +- Update examples for central examples page (PR #40) + +## v0.2.2 - 2023-03-29 + +### Authors + +- [@lilyminium] +- [@Yoshanuikabundi] + +### Reviewers +- [@lilyminium] + +### Added +- `GNNModel.load` (PR #26) +- `GNNModel.save` function (PR #29) +- General documentation (PR #21, PR #33) +- Documentation of creation of custom features (PR #36) + +### Fixed + +- Fix edge ordering in NXMol graph (Issue #28, PR #34) + +### Changed + +- Migrate away from pkg_resources to importlib_resources (PR #35) +- Expose base classes and hide metaclasses (PR #32) +- Update examples for central examples page (PR #40) + +## v0.2.1 - 2023-03-02 + +### Authors + +- [@lilyminium] + +### Reviewers +- [@mattwthompson] + +### Added +- `GNNModel.load` function (PR #26) +- `convolution_dropout` and `readout_dropout` keywords to GNNModel (PR #26) + +### Fixed + +- Versioneer `__version__` string (PR #25) + +## v0.2.0 - 2023-02-05 + +### Authors + +- [@SimonBoothroyd] +- [@jthorton] +- [@mattwthompson] +- [@lilyminium] + +### Added + +- New toolkit wrappers (PR #14, PR #16) + +### Fixed + + +### Changed + +- Refactored code so DGL is not required for install or model inference (PR #23) + +### Deprecated + + +### Removed + + +[@lilyminium]: https://github.com/lilyminium +[@mattwthompson]: https://github.com/mattwthompson +[@Yoshanuikabundi]: https://github.com/Yoshanuikabundi +[@IAlibay]: https://github.com/IAlibay +[@jthorton]: https://github.com/jthorton +[@SimonBoothroyd]: https://github.com/SimonBoothroyd diff --git a/docs/index.md b/docs/index.md index 0b34c9eb..771c1f19 100644 --- a/docs/index.md +++ b/docs/index.md @@ -73,6 +73,7 @@ hidden: true caption: Developer's Guide --- +CHANGELOG.md dev.md toolkit_wrappers.md ::: @@ -107,4 +108,4 @@ so we must use eval-rst here .. raw:: html -``` \ No newline at end of file +```