copick-utils 0.6.0__tar.gz → 1.0.0__tar.gz

copick_utils-1.0.0/.github/dependabot.yml

@@ -0,0 +1,16 @@
+version: 2
+updates:
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: fix
+      prefix-development: chore
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: fix
+      prefix-development: chore

copick_utils-1.0.0/.github/workflows/conventional-commits.yml

@@ -0,0 +1,19 @@
+# Validates PR title follows conventional commits
+name: conventional-commits
+on:
+  pull_request:
+    branches: [main]
+    types:
+      - edited
+      - opened
+      - synchronize
+      - reopened
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  conventional_commit_title:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: chanzuckerberg/github-actions/.github/actions/conventional-commits@v6.10.0

copick_utils-1.0.0/.github/workflows/py-formatting.yml

@@ -0,0 +1,23 @@
+name: Python Linting
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre_commit_checks:
+    name: pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12.5"
+      - name: Install action-validator with asdf
+        uses: asdf-vm/actions/install@v4
+        with:
+          tool_versions: |
+            action-validator 0.6.0
+      - name: check linting
+        uses: pre-commit/action@v3.0.1

copick_utils-1.0.0/.github/workflows/release-please.yml

@@ -0,0 +1,64 @@
+name: Create Release PRs
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  release-please:
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: release please
+        uses: googleapis/release-please-action@v4
+        id: release
+        with:
+          manifest-file: ".release-please.manifest.json"
+          config-file: "release-please.config.json"
+          target-branch: "main"
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+    outputs:
+      paths_released: ${{ steps.release.outputs.paths_released }}
+
+  publish-pypi-package:
+    name: Build and publish Python package to PyPI
+    runs-on: ubuntu-latest
+    needs: release-please
+    if: contains(needs.release-please.outputs.paths_released, '.')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/copick-utils
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - name: Checkout ref branch
+        uses: actions/checkout@v5
+        with:
+          ref: ${{ github.ref }}
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.7.13"
+          python-version: "3.12"
+
+      - name: build
+        run: |
+          uv build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist

copick_utils-1.0.0/.gitignore

@@ -0,0 +1,180 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Mac stuff
+.DS_Store
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Ignore Downloaded SAM2 Weights
+saber/checkpoints/*
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc

copick_utils-1.0.0/.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 23.9.1
+  hooks:
+  - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.292
+  hooks:
+  - id: ruff
+    args:
+    - --fix
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: check-toml
+  - id: check-yaml
+    exclude: 'mkdocs.yml'
+  - id: check-json
+  - id: check-merge-conflict
+  - id: end-of-file-fixer
+  - id: trailing-whitespace

copick_utils-1.0.0/.release-please.manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "1.0.0"
+}

copick_utils-1.0.0/CHANGELOG.md

@@ -0,0 +1,36 @@
+# Changelog
+
+## [1.0.0](https://github.com/copick/copick-utils/compare/copick-utils-v0.6.1...copick-utils-v1.0.0) (2025-10-16)
+
+
+### ⚠ BREAKING CHANGES
+
+* Conversion, logical and processing commands for copick-utils CLI ([#24](https://github.com/copick/copick-utils/issues/24))
+
+### ✨ Features
+
+* Conversion, logical and processing commands for copick-utils CLI ([#24](https://github.com/copick/copick-utils/issues/24)) ([d455fd2](https://github.com/copick/copick-utils/commit/d455fd217f4cd4edf18cfe8da48d951799fa272a))
+
+
+### 🐞 Bug Fixes
+
+* bump actions/checkout from 4 to 5 ([#22](https://github.com/copick/copick-utils/issues/22)) ([287ac56](https://github.com/copick/copick-utils/commit/287ac566545d5c8b496dfdc0ae7e18456337de52))
+* bump actions/setup-python from 5 to 6 ([#25](https://github.com/copick/copick-utils/issues/25)) ([f3ed071](https://github.com/copick/copick-utils/commit/f3ed071dafa9469daee9f62a9a06319de4c76d63))
+* bump astral-sh/setup-uv from 6 to 7 ([#30](https://github.com/copick/copick-utils/issues/30)) ([b3028ef](https://github.com/copick/copick-utils/commit/b3028ef908f0e0d42cf418abb5169ab3a87556eb))
+* bump chanzuckerberg/github-actions from 6.4.0 to 6.5.0 ([#20](https://github.com/copick/copick-utils/issues/20)) ([13056ae](https://github.com/copick/copick-utils/commit/13056ae6ee0fc0132c20b5f0539614c9d4d4aa24))
+* bump chanzuckerberg/github-actions from 6.5.0 to 6.6.0 ([#23](https://github.com/copick/copick-utils/issues/23)) ([2c6a994](https://github.com/copick/copick-utils/commit/2c6a99497098073cecb52b5094da9f6ede040c4a))
+* bump chanzuckerberg/github-actions from 6.6.0 to 6.10.0 ([#29](https://github.com/copick/copick-utils/issues/29)) ([bb50f1e](https://github.com/copick/copick-utils/commit/bb50f1ee9070cf33cee6d78e64aefe5063e5f0eb))
+
+## [0.6.1](https://github.com/copick/copick-utils/compare/copick-utils-v0.6.0...copick-utils-v0.6.1) (2025-07-16)
+
+
+### 🐞 Bug Fixes
+
+* bump actions/checkout from 3 to 4 ([#19](https://github.com/copick/copick-utils/issues/19)) ([570072f](https://github.com/copick/copick-utils/commit/570072f708ea47b54d00fcc24451401896c91e25))
+* bump actions/setup-python from 4 to 5 ([#17](https://github.com/copick/copick-utils/issues/17)) ([95c4784](https://github.com/copick/copick-utils/commit/95c47842e6a271ae40f69a9f9a578ef55d3d318b))
+* bump asdf-vm/actions from 3 to 4 ([#18](https://github.com/copick/copick-utils/issues/18)) ([039b576](https://github.com/copick/copick-utils/commit/039b5761c4bc6b128f1bfef1aa2e7bf612f42ea3))
+
+
+### 🧹 Miscellaneous Chores
+
+* Set up CI for copick-utils ([#14](https://github.com/copick/copick-utils/issues/14)) ([0fbcfbb](https://github.com/copick/copick-utils/commit/0fbcfbb5bc12261da52e0850531195049328c2f9))

{copick_utils-0.6.0 → copick_utils-1.0.0}/PKG-INFO

@@ -1,15 +1,25 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: copick-utils
-Version: 0.6.0
+Version: 1.0.0
 Summary: Utilities for copick
-License: MIT
-Author: Kyle Harrington
-Author-email: czi@kyleharrington.com
-Requires-Python: >=3.9
+Project-URL: Repository, https://github.com/KyleHarrington/copick-utils.git
+Project-URL: Issues, https://github.com/KyleHarrington/copick-utils/issues
+Project-URL: Documentation, https://github.com/KyleHarrington/copick-utils#readme
+Author-email: Kyle Harrington <czi@kyleharrington.com>, Jonathan Schwartz <jonathan.schwartz@czii.org>
+License: MIT License
+        
+        Copyright (c) 2024-present Kyle Harrington <czi@kyleharrington.com>
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+License-File: LICENSE
+Keywords: annotation,copick,cryo-et,cryoet,tomography,utilities
 Classifier: Development Status :: 4 - Beta
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -17,10 +27,27 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
-Requires-Dist: copick (>=0.8.0)
-Project-URL: Documentation, https://github.com/KyleHarrington/copick-utils#readme
-Project-URL: Issues, https://github.com/KyleHarrington/copick-utils/issues
-Project-URL: Source, https://github.com/KyleHarrington/copick-utils
+Requires-Python: >=3.9
+Requires-Dist: click
+Requires-Dist: click-option-group
+Requires-Dist: copick>=1.16.0
+Requires-Dist: manifold3d
+Requires-Dist: mapbox-earcut
+Requires-Dist: numpy
+Requires-Dist: rtree
+Requires-Dist: scikit-image
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: shapely
+Requires-Dist: tqdm
+Requires-Dist: trimesh
+Requires-Dist: zarr
+Provides-Extra: dev
+Requires-Dist: black>=25.1.0; extra == 'dev'
+Requires-Dist: hatch-vcs>=0.4.0; extra == 'dev'
+Requires-Dist: hatchling>=1.25.0; extra == 'dev'
+Requires-Dist: pre-commit>=4.2.0; extra == 'dev'
+Requires-Dist: ruff>=0.12.0; extra == 'dev'
 Description-Content-Type: text/markdown
 
 # copick-utils
@@ -69,4 +96,3 @@ This project adheres to the Contributor Covenant [code of conduct](https://githu
 ## Reporting Security Issues
 
 If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
-

copick_utils-1.0.0/SECURITY.md

@@ -0,0 +1,3 @@
+## Reporting Security Issues
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).