docs and chore: add examples and consolidate constants #5
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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.
* clean: clean-up CI * ci: restrict workflow permissions
… example * refactor: disentangle CLI from package code * docs: update readme with PDB training example * docs: further documentation improvements
* 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
Co-authored-by: Kieran Didi <[email protected]>
* 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 <[email protected]> Co-authored-by: Buddha7771 <[email protected]> Co-authored-by: Rachel Clune <[email protected]> Co-authored-by: Rachel Clune <[email protected]> Co-authored-by: Simon Mathis <[email protected]> Co-authored-by: Kieran Didi <[email protected]>
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production branch with cleanup & patches from staging
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) * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Buddha7771 <[email protected]> Co-authored-by: Rachel Clune <[email protected]> Co-authored-by: Rachel Clune <[email protected]> Co-authored-by: Simon Mathis <[email protected]> Co-authored-by: Kieran Didi <[email protected]> --------- Co-authored-by: Kieran Didi <[email protected]> Co-authored-by: Nathaniel Corley <[email protected]> Co-authored-by: Nathaniel Corley <[email protected]> Co-authored-by: Buddha7771 <[email protected]> Co-authored-by: Rachel Clune <[email protected]> Co-authored-by: Rachel Clune <[email protected]> * fix: prevent chain_ids in outer scope from being overridden by loop --------- Co-authored-by: Simon Mathis <[email protected]> Co-authored-by: Kieran Didi <[email protected]> Co-authored-by: Nathaniel Corley <[email protected]> Co-authored-by: Nathaniel Corley <[email protected]> Co-authored-by: Buddha7771 <[email protected]> Co-authored-by: Rachel Clune <[email protected]> Co-authored-by: Rachel Clune <[email protected]>
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