Fetch the state of cellfinder, before functionality change.

.github/workflows/test_and_deploy.yml

@@ -0,0 +1,107 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - "main"
+    tags:
+      - "*"
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      coredev:
+        description: 'Tests with development version of cellfinder-core?'
+        required: true
+        default: 'false'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  linting:
+    name: Linting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  manifest:
+    name: Check manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/check_manifest@v2
+
+  test:
+    needs: [linting,manifest]
+    runs-on: ${{ matrix.os }}
+    env:
+      INPUT_COREDEV: ${{ github.event.inputs.coredev }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Run across a mixture of Python versions and operating systems
+        include:
+        - os: macos-latest
+          python-version: "3.10"
+        - os: windows-latest
+          python-version: "3.9"
+        - os: ubuntu-latest
+          python-version: "3.8"
+    steps:
+      - uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+  build_sdist_wheels:
+    name: Build source distribution
+    needs: [test]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
+
+  deploy:
+    needs: [build_sdist_wheels]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.TWINE_API_KEY }}
+
+  build-and-push-docker:
+    needs: deploy
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.gitignore

@@ -0,0 +1,126 @@
+# Custom config files
+*.conf.custom
+
+# Byte-compiled / optimized / DLL files
+**/__pycache__/**
+*.py[cod]
+*$py.class
+
+# Cython
+*.c
+*.cpp
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+doc/build/
+
+# pydocmd
+_build/
+mkdocs.yml
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.envrc
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+.idea/
+
+*.~lock.*
+
+pip-wheel-metadata/
+
+*.DS_Store
+
+*.vscode/

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+# Configuring https://pre-commit.ci/
+ci:
+    autoupdate_schedule: monthly
+
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: requirements-txt-fixer
+          - id: trailing-whitespace
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.0.286
+      hooks:
+        - id: ruff
+    - repo: https://github.com/psf/black
+      rev: 23.7.0
+      hooks:
+          - id: black
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.5.1
+      hooks:
+          - id: mypy
+            additional_dependencies:
+                - types-setuptools
+                - types-requests

Dockerfile

@@ -0,0 +1,4 @@
+FROM tensorflow/tensorflow:latest-gpu
+LABEL maintainer="[email protected]"
+RUN pip install cellfinder
+CMD ["bash"]

LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2020, University College London
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,18 @@
+include README.md
+include LICENSE
+
+exclude *.yaml
+exclude *.yml
+exclude Dockerfile
+exclude *.ini
+
+recursive-include cellfinder *.py
+include cellfinder/config/*
+
+global-include *.pxd
+
+prune tests
+prune resources
+
+prune .github
+prune .tox