Merge with atlasgen #199
Merged
Merge with atlasgen #199
Conversation
This file contains 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
add 50um to allen mouse
Update Kim mouse atlas
Add osten mouse atlas
Fix extract_largest_region and compare_mesh_volume
* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.9...v0.2.0) - [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Add manifest to CI * Standardise tox.ini into pyproject
* first test functions for validate_mesh_structure_pairs * storing atlases and successful/failed validation functions in a data frame * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * restoring test_validation.py to the original merged version. Chages are implemented on another branch * validate_atlases.py: going back to the version on main, appending only the name of the successful and failed functions (not the function object) to lists in validate_atlases function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * populating dictionaries in for loop, writing JSON files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * saving JSON files to ~/.brainglobe/atlases/validation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * printing where to find the result files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update bg_atlasgen/validate_atlases.py Co-authored-by: Alessandro Felder <[email protected]> * Update bg_atlasgen/validate_atlases.py removing unused variables Co-authored-by: Alessandro Felder <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * saving only one JSON file with all the information * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * uncommenting test functions --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder <[email protected]>
This reverts commit 120c3b2.
for more information, see https://pre-commit.ci
…instead of all_validation_functions (#119)
24 tasks
* first test functions for validate_mesh_structure_pairs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adding docstring * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * writing docstrings to explain the behaviour of the test functions * validate_atlases.py: updated validate_mesh_structure_pairs function, test_validation.py: updated tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * spliting validate_mesh_structure_pairs function, checking mesh files and structures separately * writing tests for catch_missing_mesh_files and catch_missing_structures validation functions * creating an atlas with a missing structure to test catch_missing_structures function * Update tests/test_unit/test_validation.py Co-authored-by: Alessandro Felder <[email protected]> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder <[email protected]>
This reverts commit 9d5317d.
alessandrofelder
approved these changes
Feb 23, 2024
Co-authored-by: Alessandro Felder <[email protected]>
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.
Concerns brainglobe/BrainGlobe#43
This will:
bg-atlasgeninto this repository. It will become theatlas_generationsubmodule.brainglobe-atlasapiAfter merging:
brainglobemetapackage on conda-forge brainglobe-meta#40 will need to have it's text updated to reflect the new package structure.brainglobe-atlasapifirst release rather thanbg-atlasapiTODO: