DOC: Use pydata-sphinx-theme #2243

pllim · 2023-06-07T01:51:25Z

Description

Rendered preview: https://jdaviz--2243.org.readthedocs.build/en/2243/

This pull request is to switch to pydata-sphinx-theme that has dark mode, modern design, and mobile friendly. This is the theme that major scientific Python packages (e.g., numpy, scipy, matplotlib) have adopted. Also see https://pydata-sphinx-theme.readthedocs.io for more info on the theme.

I had to add some new pages so the TOC on both left and right sidebars, and top bar, would make more sense.

Similar effort is happening at astropy/astropy#14867 .

p.s. Dark mode!

Change log entry

Is a change log needed? If yes, is it added to CHANGES.rst? If you want to avoid merge conflicts,
list the proposed change log here for review and add to CHANGES.rst before merge. If no, maintainer
should add a no-changelog-entry-needed label.

Checklist for package maintainer(s)

This checklist is meant to remind the package maintainer(s) who will review this pull request of some common things to look for. This list is not exhaustive.

Are two approvals required? Branch protection rule does not check for the second approval. If a second approval is not necessary, please apply the trivial label.
Do the proposed changes actually accomplish desired goals? Also manually run the affected example notebooks, if necessary.
Do the proposed changes follow the STScI Style Guides?
Are tests added/updated as required? If so, do they follow the STScI Style Guides?
Are docs added/updated as required? If so, do they follow the STScI Style Guides?
Did the CI pass? If not, are the failures related?
Is a milestone set? Set this to bugfix milestone if this is a bug fix and needs to be released ASAP; otherwise, set this to the next major release milestone.
After merge, any internal documentations need updating (e.g., JIRA, Innerspace)? 🐱

codecov · 2023-06-07T02:14:26Z

Codecov Report

Patch and project coverage have no change.

Comparison is base (4cf39b7) 91.63% compared to head (aa72c15) 91.63%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2243   +/-   ##
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  Coverage   91.63%   91.63%           
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  Files         148      148           
  Lines       16551    16551           
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  Hits        15166    15166           
  Misses       1385     1385

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camipacifici · 2023-06-07T18:33:50Z

Ori and myself approve! It looks great!

kecnry · 2023-06-07T18:38:30Z

One downside: just from the main landing page, the navigation to the individual config-landing pages is not as clear (have to click or scroll down to user guide, whereas previously they appear in the navigation on the left side of the screen). We also lose the main logo (although they do exist for the individual configs). Were these changes intentional or just a consequence of this theme?

pllim · 2023-06-07T18:40:56Z

I moved the main logo to top left because it was taking up too much space. If you want, I can add it back to index page.

Similar complains about the index page navigation was raised over at astropy and now they want "cards" so it can look like https://numpy.org/doc/stable/ . If your request is the same, I'll have to see how Simon Conseil do it over there first.

that has dark mode, modern design, and mobile friendly DOC: No longer need tomli DOC: Now requires sphinx-astropy 1.9.1

with icons

in mobile mode

cshanahan1 · 2023-06-08T13:34:11Z

i am trying to review this but im having trouble building the docs locally

i pulled @pllim 's branch and installed with doc dependencies, but am getting this error when i try to 'make html'

Traceback (most recent call last): File "/Users/cshanahan/miniconda3/envs/jdaviz_dev/lib/python3.10/site-packages/traitlets/traitlets.py", line 653, in get value = obj._trait_values[self.name] KeyError: 'layout'

instead of a giant logo above the title

kecnry · 2023-06-08T14:05:03Z

docs/conf.py


 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = ''
+html_favicon = 'logos/specviz2d.ico'


hmmm, do we have any general jdaviz icon we can use?

That is not a question I can answer. I could not find one in the current logo stash.

@Jenneh - do you have anything (or can easily modify anything) for this? Its the icon that shows on the tabs in the browser, so needs to be square and work well at small sizes.

(but doesn't need to block this PR, using specviz2d logo is still more appropriate than the astropy logo that used to be there - although I am seeing a white instead of transparent background which would also be nice to fix)

what about the icon thats currently on the left hand side of the top menu, the one that says 'jdaviz' and has the 4 little icons under it (why not 5, by the way?)

Keep in mind that this icon goes on the browser tab. There is very little space, so a full Jdaviz logo would be illegible.

why not 5, by the way?

I think the 5th is a combination of the other two? 🤷

javerbukh

Looks good and we can always improve it more as we go, thank you!

cshanahan1

other than the browser tab icon, i think this is a good improvement!

* Added .ico and .svg files * app-wide display unit in specviz (#2048) * basic app-wide display unit in specviz (not all plugins are updated yet) * unit-aware select component which maps to glue-supported unit strings * implement use_display_units option for get_data, get_subsets Co-authored-by: Jesse Averbukh <[email protected]> Co-authored-by: Kyle Conroy <[email protected]> * bump glue-core to necessary version for display units * change PR number in changelog to main PR * Display units line analysis (#2128) * emit event when display unit changed * update line analysis for unit changes * cubeviz/slice plugin unit conversion support (we might want to generalize some of this logic more into the mark's _update_data when adding support for spectral lines as well) * Display units support for markers plugin (#2130) * update markers plugin for display units * move unit-updating logic to mark itself * LineUncertainties to be unit-aware * fix support for markers in cubeviz * display units: fix failing tests (#2132) * fix error raised when spectrum uncertainty is None * fix RTD build failure because of missing mixin available in import * fix test setting display unit now that um is preferred to micron * add disabled unit conversion plugin to mosviz * avoid unit-conversion error in cubeviz tests * bump versions of glue/glue-jupyter * fix deg intialization in cubeviz slice plugin * add LinesAutoUnit to __all__ so RTD can find it * add use_display_units kwarg to get_spectral_regions * fix setting display units for unitless data * Apply suggestions from code review Co-authored-by: P. L. Lim <[email protected]> * Display units: line lists (#2148) * BaseSpectrumVerticalLine to inherit unit-support from PluginMark * convert units on internal rest value * code cleanup * remove unit conversion plugin from all bug specviz * for initial implementation - eventually we'll want to implement across all plugins/viewers * get_display_unit fallback for configs without unit conversion plugin * Update glue-core dependency * Update Subset Tools plugin to use display units (#2195) * bump glue-core to necessary version for display units * cubeviz/slice plugin unit conversion support (we might want to generalize some of this logic more into the mark's _update_data when adding support for spectral lines as well) * display units: fix failing tests (#2132) * fix error raised when spectrum uncertainty is None * fix RTD build failure because of missing mixin available in import * fix test setting display unit now that um is preferred to micron * add disabled unit conversion plugin to mosviz * avoid unit-conversion error in cubeviz tests * bump versions of glue/glue-jupyter * fix deg intialization in cubeviz slice plugin * add LinesAutoUnit to __all__ so RTD can find it * add use_display_units kwarg to get_spectral_regions * fix setting display units for unitless data * Apply suggestions from code review Co-authored-by: P. L. Lim <[email protected]> * remove unit conversion plugin from all bug specviz * for initial implementation - eventually we'll want to implement across all plugins/viewers * Working on unit conversion handling in subset plugin * Get subset updating working in non-default units * Add changelog * Update jdaviz/configs/default/plugins/subset_plugin/subset_plugin.vue Co-authored-by: Kyle Conroy <[email protected]> --------- Co-authored-by: Kyle Conroy <[email protected]> Co-authored-by: P. L. Lim <[email protected]> * allow downstream apps to set what classes are considered native marks * Fix unit conversion for PluginMarks and y-limits (#2215) * Fix unit conversion for PluginMarks and y-limits * Only use equivalency if it's a spec viewer * Store wavelength unit on data update * Remove redundant line * Better check in marks * Replace subset_to_apply in docs where possible (#2223) * Replace subset_to_apply in docs where possible (#2223) * Avoid trying to convert units of empty marks arrays * Add open method to automatically detect config and load data * Update demo notebooks * Codestyle * Add autoconfig test coverage * Revert "Update demo notebooks" This reverts commit cc513b3. * Add mention of open to relevant example notebooks * Prepare to support open via cli * Remove the need to open file twice for autoconfig detection * Fix Helper vs App Docstring * TST: Change PIP_EXTRA_INDEX_URL because packages moved where they upload nightly builds. * Display units: model fitting (#2216) * model component compatibility based on display units * equation validity based on display units * allow re-estimating model parameters to update compat checks * test coverage * get_data(use_display_units) to pass spectral_density equivalency * handle whitespace in model equation * Add clarity for kwargs * plugin results: support overwriting when data loaded in multiple viewers (#2222) * reverts removal of call to set_plot_axes when loading data into viewer (#2235) * fixes a bug in the axes labels on cube viewers in cubeviz as well as setting the correct attributes in lcviz * Subsume failing identifier test into autoconfig test * Update subset plugin UI (#2234) * Update subset plugin UI * Apply suggestions from code review Co-authored-by: Kyle Conroy <[email protected]> --------- Co-authored-by: Kyle Conroy <[email protected]> * Changelog * Add docs page to explain how to create jdaviz-readable products (#2228) * Add page for data products * Update index * Fix title * Capital letters * Address first review comments * Edit format * Apply suggestions from code review Co-authored-by: P. L. Lim <[email protected]> * Including reference in import_data * Update docs/create_products.rst * Update docs/create_products.rst --------- Co-authored-by: Camilla Pacifici <[email protected]> Co-authored-by: P. L. Lim <[email protected]> Co-authored-by: Ricky O'Steen <[email protected]> * FEAT: Load annulus from file and allow IMPORT DATA to load reg files. Annulus support provided by glue-viz/glue#2403 and glue-viz/glue-astronomy#92 Add test for exception. Bump minimum requirements for glue-core and glue-astronomy. * disallow gaussian smooth output as input * BUG: Fix ellipse translation in app.get_subsets() * DOC: Use pydata-sphinx-theme (#2243) * DOC: Use pydata-sphinx-theme that has dark mode, modern design, and mobile friendly DOC: No longer need tomli DOC: Now requires sphinx-astropy 1.9.1 * Add cards to index page with icons * Remove iframe hardcoding so it scales in mobile mode * DOC: Insert small logo next to title instead of a giant logo above the title * Add app method to simplify spectral subset (#2237) * Add app method to simplify spectral subset Add simplify button to subset plugin * Fix xor bug exposed by simplify button * Fix style checks * Remove print statements * Add tooltip to simplify button * Make button appear only if the subset can be simplified * Make simplify button appear only when applicable * Apply suggestions from code review Co-authored-by: P. L. Lim <[email protected]> * Update changes file --------- Co-authored-by: P. L. Lim <[email protected]> * Fix missed conflict --------- Co-authored-by: Jennifer Kotler <[email protected]> Co-authored-by: P. L. Lim <[email protected]> Co-authored-by: Jesse Averbukh <[email protected]> Co-authored-by: Ricky O'Steen <[email protected]> Co-authored-by: Ricky O'Steen <[email protected]> Co-authored-by: Duy Nguyen <[email protected]> Co-authored-by: Camilla Pacifici <[email protected]> Co-authored-by: Camilla Pacifici <[email protected]>

pllim added the no-changelog-entry-needed changelog bot directive label Jun 7, 2023

pllim added this to the 3.6 milestone Jun 7, 2023

github-actions bot added the documentation Explanation of code and concepts label Jun 7, 2023

pllim force-pushed the yessss-dark-mode-doc branch from c5c678e to 080f585 Compare June 7, 2023 01:56

pllim marked this pull request as ready for review June 7, 2023 02:08

pllim requested review from duytnguyendtn, rosteen, javerbukh, kecnry, bmorris3, haticekaratay and cshanahan1 as code owners June 7, 2023 02:08

kecnry assigned javerbukh, camipacifici and cshanahan1 Jun 7, 2023

pllim force-pushed the yessss-dark-mode-doc branch from 9849dd1 to 66f218a Compare June 7, 2023 22:56

pllim mentioned this pull request Jun 8, 2023

Added .ico and .svg files #1912

Merged

9 tasks

pllim added 2 commits June 7, 2023 21:29

DOC: Use pydata-sphinx-theme

c94b4af

that has dark mode, modern design, and mobile friendly DOC: No longer need tomli DOC: Now requires sphinx-astropy 1.9.1

Add cards to index page

fed3563

with icons

pllim force-pushed the yessss-dark-mode-doc branch from 66f218a to fed3563 Compare June 8, 2023 01:50

Remove iframe hardcoding so it scales

7239c1e

in mobile mode

DOC: Insert small logo next to title

aa72c15

instead of a giant logo above the title

kecnry reviewed Jun 8, 2023

View reviewed changes

javerbukh approved these changes Jun 8, 2023

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pllim added the Ready for final review label Jun 8, 2023

cshanahan1 approved these changes Jun 8, 2023

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pllim merged commit ba01f97 into spacetelescope:main Jun 8, 2023

pllim deleted the yessss-dark-mode-doc branch June 8, 2023 15:38

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DOC: Use pydata-sphinx-theme #2243

DOC: Use pydata-sphinx-theme #2243

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DOC: Use pydata-sphinx-theme #2243

DOC: Use pydata-sphinx-theme #2243

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