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Updating/modernising documentation: part 1 #785

Merged
merged 107 commits into from
Apr 21, 2024
Merged

Updating/modernising documentation: part 1 #785

merged 107 commits into from
Apr 21, 2024

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apontzen
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@apontzen apontzen commented Mar 19, 2024 •
edited

Updating all documentation ahead of pynbody v2 release

Tutorials etc

  • Quick-start
  • Reading data
  • Filtering data
  • Linking snapshots
  • Profiles
  • Rotation curves
  • Images
  • Halos
  • HMF
  • Performance
  • Configuration
  • Threading etc
  • Derived quantities

Reference documentation

  • analysis
    • angmom
    • cosmology
    • decomp
    • gravity
    • halo
    • hifrac
    • hmf
    • interpolate
    • ionfrac
    • luminosity
    • pkdgrav_cosmo
    • profile
    • ramses_util
    • theoretical_profiles
  • array
  • bridge
  • chunk
  • filt
  • gravity
  • halo
  • kdtree
  • openmp
  • plot
    • gas
    • generic
    • metals
    • profile
    • sph
    • stars
    • util
  • snapshot
  • sph
  • util
  • configuration
  • dependencytracker
  • derived
  • family
  • simdict
  • transformation
  • units

@apontzen apontzen marked this pull request as draft March 19, 2024 14:00
@apontzen apontzen force-pushed the update-docs branch 2 times, most recently from 822f8c1 to 4d44107 Compare March 24, 2024 15:49
dependabot bot and others added 22 commits April 1, 2024 22:23
@dependabot
Bump pypa/cibuildwheel from 2.16.2 to 2.17.0
5ffee73 
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.16.2 to 2.17.0.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](pypa/cibuildwheel@v2.16.2...v2.17.0)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14
ac0771f 
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.8.12...v1.8.14)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@apontzen
WIP: updating/modernising documentation
650aed7
@apontzen
Painful work on getting sphinx autodoc working
89b53bd
@apontzen
Continued progress on documentation
4678d88
@apontzen
Sorting out docs for the bridge module
0940e8f
@apontzen
Fix issues arising from work on bridge
b8e1af0
@apontzen
Formatting fixes
98173a9
@apontzen
Formatting fixes
516a346
@apontzen
Fix documentation for chunk
cf880ef
@apontzen
Formatting and installation fixes
0eebc4b
@apontzen
Fix filt documentation / code style
a0982f4 
Add a couple of tests
@apontzen
Fix gravity documentation and remove non-working routines
c22579a
@apontzen
Documentation and streamlining for halo (reference + tutorial)
c91513c
@apontzen
Fix python 3.9 and add module docstrings for halo catalogues
f89e420
@apontzen
Update bridge tutorial and use the impetus to rationalise the interface
dc638d4
@apontzen
Fix formatting
cda0528
@apontzen
Fix recursion bug in __array_function__
15e21fa
@apontzen
Updating filters/subsnap docs
15d59d4
@apontzen
Testing/fixing mean_by_mass and removing it from the SimArray int…
68fbe4a 
…erface

This has been quietly broken for some time (possibly forever!)
@apontzen
Fix problem with geometrical queries on empty simulations
ff797b8
@apontzen
Fix filters documentation
6c36e8a
pre-commit-ci bot and others added 4 commits April 8, 2024 16:36
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate
f949867 
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0)
- [github.com/asottile/pyupgrade: v3.15.1 → v3.15.2](asottile/pyupgrade@v3.15.1...v3.15.2)
- [github.com/nbQA-dev/nbQA: 1.8.4 → 1.8.5](nbQA-dev/nbQA@1.8.4...1.8.5)
@apontzen
Fix snapshot and OpenMP documentation.
e43e2d6 
Add back deep-dive tutorial on derived quantities
@apontzen
Merge pull request #793 from pynbody/dependabot/github_actions/pypa/g…
2e49ab0 
…h-action-pypi-publish-1.8.14

Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14
@apontzen
Merge pull request #792 from pynbody/dependabot/github_actions/pypa/c…
9271a90 
…ibuildwheel-2.17.0

Bump pypa/cibuildwheel from 2.16.2 to 2.17.0
@apontzen
Sort out profile tutorial
e1f0203
@apontzen
Attempt to force-fix readthedocs by manually copying images
b4f985e
@apontzen
Further work on docs, and add more debug info to RTD output
b9d319e
@apontzen
Even more bizarre workaround for readthedocs images not saving plots …
ed22b6f 
…in sensible way
@apontzen
Update configuration
a081ede
@apontzen
Fix copy button
9181e26
@apontzen
Work on transformation module documentation and streamlining
791a03e
@apontzen
Work on improving transformation system
77d8b30
@apontzen
Work on transformation module documentation and streamlining
0bb66e0
@apontzen
Working on transformations in analysis modules
de3a642
@apontzen
Fix issue where sideon assumed numpy input but other iterable could b…
b641ee5 
…e provided
@apontzen
Finish documentation for analysis.halo, and tidy up
13e616b
@apontzen
Documentation and tidying of analysis.angmom
be50b4b
@apontzen
Fix unit tests
9794180
@apontzen
Update documentation in analysis.cosmology
01dc4ae
@apontzen
Update documentation in analysis.decomp
74038e2 
Fix a logic bug in transformations discovered while doing so, and add unit test
@apontzen
Fix an exception message
6fa2394
@apontzen
Fix issue with mis-detecting AHF file format
c968476
@apontzen
Fix issue with finding multi-file halo finder outputs for TNG
32545b8
@apontzen
Doc copyright line cannot have link in it
04e3fd7
@apontzen
Update family documentation
118d66b
@apontzen
Improve units rendering to latex and add test
641f58d
@apontzen
Further improvement to latex unit rendering
850415c
@apontzen
Fix errors generated by rebasing
432b28b
@apontzen
Merge remote-tracking branch 'origin/update-docs' into update-docs
14bbd7d 
# Conflicts:
#	pynbody/__init__.py
#	pynbody/halo/hbtplus.py
#	tests/array_test.py
@apontzen apontzen marked this pull request as ready for review April 21, 2024 18:43
@apontzen apontzen merged commit 490dead into master Apr 21, 2024
16 of 29 checks passed
@apontzen apontzen deleted the update-docs branch April 21, 2024 18:44
@apontzen apontzen changed the title WIP: updating/modernising documentation Updating/modernising documentation: part 1 Apr 21, 2024
@apontzen apontzen mentioned this pull request Apr 21, 2024
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