Reorganize the tests into unit/functional/integration/external

.ci/environment-ci.yml

@@ -1,3 +1,4 @@
+
 # This environment is smaller than the dev environment.
 #
 # Until conda supports creating env from pyproject.toml
@@ -10,23 +11,6 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - ipykernel
-  - nbconvert
+  - jupyterlab
   - nbformat>=5.1.2
-  - pyyaml
-  - toml
-  - markdown-it-py
-  - mdit-py-plugins
-  - pip
-  - pytest
-  - pytest-randomly
-  - pytest-cov
-  - coverage
-  - flake8
-  - autopep8
-  - black
-  - isort
   - pandoc==2.16.2
-  - sphinx-gallery<0.8
-  - pre-commit
-  - gitpython

codecov.yml → .github/codecov.yml

@@ -1,21 +1,20 @@
 codecov:
-    notify:
-        after_n_builds: 11
+  notify:
+    after_n_builds: 11
 
 comment:
   after_n_builds: 11
 
 coverage:
   status:
     project:
-      default: false  # disable the default status that measures entire project
       tests:
         paths:
           - "tests/"
         target: 100%
       source:
         paths:
-          - "jupytext/"
+          - "src/jupytext/"
         target: 97%
         threshold: 0.002
     patch:

.github/workflows/step_build.yml

@@ -29,7 +29,7 @@ jobs:
           python -m pip install build wheel
 
           # NOTE: These builds and verifications of the builds can be done more
-          # robustily with jupyter-releaser.
+          # robustly with jupyter-releaser.
           #
           # Removed the check on size of package as we are distributing tests/ with
           # sdist now and they are around 8MB. Seems like original check was to make

.github/workflows/step_tests-conda.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest', 'macos-latest', 'windows-latest' ]
-        python-version: [ 3.9 ]
+        python-version: [ 3.11 ]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -38,9 +38,8 @@ jobs:
           use-only-tar-bz2: true
 
       - name: Install from source
-        # This is required for the pre-commit tests
         shell: pwsh
-        run: python -m pip install -e '.[test-cov]'
+        run: python -m pip install -e '.[test-external,test-cov]'
 
       - name: Create kernel
         shell: pwsh

.github/workflows/step_tests-pip.yml

@@ -18,7 +18,6 @@ jobs:
       matrix:
         python-version: [ "3.8", "3.9", "3.10", "3.11" ]
         markdown-it-py-version: ["~=2.0"]
-        kernel: [true]
         include:
           - python-version: "3.12-dev"
             experimental: true
@@ -28,14 +27,13 @@ jobs:
             markdown-it-py-version: ""
           - python-version: "3.x"
             markdown-it-py-version: "~=3.0"
-          - python-version: "3.11"
+          - python-version: "3.x"
             markdown-it-py-version: "~=4.0"
             experimental: true
           - python-version: "3.x"
-            kernel: false
+            no_kernel: true
           - python-version: "3.x"
             quarto: true
-            kernel: true
 
     steps:
       - name: Checkout
@@ -46,11 +44,11 @@ jobs:
         with:
           python_version: ${{ matrix.python-version }}
 
-      - name: Install from source (required for the pre-commit tests)
-        run: python -m pip install -e '.[test-cov]' ${{ matrix.markdown-it-py-version && format('markdown-it-py{0}', matrix.markdown-it-py-version) }}
+      - name: Install from source
+        run: python -m pip install -e '.[test-cov,test-external]' ${{ matrix.markdown-it-py-version && format('markdown-it-py{0}', matrix.markdown-it-py-version) }}
 
       - name: Install a Jupyter Kernel
-        if: ${{ matrix.kernel }}
+        if: ${{ !matrix.no_kernel }}
         run: python -m ipykernel install --name python_kernel --user
 
       - name: Install Quarto
@@ -66,6 +64,7 @@ jobs:
       - name: Test lab extension
         run: |
           # Check extension
+          pip install jupyterlab
           jupyter labextension list
           jupyter labextension list 2>&1 | grep -ie "jupyterlab-jupytext.*OK"
           python -m jupyterlab.browser_check

.github/workflows/step_tests-ui.yml

@@ -20,14 +20,16 @@ jobs:
       - name: Base Setup
         uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
 
-      - name: Install from source (required for the pre-commit tests)
-        run: python -m pip install -e '.[test-cov]'
+      - name: Install from source
+        run: python -m pip install -e .
 
       - name: Install galata
         working-directory: jupyterlab/packages/jupyterlab-jupytext-extension/ui-tests
         env:
           PLAYWRIGHT_SKIP_BROWSER_DOWNLOAD: 1
-        run: jlpm install
+        run: |
+          pip install jupyterlab
+          jlpm install
 
       - name: Install browser
         working-directory: jupyterlab/packages/jupyterlab-jupytext-extension/ui-tests

.github/workflows/step_tests_categories-pip.yml

@@ -0,0 +1,50 @@
+name: test-categories
+run-name: Run Unit/Functional/Integration and External tests using Pip
+
+on:
+  workflow_call:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}-pip-test
+  cancel-in-progress: true
+
+jobs:
+  test-pip:
+    continue-on-error: ${{ matrix.experimental || false }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Base Setup
+        uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
+        with:
+          python_version: ${{ matrix.python-version }}
+
+      - name: Install from source
+        run: python -m pip install -e '.[test-cov]' markdown-it-py~=3.0
+
+      - name: Unit tests
+        run: pytest tests/unit --cov=src/jupytext --cov-report=xml
+
+      - name: Functional tests
+        run: pytest tests/functional --cov=src/jupytext --cov-report=xml
+
+      - name: Install the integration test dependencies
+        run: python -m pip install -e '.[test-integration]'
+
+      - name: Install a Jupyter Kernel
+        run: python -m ipykernel install --name python_kernel --user
+
+      - name: Integration tests
+        run: pytest tests/integration --cov=src/jupytext --cov-report=xml
+
+      - name: Install the external test dependencies
+        run: python -m pip install -e '.[test-external]'
+
+      - name: External tests
+        run: pytest tests/external --cov=src/jupytext --cov-report=xml
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3

.pre-commit-config.yaml

@@ -13,7 +13,7 @@
 exclude: >
     (?x)^(
       demo/.*|
-      tests/notebooks/.*|
+      tests/data/notebooks/.*|
     )$
 repos:
 

docs/contributing.md

@@ -20,5 +20,5 @@ You want to submit an enhancement on Jupytext? Unless this is a small change, we
 A pull request for which you do not need to contact us in advance is the addition of a new language to Jupytext. In principle that should be easy - you would only have to:
 - document the language extension and comment by adding one line to `_SCRIPT_EXTENSIONS` in `jupytext/languages.py`.
 - add the language to `docs/languages.md`
-- contribute a sample notebook in `tests/notebooks/ipynb_[language]`.
-- run the tests suite (create a [development environment](developing.md), then execute `pytest` locally). The tests will generate various text representations corresponding to your notebook under  `tests/notebooks/mirror/`. Please verify that these files are valid scripts, and include them in your PR.
+- contribute a sample notebook in `tests/data/notebooks/inputs/ipynb_[language]`.
+- run the tests suite (create a [development environment](developing.md), then execute `pytest` locally). The tests will generate various text representations corresponding to your notebook under  `tests/data/notebooks/outputs/`. Please verify that these files are valid scripts, and include them in your PR.

docs/using-pre-commit.md

@@ -62,5 +62,5 @@ repos:
       language_version: python3
 ```
 
-Tested examples of how to use the pre-commit hook are available in our [tests](https://github.com/mwouts/jupytext/tree/main/tests) -
-see for instance [test_pre_commit_1_sync_with_config.py](https://github.com/mwouts/jupytext/blob/main/tests/test_pre_commit_1_sync_with_config.py).
+Tested examples of how to use the pre-commit hook are available in our [tests](https://github.com/mwouts/jupytext/tree/main/tests/functional/pre-commit) -
+see for instance [test_pre_commit_1_sync_with_config.py](https://github.com/mwouts/jupytext/blob/main/tests/functional/pre-commit/test_pre_commit_1_sync_with_config.py).

environment.yml

@@ -6,23 +6,6 @@ dependencies:
   - python>=3.8
   - jupyterlab>=4.0.0
   - nbformat>=5.1.2
-  - pyyaml
-  - toml
-  - markdown-it-py>=1.0.0,<3.0.0
-  - mdit-py-plugins
-  - nbconvert
-  - ipykernel
-  - pytest
-  - pytest-xdist
-  - pytest-randomly
-  - pytest-cov
   - pre-commit
-  - gitpython
-  - pylint
-  - flake8
-  - black==23.11.0
-  - isort==5.12.0
-  - autopep8
-  - sphinx-gallery<0.8
-  - pandoc==2.16.2
   - nodejs>=20
+  - pandoc==2.16.2

pyproject.toml

@@ -46,31 +46,44 @@ Documentation = "https://jupytext.readthedocs.io"
 
 [project.optional-dependencies]
 # Test related dependencies
-# TODO: Split them into unit, integration and functional tests groups
 test = [
-    "autopep8",
-    "black",
-    "isort",
-    "ruff",
-    "flake8",
-    "pytest",
-    "pytest-randomly",
-    "gitpython",
-    "jupyterlab",
-    "notebook",
-    "nbconvert",
-    # jupyter-fs==0.4.0 is async, which is not supported by Jupytext ATM
-    "jupyter-fs<0.4.0",
-    "ipykernel",
-    "pre-commit",
+  "pytest",
+  "pytest-randomly"
+]
+test-functional = [
+  "jupytext[test]",
+]
+test-integration = [
+  "jupytext[test-functional]",
+  "jupyter-server",
+  # jupytext --execute
+  "nbconvert",
+  "ipykernel",
+]
+test-external = [
+  "jupytext[test-integration]",
+  # jupytext --pipe and --check
+  "autopep8",
+  "black",
+  "isort",
+  "flake8",
+  # Sphinx gallery
+  "sphinx-gallery<0.8",
+  # Pre-commit tests
+  "gitpython",
+  "pre-commit",
+  # Interaction with other contents managers
+  # jupyter-fs==0.4.0 is async, which is not supported by Jupytext ATM
+  "jupyter-fs<0.4.0"
 ]
 # Coverage requirements
 test-cov = [
-    "jupytext[test]",
+    "jupytext[test-integration]",
     "pytest-cov>=2.6.1",
 ]
 dev = [
     "jupytext[test]",
+    "pre-commit"
 ]
 # Documentation dependencies
 docs = [
@@ -103,9 +116,7 @@ path = "src/jupytext/version.py"
 # Following config is related to JupyterLab extension
 [tool.hatch.build.targets.sdist]
 artifacts = ["jupyterlab/jupyterlab_jupytext/labextension"]
-# Exclude tests (contains Notebooks that have a total size of ~8MB) to reduce sdist
-# tarball. (See #1142)
-exclude = ["tests", "demo", "**/.yarn", "**/node_modules"]
+exclude = ["demo", "**/.yarn", "**/node_modules"]
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/jupytext", "src/jupytext_config", "jupyterlab/jupyterlab_jupytext"]
@@ -163,7 +174,7 @@ ignore = ["W002"]
 [tool.ruff]
 line-length = 127
 exclude = [
-    "tests/notebooks/*",
+    "tests/data/notebooks/*",
 ]
 # Seems like W503 is not implemented in ruff
 # ref: https://github.com/astral-sh/ruff/issues/4125
@@ -172,9 +183,41 @@ ignore = [
 ]
 
 [tool.pytest.ini_options]
+markers = [
+    "requires_jupytext",
+    "requires_black",
+    "requires_isort",
+    "requires_flake8",
+    "requires_autopep8",
+    "requires_nbconvert",
+    "requires_myst",
+    "requires_no_myst",
+    "requires_quarto",
+    "requires_pandoc",
+    "requires_no_pandoc",
+    "requires_sphinx_gallery",
+    "requires_user_kernel_python3",
+    "requires_ir_kernel",
+    "skip_on_windows",
+    "pre_commit",
+]
 filterwarnings = [
     # Uncomment this "error" to turn all unfiltered warnings into errors
     # "error",
+    # Our cwd_tmpdir fixture
+    "ignore:pathlib.Path.__enter__\\(\\) is deprecated and scheduled for removal in Python 3.13:DeprecationWarning",
+    # Pre-commit
+    "ignore:read_text is deprecated. Use files\\(\\) instead:DeprecationWarning",
+    "ignore:open_text is deprecated. Use files\\(\\) instead:DeprecationWarning",
+    # Jupyter
+    "ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning",
+    # Jupyter notebook
+    "ignore:Support for bleach <5 will be removed in a future version of nbconvert:DeprecationWarning",
+    # jupyterfs
+    "ignore:run_pre_save_hook is deprecated, use run_pre_save_hooks instead:DeprecationWarning",
+    "ignore:run_post_save_hook is deprecated, use run_post_save_hooks instead:DeprecationWarning",
+    "ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning",
+    "ignore:pkg_resources is deprecated as an API:DeprecationWarning",
     # use single quote to denote raw strings in toml
     # (10 warnings)
     'ignore:Passing unrecognized arguments to super\(KernelSpec\).__init__:DeprecationWarning',

src/jupytext/parse_version.py

@@ -1,11 +1,10 @@
 def parse_version(version, custom_error=ImportError):
     try:
-        from pkg_resources import parse_version as parse
+        from packaging.version import parse
     except ImportError:
         try:
-            from packaging.version import parse
+            from pkg_resources import parse_version as parse
         except ImportError:
-            raise custom_error("Please install either pkg_resources or packaging")
+            raise custom_error("Please install either packaging or pkg_resources")
 
-    print(version)
     return parse(version)