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* Merge `brainreg-napari` into `brainreg` (#145) * initial commit * adds gui * removes deprecated folder * Update README.md * Update README.md * adds brainreg to requirements * renames gui label from register to brainreg * renames register to brainreg-register * adds brainglobe repo to setup.py * Delete requirements.txt * makes output destination selectable in GUI * Update entry point * removes sort_input_file option * Update setup.py * updates project urls in setup.cfg * Update support link * fixes output path to directory * re adds sort_input_file as hardcoded variable * adds atlas options as dropdown * adds showing the results of registration * removed a global declaration * minor refactoring * deleted commented code * fixes logging output * only loads relevant output data * outputs scaled overlay of boundaries and atlas * imports and groups segment plugin with register * lowers requirements from python >=3.7 to >=3.6 and removes project url from setup.py * removes superfluous pixel args from logging * Update readme, setup.py & general reformatting (#16) * update gitignore * Update setup.py * update readme * format with black * remove docs * remove unused import * delete tests for now * format imports * Release (#18) * Update setup.py * add bump2version config * Bump version: 0.0.1 → 0.0.2-rc0 * remove reqs from manifest * disable tests on GH actions for now * fixes reset_defaults by ignoring atlas dropdown * adds additional channels functionality * Update OS compatibility & update use of napari API * Bump (#23) * Bump version: 0.0.2-rc1 → 0.0.2-rc2 * Bump version: 0.0.2-rc2 → 0.0.2-rc3 * Bump version: 0.0.2-rc3 → 0.0.3-rc0 * Add tooltips (#25) * change default parameter names * Add tooltips * Bump version: 0.0.3-rc0 → 0.0.4-rc0 * Update README.md * Update broken image URL * Add categories and preview page workflow for the napari hub (#27) * adds EDAM Bioimaging labels * adds Action for napari hub preview service * Update citation * Update README.md * Convert to npe2 * Add pyqt library setup * Fix manifest * Add basic smoke test * Add link to contributing guide * Add pre-commit * Fix manifest * Add sample data * Add example script * Fix pre-commit and manifest * Use g-node.org for sample data * Clean up example Make noqa more specific * Set plugin values from metadata * Add a test for sample data * Add pooch to requirements Move pooch req comment * Test loading sample data through napari * Set sensible contrast limits * pre-commit fixes * Add Python 3.10 support, drop 3.7 support * Add an integration test Type block * Fix getting additional layers * Factor out add_image_layers function * Remove arguments from run() * Refactor blocking/non-blocking behaviour * Store metadata in napari layers * Use re-usable action for running tests * Give better name to add_image_layers * Add error if trying to load non-existent registration * Return layers from add_registered_image_layers * Bump version: 0.0.4-rc0 → 0.0.5-rc0 * Input orientation check (#44) * Add many features: - debug mode - interactive way of checking input orientation - brain geometry - save annotations with original orientation * add comments and docstring. * Crop the reference atlas when using interactive orientation check with half brains. * Fix a bug where run throw an error. * Fix typo in docstrings * format * Add info to use if data not loaded before checking orientation * Update docstrings Co-authored-by: Jules Scholler <jules.scholler@wysscenter.ch> * Update readme * format readme * Add codecov badge * Added citation file (#45) * Added citation file * Changes according to PR comments * Updated Citation file Updated citation file to have the preferred citation coming from the article/book when available Co-authored-by: Simão sá <simaosa@Simaos-MacBook-Pro.local> * Update packaging (#46) * update pre-commit config * update args for new brainreg version * lint * update manifest * Bump version: 0.0.5-rc0 → 0.0.5-rc1 * update testing * update packaging * update requirements * update manifest * move entry point to pyproject.toml * update hub preview version * update release for use with setuptools_scm * migrate from BG to neuroinformatics actions * add setuptools_scm to dev requirements * reduce number of tested version * update python versions tested * update release * [Napari HUB cli] Metadata enhancement suggestions (#47) * Copy "Display Name" from secondary to primary file Display Name was found in a secondary file and copied in the primary one: * (found here) "pyproject.toml" * (copied here) "brainreg_napari/napari.yaml" * Copy "Summary Sentence" from secondary to primary file Summary Sentence was found in a secondary file and copied in the primary one: * (found here) "pyproject.toml" * (copied here) ".napari/config.yml" * Use standard pre-commit config (#51) * Add standard pre-commit config * Automated pre-commit fixes * Testing clean (#50) * Use composite test action Fix use-xvfb argument * Clean tox.ini * Don't fail fast * Remove old setup steps * Clean up dev dependencies Add pyqt5 back as a dev dep * Try passing display env Put back passenv in tox * Use selected atlas to check orientation * Add orientation check tests * [pre-commit.ci] pre-commit autoupdate (#57) updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.240 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.240...v0.0.272) - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0) - [github.com/pre-commit/mirrors-mypy: v0.991 → v1.3.0](pre-commit/mirrors-mypy@v0.991...v1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update links (#56) * Update README.md * [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> * Update dependency (imlib -> brainglobe-utils) (#58) * [pre-commit.ci] pre-commit autoupdate (#59) updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275) - [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.4.1](pre-commit/mirrors-mypy@v1.3.0...v1.4.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#60) updates: - https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit - [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](astral-sh/ruff-pre-commit@v0.0.275...v0.0.276) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#61) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.276 → v0.0.277](astral-sh/ruff-pre-commit@v0.0.276...v0.0.277) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#62) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.277 → v0.0.278](astral-sh/ruff-pre-commit@v0.0.277...v0.0.278) - [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#63) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.278 → v0.0.280](astral-sh/ruff-pre-commit@v0.0.278...v0.0.280) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#65) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.280 → v0.0.281](astral-sh/ruff-pre-commit@v0.0.280...v0.0.281) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#66) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.281 → v0.0.282](astral-sh/ruff-pre-commit@v0.0.281...v0.0.282) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#67) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284) - [github.com/pre-commit/mirrors-mypy: v1.4.1 → v1.5.0](pre-commit/mirrors-mypy@v1.4.1...v1.5.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#68) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285) - [github.com/pre-commit/mirrors-mypy: v1.5.0 → v1.5.1](pre-commit/mirrors-mypy@v1.5.0...v1.5.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#70) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update .pre-commit-config.yaml (#71) * [pre-commit.ci] pre-commit autoupdate (#72) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.286 → v0.0.287](astral-sh/ruff-pre-commit@v0.0.286...v0.0.287) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#74) updates: - [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.292](astral-sh/ruff-pre-commit@v0.0.287...v0.0.292) - [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Test on Python 3.11 (#49) * Use composite test action Fix use-xvfb argument * Clean tox.ini * Don't fail fast * Remove old setup steps * Clean up dev dependencies Add pyqt5 back as a dev dep * Try passing display env Put back passenv in tox * Test on Python 3.11 * Update Python versions --------- Co-authored-by: Adam Tyson <code@adamltyson.com> * Delete .github/workflows/plugin_preview.yml (#75) * Write safe concat function * Use safe concat of dataframes * Fix logic of safe concat method * pre-commit pass * Add unit test to aplease codecov overlords * Restructure as brainreg/core, adjust imports accordingly * Make package installable again * Fix test import * Rework package structure to be compatible with brainreg-core * Update example code with new structure * Rename napari plugin to drop the -napari suffix * Exclude the to-be-reconciled READMEs from the manifest --------- Co-authored-by: stephen <stephen.lenzi@gmail.com> Co-authored-by: Adam Tyson <code@adamltyson.com> Co-authored-by: Adam Tyson <adam.tyson@ucl.ac.uk> Co-authored-by: Justin Kiggins <justin.kiggins@gmail.com> Co-authored-by: David Stansby <dstansby@gmail.com> Co-authored-by: Patrick Roddy <patrickjamesroddy@gmail.com> Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> Co-authored-by: Jules Scholler <jules.scholler@wysscenter.ch> Co-authored-by: Simão Bolota <99416933+SimaoBolota-MetaCell@users.noreply.github.com> Co-authored-by: Simão sá <simaosa@Simaos-MacBook-Pro.local> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Reconcile the `core` and `napari` READMEs (#147) * Parse existing brainreg readme * Incorporate plugin readme and update manifest * Apply Adam's updates Co-authored-by: Adam Tyson <code@adamltyson.com> --------- Co-authored-by: Adam Tyson <code@adamltyson.com> * Reconcile the `core` and `napari` READMEs (#147) * Parse existing brainreg readme * Incorporate plugin readme and update manifest * Apply Adam's updates Co-authored-by: Adam Tyson <code@adamltyson.com> --------- Co-authored-by: Adam Tyson <code@adamltyson.com> * Update README.md * Update with brainreg-segment rename to brainglobe-segmentation (#149) * Update with brainreg-segment rename to brainglobe-segmentation * Update pyproject.toml --------- Co-authored-by: stephen <stephen.lenzi@gmail.com> Co-authored-by: Adam Tyson <code@adamltyson.com> Co-authored-by: Adam Tyson <adam.tyson@ucl.ac.uk> Co-authored-by: Justin Kiggins <justin.kiggins@gmail.com> Co-authored-by: David Stansby <dstansby@gmail.com> Co-authored-by: Patrick Roddy <patrickjamesroddy@gmail.com> Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> Co-authored-by: Jules Scholler <jules.scholler@wysscenter.ch> Co-authored-by: Simão Bolota <99416933+SimaoBolota-MetaCell@users.noreply.github.com> Co-authored-by: Simão sá <simaosa@Simaos-MacBook-Pro.local> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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