feat: Update jinja templates, add versions to cookiecutter.json as hi…

…dden variables
alexandrainst · Jul 16, 2024 · 3e671c6 · 3e671c6
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diff --git a/README.md b/README.md
@@ -1,4 +1,11 @@
-<a href="https://github.com/alexandrainst/{{ cookiecutter.project_name }}"><img src="https://github.com/alexandrainst/alexandra-ml-template/blob/main/%7B%7Bcookiecutter.project_name%7D%7D/gfx/alexandra_logo.png" width="239" height="175" align="right" /></a>
+<a href="https://github.com/alexandrainst/{{ cookiecutter.project_name }}">
+<img
+	src="https://github.com/alexandrainst/{{ cookiecutter.project_name }}/raw/main/gfx/alexandra_logo.png"
+	width="239"
+	height="175"
+	align="right"
+/>
+</a>
 # Alexandra Institute Machine Learning Repository Template
 
 This repository is a template for a Python-based data science project within the
@@ -56,64 +63,3 @@ browser.
 
 The cookiecutter allows the user to choose between `poetry` and `pip` for managing
 dependencies. In both cases, `pyproject.toml` will be used for all dependencies.
-
-
-## Tools used in this project
-* [Poetry](https://towardsdatascience.com/how-to-effortlessly-publish-your-python-package-to-pypi-using-poetry-44b305362f9f): Dependency management
-* [hydra](https://hydra.cc/): Manage configuration files
-* [pre-commit plugins](https://pre-commit.com/): Automate code reviewing formatting
-* [pdoc](https://github.com/pdoc3/pdoc): Automatically create an API documentation for your project
-
-
-## Project Structure
-```
-.
-├── .devcontainer
-│   └── devcontainer.json
-├── .github
-│   └── workflows
-│       ├── ci.yaml
-│       └── docs.yaml
-├── .gitignore
-├── .pre-commit-config.yaml
-├── CODE_OF_CONDUCT.md
-├── CONTRIBUTING.md
-├── Dockerfile
-├── LICENSE
-├── README.md
-├── config
-│   ├── __init__.py
-│   ├── config.yaml
-│   └── hydra
-│       └── job_logging
-│           └── custom.yaml
-├── data
-│   ├── final
-│   │   └── .gitkeep
-│   ├── processed
-│   │   └── .gitkeep
-│   └── raw
-│       └── .gitkeep
-├── docs
-│   └── .gitkeep
-├── gfx
-│   ├── .gitkeep
-│   └── alexandra_logo.png
-├── makefile
-├── models
-│   └── .gitkeep
-├── notebooks
-│   └── .gitkeep
-├── poetry.toml
-├── pyproject.toml
-├── src
-│   ├── scripts
-│   │   ├── fix_dot_env_file.py
-│   │   └── your_script.py
-│   └── {{cookiecutter.project_name}}
-│       ├── __init__.py
-│       └── your_module.py
-└── tests
-    ├── __init__.py
-    └── test_dummy.py
-```
diff --git a/cookiecutter.json b/cookiecutter.json
@@ -6,5 +6,27 @@
     "open_source": "Is this a public open source project? (y/n, default: n)",
     "python_version": "3.11",
     "dependency_manager": "Which dependency manager do you use? (pip/poetry, default: poetry)",
+    "pre_commit_hooks": "Do you want to use pre-commit hooks? (y/n, default: y)",
+    "_poetry_version": "1.8.2",
+    "_poetry_core_version": "1.0.0",
+    "_setuptools_version": "68.0.0",
+    "_hydra_version": "1.3.2",
+    "_pytest_version": "8.1.1",
+    "_pytest_cov_version": "4.1.0",
+    "_pre_commit_version": "3.6.2",
+    "_pdoc_version": "14.1.0",
+    "_readme_coverage_badger_version": "0.1.2",
+    "_click_version": "8.1.7",
+    "_ruff_version": "0.3.2",
+    "_mypy_version": "1.9.0",
+    "_nbstripout_version": "0.7.1",
+    "_coverage_version": "5.5",
+    "_toml_version": "0.10.2",
+    "_pygrep_hooks_version": "1.10.0",
+    "_pre_commit_hooks_version": "4.6.0",
+    "_checkout_action_version": "4",
+    "_setup_python_action_version": "5",
+    "_pre_commit_action_version": "3.0.1",
+    "_deploy_pages_action_version": "4",
     "_copy_without_render": []
 }
diff --git a/{{cookiecutter.project_name}}/.github/workflows/ci.yaml b/{{cookiecutter.project_name}}/.github/workflows/ci.yaml
@@ -13,32 +13,51 @@ on:
 jobs:
   code-check:
     if: github.event.pull_request.draft == false
-    runs-on: {{'ubuntu-latest' if cookiecutter.open_source == 'y' else '[self-hosted, self-hosted-ubuntu-latest]'}}
+    {% if cookiecutter.open_source == 'y' -%}
+    runs-on: ubuntu-latest
+    {% else -%}
+  runs-on: [self-hosted, self-hosted-ubuntu-latest]
+    {% endif -%}
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-      - uses: pre-commit/action@v3.0.1
+      - uses: actions/checkout@v{{ cookiecutter._checkout_action_version }}
+      - uses: actions/setup-python@v{{ cookiecutter._setup_python_action_version }}
+      - uses: pre-commit/action@v{{ cookiecutter._pre_commit_action_version }}
 
   pytest:
     if: github.event.pull_request.draft == false
     strategy:
         matrix:
-            os: [{{'windows-latest, macos-latest, ubuntu-latest' if cookiecutter.open_source == 'y' else 'self-hosted-ubuntu-latest'}}]
+            {% if cookiecutter.open_source == 'y' -%}
+            os: [windows-latest, macos-latest, ubuntu-latest]
+            {% else -%}
+            os: [self-hosted-ubuntu-latest]
+            {% endif -%}
             python-version: ["{{ cookiecutter.python_version }}"]
     runs-on: {% raw %}${{ matrix.os }}{% endraw %}
     steps:
-      - uses: actions/checkout@v4
-{{'\n      - name: Install Poetry\n        run: pipx install poetry==1.8.2\n\n' if cookiecutter.dependency_manager != 'pip'}}
+      - uses: actions/checkout@v{{ cookiecutter._checkout_action_version }}
+      {% if cookiecutter.dependency_manager != 'pip' -%}
+      - name: Install Poetry
+        run: pipx install poetry=={{ cookiecutter._poetry_version }}
+      {% endif -%}
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v{{ cookiecutter._setup_python_action_version }}
         with:
           python-version: {% raw %}${{ matrix.python-version }}{% endraw %}
-          cache: {{'"poetry"' if cookiecutter.dependency_manager != 'pip' else 'pip'}}
+          cache: {{'poetry' if cookiecutter.dependency_manager != 'pip' else 'pip'}}
 
       - name: Install Dependencies
         run: |
-          {{'poetry env use ' if cookiecutter.dependency_manager != 'pip' else 'python'}}{% raw %}"${{ matrix.python-version }}"{% endraw %}{{'' if cookiecutter.dependency_manager != 'pip' else ' -m venv .venv'}}
-          {{'poetry install' if cookiecutter.dependency_manager != 'pip' else '. .venv/bin/activate && pip install .[dev]'}}
-
+          {% if cookiecutter.dependency_manager != 'pip' -%}
+          poetry env use {% raw %}"${{ matrix.python-version }}"{% endraw %}
+          poetry install
+          {% else -%}
+          python3 -m venv .venv
+          . .venv/bin/activate && pip install .[dev]
+          {% endif %}
       - name: Test with pytest
-        run: {{'poetry run' if cookiecutter.dependency_manager != 'pip' else '. .venv/bin/activate && python -m'}} pytest
+        {% if cookiecutter.dependency_manager != 'pip' -%}
+        run: poetry run pytest
+        {% else -%}
+        run: . .venv/bin/activate && python -m pytest
+        {% endif -%}
diff --git a/...oject_name}}/.github/workflows/{{'docs.yaml' if cookiecutter.open_source == 'y' else ''}} b/...oject_name}}/.github/workflows/{{'docs.yaml' if cookiecutter.open_source == 'y' else ''}}
@@ -15,22 +15,32 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-{{'\n      - name: Install Poetry\n        run: pip3 install poetry==1.8.2\n' if cookiecutter.dependency_manager != 'pip' else ''}}
+      - uses: actions/checkout@v{{ cookiecutter._checkout_action_version }}
+      {% if cookiecutter.dependency_manager != 'pip' -%}
+      - name: Install Poetry
+        run: pip3 install poetry=={{ cookiecutter._poetry_version }}
+      {% endif -%}
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v{{ cookiecutter._setup_python_action_version }}
         with:
           python-version: "{{ cookiecutter.python_version }}"
           cache: {{'"poetry"' if cookiecutter.dependency_manager != 'pip' else 'pip'}}
 
       - name: Install Dependencies
         run: |
-          {{'poetry env use ' if cookiecutter.dependency_manager != 'pip' else 'python'}}"{{ cookiecutter.python_version }}"{{'' if cookiecutter.dependency_manager != 'pip' else ' -m venv .venv'}}
-          {{'poetry install --no-interaction --no-cache' if cookiecutter.dependency_manager != 'pip' else '. .venv/bin/activate && python -m pip install .[dev]'}}
-
+          {% if cookiecutter.dependency_manager != 'pip' -%}
+          poetry env use "{{ cookiecutter.python_version }}"
+          poetry install --no-interaction --no-cache
+          {% else -%}
+          python3 -m venv .venv
+          . .venv/bin/activate && python -m pip install .[dev]
+          {% endif -%}
       - name: Build documentation
-        run: {{'poetry run' if cookiecutter.dependency_manager != 'pip' else '. .venv/bin/activate && python -m'}} pdoc --docformat google src/{{ cookiecutter.project_name }} -o docs
-
+        {% if cookiecutter.dependency_manager != 'pip' -%}
+        run: poetry run pdoc --docformat google src/{{ cookiecutter.project_name }} -o docs
+        {% else -%}
+        run: . .venv/bin/activate && python -m pdoc --docformat google src/{{ cookiecutter.project_name }} -o docs
+        {% endif -%}
       - name: Compress documentation
         run: tar --directory docs/ -hcf artifact.tar .
 
@@ -53,4 +63,4 @@ jobs:
       url: {% raw %}${{ steps.deployment.outputs.page_url }}{% endraw %}
     steps:
       - id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v{{ cookiecutter._deploy_pages_action_version }}
diff --git a/{{cookiecutter.project_name}}/.pre-commit-config.yaml b/{{cookiecutter.project_name}}/.pre-commit-config.yaml
@@ -1,16 +1,16 @@
 repos:
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
+    rev: v{{ cookiecutter._pygrep_hooks_version }}
     hooks:
       - id: python-use-type-annotations
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v{{ cookiecutter._pre_commit_hooks_version }}
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: debug-statements
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.2
+    rev: v{{ cookiecutter._ruff_version }}
     hooks:
       - id: ruff
         args:
@@ -26,11 +26,11 @@ repos:
           - pyi
           - jupyter
 -   repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: {{ cookiecutter._nbstripout_version }}
     hooks:
     -   id: nbstripout
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v{{ cookiecutter._mypy_version }}
     hooks:
     -   id: mypy
         args:

diff --git a/{{cookiecutter.project_name}}/Dockerfile b/{{cookiecutter.project_name}}/Dockerfile
@@ -1,11 +1,27 @@
 FROM python:{{ cookiecutter.python_version }}-slim-bookworm
-{{'\n# Install poetry\nRUN pip install "poetry==1.8.2"\n' if cookiecutter.dependency_manager != 'pip'}}
+
+{%- if cookiecutter.dependency_manager != 'pip' %}
+
+# Install Poetry
+RUN pip install "poetry=={{ cookiecutter._poetry_version }}"
+{%- endif %}
+
 # Move the files into the container
 WORKDIR /project
 COPY . /project
 
 # Install dependencies
-{{'RUN poetry env use python' if cookiecutter.dependency_manager != 'pip'}}{{cookiecutter.python_version if cookiecutter.dependency_manager != 'pip'}}{{'\nRUN poetry install --no-interaction --no-cache --without dev' if cookiecutter.dependency_manager != 'pip' else 'RUN pip install .'}}
+{% if cookiecutter.dependency_manager != 'pip' -%}
+RUN poetry env use python {{ cookiecutter.python_version }}
+RUN poetry install --no-interaction --no-cache --without dev
+{%- else -%}
+RUN python3 -m venv .venv
+RUN . .venv/bin/activate && pip install .
+{%- endif %}
 
 # Run the script
-CMD {{'poetry run ' if cookiecutter.dependency_manager != 'pip'}}python src/scripts/your_script.py
+{% if cookiecutter.dependency_manager != 'pip' -%}
+CMD poetry run python src/scripts/main.py
+{%- else -%}
+CMD . .venv/bin/activate && python src/scripts/main.py
+{%- endif %}
diff --git a/{{cookiecutter.project_name}}/README.md b/{{cookiecutter.project_name}}/README.md
@@ -1,13 +1,24 @@
-<a href="https://github.com/alexandrainst/{{ cookiecutter.project_name }}"><img src="https://github.com/alexandrainst/{{ cookiecutter.project_name }}/raw/main/gfx/alexandra_logo.png" width="239" height="175" align="right" /></a>
+<a href="https://github.com/alexandrainst/{{ cookiecutter.project_name }}">
+<img
+	src="https://github.com/alexandrainst/{{ cookiecutter.project_name }}/raw/main/gfx/alexandra_logo.png"
+	width="239"
+	height="175"
+	align="right"
+/>
+</a>
 # {{cookiecutter.project_name}}
 
 {{cookiecutter.project_description}}
 
 ______________________________________________________________________
-[![Code Coverage](https://img.shields.io/badge/Coverage-0%25-red.svg)](https://github.com/alexandrainst/{{cookiecutter.project_name}}/tree/main/tests){{'\n[![Documentation](https://img.shields.io/badge/docs-passing-green)](https://alexandrainst.github.io/' if cookiecutter.open_source == 'y'}}{{cookiecutter.project_name if cookiecutter.open_source == 'y'}}{{'/' if cookiecutter.open_source == 'y'}}{{ cookiecutter.project_name if cookiecutter.open_source == 'y'}}{{'.html)\n[![License](https://img.shields.io/github/license/alexandrainst/' if cookiecutter.open_source == 'y'}}{{cookiecutter.project_name if cookiecutter.open_source == 'y'}}{{')](https://github.com/alexandrainst/' if cookiecutter.open_source == 'y'}}{{cookiecutter.project_name if cookiecutter.open_source == 'y'}}{{'/blob/main/LICENSE)\n[![LastCommit](https://img.shields.io/github/last-commit/alexandrainst/' if cookiecutter.open_source == 'y'}}{{cookiecutter.project_name if cookiecutter.open_source == 'y'}}{{')](https://github.com/alexandrainst/' if cookiecutter.open_source == 'y'}}{{cookiecutter.project_name if cookiecutter.open_source == 'y'}}{{'/commits/main)\n[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg)](https://github.com/alexandrainst/' if cookiecutter.open_source == 'y'}}{{cookiecutter.project_name if cookiecutter.open_source == 'y'}}{{'/blob/main/CODE_OF_CONDUCT.md)' if cookiecutter.open_source == 'y'}}
-
-
-Developer(s):
+[![Code Coverage](https://img.shields.io/badge/Coverage-0%25-red.svg)](https://github.com/alexandrainst/{{cookiecutter.project_name}}/tree/main/tests)
+{% if cookiecutter.open_source == 'y' -%}
+[![Documentation](https://img.shields.io/badge/docs-passing-green)](https://alexandrainst.github.io/{{cookiecutter.project_name}}/{{cookiecutter.project_name}}.html)
+[![License](https://img.shields.io/github/license/alexandrainst/{{cookiecutter.project_name}})](https://github.com/alexandrainst/{{cookiecutter.project_name}}/blob/main/LICENSE)
+[![LastCommit](https://img.shields.io/github/last-commit/alexandrainst/{{cookiecutter.project_name}})](https://github.com/alexandrainst/{{cookiecutter.project_name}}/commits/main)
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg)](https://github.com/alexandrainst/{{cookiecutter.project_name}}/blob/main/CODE_OF_CONDUCT.md)
+{% endif %}
+Developer:
 
 - {{cookiecutter.author_name}} ({{cookiecutter.email}})
 
@@ -18,25 +29,45 @@ Developer(s):
 
 1. Run `make install`, which sets up a virtual environment and all Python dependencies therein.
 2. Run `source .venv/bin/activate` to activate the virtual environment.
-3. (Optional) Run `make install-pre-commit`, which installs pre-commit hooks for linting, formatting and type checking.{{'\n4. (Optional) Run `make add-rag` to add RAG functionality from [ragger](https://github.com/alexandrainst/ragger).' if cookiecutter.open_source != 'y'}}
-
+3. (Optional) Run `make install-pre-commit`, which installs pre-commit hooks for linting, formatting and type checking.
+{% if cookiecutter.open_source != 'y' -%}
+4. (Optional) Run `make add-rag` to add RAG functionality from [ragger](https://github.com/alexandrainst/ragger).
+{% endif %}
 ### Adding and Removing Packages
 
 To install new PyPI packages, run:
 ```
-{{'poetry add' if cookiecutter.dependency_manager != 'pip' else 'pip install'}} <package-name>
+{% if cookiecutter.dependency_manager != 'pip' -%}
+poetry add <package-name>
+{% else -%}
+pip install <package-name>
+{% endif -%}
 ```
 
 To remove them again, run:
 ```
-{{'poetry remove' if cookiecutter.dependency_manager != 'pip' else 'pip uninstall'}} <package-name>
-```{{'\n\nTo freeze dependencies into pyproject.toml, run:\n```\nmake freeze\n```' if cookiecutter.dependency_manager == 'pip'}}
-
+{% if cookiecutter.dependency_manager != 'pip' -%}
+poetry remove <package-name>
+{% else -%}
+pip uninstall <package-name>
+{% endif -%}
+```
+{% if cookiecutter.dependency_manager == 'pip' -%}
+To freeze dependencies into `requirements.txt`, run:
+```
+make freeze
+```
+{% endif %}
 To show all installed packages, run:
 ```
-{{'poetry show' if cookiecutter.dependency_manager != 'pip' else 'pip list'}}
+{% if cookiecutter.dependency_manager != 'pip' -%}
+poetry show
+{% else -%}
+pip list
+{% endif -%}
 ```
 
+
 ## All Built-in Commands
 
 The project includes the following convenience commands:
@@ -47,8 +78,10 @@ The project includes the following convenience commands:
 - `make type-check`: Type check the code using `mypy`.
 - `make test`: Run tests using `pytest` and update the coverage badge in the readme.
 - `make docker`: Build a Docker image and run the Docker container.
+{% if cookiecutter.open_source != 'y' -%}
 - `make add-rag`: Add RAG functionality from [ragger](https://github.com/alexandrainst/ragger).
 - `make update-rag`: Update RAG functionality from [ragger](https://github.com/alexandrainst/ragger).
+{% endif -%}
 - `make docs`: Generate HTML documentation using `pdoc`.
 - `make view-docs`: View the generated HTML documentation in a browser.
 - `make tree`: Show the project structure as a tree.
@@ -94,8 +127,8 @@ file is also a Python script, rather than a module.
 ### Docker Setup
 
 A Dockerfile is included in the new repositories, which by default runs
-`src/scripts/your_script.py`. You can build the Docker image and run the Docker
-container by running `make docker`.
+`src/scripts/main.py`. You can build the Docker image and run the Docker container by
+running `make docker`.
 
 ### Automatic Documentation
 

diff --git a/{{cookiecutter.project_name}}/config/__init__.py b/{{cookiecutter.project_name}}/config/__init__.py
@@ -1 +1 @@
-"""Config files to be used with hydra."""
+"""Config files to be used with Hydra."""
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		"""Config files to be used with hydra."""
		"""Config files to be used with Hydra."""