Merged
Conversation
- Include git hash in version string for better build traceability. - Standardize version/help flags and add citations to all CLI tools. - containerization scripts with custom tag support and non-interactive modes. - Update docs with uv setup instructions and final PyPI installation steps and misc. - Fix argument error in automatic checkpoint download during inpainting.
m-reuter
reviewed
Feb 20, 2026
Contributor
There was a problem hiding this comment.
Pull request overview
This PR prepares for a release by standardizing CLI --help/--version behavior (including build traceability via git hash), improving containerization scripts for CI/non-interactive usage, and updating documentation around installation and contribution workflows.
Changes:
- Centralize version reporting and add
-v/--versionsupport across multiple CLI entrypoints (including git hash when available). - Update containerization scripts to support custom image tags and more non-interactive/test-friendly execution.
- Refresh Sphinx docs for PyPI installation, uv-based contributor setup, and troubleshooting guidance; fix checkpoint download arg-parsing behavior during inpainting.
Reviewed changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated 8 comments.
Show a summary per file
| File | Description |
|---|---|
| neurolit/utils/download_checkpoints.py | Adds argparse handling + standardized help/version output for checkpoint downloader; supports being called from other CLIs without argument conflicts. |
| neurolit/scripts/run_lit_containerized.sh | Adds --tag support and non-interactive docker run; refactors version/tag resolution and singularity pull image selection. |
| neurolit/scripts/lesion_postprocessing.py | Adds version flag and improves backup handling for symlinks in postprocessing outputs. |
| neurolit/postprocessing/lesion_to_surface.py | Adds --version flag and citation text in module docstring. |
| neurolit/postprocessing/lesion_to_segmentation.py | Adds --version flag and citation epilog in CLI help. |
| neurolit/cli.py | Switches to centralized version helper; fixes checkpoint download invocation to avoid arg-parsing errors. |
| neurolit/_version.py | Introduces get_version_with_hash() helper for consistent version strings across tools. |
| doc/usage.rst | Updates mask dilation guidance and troubleshooting text. |
| doc/installation.rst | Updates PyPI and source installation sections for release readiness. |
| doc/index.rst | Updates top-level docs image formatting and PyPI install snippet. |
| doc/contributing.rst | Updates contributor setup steps to uv-based workflow. |
| CONTRIBUTING.md | Updates documentation build instructions to use uv. |
| containerization/build_docker.sh | Adds --tag support and refactors docker build options handling. |
| containerization/Dockerfile_experimental | Removes experimental Dockerfile (cleanup ahead of release). |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
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.
This is mostly documentation and testing prior to release
Various changes, e.g.