Reenable and fix tests with Jupyter. (#535)

Author: tobiasraabe

.github/workflows/main.yml

@@ -50,7 +50,7 @@ jobs:
 
       - name: Run unit tests and doctests.
         shell: bash -l {0}
-        run: tox -e pytest -- -m "unit or (not integration and not end_to_end)" --cov=src --cov=tests --cov-report=xml -n auto
+        run: tox -e test -- -m "unit or (not integration and not end_to_end)" --cov=src --cov=tests --cov-report=xml -n auto
 
       - name: Upload unit test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v3
@@ -59,7 +59,7 @@ jobs:
 
       - name: Run integration tests.
         shell: bash -l {0}
-        run: tox -e pytest -- -m integration --cov=src --cov=tests --cov-report=xml -n auto
+        run: tox -e test -- -m integration --cov=src --cov=tests --cov-report=xml -n auto
 
       - name: Upload integration test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v3
@@ -68,7 +68,7 @@ jobs:
 
       - name: Run end-to-end tests.
         shell: bash -l {0}
-        run: tox -e pytest -- -m end_to_end --cov=src --cov=tests --cov-report=xml -n auto
+        run: tox -e test -- -m end_to_end --cov=src --cov=tests --cov-report=xml -n auto
 
       - name: Upload end_to_end test coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v3

docs/source/changes.md

@@ -21,6 +21,7 @@ releases are available on [PyPI](https://pypi.org/project/pytask) and
 - {pull}`524` improves some linting and formatting rules.
 - {pull}`525` enables pytask to work with remote files using universal_pathlib.
 - {pull}`528` improves the codecov setup and coverage.
+- {pull}`535` reenables and fixes tests with Jupyter.
 
 ## 0.4.4 - 2023-12-04
 
@@ -68,7 +69,7 @@ releases are available on [PyPI](https://pypi.org/project/pytask) and
 - {pull}`465` adds test to ensure internal tracebacks are removed by reports.
 - {pull}`466` implements hashing for files instead of modification timestamps.
 - {pull}`470` moves `.pytask.sqlite3` to `.pytask`.
-- {pull}`472` adds `is_product` to {meth}`PNode.load`.
+- {pull}`472` adds `is_product` to {meth}`~pytask.PNode.load`.
 - {pull}`473` adds signatures to nodes which decouples an identifier from a name.
 - {pull}`477` updates the PyPI action.
 - {pull}`478` replaces black with ruff-format.
@@ -94,9 +95,9 @@ releases are available on [PyPI](https://pypi.org/project/pytask) and
   is not present.
 - {pull}`387` replaces pony with sqlalchemy.
 - {pull}`391` removes `@pytask.mark.parametrize`.
-- {pull}`394` allows to add products with {obj}`typing.Annotation` and
+- {pull}`394` allows to add products with {obj}`typing.Annotated` and
   {obj}`~pytask.Product`.
-- {pull}`395` refactors all occurrences of pybaum to {mod}`_pytask.tree_util`.
+- {pull}`395` refactors all occurrences of pybaum to `_pytask.tree_util`.
 - {pull}`396` replaces pybaum with optree and adds paths to the name of
   {class}`pytask.PythonNode`'s allowing for better hashing.
 - {pull}`397` adds support for {class}`typing.NamedTuple` and attrs classes in
@@ -123,7 +124,7 @@ releases are available on [PyPI](https://pypi.org/project/pytask) and
 - {pull}`421` removes the deprecation warning when `produces` is used as an magic
   function keyword to define products.
 - {pull}`423` adds a notebook to explain the functional interface.
-- {pull}`424` fixes problems with {func}`~_pytask.path.import_path`.
+- {pull}`424` fixes problems with `~_pytask.path.import_path`.
 - {pull}`426` publishes the {mod}`pytask.tree_util` module.
 - {pull}`427` fixes type annotations for {attr}`pytask.PTask.depends_on` and
   {attr}`pytask.PTask.produces`.

docs/source/conf.py

@@ -41,6 +41,7 @@
     "IPython.sphinxext.ipython_console_highlighting",
     "IPython.sphinxext.ipython_directive",
     "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
     "sphinx.ext.extlinks",
     "sphinx.ext.intersphinx",
     "sphinx.ext.linkcode",

docs/source/reference_guides/api.md

@@ -285,10 +285,11 @@ To mark any callable as a task use
 .. autofunction:: pytask.task
 ```
 
-Task are currently represented by the following class:
+Task are currently represented by the following classes:
 
 ```{eval-rst}
 .. autoclass:: pytask.Task
+.. autoclass:: pytask.TaskWithoutPath
 ```
 
 Currently, there are no different types of tasks since changing the `.function`
@@ -369,12 +370,8 @@ resolution and execution.
 ## Tree utilities
 
 ```{eval-rst}
-.. autofunction:: pytask.tree_util.PyTree
-.. autofunction:: pytask.tree_util.tree_flatten_with_path
-.. autofunction:: pytask.tree_util.tree_leaves
-.. autofunction:: pytask.tree_util.tree_map
-.. autofunction:: pytask.tree_util.tree_map_with_path
-.. autofunction:: pytask.tree_util.tree_structure
+.. automodule:: pytask.tree_util
+    :members:
 ```
 
 ## Typing

environment.yml

@@ -28,7 +28,7 @@ dependencies:
   - ipywidgets
   - jupyterlab
   - matplotlib
-  - nbval
+  - nbmake
   - pre-commit
   - pygraphviz
   - pytest

pyproject.toml

@@ -1,13 +1,9 @@
 [build-system]
 build-backend = "setuptools.build_meta"
-requires = [
-  "setuptools>=45",
-  "setuptools_scm[toml]>=6",
-  "wheel",
-]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 
 [tool.setuptools_scm]
-write_to = "src/_pytask/_version.py"
+version_file = "src/_pytask/_version.py"
 
 [project]
 name = "pytask"
@@ -72,6 +68,7 @@ docs = [
 ]
 test = [
   "deepdiff",
+  "nbmake",
   "pexpect",
   "pytest",
   "pytest-cov",
@@ -149,15 +146,13 @@ ignore = [
 convention = "numpy"
 
 [tool.pytest.ini_options]
-addopts = ["--doctest-modules"]
-testpaths = ["src", "tests"]
+testpaths = ["tests"]
 markers = [
     "wip: Tests that are work-in-progress.",
     "unit: Flag for unit tests which target mainly a single function.",
     "integration: Flag for integration tests which may comprise of multiple unit tests.",
     "end_to_end: Flag for tests that cover the whole program.",
 ]
-norecursedirs = [".idea", ".tox"]
 filterwarnings = [
     "ignore:'@pytask.mark.*. is deprecated:FutureWarning",
     "ignore:The --rsyncdir command line argument:DeprecationWarning",

src/_pytask/console.py

@@ -222,7 +222,7 @@ def get_file(  # noqa: PLR0911
             return get_file(function.__wrapped__)
     source_file = inspect.getsourcefile(function)
     if source_file:  # pragma: no cover
-        if "<stdin>" in source_file:
+        if "<stdin>" in source_file or "ipykernel" in source_file:
             return None
         if "<string>" in source_file:
             try:

src/_pytask/node_protocols.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-from abc import abstractmethod
 from typing import Any
 from typing import Callable
 from typing import Protocol
@@ -27,7 +26,6 @@ class PNode(Protocol):
     def signature(self) -> str:
         """Return the signature of the node."""
 
-    @abstractmethod
     def state(self) -> str | None:
         """Return the state of the node.
 
@@ -80,7 +78,6 @@ class PTask(Protocol):
     def signature(self) -> str:
         """Return the signature of the node."""
 
-    @abstractmethod
     def state(self) -> str | None:
         """Return the state of the node.
 

tests/test_jupyter/test_functional_interface.ipynb

@@ -64,7 +64,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

tests/test_jupyter/test_functional_interface_w_relative_path.ipynb

@@ -64,7 +64,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

tox.ini

@@ -1,14 +1,22 @@
 [tox]
-envlist = pytest
+requires = tox>=4
+envlist = docs, test
 
 [testenv]
 passenv = CI
-usedevelop = true
+package = wheel
 
-[testenv:pytest]
+[testenv:test]
 extras = all, test
 deps =
     pygraphviz;platform_system != "Windows"
 
 commands =
-    pytest {posargs}
+    pytest --nbmake {posargs}
+
+
+[testenv:docs]
+extras = docs, test
+commands =
+    - sphinx-build -n -T -b html -d {envtmpdir}/doctrees docs/source docs/build/html
+    - sphinx-build -n -T -b doctest -d {envtmpdir}/doctrees docs/source docs/build/html