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

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+ignore = E203, E231, W503, E722
+max-line-length = 79
+exclude = __init__.py,build,.eggs

.github/workflows/plugin_preview.yml

@@ -16,6 +16,6 @@ jobs:
         uses: actions/checkout@v2
 
       - name: napari hub Preview Page Builder
-        uses: chanzuckerberg/[email protected].5
+        uses: chanzuckerberg/[email protected]
         with:
           hub-ref: main

.github/workflows/test_and_deploy.yml

@@ -1,59 +1,98 @@
 name: tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - '*'
+    tags:
+      - '*'
+  pull_request:
 
 jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: brainglobe/actions/lint@v1
+      - uses: neuroinformatics-unit/actions/lint@v1.2.0
 
   manifest:
     name: Check Manifest
     runs-on: ubuntu-latest
     steps:
-      - uses: brainglobe/actions/check_manifest@v1
+      - uses: neuroinformatics-unit/actions/check_manifest@v1.2.0
 
   test:
-    needs: [linting, manifest]
+    needs: [ linting, manifest ]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # Run all supported Python versions on linux and windows
+        # Run all supported Python versions on linux
         python-version: ["3.8", "3.9", "3.10"]
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest]
+        # Test on Windows and macOS on only one OS to save time (and CI minutes)
+        include:
+        - os: macos-latest
+          python-version: "3.10"
+        - os: windows-latest
+          python-version: "3.10"
 
     steps:
-      # Setup pyqt libraries
-      - uses: tlambert03/setup-qt-libs@v1
-      # Run tests
-      - uses: brainglobe/actions/test@v1
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-  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@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
+      # 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
-          pip install -U setuptools setuptools_scm wheel twine
-      - name: Build and publish
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: python -m tox
         env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
-        run: |
-          git tag
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v2
+
+  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@main
+
+
+  upload_all:
+    name: Publish build distributions
+    needs: [build_sdist_wheels]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v3
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/[email protected]
+      with:
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.1.0
+      rev: v4.3.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -15,16 +15,19 @@ repos:
             args: [--fix=lf]
           - id: requirements-txt-fixer
           - id: trailing-whitespace
-    - repo: https://gitlab.com/pycqa/flake8
-      rev: 3.9.2
+            # bump2version produces whitespace in setup.cfg, so exclude to
+            # not inferfere with versioning
+            exclude: setup.cfg
+    - repo: https://github.com/pycqa/flake8
+      rev: 5.0.4
       hooks:
           - id: flake8
     - repo: https://github.com/psf/black
-      rev: 22.3.0
+      rev: 22.10.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.931
+      rev: v0.990
       hooks:
           - id: mypy
             additional_dependencies:

CITATION.CFF

@@ -9,19 +9,19 @@ authors:
   given-names: "M."
 - family-names: "Rousseau"
   given-names: "C."
-- family-names: "Cossell"  
+- family-names: "Cossell"
   given-names: "L."
-- family-names: "Tsitoura"  
+- family-names: "Tsitoura"
   given-names: " C."
-- family-names: "Lenzi"  
+- family-names: "Lenzi"
   given-names: " S."
-- family-names: "Obenhaus"  
+- family-names: "Obenhaus"
   given-names: "H."
-- family-names: "Claudi"  
+- family-names: "Claudi"
   given-names: "F."
-- family-names: "Branco"  
+- family-names: "Branco"
   given-names: "T."
-- family-names: "Margrie"  
+- family-names: "Margrie"
   given-names: "T."
 url: https://github.com/brainglobe/brainreg-napari
 preferred-citation:
@@ -40,19 +40,19 @@ preferred-citation:
         given-names: "M."
       - family-names: "Rousseau"
         given-names: "C."
-      - family-names: "Cossell"  
+      - family-names: "Cossell"
         given-names: "L."
-      - family-names: "Tsitoura"  
+      - family-names: "Tsitoura"
         given-names: " C."
-      - family-names: "Lenzi"  
+      - family-names: "Lenzi"
         given-names: "S."
-      - family-names: "Obenhaus"  
+      - family-names: "Obenhaus"
         given-names: "H."
-      - family-names: "Claudi"  
+      - family-names: "Claudi"
         given-names: "F."
-      - family-names: "Branco"  
+      - family-names: "Branco"
         given-names: "T."
-      - family-names: "Margrie"  
+      - family-names: "Margrie"
         given-names: "T."
 references:
   - type: article
@@ -70,13 +70,13 @@ references:
         given-names: "A."
       - family-names: "Jorge"
         given-names: "M."
-      - family-names: "Osten"  
+      - family-names: "Osten"
         given-names: "P."
-      - family-names: "Ourselin"  
+      - family-names: "Ourselin"
         given-names: "S."
-      - family-names: "Modat"  
+      - family-names: "Modat"
         given-names: "M."
-      - family-names: "Margrie"  
+      - family-names: "Margrie"
         given-names: "T."
 references:
   - type: article
@@ -94,9 +94,9 @@ references:
         given-names: "L."
       - family-names: "Tyson"
         given-names: "A."
-      - family-names: "Branco"  
+      - family-names: "Branco"
         given-names: "T."
-      - family-names: "Margrie"  
+      - family-names: "Margrie"
         given-names: "T."
-      - family-names: "Portugues"  
+      - family-names: "Portugues"
         given-names: "R."

MANIFEST.in

@@ -3,10 +3,12 @@ include README.md
 include tox.ini
 include brainreg_napari/napari.yaml
 include .napari/config.yml
+include CITATION.CFF
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-exclude .napari *
 exclude .pre-commit-config.yaml
+exclude .flake8
 recursive-exclude examples *

brainreg_napari/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.0.5-rc0"

brainreg_napari/register.py

@@ -30,6 +30,8 @@
     initialise_brainreg,
 )
 
+PRE_PROCESSING_ARGS = None
+
 
 def add_registered_image_layers(
     viewer: napari.Viewer, *, registration_directory: pathlib.Path
@@ -440,6 +442,7 @@ def run():
                 data_orientation,
                 atlas.metadata["orientation"],
                 niftyreg_args,
+                PRE_PROCESSING_ARGS,
                 scaling,
                 load_parallel,
                 sort_input_file,

pyproject.toml

@@ -1,4 +1,77 @@
+[project]
+name = "brainreg-napari"
+authors = [{name = "Adam Tyson, Stephen Lenzi", email= "[email protected]"}]
+description = "Multi-atlas whole-brain microscopy registration"
+readme = "README.md"
+requires-python = ">=3.8.0"
+dynamic = ["version"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Framework :: napari",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Operating System :: OS Independent",
+    ]
+
+license = {text = "BSD-3-Clause"}
+dependencies = [
+    "napari",
+    "napari-plugin-engine >= 0.1.4",
+    "magicgui",
+    "qtpy",
+    "brainglobe-napari-io",
+    "brainreg",
+    "brainreg-segment",
+    "pooch>1",  # For sample data
+]
+
+[project.optional-dependencies]
+dev = [
+        "black",
+        "pytest-cov",
+        "pytest",
+        "pytest-qt",
+        "napari",
+        "pyqt5",
+        "tox",
+        "gitpython",
+        "coverage>=5.0.3",
+        "bump2version",
+        "pre-commit",
+        "flake8",
+        "check-manifest",
+        "setuptools_scm",
+]
+
+[project.urls]
+homepage = "https://brainglobe.info"
+bug_tracker = "https://github.com/brainglobe/brainreg-napari/issues"
+documentation = "https://docs.brainglobe.info/brainreg-napari"
+source_code = "https://github.com/brainglobe/brainreg-napari"
+user_support = "https://forum.image.sc/tag/brainglobe"
+twitter = "https://twitter.com/brain_globe"
+
+[project.entry-points."napari.manifest"]
+brainreg-napari = "brainreg_napari:napari.yaml"
+
+[build-system]
+requires = [
+    "setuptools>=45",
+    "wheel",
+    "setuptools_scm[toml]>=6.2",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+
 [tool.black]
+target-version = ['py38', 'py39', 'py310']
 skip-string-normalization = false
 line-length = 79
 exclude = '''
@@ -8,10 +81,7 @@ exclude = '''
     | \.git
     | \.hg
     | \.mypy_cache
-    | \.tox
-    | \.venv
     | _build
-    | buck-out
     | build
     | dist
   )/