Add pre-commit hooks

.flake8

@@ -2,4 +2,4 @@
 # https://github.com/PyCQA/flake8/issues/234
 [flake8]
 exclude = docs,venv
-max-line-length = 100
+max-line-length = 100

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -25,7 +25,7 @@ body:
         cachedir: .pytest_cache
         rootdir: /root/shared
         plugins: anyio-3.6.1, cov-3.0.0
-        collected 1 item                                                                                               
+        collected 1 item
 
         test/test_code.py::test_addition PASSED
         ============================================== 1 passed in 0.01s ===============================================
@@ -49,7 +49,7 @@ body:
       placeholder: i.e. "I'm Ubuntu 20.04" or "Im using Windows 11"
   - type: textarea
     id: extra
-    attributes: 
+    attributes:
       label: Additional information
       description: If you have any additional information, please add it here.
       placeholder: You can drag and drop files here to attach them

.github/workflows/build_docs.yml

@@ -21,7 +21,7 @@ jobs:
 
       - name: Install dependencies
         run: python -m pip install ".[test,docs]"
-                
+
       - name: Build docs
         run: make doc
 
@@ -32,4 +32,4 @@ jobs:
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ${{ env.PUBLISH_DIR }}
+          publish_dir: ${{ env.PUBLISH_DIR }}

.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: requirements-txt-fixer
+
+  - repo: https://github.com/asottile/reorder_python_imports
+    rev: v3.8.3
+    hooks:
+      - id: reorder-python-imports
+
+  - repo: https://github.com/psf/black
+    rev: 22.8.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.0.0
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/asottile/add-trailing-comma
+    rev: v2.3.0
+    hooks:
+      - id: add-trailing-comma
+
+  - repo: https://github.com/asottile/setup-cfg-fmt
+    rev: v2.0.0
+    hooks:
+      - id: setup-cfg-fmt
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.981
+    hooks:
+      - id: mypy

CITATION.cff

@@ -6,4 +6,4 @@ authors:
   orcid: "https://orcid.org/0000-0001-6489-8858"
 title: "Template for reproducible research"
 version: 0.1.0
-date-released: 2022-09-13
+date-released: 2022-09-13

CONTRIBUTING.md

@@ -1,9 +1,8 @@
 # Contributing
 
-To contribute to this repository: 
+To contribute to this repository:
 1. Create a [fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) of the repository.
 2. [Clone](https://docs.github.com/en/get-started/quickstart/fork-a-repo#cloning-your-forked-repository) the forked repository.
 3. Checkout a new branch (using `git checkout -b name_of_branch`), where name of branch should be replaced by `your_github_username/description_of_feature`. For instance, `jorgensd/add_guidelines`.
 4. Add your contribution and push it to your fork.
 5. Make a [pull request from your fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork).
-

Dockerfile

@@ -36,4 +36,4 @@ USER root
 RUN chown -R ${NB_UID} ${HOME}
 
 USER ${NB_USER}
-ENTRYPOINT []
+ENTRYPOINT []

Makefile

@@ -1,8 +1,8 @@
-# List of Python demos (without file extenion) from the repo `demo` to include in the jupyterbook. 
+# List of Python demos (without file extenion) from the repo `demo` to include in the jupyterbook.
 # These files should be listed in `docs/_toc.yml`
 DEMOS = demo
 
-doc: # Generate Sphinx HTML documentation, including API docs 
+doc: # Generate Sphinx HTML documentation, including API docs
 # We use --set-kernel with jupytext to make it possible for binder to pick it up
 	@for demo in ${DEMOS}; do \
 		jupytext --to=ipynb --set-kernel=python3 demo/$$demo.py --output=docs/$$demo.ipynb ;\

README.md

@@ -7,4 +7,3 @@ The documentation for this repository can be found [here](https://jorgensd.githu
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jorgensd/reproducibility/gh-pages?labpath=_sources)
 [![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://jorgensd.github.io/reproducibility)
 [![MIT License](https://img.shields.io/github/license/jorgensd/reproducibility)](LICENSE)
-

demo/demo.py

@@ -4,17 +4,13 @@
 #
 # SPDX-License-Identifier:    MIT
 # -
-
 # + [markdown]
 # We start a new cell explicitly by using the "+" sign and can explicitly end
 # it by using the "-" sign.
 # -
-
 # If we do not use explicit indicators for starting or ending a cell, it creates a
 # new cell whenever there is a blank line
-
 # This is a new cell
-
 # Comments can be added to code by not adding a new line before the code
 import mypackage
 

docs/_config.yml

@@ -36,6 +36,3 @@ sphinx:
   - 'sphinx.ext.autodoc'
   - 'sphinx.ext.napoleon'
   - 'sphinx.ext.viewcode'
-
-
-

docs/_toc.yml

@@ -9,6 +9,7 @@ parts:
     - file: "part1/linting"
     - file: "part1/typing"
     - file: "part1/testing"
+    - file: "part1/pre_commit.md"
 
   - caption: Github tools
     chapters:

docs/api.rst

@@ -2,4 +2,4 @@ API Reference
 =============
 
 .. automodule:: mypackage
-    :members:
+    :members:

docs/part1/packaging.md

@@ -10,19 +10,19 @@ We recommend using the source layout. See [this chapter](https://py-pkgs.org/04-
 A [toml](https://toml.io/en/) (Tom's Obivous Minimal Language) file is a plain-text file, consisting of [tables](https://toml.io/en/v1.0.0#table)
 which are a selection of key-value pairs.
 
-An example is 
+An example is
 ```toml
 [project]
 name = "catch_us"
 authors = [
     {name = "Per Ulv", email = "per@acme.no"},
     {name = "Bippe Stankelbein", email = "bippe@roadrunner.no"}
     ]
-version = "x.y.z" 
+version = "x.y.z"
 description = "Meep Meep"
-# "readme" the description field in your package, 
+# "readme" the description field in your package,
 # see: https://python-poetry.org/docs/pyproject/#readme
-readme = "README.md" 
+readme = "README.md"
 requires-python = ">=3.8"
 # Path to license file, see: https://spdx.org/licenses/
 # for a selection of licenses
@@ -51,4 +51,4 @@ test = ["pytest"]
 Then, when installing the package, you call `pip3 install .[test]` instead of `pip3 install .` to get the additional dependencies.
 
 ### Other tables
-For options related to coverage reports and code consistency, see the [Coverage](./coverage) and [Linting](./linting.md) section, respectively.
+For options related to coverage reports and code consistency, see the [Coverage](./coverage) and [Linting](./linting.md) section, respectively.

docs/part1/pre_commit.md

@@ -0,0 +1,21 @@
+# Pre-commit hooks
+
+Using pre-commit hooks is a great way to make sure that the code you commit to the repo follows some common style. This way, you will not end up changing the style back and forth when collaborating with other people.
+
+The file `.pre-commit-config.yaml` in the root of the repo contains a set of default pre-commit hooks. You can find more hooks in the [pre-commit home page](https://pre-commit.com/hooks.html).
+
+To install the pre-commit hook you first need to install pre-commit
+```
+python -m pip install pre-commit
+```
+and then install the pre-commit hook
+```
+pre-commit install
+```
+The pre-commit hook will only run on the files you commit to the repo. To run the pre-commit hook on all the files in your repo, you can execute the command.
+```
+pre-commit run --all
+```
+
+## Running pre-commit in CI
+You can also run the pre-commit hooks as a part of your continuous integration. You can check out the [GitHub action](https://github.com/pre-commit/action), or you can set up at webhook using [pre-commit.ci](https://pre-commit.ci).

docs/part1/testing.md

@@ -1 +1 @@
-# Testing
+# Testing

docs/part1/typing.md

@@ -1 +1 @@
-# Python typing
+# Python typing

docs/part2/citeable.md

@@ -1,4 +1,3 @@
 # Make a repository citable
-The easiest way to make your repository citable is to add a `CITATION.cff` file to the repository, as it is supported by both 
+The easiest way to make your repository citable is to add a `CITATION.cff` file to the repository, as it is supported by both
 [Zenodo's](https://zenodo.org/) and it's [Github integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content) and [Github](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files) itself.
-

docs/part2/github.md

@@ -1,2 +1 @@
 # Github tools
-

docs/part2/issues.md

@@ -1,4 +1,2 @@
 # Issue template
 See [Adding an issue template](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository) for more information.
-
-

docs/part3/auto_api.md

@@ -1 +1 @@
-# Auto-generation
+# Auto-generation

docs/part3/auto_demos.md

@@ -14,4 +14,4 @@ This is illustrated in the following auto-converted demo.
 
 # Auto-conversion of demos
 
-In the [Makefile](https://github.com/jorgensd/reproducibility/blob/main/Makefile) one can find the instructions for auto-converting the demos and building the book.
+In the [Makefile](https://github.com/jorgensd/reproducibility/blob/main/Makefile) one can find the instructions for auto-converting the demos and building the book.

docs/part3/publishing.md

@@ -4,5 +4,4 @@
 
 ## `_toc.yml`
 
-## `_config.yml` 
-
+## `_config.yml`

pyproject.toml

@@ -9,10 +9,10 @@ authors = [
     {name = "Jørgen S. Dokken", email = "dokken@simula.no"},
     {name = "Henrik N. Finsberg", email = "henriknf@simula.no"}
     ]
-version = "0.1.0" 
+version = "0.1.0"
 description = "Minimal package for adding two numbers"
 # "readme" the description field in your package, see: https://python-poetry.org/docs/pyproject/#readme
-readme = "README.md" 
+readme = "README.md"
 requires-python = ">=3.8"
  # Path to license file, see: https://spdx.org/licenses/ for options
 license = {file = "LICENSE"}
@@ -46,7 +46,7 @@ pypi = [
 [tool.mypy]
 ignore_missing_imports = true # Does not show errors when importing untyped libraries
 exclude = [ # We only want mypy to consider files that are not generated in installing or building documentation
-    "docs/", 
+    "docs/",
     "build/"
 ]
 files = [  # Folder to which files that should be checked by mypy
@@ -58,4 +58,4 @@ files = [  # Folder to which files that should be checked by mypy
 addopts = "--cov=mypackage --cov-report html --cov-report term-missing -v"
 testpaths = [
     "test"
-]
+]

src/mypackage/__init__.py

@@ -1,12 +1,11 @@
-
 # Copyright (C) 2022 Jørgen Schartum Dokken
 #
 # This file is part of my_package
 # SPDX-License-Identifier:    MIT
-
 import importlib.metadata
 
-from .functions import addition, print_add
+from .functions import addition
+from .functions import print_add
 
 __version__ = importlib.metadata.version(__package__)
 

src/mypackage/functions.py

@@ -1,5 +1,3 @@
-
-
 # Copyright (C) 2022 Jørgen Schartum Dokken
 #
 # This file is part of mypackage
@@ -9,12 +7,12 @@
 
 
 def addition(a: int, b: int) -> int:
-    """ Computes a+b """
+    """Computes a+b"""
     return a + b
 
 
 def print_add(a: int, b: int) -> int:
-    """ Computes and prints a + b"""
+    """Computes and prints a + b"""
     c = a + b
     print(c)
     return c

test/test_code.py

@@ -2,7 +2,6 @@
 #
 # This file is part of my_package
 # SPDX-License-Identifier:    MIT
-
 from mypackage import addition