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commit 83083f4 Author: Fernando Cervantes Sanchez <[email protected]> Date: Tue Jul 16 17:43:23 2024 -0400 Added edit scale to editor commit c94cd09 Author: Fernando Cervantes Sanchez <[email protected]> Date: Mon Jul 15 18:56:29 2024 -0400 Working on adding editable scale for layers commit 9e51908 Author: Fernando Cervantes Sanchez <[email protected]> Date: Fri Jul 12 17:04:44 2024 -0400 Made torch optional and fixing mask scales commit 17a5b91 Author: Fernando Cervantes Sanchez <[email protected]> Date: Thu Jul 11 17:32:56 2024 -0400 Organized classes into modules commit 33dc20a Author: Fernando Cervantes Sanchez <[email protected]> Date: Wed Jul 10 17:03:40 2024 -0400 Adding configurable cellpose method commit cd80549 Author: Fernando Cervantes Sanchez <[email protected]> Date: Wed Jul 10 11:55:58 2024 -0400 Testing convertion of repository into napari plugin commit ba0ab02 Author: Fernando Cervantes Sanchez <[email protected]> Date: Mon Jul 8 17:56:09 2024 -0400 Migrated code to napari cookie cutter scheme
TheJacksonLaboratory · Jul 16, 2024 · 8e37ca4 · 8e37ca4
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diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -0,0 +1,91 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+      - npe2
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+      - npe2
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: aganders3/headless-gui@v2
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy:
+    # this will run when you have tagged a commit, starting with "v*"
+    # and requires that you have put your twine API key in your
+    # github secrets (see readme for details)
+    needs: [test]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+        run: |
+          git tag
+          python -m build .
+          twine upload dist/*
diff --git a/.gitignore b/.gitignore
@@ -24,7 +24,6 @@ share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -158,8 +157,23 @@ cython_debug/
 #  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/
-/data
-examples.py
-/.vscode
+.idea/
+venv/
+.vscode/
+
+# Test image files and models
 *.zarr
+/data
 /models
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py
diff --git a/.napari-hub/DESCRIPTION.md b/.napari-hub/DESCRIPTION.md
@@ -0,0 +1,9 @@
+<!-- This file is a placeholder for customizing description of your plugin 
+on the napari hub if you wish. The readme file will be used by default if
+you wish not to do any customization for the napari hub listing.
+
+If you need some help writing a good description, check out our 
+[guide](https://github.com/chanzuckerberg/napari-hub/wiki/Writing-the-Perfect-Description-for-your-Plugin)
+-->
+
+The developer has not yet provided a napari-hub specific description.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: ^\.napari-hub/.*
+      - id: check-yaml # checks for correct yaml syntax for github actions ex.
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.1
+    hooks:
+      - id: ruff
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+  - repo: https://github.com/tlambert03/napari-plugin-checks
+    rev: v0.3.0
+    hooks:
+      - id: napari-plugin-checks
+  # https://mypy.readthedocs.io/en/stable/
+  # you may wish to add this as well!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.9.0
+  #   hooks:
+  #     - id: mypy
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
diff --git a/README.md b/README.md
@@ -1,2 +1,62 @@
 # Active Learning tools for ML models fine-tuning
 Active learning tools for fine-tuning ML models
+
+[![License MIT](https://img.shields.io/pypi/l/napari-activelearning.svg?color=green)](https://github.com/fercer/napari-activelearning/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-activelearning.svg?color=green)](https://pypi.org/project/napari-activelearning)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-activelearning.svg?color=green)](https://python.org)
+[![tests](https://github.com/fercer/napari-activelearning/workflows/tests/badge.svg)](https://github.com/fercer/napari-activelearning/actions)
+[![codecov](https://codecov.io/gh/fercer/napari-activelearning/branch/main/graph/badge.svg)](https://codecov.io/gh/fercer/napari-activelearning)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-activelearning)](https://napari-hub.org/plugins/napari-activelearning)
+
+A plugin for running a complete active learning workflow
+
+----------------------------------
+
+This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/cookiecutter-napari-plugin#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-activelearning` via [pip]:
+
+    pip install napari-activelearning
+
+
+
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [MIT] license,
+"napari-activelearning" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/
diff --git a/activelearning/__init__.py b/activelearning/__init__.py
diff --git a/activelearning/alutils.py b/activelearning/alutils.py