update to npe2 (#7)

* update to npe2 * add test * make extension handling consistent between napari.yaml and reader itself * fix bug introduced in reader * add deps
alisterburt · Jun 8, 2023 · ff25cd9 · ff25cd9
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commit ff25cd9
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diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -3,26 +3,88 @@
 
 name: tests
 
-on: push
+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:
-  ubuntu-latest:
-    runs-on: ubuntu-latest
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         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
-          pip install setuptools tox tox-gh-actions
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
       - name: Test with tox
-        run: tox
+        uses: aganders3/headless-gui@v1
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
       - name: Coverage
-        uses: codecov/codecov-action@v1
+        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@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        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/napari_mrcfile_reader/__init__.py b/napari_mrcfile_reader/__init__.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,58 @@
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.setuptools_scm]
+write_to = "src/napari_mrcfile_reader/_version.py"
+
+[tool.black]
+line-length = 79
+target-version = ['py38', 'py39', 'py310']
+
+
+[tool.ruff]
+line-length = 79
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py38"
+fix = true
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.cfg b/setup.cfg
@@ -0,0 +1,59 @@
+[metadata]
+name = napari-mrcfile-reader
+
+description = Read MRC2014 files in napari using mrcfile.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/alisterburt/napari-mrcfile-reader
+author = Alister Burt
+author_email = [email protected]
+license = BSD-3-Clause
+license_files = LICENSE
+classifiers =
+    Development Status :: 2 - Pre-Alpha
+    Framework :: napari
+    Intended Audience :: Developers
+    License :: OSI Approved :: BSD License
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Topic :: Scientific/Engineering :: Image Processing
+project_urls =
+    Bug Tracker = https://github.com/alisterburt/napari-mrcfile-reader/issues
+    Documentation = https://github.com/alisterburt/napari-mrcfile-reader#README.md
+    Source Code = https://github.com/alisterburt/napari-mrcfile-reader
+    User Support = https://github.com/alisterburt/napari-mrcfile-reader/issues
+
+[options]
+packages = find:
+install_requires =
+    numpy
+    mrcfile
+
+python_requires = >=3.8
+include_package_data = True
+package_dir =
+    =src
+setup_requires = setuptools_scm
+# add your package requirements here
+
+[options.packages.find]
+where = src
+
+[options.entry_points]
+napari.manifest =
+    napari-mrcfile-reader = napari_mrcfile_reader:napari.yaml
+
+[options.extras_require]
+testing =
+    tox
+    pytest  # https://docs.pytest.org/en/latest/contents.html
+    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+
+
+[options.package_data]
+* = *.yaml
diff --git a/setup.py b/setup.py
diff --git a/napari_mrcfile_reader/_tests/__init__.py → src/__init__.py b/napari_mrcfile_reader/_tests/__init__.py → src/__init__.py
diff --git a/src/napari_mrcfile_reader/__init__.py b/src/napari_mrcfile_reader/__init__.py
@@ -0,0 +1,11 @@
+
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+from ._reader import napari_get_reader
+
+__all__ = (
+    "napari_get_reader",
+    )
diff --git a/napari_mrcfile_reader/mrcfile_reader.py → src/napari_mrcfile_reader/_reader.py b/napari_mrcfile_reader/mrcfile_reader.py → src/napari_mrcfile_reader/_reader.py
@@ -1,21 +1,16 @@
 """
-This module is an mrc file reader plugin for napari.
+This module is an example of a barebones numpy reader plugin for napari.
 
-It implements the ``napari_get_reader`` hook specification to create
-a reader plugin.
-see: https://napari.org/docs/plugins/hook_specifications.html
-
-Replace code below accordingly.  For complete documentation see:
-https://napari.org/docs/plugins/for_plugin_developers.html
+It implements the Reader specification, but your plugin may choose to
+implement multiple readers or even other plugin contributions. see:
+https://napari.org/stable/plugins/guides.html?#readers
 """
-import numpy as np
-from napari_plugin_engine import napari_hook_implementation
 import mrcfile
+import numpy as np
 
 
-@napari_hook_implementation
 def napari_get_reader(path):
-    """A basic implementation of the napari_get_reader hook specification.
+    """A basic implementation of a Reader contribution.
 
     Parameters
     ----------
@@ -35,7 +30,15 @@ def napari_get_reader(path):
         path = path[0]
 
     # if we know we cannot read the file, we immediately return None.
-    extensions = ".mrc", ".mrcs", ".map"
+    extensions = (
+        '.mrc',
+        '.mrcs',
+        '.map',
+        '.st',
+        '.rec',
+        '.preali',
+        '.ali',
+    )
     if not path.endswith(extensions):
         return None
 

diff --git a/...file_reader/_tests/test_mrcfile_reader.py → ...pari_mrcfile_reader/_tests/test_reader.py b/...file_reader/_tests/test_mrcfile_reader.py → ...pari_mrcfile_reader/_tests/test_reader.py
@@ -1,14 +1,17 @@
-import numpy as np
 import mrcfile
+import numpy as np
+
 from napari_mrcfile_reader import napari_get_reader
 
 
 # tmp_path is a pytest fixture
 def test_reader(tmp_path):
-    # write a fake MRC file using mrcfile
+    """An example of how you might test your plugin."""
+
+    # write some fake data using your supported file format
     my_test_file = str(tmp_path / "myfile.mrc")
     original_data = np.random.rand(20, 20).astype(np.float32)
-    mrcfile.new(my_test_file, original_data)
+    mrcfile.write(my_test_file, original_data)
 
     # try to read it back in
     reader = napari_get_reader(my_test_file)

diff --git a/src/napari_mrcfile_reader/napari.yaml b/src/napari_mrcfile_reader/napari.yaml
@@ -0,0 +1,19 @@
+name: napari-mrcfile-reader
+display_name: napari-mrcfile-reader
+contributions:
+  commands:
+    - id: napari-mrcfile-reader.get_reader
+      python_name: napari_mrcfile_reader._reader:napari_get_reader
+      title: Open data with napari-mrcfile-reader
+  readers:
+    - command: napari-mrcfile-reader.get_reader
+      accepts_directories: false
+      filename_patterns: [
+        '*.mrc',
+        '*.mrcs',
+        '*.map',
+        '*.st',
+        '*.rec',
+        '*.preali',
+        '*.ali',
+      ]