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9de015a
Create conf.py for sphinx
joe-from-mtl Dec 16, 2024
0fe1f70
Create requirements for sphinx
joe-from-mtl Dec 16, 2024
31dea93
Update .readthedocs.yaml to use sphinx specific requirements
joe-from-mtl Dec 16, 2024
f678d1a
Renamed the sphinx requirements file
joe-from-mtl Dec 16, 2024
0534209
Adding a base documentation file for Sphinx
joe-from-mtl Dec 16, 2024
94cb3e7
Adding a script documentation as an example
joe-from-mtl Dec 16, 2024
5ea798c
Adding the linum requirements to build the doc
joe-from-mtl Dec 16, 2024
2d8c59f
Sphing was complaining that there were no versions for this package
joe-from-mtl Dec 16, 2024
b32bb53
Latest python version is causing a problem with some dependencies
joe-from-mtl Dec 16, 2024
3800e5c
Scripts were not appearing in the compiled doc
joe-from-mtl Dec 16, 2024
91b0565
Adding the script name
joe-from-mtl Dec 16, 2024
26d2701
Adding the linumpy automodule documentation
joe-from-mtl Dec 16, 2024
77f37e8
Adding the linumpy automodule documentation
joe-from-mtl Dec 16, 2024
28c6ebd
Using autosummary for the API documentation
joe-from-mtl Dec 16, 2024
c376dec
Including linumpy
joe-from-mtl Dec 16, 2024
cf72a1a
Trying autosummary
joe-from-mtl Dec 16, 2024
be01d2c
Supporting numpy style documentation
joe-from-mtl Dec 16, 2024
119b9e7
Napoleon settings
joe-from-mtl Dec 16, 2024
08299d1
Autodoc and autosummary with templates
joe-from-mtl Dec 16, 2024
7e7fdef
Error with autosummary formating
joe-from-mtl Dec 16, 2024
7c90595
Generating an API documentation, and adding script docs
joe-from-mtl Dec 17, 2024
51273ba
Missing dependency
joe-from-mtl Dec 17, 2024
7da8c0a
Formatting docstring
joe-from-mtl Dec 17, 2024
419ff65
Formatting docstring
joe-from-mtl Dec 17, 2024
4c7cec6
Removing the pip install option for now
joe-from-mtl Dec 17, 2024
be46990
Adding a usage example and removing the shell scripts
joe-from-mtl Dec 17, 2024
430ff79
Formatting the docstring according to numpy style
joe-from-mtl Dec 17, 2024
09a9985
Formatting the docstring according to numpy style
joe-from-mtl Dec 17, 2024
415d790
Merge remote-tracking branch 'origin/sphinx-config' into sphinx-config
joe-from-mtl Dec 17, 2024
41a464a
Removing old scripts and renaming a few to make things clearer (issue…
joe-from-mtl Dec 17, 2024
6e5f947
Adapting the script name for issue #30
joe-from-mtl Dec 17, 2024
7054921
Adapting the documentation based on the removed and renamed scripts (…
joe-from-mtl Dec 17, 2024
a806bd8
Adapting the documentation to use numpy style
joe-from-mtl Dec 17, 2024
46f6a38
Formatting
joe-from-mtl Dec 17, 2024
053f0ee
Formatting according to PEP8
joe-from-mtl Dec 17, 2024
8451f1c
Adding a convention for the axis order
joe-from-mtl Dec 17, 2024
92026ec
Formatting for PEP8
joe-from-mtl Dec 17, 2024
4087527
Formatting for PEP8
joe-from-mtl Dec 17, 2024
22338b5
Adding a script that was removed by error from the 3D pipeline
joe-from-mtl Dec 17, 2024
6edeb53
Update docs/CONTRIBUTING.md to use .ome.zarr
joe-from-mtl Dec 17, 2024
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2 changes: 1 addition & 1 deletion docs/CONTRIBUTING.md
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We should also mention somewhere than the zarr chunk size is often chosen to match the raw tile size. This is important for the processing pipeline.

Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# `linumpy` coding standards

* We use the [PEP8](https://peps.python.org/pep-0008/) coding standard
* OME-Zarr format extension should be `ome.zarr`, as shown in the NGFF documentation ([URL](https://ngff.openmicroscopy.org/0.4/index.html#bf2raw-layout))
* OME-Zarr format extension should be `.ome.zarr`, as shown in the NGFF documentation ([URL](https://ngff.openmicroscopy.org/0.4/index.html#bf2raw-layout))
* All scripts/methods should explicitly document the expected resolutions and dimensions units
* We use Numpy style docstrings: https://numpydoc.readthedocs.io/en/latest/format.html
* The axis order should be Z, Y, X
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