Merged
Conversation
Contributor
There was a problem hiding this comment.
Pull Request Overview
This PR expands documentation across the openDVP project, focusing on installation guides, workflow documentation, and contribution guidelines. The changes reorganize and enhance documentation structure while making minor dependency version adjustments.
- Adds comprehensive installation and setup guides for openDVP, MCMICRO, and SOPA workflows
- Creates new experimental and computational workflow documentation sections
- Adds contribution guide and improves navigation structure
Reviewed Changes
Copilot reviewed 17 out of 19 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| pyproject.toml | Changes napari-spatialdata dependency from flexible (~=) to exact (==) version and removes anndata version constraint |
| docs/index.md | Removes empty line, increases maxdepth to 3, and adds ContributionGuide to toctree |
| docs/conf.py | Adds navigation_depth configuration for theme |
| docs/Workflows/uv_tutorial.md | Removes entire uv tutorial file (content moved elsewhere) |
| docs/Workflows/index.md | Removes empty line and adds toctree for Experimental and Computational subdirectories |
| docs/Workflows/Experimental/index.md | Adds empty lines and toctree for experimental workflow documentation |
| docs/Workflows/Experimental/Experimental_Tissue_and_Slides.md | New file documenting tissue preparation and slide selection guidance |
| docs/Workflows/Experimental/Experimental_Imaging.md | New file documenting imaging modalities and microscope settings |
| docs/Workflows/Computational/index.md | New file organizing computational workflow documentation with links to tutorials |
| docs/Workflows/Computational/InstallOpenDVP.md | New file consolidating installation instructions from removed uv_tutorial.md |
| docs/Workflows/Computational/GettingStartedWithSOPA.md | Major expansion with detailed SOPA setup and usage instructions |
| docs/Workflows/Computational/GettingStartedWithMCMICRO.md | Major expansion with comprehensive MCMICRO installation and configuration guide |
| docs/Tutorials/T5_Thresholding_tutorial.ipynb | New empty tutorial notebook placeholder |
| docs/Tutorials/T4_Segmask_to_shapes.ipynb | New empty tutorial notebook placeholder |
| docs/ContributionGuide.md | New comprehensive contribution guide for developers |
| README.md | Updates Python version requirements from 3.10+ to 3.11-3.12 and adds conda environment creation |
| src/opendvp/io/DIANN_to_adata.py | Adds two TODO comments for future improvements |
Comments suppressed due to low confidence (1)
docs/Workflows/Computational/GettingStartedWithSOPA.md:1
- Corrected spelling of 'wih' to 'with'.
# Getting started with SOPA
Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.
|
|
||
| ### Windows users | ||
| - More modality compatibility leads to complexity of setup. | ||
| - SOPA cannot perform **Illumination correction**, **Stitching and Registration**, or **Background Subtraction**.(Jose is considering helping out SOPA devs with these). |
There was a problem hiding this comment.
Corrected spelling of 'ration' to 'ratio' in 'signal-to-noise ration'.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.