Simplify generation repo using README as index (#11)

* Simplify generation repo using README as index

* Fix path

Author: jorgensd

.github/workflows/build_docs.yml

@@ -23,7 +23,7 @@ concurrency:
 
 env:
   # Directory that will be published on github pages
-  PUBLISH_DIR: ./docs/_build/html
+  PUBLISH_DIR: ./_build/html
 
 jobs:
 
@@ -43,7 +43,7 @@ jobs:
         run: python3 -m pip install -r requirements.txt
 
       - name: Build docs
-        run: 	jupyter book build -W docs
+        run: 	jupyter book build -W .
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1

.gitignore

@@ -127,3 +127,5 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+_build/

README.md

@@ -1,10 +1,11 @@
-# Template repository for reproducible research
+# Template repository for Python packages
+
 Repository using [Cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) for project templates.
 
 ## Installation
 To use this repository, you need to install cookiecutter. This can be done with `pip`
 ```bash
-pip install cookiecutter
+python3 -m pip install cookiecutter
 ```
 For other installation options, see: [Cookiecutter installation](https://cookiecutter.readthedocs.io/en/stable/installation.html)
 
@@ -14,7 +15,25 @@ You also need to have `git` installed on your system, see:
 ## Usage
 To use this repository with cookiecutter you can call:
 ```bash
-cookiecutter gh:scientificcomputing/template-repo
+cookiecutter gh:scientificcomputing/generate-python-package
 ```
 and fill out the list of options.
-See: [https://scientificcomputing.github.io/template-repo](https://scientificcomputing.github.io/template-repo) for documentation.
+
+# Options for cookiecutter
+The following options are available when using the cookiecutter:
+
+1. __Full Name__: Will appear in the `pyproject.toml` file as the author. Will also be used as author of the documentation generated by [jupyter-book](https://scientificcomputing.github.io/reproducibility/part3/publishing.html).
+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. __repository\_name__: Name of the repository
+6. __package\_name__: Name of the python package.
+7. __project\_short\_description__: Using 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).
+11. __use\_argparse__: Makes it possible to run the package as `module_name` or `python -m module_name` with inputs from the command line.
+12. __build\_docs__: Build a webpage with documentation (including a package API).
+13. __use_pre_commit__: Set up [pre-commit hooks](https://pre-commit.com) that will run some tests every time you make a commit.
+14. __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).
+15. __open\_source\_license__: Choose a open source license for your code

docs/_config.yml _config.ymldocs/_config.yml renamed to _config.yml

@@ -29,4 +29,6 @@ sphinx:
   extra_extensions:
   - 'sphinx.ext.autodoc'
   - 'sphinx.ext.napoleon'
-  - 'sphinx.ext.viewcode'
+  - 'sphinx.ext.viewcode'
+
+exclude_patterns: ["**cookiecutter.repository_name**"] 

_toc.yml

@@ -0,0 +1,2 @@
+format: jb-book
+root: README