Add docs build and populate content #39

willGraham01 · 2024-07-09T09:46:59Z

Description

What is this PR

Bug fix
Addition of a new feature
Other

Why is this PR needed?

Allows us to host more expansive documentation than just that in the README.

What does this PR do?

Adds a docs build and publish workflow
Adds scope to write fuller documentation for the plugin(s) that are developed here.

References

How has this PR been tested?

Please explain how any new code has been tested, and how you have ensured that no existing functionality has changed.

Is this a breaking change?

Does this PR require an update to the documentation?

Checklist:

The code has been tested locally
Tests have been added to cover all new functionality (unit & integration)
The documentation has been updated to reflect any changes
The code has been formatted with pre-commit

codecov · 2024-07-09T09:51:29Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.66%. Comparing base (901e4a4) to head (076d2c1).

Additional details and impacted files

@@               Coverage Diff               @@
##           ARC-dev-branch      #39   +/-   ##
===============================================
  Coverage           89.66%   89.66%           
===============================================
  Files                   8        8           
  Lines                 484      484           
===============================================
  Hits                  434      434           
  Misses                 50       50

☔ View full report in Codecov by Sentry.
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…endering

K-Meech · 2024-07-09T15:44:32Z

Do we want to update the installation instructions on the top index.md? Currently they refer to installing from pip, rather than from a locally cloned repo.

K-Meech · 2024-07-09T15:45:49Z

Also seems like sphinx doesn't understand emojis unfortunately (last line of the group_layers index.md)

willGraham01 · 2024-07-10T08:14:50Z

Do we want to update the installation instructions on the top index.md? Currently they refer to installing from pip, rather than from a locally cloned repo.

This is probably a question for @alessandrofelder as to whether he wants to release the plugin on PyPI and napari hub, or would prefer it stayed as a local installation thing. If we want to get people testing the plugin, I would guess an alpha-release would be best. CI should be setup to handle this (save for the first push to PyPI) - though we might want a slightly more informative name for the plugin 😂

alessandrofelder

This is great - thanks a lot @K-Meech and @willGraham01

@K-Meech

* Pull sample blobs code * Strip away everything except the open-able widget * Some basic structures that track the existing layers * BROKEN: Image layers don't play nice but I did combine the emitter objects * HACK: Napari will now load up, but this hasn't really fixed the naming issue. I've just hacked in a missing attribute to all of the GroupLayer children - they need to have a Node mixin to behave properly * I can see when layers are added, and have some kind of list. Still get SEG-faults or index errors when moving groups within groups, particularly empty group into empty group. * Recognises add/remove layers from viewer and auto-adds to the group layers view. Still seg-fault bug when nesting two empty group layers * Rename classes to be closer to development language * Rename and move items to break things up * Link up group layer selection with layer tab * Reliable testing framework * Fix our failing test suite (#13) * Edit file name to be specific to our use case * Rename single test * Add checks on napari `main` (#18) * Add workflow step to run tests on head of napari * Add optional dependency on napari-latest which fetches napari from the git repo directly * Create an optional install that uses HEAD of napari, add it to list of tests * Add note that napari-latest install is available to README * Update README.md Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> --------- Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> * Add conftest and some fixtures for testing (#15) * Add conftest.py for shared fixtures and do a quick model check for our QtGroupLayerModel * Typehints don't carry through fixtures * Allow renaming of layers / group layers (#19) * allow renaming of groups and layers * keep prefix for group layers and update setRoot * remove unused tree_model * add initial tests for renaming * add test for editing state on double click * move tests into test_group_layer_widget * Correctly Subclass our `GroupLayer` (#20) * Ensure GroupLayer subclasses from our own subclass of Node * Define ambiguously inherited attributes (IE ensure I don't break KM's tests) * Actually use the nested structure fixture so ruff doesn't get angry * Reorganise the test suite fixture layout since it's starting to get bloated * Basic tests to check is_group and strict typing * Self-review * Allow _check_if_already_tracking to be optionally recursive. Write test for method. * Update src/napari_experimental/group_layer.py Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * Dammit linter --------- Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * Adds independent layer controls to widget (#22) * add group layer controls * fix controls for latest changes to group layer * remove syncing of selection * add tests for group layer controls * fix TypeError * expand docstrings * react to sub-groups * add overview and todo sections to readme (#31) * Sync GroupLayer and Main Viewer layer orders (#26) * Allow group_layer to return a flat index * Enforce layer order updates through the GroupLayer events * Rework how items are added to GroupLayers to make things more explicit * Remove unused function * Docstring Tidy (#27) * Some docstrings for _widget * Docstrings for GroupLayerNode class * docstrings for group_layer_qt * Docstrings for group_layer.py * Add attributes and methods to classes where necessary * Missed a rename * Add tests for widget activity * Test for layer deletion sync * Ruff for 3.9 disagrees with 3.11 * strict keyword not in Py3.9 * Update test_and_deploy.yml (#32) (#33) * Fix Errors when Moving Layers (#28) * Allow group_layer to return a flat index * Enforce layer order updates through the GroupLayer events * Rework how items are added to GroupLayers to make things more explicit * Remove unused function * Docstring Tidy (#27) * Some docstrings for _widget * Docstrings for GroupLayerNode class * docstrings for group_layer_qt * Docstrings for group_layer.py * Add attributes and methods to classes where necessary * Missed a rename * Write method that fixes the min failing example * Hey look, a docstring! * Remove double-counting of positions after destination * Test revise index method, remove redundant variable passed * Maybe this is correct if I have a flat index sort a priori * Fix ordering issue and allow for Groups to be assigned a flatindex * Add 2nd test to check moving items out of different subgroups still tracks order correctly * Remove un-necessary variable * Remove commented-out experimental code * Apply suggestions from @K-Meech code review * Add `Implementation` section to README (#34) * MDLint + alessandrofelder -> brainglobe in README * Create implementation deatils section * Group and Node subclassing explanations * Notes on indexing conventions * Update README.md Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> --------- Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * Add right click menu and styling (#29) * add group layer delegate * rename group layer delegate * add context for right click menu * working minimal right click menu * fix syncing of selection * update docstrings and remove unused functions * fix double click edit * simplify right click actions and context to fix tests * update docstrings * Force widget in tests to have a parent (#35) * Allows toggling visibility of group layers (#30) * toggle visiblity for group layers * add tests for visiblity * update docstrings * fix failing tests * remove logger and thumbnail role * fix view controls when switching from group to layer --------- Co-authored-by: Will Graham <32364977+willGraham01@users.noreply.github.com> * `main` and `ARC-dev-branch` merge commit reconcile (#37) * Fix bugs relating to empty `GroupLayers` (#38) * Fix seg-faults and broken drag-and-drop via overwriting index method * Switch to unique ID trackers over reimplementing method. Allows safe overwride of __eq__ and __hash__ * Remove one bug from the README broken features section --------- Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> * Add docs build and populate content (#39) * Basic Sphinx build and docs structure * Workflow to publish docs on pushes to main * Separate sphinx requirements from package requirements * Add building the docs section * Reorganise group_layers docs * Docs API for Groups & Nodes, some source docstring updates for text rendering * Placeholder for widget docs * Write widget docs page * Add note on hashing things * expand docs for group layers, delegates and context menu (#40) --------- Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> --------- Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

willGraham01 added 3 commits July 9, 2024 10:33

Basic Sphinx build and docs structure

780c18e

Workflow to publish docs on pushes to main

3839f74

Separate sphinx requirements from package requirements

66e4c63

willGraham01 added 5 commits July 9, 2024 11:02

Add building the docs section

723cde1

Reorganise group_layers docs

18e005f

Docs API for Groups & Nodes, some source docstring updates for text r…

65ebe48

…endering

Placeholder for widget docs

3a0157d

Write widget docs page

7badfc7

alessandrofelder requested review from alessandrofelder and removed request for alessandrofelder July 9, 2024 13:05

Add note on hashing things

41550d5

expand docs for group layers, delegates and context menu (#40)

076d2c1

willGraham01 requested a review from alessandrofelder July 10, 2024 08:20

alessandrofelder approved these changes Jul 10, 2024

View reviewed changes

alessandrofelder merged commit d852765 into ARC-dev-branch Jul 10, 2024
18 checks passed

alessandrofelder deleted the wgraham/basic-docs branch July 10, 2024 11:00

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Add docs build and populate content #39

Add docs build and populate content #39

willGraham01 commented Jul 9, 2024

codecov bot commented Jul 9, 2024 •

edited

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K-Meech commented Jul 9, 2024

K-Meech commented Jul 9, 2024

willGraham01 commented Jul 10, 2024

alessandrofelder left a comment

Add docs build and populate content #39

Add docs build and populate content #39

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willGraham01 commented Jul 9, 2024

Description

References

How has this PR been tested?

Is this a breaking change?

Does this PR require an update to the documentation?

Checklist:

codecov bot commented Jul 9, 2024 • edited Loading

Codecov Report

K-Meech commented Jul 9, 2024

K-Meech commented Jul 9, 2024

willGraham01 commented Jul 10, 2024

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codecov bot commented Jul 9, 2024 •

edited

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