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Review notebook documentation #260

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manulera opened this issue Sep 5, 2024 · 6 comments
Closed

Review notebook documentation #260

manulera opened this issue Sep 5, 2024 · 6 comments
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documentation Hackathon-2024

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@manulera
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manulera commented Sep 5, 2024

Soon we will have some jupyter notebooks with documentation on how to get started with pydna (from issue #244).

A task for the hackathon could be to go through this documentation and check if there are missing things, something could be added, there are errors, etc. Several people could review.
@manulera manulera changed the title Review pydna documentation Review ntoebook documentation Sep 5, 2024
@manulera manulera changed the title Review ntoebook documentation Review notebook documentation Sep 5, 2024
@BjornFJohansson
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I would love to do this. Are the notebooks available somewhere?

@manulera
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HI @BjornFJohansson I put a link to the notebooks in last call's notes. Here is the link:

https://github.com/JeffXiePL/pydna/tree/docs_peilun/docs/notebooks

These are in @JeffXiePL's fork in a branch called docs_peilun. He still wants to make some final touches to them before making a PR. I think we can wait for that before reviewing

@JeffXiePL
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Hi Manu and Bjorn:

I've finished with a draft of the documentations. Please feel free to review whenever. Two things are still missing, which I could not get right: 1) example for the Gibson Assembly, which I describe in more detail at this issue. 2) cripsr page.

Thank you, Manu and Bjorn, for your help and answering my questions!

@manulera
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Great, I can have a look at it tomorrow!

JeffXiePL added a commit to JeffXiePL/pydna that referenced this issue Sep 18, 2024
@JeffXiePL
Merge pull request #5 from manulera/feedback_manu
d6c360f 
feedback changes for pydna-group#260
manulera added a commit that referenced this issue Sep 30, 2024
@manulera @JeffXiePL
Documentation notebooks (#271)
2187bfd 
* 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]>
@manulera
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These will now be merged into dev_bjorn since the fork also had some small bug fixes. You can review them there at docs/notebooks.

manulera added a commit that referenced this issue Sep 30, 2024
@manulera @JeffXiePL
Documentation notebooks 2 (#272)
a629c82 
* 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]>
@JeffXiePL JeffXiePL mentioned this issue Sep 30, 2024
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@JeffXiePL
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For anyone reading/reviewing the documentations, just a note that there are some minor to-dos left, but the bulk of the documentation is complete. Please feel free to use/update the documentations.

@hiyama341 hiyama341 mentioned this issue Oct 4, 2024
Merged
manulera added a commit that referenced this issue Oct 4, 2024
@hiyama341 @manulera
New CRISPR example notebook (#260) (#284)
b26f931 
* 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]>
manulera added a commit that referenced this issue Oct 8, 2024
@manulera @JeffXiePL
Documentation notebooks 2 (#272)
3514427 
* 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]>
manulera added a commit that referenced this issue Oct 8, 2024
@hiyama341 @manulera
New CRISPR example notebook (#260) (#284)
26bb292 
* 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]>
@manulera manulera closed this as completed Oct 9, 2024
manulera added a commit that referenced this issue Oct 24, 2024
@manulera @BjornFJohansson
@JeffXiePL @jxu10 @hiyama341 @dependabot @dgruano
Release? (#306)
0a9fe6e 
* 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]>
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@BjornFJohansson @manulera @JeffXiePL