Fix action #311
Merged
Fix action #311
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## dev_bjorn #311 +/- ##
==========================================
Coverage 93.63% 93.63%
==========================================
Files 40 40
Lines 3926 3926
Branches 589 589
==========================================
Hits 3676 3676
Misses 198 198
Partials 52 52 |
manulera
added a commit
that referenced
this pull request
Oct 24, 2024
* added new translation function * new orfs method for Seq based on three_frame_orfs function * new orfs_to_features method for Dseqrecord * new extract_from_text functions that also returns the intervening text between sequences * bugfix orfs for Seq and Dsecrecord * added crispr tests * added pairwise for older Python versions * older type hint * Deploying to gh-pages from @ da3e7e9 🚀 * Deploying to gh-pages from @ 5be4f9d 🚀 * Deploying to gh-pages from @ b37a17c 🚀 * Deploying to gh-pages from @ 11aae3c 🚀 * Deploying to gh-pages from @ 0f95223 🚀 * try to build docs locally on gh-pages * try to build gh pages * try to build gh pages * fix * added sphinx ext * Deploying to gh-pages from @ bc08a36 🚀 * try fix docs * build docs * clean * redirect docs badge to action * redirect docs badge to action * fix readme links * fix readme * fix * try to fix test error * fix bug that recognized parts of re enzyme names as other enzymes * added comment with number of enzymes * changed number of expected enzymes to the correct number 621 * more informative error msg * closes #216 (2) * closes #196 * vscode and poetry settings added * fix test * add locations_overlap to utils * Issue 238 (#239) * closes #238 * fix notebook * closes #240 * atomically write default config * optimisation for #237 * fix python 3.8 typing * include neb calculator and its tests * fix design and add tests * example commit for #176 * Documentation notebooks 2 (#272) * Documentation notebooks (#271) * added documentation for dseq.py * fixed docs for Dseq.py * fixed docs for Dseq.py * add hook * fix exclusions and run hook * strip outputs of Dseq.ipynb * update Dseq notebook * placed notebooks in docs * added looped and shifted methods in Dseq docs * added docs for importing files using pydna * added some Dseqrecord docs * added docs+examples for Dseq_Features * added origin spanning feats and removing feats for Dseq_Features * some comments and todos * added restriction page * updated Importing_Seq page * updated Dseq_Feature Page w/examples * added restrict+ligate notebook * added some PCR notes * added examples, prints * added tm and design * fixed tm_default docs * added gibson assembly * some comments on current progress * gibson * fixed comments, added gibson example and CRISPR * added Restriction example * added Gibson example * closes #256 * run pre-commit * alternative example for gibson * gibson updated example * modified crispr * modified crispr * feedback changes for #260 * best practices for qualifiers --------- Co-authored-by: Pei-Lun Xie <[email protected]> Co-authored-by: Pei-Lun Xie <[email protected]> * remove unnecessary file * remove dir exclusions * exclude test notebooks --------- Co-authored-by: Pei-Lun Xie <[email protected]> Co-authored-by: Pei-Lun Xie <[email protected]> * update contribution guidelines (#274) * update CI action to enforce hooks (#277) * update CI action to enforce hooks * update action * update: Added google badge to all notebooks issue #266 (#275) * fourth trt * final file added * update: added installation of pydna * added seguid stamp to Genbank sequence files * fix test sequence file * dependabot monthly * New CRISPR example notebook (#260) (#284) * fourth trt * final file added * update: added installation of pydna * update: added CRIPSR examples in notebooks issue #259 * update: added google badge issue #266 * Polished Example CRISPR notebook --------- Co-authored-by: Manuel Lera-Ramirez <[email protected]> * Updated notebooks (#295) * updated example_restriction (#285) Co-authored-by: Pei-Lun Xie <[email protected]> * small fixes (#294) * allow run all on notebooks that have pip install for google colab --------- Co-authored-by: Pei-Lun Xie <[email protected]> * progress towards #261 * WIP * remove code image from README for #261 * more README updates + make requirements.txt * add requirements file * fix configuration * typing for PrettyTable * typing for codon dicts * typing for Seq * typing for FakeSeq * typing for Genbank * typing for sequence_picker module * typing for common_sub_strings module * typing for Assembly.__init__ and Assembly.__repr__ * Bump pillow from 10.3.0 to 10.4.0 Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.3.0 to 10.4.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@10.3.0...10.4.0) --- updated-dependencies: - dependency-name: pillow dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * Bump autopep8 from 2.1.0 to 2.3.1 Bumps [autopep8](https://github.com/hhatto/autopep8) from 2.1.0 to 2.3.1. - [Release notes](https://github.com/hhatto/autopep8/releases) - [Commits](hhatto/autopep8@v2.1.0...v2.3.1) --- updated-dependencies: - dependency-name: autopep8 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * Bump black from 24.4.2 to 24.8.0 Bumps [black](https://github.com/psf/black) from 24.4.2 to 24.8.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@24.4.2...24.8.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * Bump sphinx-rtd-theme from 2.0.0 to 3.0.0 Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 2.0.0 to 3.0.0. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](readthedocs/sphinx_rtd_theme@2.0.0...3.0.0) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump prettytable from 3.10.0 to 3.11.0 Bumps [prettytable](https://github.com/jazzband/prettytable) from 3.10.0 to 3.11.0. - [Release notes](https://github.com/jazzband/prettytable/releases) - [Changelog](https://github.com/jazzband/prettytable/blob/main/CHANGELOG.md) - [Commits](prettytable/prettytable@3.10.0...3.11.0) --- updated-dependencies: - dependency-name: prettytable dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * closes #261 (#297) * tests for #281 #279, add type to pcr (#298) * update codecov action for #242 * Issue 270 (#301) * closes #270 * closes #269 by adding an example notebook + extra tests * closes #288, includes the graphics in docs notebook * added example.ipynb to tests folder * removed example.ipynb * deal with Tm = 0 * fix notebook export related to #279 * New docs (#304) * new docs * update action * update action * fix typo in action * update README + closes #305 * improve docs * document how docs work * fix autogen_docs.sh * fix crispr docstring * Fix link in README (#310) * Fix action (#311) * fix action * fix action --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: BjornFJohansson <[email protected]> Co-authored-by: BjornFJohansson <[email protected]> Co-authored-by: Pei-Lun Xie <[email protected]> Co-authored-by: Jerry Xu <[email protected]> Co-authored-by: Pei-Lun Xie <[email protected]> Co-authored-by: Lucas Levassor <[email protected]> Co-authored-by: Kawin <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel García Ruano <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This commit fixes the action, which before was running the hooks not on the files changed in the latest commit, but on others (perhaps with respect to master?).