Restructure and rename some arguments. Add Docker support

Author: jorgensd

.flake8

@@ -2,5 +2,5 @@
 # https://github.com/PyCQA/flake8/issues/234
 [flake8]
 exclude = docs
-          {{cookiecutter.module_name}}
+          {{cookiecutter.repository_name}}
 max-line-length = 100

cookiecutter.json

@@ -2,14 +2,16 @@
     "full_name": "Jørgen S. Dokken",
     "email": "[email protected]",
     "github_username": "jorgensd",
-    "project_name": "Package Name",
-    "module_name": "{{ cookiecutter.project_name.lower().replace(' ', '_').replace('-', '_') }}",
+    "project_name": "Research Project 1",
+    "repository_name": "{{ cookiecutter.project_name.lower().replace(' ', '_').replace('-', '_') }}",
+    "module_name": "{{cookiecutter.repository_name}}",
     "project_short_description": "Tools ensuring reproducible and standarized Python packaging.",
     "version": "0.1.0",
     "linting": "y",
     "testing": ["pytest", "pytest-cov", "none"],
     "use_argparse": "y",
     "build_docs": "y",
+    "docker": "y",
     "open_source_license": ["MIT", "GPL-3.0", "Other"],
     "_copy_without_render": [".github/*"]
   }

docs/options.md

@@ -5,11 +5,13 @@ The following options are available when using the cookiecutter:
 2. __Email__: Will be used in `pyproject.toml` for package information.
 3. __github\_username__: Will be used to fetch the correct links for the documentation and [license badge](https://scientificcomputing.github.io/reproducibility/part5/badges.html#licence).
 4. __project\_name__: Used in various headers of the documentation
-5. __module\_name__: Name of the python module.
-6. __project\_short\_description__: Usin in `pyproject.toml`
-7. __version__: The initial version of the software.
-8. __linting__: Enable linting, i.e. [mypy](https://scientificcomputing.github.io/reproducibility/part1/typing.html) and [flake8](https://scientificcomputing.github.io/reproducibility/part1/linting.html). This also enables the "Check Formatting" Github action.
-9. __testing__: Creates a test folder with an initial test. Also adds [optional installation dependencies](https://scientificcomputing.github.io/reproducibility/part1/packaging.html#optional-dependencies) to `pyproject.toml`. Creates a "Test Package" Githib action.
+5. __repository\_name__: Name of the repository
+6. __package\_name__: Name of the python package.
+7. __project\_short\_description__: Usin in `pyproject.toml`
+8. __version__: The initial version of the software.
+9. __linting__: Enable linting, i.e. [mypy](https://scientificcomputing.github.io/reproducibility/part1/typing.html) and [flake8](https://scientificcomputing.github.io/reproducibility/part1/linting.html). This also enables the "Check Formatting" Github action.
+10. __testing__: Choose testing framework. If not `none` it creates a test folder with an initial test. Also adds [optional installation dependencies](https://scientificcomputing.github.io/reproducibility/part1/packaging.html#optional-dependencies) to `pyproject.toml`. Creates a "Test Package" Github action. If `pytest-cov` is chosen, it adds settings to generate a coverage report and publsuh them as a [Github artifact](https://scientificcomputing.github.io/reproducibility/part1/coverage.html).
 10. __use\_argparse__: Makes it possible to run the package as `module_name` or `python -m module_name` with inputs from the command line.
 11. __build\_docs__: Build a webpage with documentation (including a package API).
-12. __open\_source\_license__: Choose a open source license for your code
+12. __docker__: Adds a Dockerfile that includes the module (not including optional dependencies). Adds a [publishing workflow](https://scientificcomputing.github.io/reproducibility/part4/docker.html#github-packages).
+13. __open\_source\_license__: Choose a open source license for your code

hooks/post_gen_project.py

@@ -20,12 +20,21 @@
     'docs/api.rst',
     'docs/index.md',
     'docs/logo.png',
-    'docs'
+    'docs',
+    {% endif %}
+    {%- if cookiecutter.docker|lower != "y" %}
+    'Dockerfile',
+    '.github/workflows/docker-image.yml',
+    {% endif %}
+    {%- if cookiecutter.use_argparse|lower != "y" %}
+    'src/{{ cookiecutter.module_name }}/__main__.py',
+    'src/{{ cookiecutter.module_name }}/cli.py',
     {% endif %}
 ]
 
 for path in REMOVE_PATHS:
     path = path.strip()
+    print(path)
     if path and os.path.exists(path):
         if os.path.isdir(path):
             os.rmdir(path)

{{cookiecutter.module_name}}/.flake8 renamed to {{cookiecutter.repository_name}}/.flake8

@@ -0,0 +1,49 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches:
+      - "!*"
+    tags:
+      - "v*"
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}