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Release? #306

Merged
merged 84 commits into from
Oct 24, 2024
Merged

Release? #306

merged 84 commits into from
Oct 24, 2024

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manulera
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Hi @BjornFJohansson, I think with all recent bug fixes and improvements to the documentation, we should do a release to pypi.

It does not have to be a major release, I think, since it's mostly bug fixes and docs, and there are no breaking changes as far as I remember. Let me know what you think.

Kawin and others added 20 commits October 8, 2024 11:11
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]>
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]>
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]>
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]>
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 #270

* closes #269 by adding an example notebook + extra tests

* closes #288, includes the graphics in docs notebook
* 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
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codecov bot commented Oct 11, 2024

Codecov Report

Attention: Patch coverage is 86.50000% with 54 lines in your changes missing coverage. Please review.

Project coverage is 93.63%. Comparing base (989e76e) to head (72cd39b).
Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
src/pydna/seq.py 64.81% 19 Missing ⚠️
src/pydna/seqrecord.py 54.16% 11 Missing ⚠️
src/pydna/dseqrecord.py 60.00% 7 Missing and 1 partial ⚠️
src/pydna/parsers.py 89.36% 3 Missing and 2 partials ⚠️
src/pydna/dseq.py 94.66% 2 Missing and 2 partials ⚠️
src/pydna/readers.py 62.50% 1 Missing and 2 partials ⚠️
src/pydna/tm.py 87.50% 1 Missing and 1 partial ⚠️
src/pydna/utils.py 94.87% 2 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #306      +/-   ##
==========================================
+ Coverage   93.00%   93.63%   +0.63%     
==========================================
  Files          40       40              
  Lines        3744     3926     +182     
  Branches      562      589      +27     
==========================================
+ Hits         3482     3676     +194     
+ Misses        217      198      -19     
- Partials       45       52       +7     
Files with missing lines Coverage Δ
src/pydna/__init__.py 90.10% <100.00%> (+0.82%) ⬆️
src/pydna/_pretty.py 100.00% <100.00%> (ø)
src/pydna/amplify.py 98.67% <100.00%> (+0.01%) ⬆️
src/pydna/assembly.py 97.70% <100.00%> (+0.14%) ⬆️
src/pydna/codon.py 100.00% <100.00%> (ø)
src/pydna/common_sub_strings.py 100.00% <100.00%> (ø)
src/pydna/crispr.py 87.23% <ø> (ø)
src/pydna/design.py 97.57% <100.00%> (+0.37%) ⬆️
src/pydna/fakeseq.py 100.00% <100.00%> (+50.00%) ⬆️
src/pydna/genbank.py 100.00% <100.00%> (ø)
... and 10 more

... and 7 files with indirect coverage changes

dgruano and others added 2 commits October 15, 2024 14:11
@manulera
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Hey @BjornFJohansson any thoughts on this?

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@BjornFJohansson BjornFJohansson left a comment

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I think this is fine. There are of course lots of changes, but all tests passes.

@manulera
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Ok then! Merge it is!

@manulera manulera merged commit 0a9fe6e into master Oct 24, 2024
35 of 37 checks passed
@manulera manulera deleted the dev_bjorn branch October 24, 2024 07:52
@manulera
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By the way @BjornFJohansson what is the process you follow to release to pypi? If I want to release a next version (say 5.3.0), how do I do so?

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6 participants