Comments (11)
Jordan-Dennis
commented on August 17, 2024
1
Just an update on the docs front. The gh-pages cannot be deployed at the moment because all the docs point at the old locations under the src. structure. I will update this but not immediately.
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Jordan-Dennis
commented on August 17, 2024
I've created a new branch with the following structure:
docs/
- optical_system.md
- wavefronts/
- fresnel_wavefront.md
- physical_wavefront.md
- layers/
- ect.
Where each class get's it's own markdown file. We can change this up, but I assumed that we would not be transitioning to a (readthedocs.io) [https://readthedocs.io] web site so the heavy structuring will make it easy to find the relevant information. I was planning to writing these today, to aid my own understanding of some of the code.
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LouisDesdoigts
commented on August 17, 2024
@benjaminpope has set up a gh-pages branch for docs https://louisdesdoigts.github.io/dLux/, but I think starting out with this is a good idea, and then we can merge it together cohesively once we have most of it written.
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Jordan-Dennis
commented on August 17, 2024
Ahhh, I was wondering what the gh-pages branch was for. I'll keep writing docs on the Documentation branch for now then. But move them over long term.
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Jordan-Dennis
commented on August 17, 2024
Also how do we want to document the __init__ and __call__ dunder methods. At the moment I have been documenting both parameter sets just under a #### Parameters: label in Documentation. This is confusing because it does not specify when to provide the parameters. The other option is to have a #### Constructor: heading and then a #### Parameters: heading.
Let me know what you think.
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Jordan-Dennis
commented on August 17, 2024
Spoke with @benjaminpope and we are using mkdocs.
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Jordan-Dennis
commented on August 17, 2024
Hello again,
Just checking in with an update. The Wavefront branch now contains full documentation for the PhysicalWavefront class although this has been spread over Wavefront and PlanarWavefront (name subject to change, I just wanted something more physical). As part of the documenting I have been updating names to match the PEP 8 style guides. This will be subject to review and will probably require @LouisDesdoigts and I to sit down and review each case individually. Some examples are get_XXYY became get_pixel_grid and invertXY became invert_x_and_y. Some probably more annoying ones will be pixelscale to pixel_scale. @LouisDesdoigts I will probably make a pull request for the Wavefront branch into the GaussianWavefront branch either today or tomorrow and we can go over these details then.
Regards
Jordan
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Jordan-Dennis
commented on August 17, 2024
Hi all,
While I was updating the GitHub issue I thought I would comment on the current state of this. I have set-up the mkdocs.yml with the following structure:
nav:
- Home:
- User Documentation:
- Optical System:
- Layers:
- Create Wavefront:
- ect.
- Developer Documentation:
- Propagators:
- Propagator:
- Variable Sampling:
- Variable Sampling Propagator:
- ect.
- Fixed Sampling:
- Fixed Sampling Propagator:
- ect.
- Wavefronts:
- Wavefront:
- Physical Wavefront:
- Angular Wavefront:
- Gaussian Wavefront:These will be available from the GitHub pages by the end of the day and are pending the pull request of the Propagators branch.
Regards
Jordan
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Jordan-Dennis
commented on August 17, 2024
So this did not make it through the pull request because of the following error:
ERROR - Error building page
'developer_documentation/propagators/propagator.md': Could not
resolve equinox
Traceback (most recent call last):
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs_autorefs/plugin.py", line 78, in _get_item_url
return self._url_map[identifier]
KeyError: 'src.wavefronts.eqx.Module'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/dataclasses.py", line 945, in resolve_target
resolved = self.modules_collection[self.target_path]
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/mixins.py", line 26, in __getitem__
return self.members[parts[0]] # type: ignore[attr-defined]
KeyError: 'equinox'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/jordan/anaconda3/envs/jax/bin/mkdocs", line 8, in <module>
sys.exit(cli())
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs/__main__.py", line 192, in build_command
build.build(config.load_config(**kwargs), dirty=not clean)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs/commands/build.py", line 314, in build
_build_page(file.page, config, doc_files, nav, env, dirty)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs/commands/build.py", line 220, in _build_page
output = config['plugins'].run_event(
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs/plugins.py", line 102, in run_event
result = method(item, **kwargs)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs_autorefs/plugin.py", line 205, in on_post_page
fixed_output, unmapped = fix_refs(output, url_mapper)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs_autorefs/references.py", line 191, in fix_refs
html = AUTO_REF_RE.sub(fix_ref(url_mapper, unmapped), html)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs_autorefs/references.py", line 157, in inner
url = url_mapper(unescape(identifier))
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs_autorefs/plugin.py", line 107, in get_item_url
url = self._get_item_url(identifier, fallback)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocs_autorefs/plugin.py", line 83, in _get_item_url
new_identifiers = fallback(identifier)
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocstrings/handlers/base.py", line 508, in get_anchors
anchors = handler.get_anchors(handler.collect(identifier, fallback_config))
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/mkdocstrings_handlers/python/handler.py", line 200, in collect
doc_object = self._modules_collection[identifier]
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/mixins.py", line 27, in __getitem__
return self.members[parts[0]][parts[1:]] # type: ignore[attr-defined]
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/mixins.py", line 27, in __getitem__
return self.members[parts[0]][parts[1:]] # type: ignore[attr-defined]
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/mixins.py", line 27, in __getitem__
return self.members[parts[0]][parts[1:]] # type: ignore[attr-defined]
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/dataclasses.py", line 821, in __getitem__
return self.target[key]
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/dataclasses.py", line 921, in target
self.resolve_target()
File "/home/jordan/anaconda3/envs/jax/lib/python3.10/site-packages/griffe/dataclasses.py", line 947, in resolve_target
raise AliasResolutionError(self.target_path) from error
griffe.exceptions.AliasResolutionError: Could not resolve equinoxwhich as all mkdocs errors seem to be is very cryptic.
Any help appreciated,
Jordan
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Jordan-Dennis
commented on August 17, 2024
So I managed to fix this using the typing module.
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LouisDesdoigts
commented on August 17, 2024
The docs pages now deploy and are more or less fully populated with low-level tutorial notebooks, so I consider this to be complete
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Related Issues (20)
- Add sub headings in API docs HOT 1
- Position in binary is not flux weighted HOT 2
- `UniformSpider` API missing HOT 1
- Improve FP-precision by setting wavefront amplitude as opposed to scaling output PSFs?
- Update `ApplyJitter` class HOT 1
- pyproject.toml fixes HOT 1
- oversample in MFT? HOT 1
- change banner
- Add `CoronagraphicLayer` and `InterpolatedLayer`
- logo does not display on main README.md
- Add intrapixel sensitivity map downsampling HOT 1
- Add Convolution detector layer
- Missing `new_pixel_scale` return value in `utils.propagation.FFT` docstring
- ConcretizationTypeError in nd_coords HOT 5
- Inconsistency between parameter raising from `LayeredOpticalSystem` and `LayeredDetector`
- PointSource enforces flux as float HOT 1
- Remove all calls to `.normalise` when calculating things.
- HST-like Aperture Incorrect Size in Docs
- Add FoV method to child-classes of `ParametricOpticalSystem`
- `dlu.nandiv` fails on float inputs
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