Seperated nox sessions for templates and tests and, new testing infra…

… for generated project

.github/workflows/test_on_push.yml

@@ -1,4 +1,4 @@
-name: Test template generation
+name: Test template and generated project
 
 on:
   workflow_dispatch:
@@ -7,7 +7,6 @@ on:
     branches:
     - main
 
-
 jobs:
   style:
     runs-on: ubuntu-latest
@@ -32,7 +31,7 @@ jobs:
         os: [ubuntu-latest, macos-13, macos-14, windows-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     name:
-      Template Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
+      Template Generation/Project Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
     steps:
       - name: Checkout pybamm-cookiecutter
         uses: actions/checkout@v4
@@ -51,9 +50,13 @@ jobs:
       - name: Install nox
         run: uv pip install nox[uv]
 
-      - name: Test Template Generation
+      - name: Test template generation
+        run: |
+          nox -s template-tests
+
+      - name: Test project units
         run: |
-          nox -s test-generation
+          nox -s project-tests
 
       - name: Run coverage tests
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
@@ -87,3 +90,36 @@ jobs:
 
       - name: Check if the documentation can be built
         run: python -m nox -s docs
+
+  generated_project_tests:
+      needs: [style, template_test]
+      runs-on: ${{ matrix.os }}
+      strategy:
+        fail-fast: false
+        matrix:
+          os: [ubuntu-latest, macos-13, macos-14, windows-latest]
+          python-version: ["3.9", "3.10", "3.11", "3.12"]
+      name:
+        Generated Project Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
+      steps:
+        - name: Checkout pybamm-cookiecutter
+          uses: actions/checkout@v4
+
+        - name: Set up Python ${{ matrix.python-version }}
+          id: setup-python
+          uses: actions/setup-python@v5
+          with:
+            python-version: ${{ matrix.python-version }}
+
+        - name: Install cookiecutter and pipx
+          run: python -m pip install cookiecutter pipx
+
+        - name: Generate a project using cookiecutter
+          run: |
+            cookiecutter . --no-input
+
+        - name: Install nox and test generated project
+          working-directory: ./pybamm_example_project
+          run: |
+            pipx install nox
+            pipx run nox -s generated-project-tests

cookiecutter.json

@@ -1,5 +1,5 @@
 {
-    "project_name": "pybamm-example-project",
+    "project_name": "pybamm_example_project",
     "platform": [
         "github",
         "gitlab"
@@ -20,6 +20,7 @@
     "mypy": false,
     "__year": "{% now 'utc', '%Y' %}",
     "__project_slug": "{{ cookiecutter.project_name | lower | replace('-', '_') | replace('.', '_') }}",
+    "_copy_without_render": ["*.yml"],
     "__type": "{{ 'pure' }}",
     "__answers": "",
     "__ci": "{{ cookiecutter.platform }}",
@@ -31,7 +32,7 @@
             "gitlab": "GitLab"
         },
         "org": "The name of your organisation (or username, if you are not part of an organisation)",
-        "url": "The URL to your repository",
+     "url": "The URL to your repository",
         "full_name": "Your name",
         "email": "Your email",
         "project_short_description": "A short description of your project",

noxfile.py

@@ -36,12 +36,19 @@ def build_docs(session: nox.Session) -> None:
                 "build/html/",
             )
 
-@nox.session(name="test-generation")
+@nox.session(name="template-tests")
 def run_template_generation(session):
     """Run the tests for testing template generation"""
     session.install("setuptools", silent=False)
     session.install("-e", ".[dev]", silent=False)
-    session.run("pytest", "tests")
+    session.run("pytest", "tests/template_tests")
+
+@nox.session(name="project-tests")
+def run_project_tests(session):
+    """Run the tests for testing template generation"""
+    session.install("setuptools", silent=False)
+    session.install("-e", ".[dev]", silent=False)
+    session.run("pytest", "tests/project_tests")
 
 @nox.session(name="coverage")
 def run_coverage(session):

tests/test_project_generation.py → tests/template_tests/test_project_generation.py

@@ -12,7 +12,7 @@ def test_bake_project(cookies: Cookies):
     result = cookies.bake()
     assert result.exit_code == 0, f"Exited with code {result.exit_code}, expected 0"
     assert result.exception is None, result.exception
-    assert result.project_path.name == "pybamm-example-project"
+    assert result.project_path.name == "pybamm_example_project"
     assert result.project_path.is_dir(), f"Project directory {result.project_path} not found"
 
 

{{cookiecutter.project_name}}/.github/workflows/test_on_push.yml

@@ -0,0 +1,92 @@
+name: Project Tests
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+    - main
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Check style
+        run: |
+          python -m pip install pre-commit
+          pre-commit run -a
+
+  test_project:
+    needs: style
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-14, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    name:
+      Template Generation/Project Tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
+    steps:
+      - name: Checkout pybamm-cookiecutter
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up uv
+        uses: yezz123/setup-uv@v4
+        with:
+          uv-venv: ".venv"
+
+      - name: Install nox
+        run: uv pip install nox[uv]
+
+      - name: Test project units
+        run: |
+          nox -s generated-project-tests
+
+      - name: Test user tests
+        run: |
+          nox -s user-tests
+
+      - name: Run coverage tests
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        run: python -m nox -s coverage
+
+      - name: Upload coverage report
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: codecov/codecov-action@v4.5.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  run_doctests:
+    needs: style
+    runs-on: ubuntu-latest
+    name: Doctests (ubuntu-latest / Python 3.12)
+
+    steps:
+      - name: Check out pybamm-cookiecutter repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+          cache: 'pip'
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Check if the documentation can be built
+        run: python -m nox -s docs

{{cookiecutter.project_name}}/noxfile.py

@@ -1,20 +1,67 @@
 import nox
+from pathlib import Path
+import os
 
 # Options to modify nox behaviour
+nox.options.default_venv_backend = "uv|virtualenv"
 nox.options.reuse_existing_virtualenvs = True
 
+VENV_DIR = Path("./venv").resolve()
+
 @nox.session(name="docs")
-def build_docs(session):
+def build_docs(session: nox.Session) -> None:
     """Build the documentation and load it in a browser tab, rebuilding on changes."""
-    envbindir = session.bin
     session.install("-e", ".[docs]")
     with session.chdir("docs/"):
-        session.run(
-            "sphinx-autobuild",
-            "-j",
-            "auto",
-            "--open-browser",
-            "-qT",
-            ".",
-            f"{envbindir}/../tmp/html",
-        )
+        # For local development
+        if session.interactive:
+            session.run(
+                "sphinx-autobuild",
+                "-j",
+                "auto",
+                "--open-browser",
+                "-qT",
+                ".",
+                "build/html/",
+            )
+        # For CI testing if documentation builds
+        else:
+            session.run(
+                "sphinx-build",
+                "-b",
+                "html",
+                "-W",
+                "--keep-going",
+                ".",
+                "build/html/",
+            )
+
+@nox.session(name="generated-project-tests")
+def run_generated_project_tests(session):
+    """Run the tests for testing units inside generated project"""
+    session.install("setuptools", silent=False)
+    session.install("-e", ".[dev]", silent=False)
+    session.run("pytest", "tests/generated_project_tests")
+
+@nox.session(name="user-tests")
+def run_user_tests(session):
+    """Run the tests for testing user written tests"""
+    session.install("setuptools", silent=False)
+    session.install("-e", ".[dev]", silent=False)
+    session.run("pytest", "tests/user_tests")
+
+@nox.session(name="coverage")
+def run_coverage(session):
+    """Run the coverage tests and generate an XML report."""
+    session.install("setuptools", silent=False)
+    session.install("coverage", silent=False)
+    session.install("-e", ".[all,dev,jax]", silent=False)
+    session.run("pytest", "--cov=src/pybamm_cookiecutter", "--cov-report=xml", "tests/")
+
+@nox.session(name="dev")
+def set_dev(session):
+    """Install pybamm-cookiecutter in editable mode"""
+    session.install("virtualenv")
+    session.run("virtualenv", os.fsdecode(VENV_DIR), silent=True)
+    python = os.fsdecode(VENV_DIR.joinpath("bin/python"))
+    session.run(python, "-m", "pip", "install", "-e", ".[dev]")

{{cookiecutter.project_name}}/pyproject.toml

@@ -47,15 +47,14 @@ classifiers = [
 {%- if cookiecutter.backend == "hatch" %}
 dynamic = ["version"]
 {%- endif %}
-dependencies = ["pybamm", "cookiecutter"]
+dependencies = ["pybamm",]
 
 [project.optional-dependencies]
 dev = [
   "pytest >=6",
   "pytest-cov >=3",
   "nox[uv]",
   "pre-commit",
-  "pytest-cookies",
 ]
 docs = [
   "sphinx",

{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/__init__.py

@@ -13,18 +13,12 @@
 {# keep this line here for newline #}
 {%- if cookiecutter.mypy %}
 __all__: list[str] = [
-    "__version__",
-    "pybamm",
-    "parameter_sets",
-    "Model",
-    "models",
-]
 {%- else %}
 __all__ = [
+{%- endif %}
     "__version__",
     "pybamm",
     "parameter_sets",
     "Model",
     "models",
 ]
-{%- endif %}

{{cookiecutter.project_name}}/tests/generated_project_tests/test_entry_points.py

@@ -0,0 +1,43 @@
+import pytest
+import {{ cookiecutter.project_name }}
+import importlib.util
+import sys
+from pathlib import Path
+
+def test_parameter_sets_entry_points():
+    """Test if the parameter_sets via entry points are loaded correctly."""
+
+    entry_points = list({{ cookiecutter.project_name }}.parameter_sets)
+    parameter_sets = Path("src/{{ cookiecutter.project_name }}/parameters/input/").glob("*.py")
+    # Making a list of parameter sets in the parameters/input directory
+    parameter_sets = [x.stem for x in parameter_sets]
+
+    assert parameter_sets == entry_points, "Entry points missing either in pyproject.toml or in the input directory"
+
+def test_parameter_sets_entry_point_load():
+    """Testing if the values get loaded via parameter entry points and are equal when loaded through entry points"""
+    # Loading parameter_sets through entry points
+    parameters = {{ cookiecutter.project_name }}.parameter_sets['Chen2020']
+    # Loading parameter sets through the source file by dynamically loading Chen2020.py as a module
+    spec = importlib.util.spec_from_file_location("Chen2020mod", "src/{{ cookiecutter.project_name }}/parameters/input/Chen2020.py")
+    chen_module = importlib.util.module_from_spec(spec)
+    sys.modules["Chen2020mod"] = chen_module
+    spec.loader.exec_module(chen_module)
+    parameters_from_file = chen_module.get_parameter_values()
+    assert parameters.keys() == parameters_from_file.keys(), f"The keys in the module and local input file are not the same, expected {parameters.keys} got {parameters_from_file.keys()}"
+
+def test_model_entry_points():
+    """Test if the models via entry points are loaded correctly."""
+
+    entry_points = list({{ cookiecutter.project_name }}.models)
+    models = Path("src/{{ cookiecutter.project_name }}/models/input/").glob("*.py")
+    # Making a list Parameter sets in the parameters/input directory
+    models = [x.stem for x in models]
+
+    assert models == entry_points, "Entry points missing either in pyproject.toml or in the input directory"
+
+def test_model_entry_point_load():
+    """Testing if the model gets initialised and returned."""
+    # Loading parameter_sets through entry points
+    model_instance = {{ cookiecutter.project_name }}.Model("SPM")
+    assert model_instance is not None