Port changes from docs repo to main repo for 0.4.18 #6002

Czaki · 2023-06-23T23:35:00Z

Fixes/Closes

Closes #

Description

References

Type of change

Bug-fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Maintenance (changes required to run napari, tests, & CI smoothly)
Enhancement (non-breaking improvements of an existing feature)
Documentation (update of docstrings and deprecation information)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires a documentation update

How has this been tested?

example: the test suite for my feature covers cases x, y, and z
example: all tests pass with my change
example: I check if my changes works with both PySide and PyQt backends
as there are small differences between the two Qt bindings.

Final checklist:

My PR is the minimum possible work for the desired functionality
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
I have added tests that prove my fix is effective or that my feature works
If I included new strings, I have used trans. to make them localizable.
For more information see our translations guide.

…ead (#5195) Co-authored-by: Andy Sweet <andrew.d.sweet@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* update viewer * review Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

* add sample data page * add title and change URL location

* Add white space for images diff * Add missing images to diff * Apply event alt text! Co-authored-by: Draga Doncila Pop <17995243+DragaDoncila@users.noreply.github.com> Co-authored-by: Andy Sweet <andrew.d.sweet@gmail.com> Co-authored-by: Kandarp Khandwala <kandarpksk@users.noreply.github.com> * Copy edits and clean up * Remove white space placeholders * Remove typos and white space * Update docs/howtos/layers/shapes.md Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com> Co-authored-by: isabela-pf <irpf.design@gmail.com> Co-authored-by: Isabela Presedo-Floyd <50221806+isabela-pf@users.noreply.github.com> Co-authored-by: Draga Doncila Pop <17995243+DragaDoncila@users.noreply.github.com> Co-authored-by: Andy Sweet <andrew.d.sweet@gmail.com> Co-authored-by: Kandarp Khandwala <kandarpksk@users.noreply.github.com> Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com>

…76) * add 'sphinx_copybutton' * update requirements.txt

* Add contributable menus nap * Update docs/naps/6-contributable-menus.md Co-authored-by: alisterburt <alisterburt@gmail.com> * Fixed header info Co-authored-by: alisterburt <alisterburt@gmail.com>

@jaimergp

* Added info for conda installation problems * Update docs/tutorials/fundamentals/installation.md Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> * Update docs/tutorials/fundamentals/installation.md Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> * Conda per @jaimergp Version by @melissawm * Add note about checking napari version * Add the myst_subs for napari version * use python 3.9 in the example, add link to mamba * Don't use versions in codeblock * Fix version? * make 0.x.y version string * work around no substitution in code blocks * Tweak version Note * @Czaki trick to sub the whole strong Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com> * @Czaki fix Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com> * tweak wording * fix the non-code version substitution * Update docs/tutorials/fundamentals/installation.md Co-authored-by: Jaime Rodríguez-Guerra <jaimergp@users.noreply.github.com> Co-authored-by: Christopher Nauroth-Kreß <56394171+ch-n@users.noreply.github.com> Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> Co-authored-by: Peter Sobolewski <pete.sd@gmail.com> Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com> Co-authored-by: Jaime Rodríguez-Guerra <jaimergp@users.noreply.github.com>

This PR does some basic reorganization of some items in the Usage section of the docs, to bring more visibility to the Layers how-to guides and the napari workshop materials. This also adds a mention of the new napari-workshop-template repository. Included in this change is the move from sphinx-tabs/sphinx-panels to sphinx-design, as the first two packages are being deprecated in favor of the latter.

@Czaki

* implement python version subs per @Czaki * tweak index.md wording re: conda env * Add substitution for python version range * Use substitutions on quick_start docs * Fix quick_start installation indentation * fix index conda env and use python_version * use python_version_range in Prerequisites * add python_minimum_version subs * subs napari version in quick_start bundle links * fix link substitutions * Fix missed [ * Add a sustituted link to stable release page * rename conda substitution to conda_create_env

* Fixes gallery ToC - Orders gallery by example title - Restores left sidebar for individual example pages * Removes individual gallery examples from left sidebar

# Description Fixes a number of broken links ~and adds a link check step to CI.~ There are a few broken links still (see napari/docs#59 (comment)) but these can be fixed in a follow up. Pending is also a link check step to CI.

closes napari/docs#43

…install (#78) Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>

Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com>

* add best practices about packaging * reword a bit Co-authored-by: psobolewskiPhD <psobolewskiPhD@users.noreply.github.com> Co-authored-by: psobolewskiPhD <psobolewskiPhD@users.noreply.github.com>

This is best practice, to make sure the pip being picked up matches the current python executable. Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

Labels layer how-to, ensure imports are in code snippet so it can be copy-pasted and run.

@rwkozar

# Description This is a redo of #4827. Also includes some reorganization on the contributing guide. cc @rwkozar Co-authored-by: Rob Kozar <rwkozar88@yahoo.com> ## Type of change - [x] Fixes or improves existing content # References Closes #46 Depends on #63 for the nice sphinx-design tabs :) Co-authored-by: Rob Kozar <rwkozar88@yahoo.com> Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>

# Description Adds cards to landing pages under the usage section. Organization, wording and the order of the cards can be changed according to the review. ## Type of change - [x] Fixes or improves existing content # References Closes #87 ## Final checklist: - [x] My PR is the minimum possible work for the desired functionality

#35) # Description The first section of the workshop has been broken down into 5 articles. They are: 1. Python's assert keyword, 2. Pytest testing frameworks, 3. Napari plugins, and 4. Testing coverage. The 5th one on testing widgets is on hold for now. ## Type of change - [x] This change adds new documentation Co-authored-by: Sean Martin <martins7@tcd.ie> Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> Co-authored-by: Draga Doncila Pop <17995243+DragaDoncila@users.noreply.github.com> Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com>

Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com> Co-authored-by: Kevin Yamauchi <kevin.yamauchi@gmail.com>

# Description Closes #115

# Description change string format to f-string # References https://peps.python.org/pep-0498/

# Description The ` ` character causes various difficulties and confusion, such as the `docs/howtos/docker.md` document's "For development" header not being rendered as a header by Markdown renderers. ## Type of change - [x] Fixes or improves existing content ## Final checklist: - [x] My PR is the minimum possible work for the desired functionality

# Description Adding right-click controls, main menu options and other copy edits to napari viewer tutorial. ## Type of change - [x] Fixes or improves existing content # References None ## Final checklist: - [x] My PR is the minimum possible work for the desired functionality - [x] I have added [alt text](https://webaim.org/techniques/alttext/) to new images included in this PR --------- Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com>

# Description This adds some short docs for adding a LayerData tuple to the napari viewer. Replaces #4711.

for more information, see https://pre-commit.ci

melissawm

With the changes I note here, this builds locally and looks good as far as I can tell.

Please don't forget to add the release notes to _toc.yml 🙂

A few broken links that can be fixed now, or later (I can't suggest because these files are not part of this PR):

In docs/developers/documentation/docs_template.md, in the last line of the file, [updating the TOC](./index.md#2-update-toc) should be replaced with updating the TOC, and in docs/developers/documentation/index.md we need to add an anchor before ## 2. Update TOC to read

(update-toc)=
## 2. Update TOC

On docs/developers/documentation/index.md, replace (line 25) - A clean conda environment with a development installation of napari, see the [contributor guide](napari-contributing#setting-up-a-development-installation) for details with - A clean conda environment with a development installation of napari, see the [contributor guide](dev-installation) for details, and add

(dev-installation)=
## Setting up a development installation

on line 8 of docs/developers/contributing.md.

On docs/developers/documentation/index.md, [Examples](..../examples/README) should be replaced with [Examples](gallery)

Thank you @Czaki !

melissawm · 2023-06-24T21:46:59Z

docs/_static/version_switcher.json

+		"name": "stable (0.4.17)",
+		"version": "0.4.17",


We need to have this updated either now or after the release to add the 0.4.18 entry. Later, we also need to update the files on napari.github.io so that stable points to 0.4.18.

melissawm · 2023-06-24T21:54:16Z

docs/requirements.txt

 sphinx-external-toc
+sphinx-favicon


Needs

Suggested change

sphinx-favicon

sphinx-favicon>=1.0

sphinx-copybutton

jni · 2023-06-28T11:02:40Z

@Czaki the manifest check is failing with:

check-manifest
lists of files in version control and sdist do not match!
missing from sdist:
  docs/_static/favicon/logo-silhouette-dark-light.svg
  docs/_static/images/tribolium.mp4
suggested MANIFEST.in rules:
  recursive-include docs *.mp4
  recursive-include docs *.svg
make: *** [Makefile:22: check-manifest] Error 1

Also, the "add files to lfs" commit looks right, but the "Files" tab on the PR does not — it still shows that all files are being added...

Czaki · 2023-06-28T11:57:12Z

I have checkout these changes to separate repo and git ls-files and it looks correct. So I do not know why the interface shows this way.

jni · 2023-06-28T12:25:42Z

Cool, thank you, hopefully it's a quirk of the GH interface. 🤞 Worst case we can always rewrite the history, no big deal. 😅 😰 Let me know when you think this is ready to merge — currently there is one failure that seems sporadic, one from pre-commit which is weird...

Czaki · 2023-06-29T20:46:47Z

I think that napari/docs#192 should be merged and cherry picked. Then this could be merged.

jni · 2023-06-30T12:47:48Z

Ok I've confirmed by pulling this down without LFS that only LFS stubs are present. 🎉 🚀 Here we go!

Czaki and others added 30 commits June 24, 2023 01:17

Add option to check if plugin try to set viewer attr outside main thr…

a3d7b4f

…ead (#5195) Co-authored-by: Andy Sweet <andrew.d.sweet@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

move files from lfs to repo

63ce4c7

Add favicon and configuration (#4)

91cae59

Use imshow in getting_started (#9)

2f414b6

Update viewer tutorial, regarding the console button (#53)

4ce3648

DOC Update viewer.md (#11)

3460b63

* update viewer * review Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

add sample database page (#56)

1bd51ed

* add sample data page * add title and change URL location

Feature: add copy button for code blocks using sphinx-copybutton (#…

05021fb

…76) * add 'sphinx_copybutton' * update requirements.txt

Add NAP-6 - Proposal for contributable menus (#77)

adcdeca

* Add contributable menus nap * Update docs/naps/6-contributable-menus.md Co-authored-by: alisterburt <alisterburt@gmail.com> * Fixed header info Co-authored-by: alisterburt <alisterburt@gmail.com>

Update theme related documentation (#81)

b6ca6ee

Fixes gallery ToC (#85)

3079797

* Fixes gallery ToC - Orders gallery by example title - Restores left sidebar for individual example pages * Removes individual gallery examples from left sidebar

Fix broken links (#59)

04e8b4e

# Description Fixes a number of broken links ~and adds a link check step to CI.~ There are a few broken links still (see napari/docs#59 (comment)) but these can be fixed in a follow up. Pending is also a link check step to CI.

Clarify arm64 macOS (Apple Silicon) installation (#89)

8869f4d

closes napari/docs#43

Update contributing docs for [dev] install change needing Qt backend …

b04eb0f

…install (#78) Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>

Docs for 5195 from main repository (#7)

2445a79

Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> Co-authored-by: Melissa Weber Mendonça <melissawm@gmail.com>

add best practices about packaging (#52)

e6ed81a

* add best practices about packaging * reword a bit Co-authored-by: psobolewskiPhD <psobolewskiPhD@users.noreply.github.com> Co-authored-by: psobolewskiPhD <psobolewskiPhD@users.noreply.github.com>

Replace pip with python -m pip (#100)

32e4433

This is best practice, to make sure the pip being picked up matches the current python executable. Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

change blob example to be self contained (#101)

1aa6679

Labels layer how-to, ensure imports are in code snippet so it can be copy-pasted and run.

Update the 'ensuring correctness' mission clause (#105)

e64bb62

Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com> Co-authored-by: Kevin Yamauchi <kevin.yamauchi@gmail.com>

Update requirements and config for sphinx-favicon for 1.0 (#116)

c03d316

# Description Closes #115

change print to f-string (#117)

3f5f0a2

# Description change string format to f-string # References https://peps.python.org/pep-0498/

dstansby and others added 3 commits June 24, 2023 19:08

Docs for adding LayerData tuple to viewer (#152)

790eead

# Description This adds some short docs for adding a LayerData tuple to the napari viewer. Replaces #4711.

add files to lfs

6a14aca

update release notes

49d8a41

Czaki force-pushed the docs_0.4.18 branch from 4a4958d to 49d8a41 Compare June 24, 2023 17:33

beter distinguish docs PR

0e2a257

Czaki force-pushed the docs_0.4.18 branch from bb71d3e to 0e2a257 Compare June 24, 2023 17:37

[pre-commit.ci] auto fixes from pre-commit.com hooks

a706cea

for more information, see https://pre-commit.ci

melissawm reviewed Jun 24, 2023

View reviewed changes

Czaki added 2 commits June 25, 2023 12:27

add release notes to TOC

4bb3f91

apply changes from code review

ac82277

Carreau added this to the 0.4.18 milestone Jun 25, 2023

Czaki added 2 commits June 26, 2023 00:08

add information about new contributtors

20ee2e0

better links for new contributors

65b9741

Czaki mentioned this pull request Jun 28, 2023

v0.4.18 - release process #5911

Closed

Czaki marked this pull request as ready for review June 28, 2023 08:06

Czaki requested a review from a team as a code owner June 28, 2023 08:06

fix manifest

9f45f70

jni approved these changes Jun 28, 2023

View reviewed changes

Czaki and others added 3 commits June 29, 2023 20:50

moe import on top

fd0f1f5

Update SC information

a9b83df

Update SC information (#192)

0a88540

jni changed the title ~~Docs 0.4.18~~ Port changes from docs repo to main repo for 0.4.18 Jun 30, 2023

jni merged commit 7da1a7b into v0.4.18x Jun 30, 2023
30 of 31 checks passed

jni deleted the docs_0.4.18 branch June 30, 2023 12:49

jni mentioned this pull request Jul 8, 2023

Docs repo, hosting, git-lfs 4: revenge of the media files #6049

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Port changes from docs repo to main repo for 0.4.18 #6002

Port changes from docs repo to main repo for 0.4.18 #6002

Czaki commented Jun 23, 2023

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jni commented Jun 30, 2023

Port changes from docs repo to main repo for 0.4.18 #6002

Port changes from docs repo to main repo for 0.4.18 #6002

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Czaki commented Jun 23, 2023

Fixes/Closes

Description

References

Type of change

How has this been tested?

Final checklist:

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