🔀 Merge: Update package #20

- 🔧 Move to flit for PEP 621 packaging - 🔧 Add isort pre-commit hook - ⬆️ nbconvert-> nbclient, coverage v4 -> v5 - 📚 Use https for intersphinx URLs - 📚 DOCS: Update documentation packages - 🧪 TEST: Update codecov-action
chrisjsewell · Jan 17, 2022 · 997c04b · 997c04b
2 parents 40381be + 13815a2
commit 997c04b
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diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -26,7 +26,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8, 3.9]
 
     runs-on: ${{ matrix.os }}
 
@@ -47,10 +47,10 @@ jobs:
       run: coverage xml
 
     - name: Upload to Codecov
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7 && github.repository == 'chrisjsewell/pytest-notebook'
-      uses: codecov/codecov-action@v1
+      if: github.repository == 'chrisjsewell/pytest-notebook'
+      uses: codecov/codecov-action@v2
       with:
-        name: pytests-py3.7
+        name: pytests-notebook
         flags: pytests
         file: ./coverage.xml
         fail_ci_if_error: true
@@ -62,18 +62,18 @@ jobs:
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v2
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
-        with:
-          python-version: 3.7
-      - name: Build package
-        run: |
-          pip install wheel
-          python setup.py sdist bdist_wheel
-      - name: Publish
-        uses: pypa/gh-action-pypi-publish@v1.1.0
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_KEY }}
+    - name: Checkout source
+      uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: install flit
+      run: |
+        pip install flit~=3.4
+    - name: Build and publish
+      run: |
+        flit publish
+      env:
+        FLIT_USERNAME: __token__
+        FLIT_PASSWORD: ${{ secrets.PYPI_KEY }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,21 +3,26 @@
 
 repos:
 
-  - repo: git://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
     hooks:
     - id: check-json
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
   - repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 21.12b0
     hooks:
     - id: black
 
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.3
+    rev: 3.9.2
     hooks:
     - id: flake8
       additional_dependencies:
@@ -26,11 +31,6 @@ repos:
         - flake8_builtins
         - import-order
 
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.39"
-    hooks:
-    - id: check-manifest
-
   # - repo: local
   #   hooks:
 

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,7 +1,7 @@
 version: 2
 
 python:
-  version: 3.7
+  version: "3.8"
   install:
     - method: pip
       path: .

diff --git a/LICENSE b/LICENSE
@@ -1,5 +1,5 @@
 
-Copyright (c) 2019, Chris Sewell
+Copyright (c) 2022, Chris Sewell
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -63,6 +63,7 @@ To install the development version:
 ```shell
 >> git clone https://github.com/chrisjsewell/pytest-notebook .
 >> cd pytest-notebook
+>> pip install --upgrade pip
 >> pip install -e .
 >> # pip install -e .[code_style,testing,docs] # install extras for more features
 ```

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -38,12 +38,12 @@
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3.6", None),
-    "_pytest": ("http://doc.pytest.org/en/latest/", None),
+    "_pytest": ("https://doc.pytest.org/en/latest/", None),
     # "PIL": ("http://pillow.readthedocs.org/en/latest/", None),
-    "nbconvert": ("http://nbconvert.readthedocs.io/en/latest/", None),
-    "nbformat": ("http://nbformat.readthedocs.io/en/latest/", None),
-    "attr": ("http://www.attrs.org/en/stable/", None),
-    "coverage": ("https://coverage.readthedocs.io/en/v4.5.x/", None),
+    "nbclient": ("https://nbclient.readthedocs.io/en/latest/", None),
+    "nbformat": ("https://nbformat.readthedocs.io/en/latest/", None),
+    "attr": ("https://www.attrs.org/en/stable/", None),
+    "coverage": ("https://coverage.readthedocs.io/en/6.2/", None),
 }
 
 intersphinx_aliases = {
@@ -68,6 +68,7 @@
 
 nitpick_ignore = [
     ("py:class", "NoneType"),
+    ("py:class", "Config"),
     ("py:class", "TextIO"),
     ("py:class", "attr.ib"),
     ("py:class", "attr.s"),
@@ -77,84 +78,28 @@
     ("py:class", "_pytest.nodes.Item"),
 ]
 
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-# default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-# add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-# add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-# show_authors = False
-
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
 
-# A list of ignored prefixes for module index sorting.
-# modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built documents.
-# keep_warnings = False
-
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
 
 # -- Options for HTML output ----------------------------------------------
 
 html_theme = "sphinx_book_theme"
+html_theme_options = {
+    "repository_url": "https://github.com/chrisjsewell/pytest-notebook",
+    "repository_branch": "master",
+    "path_to_docs": "docs/source",
+    "use_edit_page_button": True,
+    "use_issues_button": True,
+    "use_repository_button": True,
+}
 jupyter_execute_notebooks = "cache"
 execution_show_tb = "READTHEDOCS" in os.environ
 execution_timeout = 60  # Note: 30 was timing out on RTD
-myst_admonition_enable = True
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = "pytest-notebookdoc"
-
-
-# -- Options for other outputs ---------------------------------------
-
-latex_documents = [
-    (
-        master_doc,
-        "pytest-notebook.tex",
-        "pytest-notebook Documentation",
-        "Chris Sewell",
-        "manual",
-    )
-]
-# latex_logo = None
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    # 'papersize': 'letterpaper',
-    # The font size ('10pt', '11pt' or '12pt').
-    # 'pointsize': '10pt',
-    # Additional stuff for the LaTeX preamble.
-    # 'preamble': '',
-    # Latex figure (float) alignment
-    # 'figure_align': 'htbp',
-}
-
-man_pages = [
-    (master_doc, "pytest-notebook", u"pytest-notebook Documentation", [author], 1)
-]
-
-texinfo_documents = [
-    (
-        master_doc,
-        "pytest-notebook",
-        u"pytest-notebook Documentation",
-        author,
-        "pytest-notebook",
-        "A pytest plugin for testing Jupyter Notebooks.",
-        "Miscellaneous",
-    )
-]
+myst_enable_extensions = ["colon_fence"]
 
 # -- Sphinx setup for other outputs ---------------------------------------
 

diff --git a/docs/source/user_guide/tutorial_coverage.md b/docs/source/user_guide/tutorial_coverage.md
@@ -21,29 +21,34 @@ This notebook was rendered with [myst-nb](https://myst-nb.readthedocs.io): {nb-d
 
 +++
 
-The core component of the notebook execution API is the {py:class}`~pytest_notebook.execution.ExecuteCoveragePreprocessor` class,
-which is a subclass of {py:class}`nbconvert.preprocessors.ExecutePreprocessor`,
+The core component of the notebook execution API is the {py:class}`~pytest_notebook.execution.CoverageNotebookClient` class,
+which is a subclass of {py:class}`nbclient.client.NotebookClient`,
 that can additionally create code [coverage](https://coverage.readthedocs.io) analytics.
 
 This class is called by {py:func}`~pytest_notebook.execution.execute_notebook`,
 which returns an {py:class}`~pytest_notebook.execution.ExecuteResult` object.
 
 ```{code-cell} ipython3
-import yaml
 from pytest_notebook.execution import execute_notebook
 from pytest_notebook.notebook import create_notebook, create_cell, dump_notebook
 ```
 
 ```{code-cell} ipython3
-notebook = create_notebook()
-notebook.cells = [
-    create_cell("""
+notebook = create_notebook(
+    metadata={
+        "kernelspec": {
+            "name": "python3",
+            "display_name": "Python 3",
+        }
+    },
+    cells=[
+        create_cell("""
 from pytest_notebook import __version__
 from pytest_notebook.notebook import create_notebook
 print(__version__)
 """
-    )
-]
+    )]
+)
 ```
 
 ```{code-cell} ipython3
@@ -56,15 +61,17 @@ result.coverage_data()
 ```
 
 ```{code-cell} ipython3
-print(yaml.dump(result.coverage_dict))
+:tags: [hide-output]
+
+result.coverage_dict
 ```
 
 The coverage can be limited to particular files or modules, by setting `cov_source`.
 
 ```{code-cell} ipython3
 result = execute_notebook(
     notebook, with_coverage=True, cov_source=['pytest_notebook.notebook'])
-print(yaml.dump(result.coverage_dict))
+result.coverage_dict
 ```
 
 ## Integration with pytest-cov
@@ -87,7 +94,7 @@ and merge the data back into the main {py:class}`~coverage.Coverage` object.
 %%pytest --disable-warnings --color=yes --cov=pytest_notebook --nb-coverage --log-cli-level=info
 
 import logging
-import importlib_resources
+from importlib import resources as importlib_resources
 from pytest_notebook import example_nbs
 
 def test_notebook(nb_regression):

diff --git a/docs/source/user_guide/tutorial_intro.md b/docs/source/user_guide/tutorial_intro.md
@@ -25,10 +25,10 @@ This notebook was rendered with [myst-nb](https://myst-nb.readthedocs.io): {nb-d
 
 The principal component of `pytest-notebook` is the
 {py:class}`~pytest_notebook.nb_regression.NBRegressionFixture` class,
-which is an [attrs](http://www.attrs.org) class, whose parameters can be instatiated or set via attibutes.
+which is an [attrs](http://www.attrs.org) class, whose parameters can be instantiated or set via attributes.
 
 ```{code-cell} ipython3
-import importlib_resources
+from importlib import resources as importlib_resources
 from pytest_notebook import example_nbs
 from pytest_notebook.nb_regression import NBRegressionFixture
 ```