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Clean/versions - #4
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…otite`, `hydrid`, `torch` and `einops` versions ci: update github actions
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nscorley
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… update CI (#4) * clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions * ci: update github actions trigger `digs` workflow manually only.
kierandidi
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* docs: load and visualize structures * chore: format * docs: update README * docs(readme): improve code block formatting * docs(readme): fix typos * Change TOC depth Just changed the TOC depth from 1 to 2 in the conf.py file to test the GitHub actions workflow. * Update README.md Updated the link to the external docs to remove 404 error. * Update README.md Changed the documentation link in the contribution section. * docs(readme): add notice * clean: remove legacy dependencies, relax various dependency versions, update CI (#4) * clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions * ci: update github actions trigger `digs` workflow manually only. * clean: clean-up CI (#6) * ci: restrict workflow permissions (#8) * clean: clean-up CI * ci: restrict workflow permissions * refactor: disentangle CLI form package code and document PDB training example * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * Build/numpy version (#10) * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * build: enable numpy 2.x, pandas 2.3 * chore: ruff * docs: fix readme (#11) * docs: two additional examples for the gallery --------- Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local> Co-authored-by: Buddha7771 <hwlee7771@gmail.com> Co-authored-by: Rachel Clune <rclune4b@gmail.com> Co-authored-by: Rachel Clune <rachel.clune@omsf.io> Co-authored-by: Simon Mathis <simon.mathis@gmail.com> Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com>
kierandidi
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* clean: remove legacy dependencies, relax various dependency versions, update CI (#4) * clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions * ci: update github actions trigger `digs` workflow manually only. * clean: clean-up CI (#6) * ci: restrict workflow permissions (#8) * clean: clean-up CI * ci: restrict workflow permissions * refactor: disentangle CLI form package code and document PDB training example * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * Build/numpy version (#10) * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * build: enable numpy 2.x, pandas 2.3 * chore: ruff * docs: fix readme (#11) * refactor: consolidate `constants` and `common` (#7) Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com> * docs: initial examples (#12) * docs: load and visualize structures * chore: format * docs: update README * docs(readme): improve code block formatting * docs(readme): fix typos * Change TOC depth Just changed the TOC depth from 1 to 2 in the conf.py file to test the GitHub actions workflow. * Update README.md Updated the link to the external docs to remove 404 error. * Update README.md Changed the documentation link in the contribution section. * docs(readme): add notice * clean: remove legacy dependencies, relax various dependency versions, update CI (#4) * clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions * ci: update github actions trigger `digs` workflow manually only. * clean: clean-up CI (#6) * ci: restrict workflow permissions (#8) * clean: clean-up CI * ci: restrict workflow permissions * refactor: disentangle CLI form package code and document PDB training example * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * Build/numpy version (#10) * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * build: enable numpy 2.x, pandas 2.3 * chore: ruff * docs: fix readme (#11) * docs: two additional examples for the gallery --------- Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local> Co-authored-by: Buddha7771 <hwlee7771@gmail.com> Co-authored-by: Rachel Clune <rclune4b@gmail.com> Co-authored-by: Rachel Clune <rachel.clune@omsf.io> Co-authored-by: Simon Mathis <simon.mathis@gmail.com> Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com> --------- Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com> Co-authored-by: Nathaniel Corley <nscorley@gmail.com> Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local> Co-authored-by: Buddha7771 <hwlee7771@gmail.com> Co-authored-by: Rachel Clune <rclune4b@gmail.com> Co-authored-by: Rachel Clune <rachel.clune@omsf.io>
Croydon-Brixton
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Sep 3, 2025
) * docs and chore: add examples and consolidate constants (#5) * clean: remove legacy dependencies, relax various dependency versions, update CI (#4) * clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions * ci: update github actions trigger `digs` workflow manually only. * clean: clean-up CI (#6) * ci: restrict workflow permissions (#8) * clean: clean-up CI * ci: restrict workflow permissions * refactor: disentangle CLI form package code and document PDB training example * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * Build/numpy version (#10) * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * build: enable numpy 2.x, pandas 2.3 * chore: ruff * docs: fix readme (#11) * refactor: consolidate `constants` and `common` (#7) Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com> * docs: initial examples (#12) * docs: load and visualize structures * chore: format * docs: update README * docs(readme): improve code block formatting * docs(readme): fix typos * Change TOC depth Just changed the TOC depth from 1 to 2 in the conf.py file to test the GitHub actions workflow. * Update README.md Updated the link to the external docs to remove 404 error. * Update README.md Changed the documentation link in the contribution section. * docs(readme): add notice * clean: remove legacy dependencies, relax various dependency versions, update CI (#4) * clean: remove `fire` and `fastparquet` legacy dependencies, relax `biotite`, `hydrid`, `torch` and `einops` versions * ci: update github actions trigger `digs` workflow manually only. * clean: clean-up CI (#6) * ci: restrict workflow permissions (#8) * clean: clean-up CI * ci: restrict workflow permissions * refactor: disentangle CLI form package code and document PDB training example * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * Build/numpy version (#10) * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements * build: enable numpy 2.x, pandas 2.3 * chore: ruff * docs: fix readme (#11) * docs: two additional examples for the gallery --------- Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local> Co-authored-by: Buddha7771 <hwlee7771@gmail.com> Co-authored-by: Rachel Clune <rclune4b@gmail.com> Co-authored-by: Rachel Clune <rachel.clune@omsf.io> Co-authored-by: Simon Mathis <simon.mathis@gmail.com> Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com> --------- Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com> Co-authored-by: Nathaniel Corley <nscorley@gmail.com> Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local> Co-authored-by: Buddha7771 <hwlee7771@gmail.com> Co-authored-by: Rachel Clune <rclune4b@gmail.com> Co-authored-by: Rachel Clune <rachel.clune@omsf.io> * fix: prevent chain_ids in outer scope from being overridden by loop --------- Co-authored-by: Simon Mathis <simon.mathis@gmail.com> Co-authored-by: Kieran Didi <58345129+kierandidi@users.noreply.github.com> Co-authored-by: Nathaniel Corley <nscorley@gmail.com> Co-authored-by: Nathaniel Corley <nscorley@Nathaniels-MacBook-Pro.local> Co-authored-by: Buddha7771 <hwlee7771@gmail.com> Co-authored-by: Rachel Clune <rclune4b@gmail.com> Co-authored-by: Rachel Clune <rachel.clune@omsf.io>
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Part of the post-release cleanup: Refines dependency version constraints in
pyproject.tomlfor improved compatibility and maintainability, and updates the CI workflow to trigger on an thestagingbranch.Dependency version updates and cleanup:
fastparquetandfirefrom the dependenciespre-commit,debugpy, andipykernelfrom thedevdependencies.pyproject.tomlto allow for greater flexibility and future updates, includingbiotite,hydride,rdkit,torch, andeinops.