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Documentation and type checking #11

Merged
merged 43 commits into from
Oct 11, 2024
Merged

Documentation and type checking #11

merged 43 commits into from
Oct 11, 2024

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jat255
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@jat255 jat255 commented Oct 11, 2024

Bumps version to 0.9.0

Does a few things primarily:

  • Auto-builds documentation using Github actions
  • Added type-checking to every module (not yet enforced with mypy or anything though)
  • Improved README and updated example Jupyter notebook
  • Added actions runners for tests using both conda (windows, mac, linux) and poetry (linux):
    • can't do CUDA tests unfortunately
    • removed docker container approach from before, so no longer reliant on aaherzing/etspy:latest image from docker hub
  • Updated license to NIST public license
  • Added coverage information (not at 100% yet, that'll come after the TomoStack API changes)

Remaining todos (after this PR):

  • make shifts and tilts properties and update docs/tests to match
  • Complete test coverage and add badge or something to show it
  • Enforce MyPy type checking in Github actions (optional, but probably a good idea)
  • Register ETSpy as a hyperspy extension
  • Build and publish pypi and conda packages

@jat255
first attempt at docs
a296074
@jat255
add ruff cache to gitignore
0725213
@jat255
fix isort on conf.py
7bf1597
@jat255
conda GH actions test
eee671c
@jat255
put environment file in conda setup action
766d3bb
@jat255
try adding CUDA to actions matrix
1a77b45
@jat255
remove CUDA (can't use on standard GH action runners)
d3800c5
@jat255
Test doc build in GH action
6e68baf
@jat255
upload built docs artifact
0d9e99d
@jat255
try check links
6c1836e
@jat255
try installing CUDA so astra-toolbox can be installed using poetry
1971466
@jat255
try setting up re-usable installation workflow
cf536ed
@jat255
add poetry to reusable actions
6693971
@jat255
add dependencies and poetry pytest runs
6c68bf2
@jat255
fix ruff issues that only sometimes appeared?
78bd53a
@jat255
test switching branch
211263c
@jat255
try committing docs to nist-pages using action
e7e34b5
@jat255
Get doc navigation working better
f171393
@jat255
add type hints to align module, add intersphinx, fix some docstrings,
9c7ceca 
formalize alignment methods into a reusable Enum
@jat255
add explicit groups for methods and classes
1447499
@jat255
Improve base.py docstrings
885bebc
@jat255
Fix align.py type issues and datasets.py docstrings
37a9226
@jat255
Improve io, recon, simulation, and utils.py docstrings (add type hints)
7338ffb 
Switch to Literal types for strings that have explicit options.
Fix inconsistent optionality of dart_iterations in TomoStack.reconstruct.
@jat255
fix remaining lint issues and get tests passing again
772059b 
re-enable 3.12 tests since pystackreg is on pypi now
@jat255
update README and add some context to API reference page
095c873
@jat255
fix various sphinx warnings to ensure a clean doc build
4b98242 
and other minor documentation edits (fix circular TomoStack import)
@jat255
Make recon.run take numpy array to be consistent with the rest of the…
7d43259 
… recon methods
@jat255
Make CommonStack explicitly abstract so it cannot be instantiated dir…
b2b2cfc 
…ectly

(better for API clarity that TomoStack and RecStack should be used instead)
@jat255
add typing_extensions for 3.10 support
bf6ce87
@jat255
First attempt at rendering notebook in documentation
2e8cd33
@jat255 jat255 marked this pull request as draft October 11, 2024 16:32
@jat255 jat255 marked this pull request as ready for review October 11, 2024 16:37
@AndrewHerzing AndrewHerzing merged commit 610387f into usnistgov:master Oct 11, 2024
15 checks passed
@jat255 jat255 deleted the build_documentation branch October 29, 2024 23:47
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@jat255 @AndrewHerzing