Merge pull request #75 from ArcanaFramework/docs-formats

Added api references for all formats to docs

Author: tclose

.github/workflows/ci-cd.yml

@@ -23,6 +23,8 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+    env:
+      PIP_BREAK_SYSTEM_PACKAGES: 1
     steps:
     - name: Checkout
       uses: actions/checkout@v2
@@ -39,13 +41,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Update build tools
-      run: python3 -m pip install --break-system-packages --upgrade pip
+      run: python3 -m pip install --upgrade pip
     - name: Install Package
-      run: python3 -m pip install --break-system-packages -e .[test]
+      run: python3 -m pip install -e .[test]
     - name: Install Extras Package
-      run: python3 -m pip install --break-system-packages -e ./extras[test]
-    - name: Change out of root directory
-      run: cd docs
+      run: python3 -m pip install -e ./extras[test]
+    - name: MyPy
+      run: mypy --install-types --non-interactive .
     - name: Pytest
       run: pytest -vvs --cov fileformats --cov-config .coveragerc --cov-report xml .
     - name: Upload coverage to Codecov

.pre-commit-config.yaml

@@ -1,28 +1,39 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
--   repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-    -   id: black
-        exclude: ^(fileformats/core/_version\.py)$
-        args:
-          - -l 88
--   repo: https://github.com/codespell-project/codespell
-    rev: v2.1.0
-    hooks:
-    -   id: codespell
-        exclude: ^(fileformats/core/_version\.py)$
-        args:
-        -   --ignore-words=.codespell-ignorewords
--   repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
-    hooks:
-    -   id: flake8
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.3.0
+      hooks:
+          - id: trailing-whitespace
+          - id: end-of-file-fixer
+          - id: check-yaml
+          - id: check-added-large-files
+    - repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+          - id: black
+            exclude: ^(fileformats/core/_version\.py)$
+            args:
+                - -l 88
+    - repo: https://github.com/codespell-project/codespell
+      rev: v2.1.0
+      hooks:
+          - id: codespell
+            exclude: ^(fileformats/core/_version\.py)$
+            args:
+                - --ignore-words=.codespell-ignorewords
+    - repo: https://github.com/PyCQA/flake8
+      rev: 4.0.1
+      hooks:
+          - id: flake8
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.11.2
+      hooks:
+          - id: mypy
+            args:
+                [
+                    --strict,
+                    --install-types,
+                    --non-interactive,
+                    --no-warn-unused-ignores,
+                ]

conftest.py

@@ -33,11 +33,11 @@
 # break at it
 if os.getenv("_PYTEST_RAISE", "0") != "0":
 
-    @pytest.hookimpl(tryfirst=True)  # type: ignore
+    @pytest.hookimpl(tryfirst=True)
     def pytest_exception_interact(call: ty.Any) -> None:
         raise call.excinfo.value
 
-    @pytest.hookimpl(tryfirst=True)  # type: ignore
+    @pytest.hookimpl(tryfirst=True)
     def pytest_internalerror(excinfo: ty.Any) -> None:
         raise excinfo.value
 

docs/source/developer.rst

@@ -272,6 +272,7 @@ when a hooked method is accessed.
  Use the `@extra` decorator on a method in the to define an extras method,
 
  .. code-block:: python
+
     from typing import Self
 
     class MyFormat(File):

docs/source/index.rst

@@ -114,7 +114,17 @@ This work is licensed under a
    :caption: Reference
    :hidden:
 
-   api.rst
+   reference/core.rst
+   reference/generic.rst
+   reference/field.rst
+   reference/application.rst
+   reference/audio.rst
+   reference/image.rst
+   reference/model.rst
+   reference/text.rst
+   reference/video.rst
+   reference/datascience.rst
+   reference/medimage.rst
 
 
 .. _Pydra: https://pydra.readthedocs.io