Further tooling: black, flake8, and precommit-hooks (#32)

* feat: add black, flake8 and precommit-hooks

* chore: run precommit-hooks on all files and fix all existing errors

* feat: improve documentation regarding contributions and intended uses of GutenTAG

* fix: pre-commit-dependency version specification

* fix: downgrade flake8 to 5.0.4 to support Python 3.7

* chore: remove obsolete gitlab CI configuration

* fix: downgrade pre-commit to 2.21 to support Python 3.7

* chore: remove additional generation configurations

(they were accidentially added in a previous commit)

.github/workflows/build.yml

@@ -12,9 +12,10 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  typecheck:
-    name: Typecheck GutenTAG on ubuntu with python 3.7
+  check:
+    name: Run checks for GutenTAG on ubuntu with python 3.7
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v3
       - name: Setup Miniconda
@@ -29,6 +30,10 @@ jobs:
       - name: Typcheck with mypy
         run: |
           python setup.py typecheck
+      - name: Lint with flake8
+        run: |
+          flake8 . --count --show-source --statistics
+
   test:
     name: Test GutenTAG on ${{ matrix.os }} with python ${{ matrix.python_version }}
     runs-on: ${{ matrix.os }}

.github/workflows/test-pr.yml

@@ -11,9 +11,10 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  typecheck:
-    name: Typecheck GutenTAG on ubuntu with python 3.7
+  check:
+    name: Run checks for GutenTAG on ubuntu with python 3.7
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v3
       - name: Setup Miniconda
@@ -28,6 +29,10 @@ jobs:
       - name: Typcheck with mypy
         run: |
           python setup.py typecheck
+      - name: Lint with flake8
+        run: |
+          flake8 . --count --show-source --statistics
+
   test:
     name: Test GutenTAG on ${{ matrix.os }} with python ${{ matrix.python_version }}
     runs-on: ${{ matrix.os }}

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.0.0
+  hooks:
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+    args: [--markdown-linebreak-ext=md]
+  - id: check-case-conflict
+  - id: mixed-line-ending
+    args: [--fix=lf]
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.920
+  hooks:
+  - id: mypy
+    files: gutenTAG
+    additional_dependencies:
+      - types-PyYAML
+      - types-jsonschema
+- repo: https://github.com/psf/black
+  rev: '23.1.0'
+  hooks:
+  - id: black
+- repo: https://github.com/pycqa/flake8
+  rev: '5.0.4'
+  hooks:
+  - id: flake8

CONTRIBUTING.md

@@ -0,0 +1,36 @@
+# Contributing
+
+## Code style and format
+
+We use [black](https://black.readthedocs.io/) to automatically format our python files.
+Please stick to the black code style.
+
+Please consider using the pre-commit hooks.
+They automatically run i.a. black for you.
+See next section.
+
+### Black quick-installation guide
+
+```bash
+pip install black
+black
+```
+
+## Running pre-commit hooks
+
+We use [pre-commit](https://pre-commit.com/) to run some checks on your files before they are commited.
+Find the configured hooks in [`.pre-commit-config.yaml`](./pre-commit-config.yaml).
+If there are errors, you have to re-add the files to the index and commit the fixed files.
+
+### Pre-commit quick-installation guide
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+Optionally, cou can then run the hooks against all files with:
+
+```bash
+pre-commit run --all-files
+```

README.md

@@ -6,6 +6,7 @@
 
 [![CI](https://github.com/HPI-Information-Systems/gutentag/actions/workflows/build.yml/badge.svg)](https://github.com/HPI-Information-Systems/gutentag/actions/workflows/build.yml)
 [![codecov](https://codecov.io/gh/HPI-Information-Systems/gutentag/branch/main/graph/badge.svg?token=6QXOCY4TS2)](https://codecov.io/gh/HPI-Information-Systems/gutentag)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![PyPI package](https://badge.fury.io/py/timeeval-gutenTAG.svg)](https://badge.fury.io/py/timeeval-gutenTAG)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 ![python version 3.7|3.8|3.9|3.10|3.11](https://img.shields.io/badge/python-3.7%20%7C%203.8%20%7C%203.9%20%7C%203.10%20%7C%203.11-blue)
@@ -93,6 +94,8 @@ If you use GutenTAG in your project or research, please cite our demonstration p
 }
 ```
 
-## To-Do
+## Contributing
 
-- [ ] negation anomaly (does a pattern not appear)
+We welcome contributions to GutenTAG.
+If you have spotted an issue with GutenTAG or if you want to enhance it, please open an issue first.
+See [Contributing](CONTRIBUTING.md) for details.

doc/advanced-features.md

@@ -2,7 +2,7 @@
 
 ## Add-Ons
 
-GutenTAG has a simple add-on feature which can be activated by using the [CLI](usage#from-cli). 
+GutenTAG has a simple add-on feature which can be activated by using the [CLI](usage#from-cli).
 
 ### Definition
 

doc/introduction/base-oscillations.md

@@ -239,7 +239,7 @@ operand: Union[float, FormulaObj]
 **Aggregation**
 
 The alternative to the `Operation` is the `Aggregation` field. This field defines an aggregation operation on the `base`. Its result is either a scalar or an array. It consists of two fields: `kind`, and `axis`.
-The `kind` field defines the kind of aggregation performed on a numpy array. The optional `axis` field defines the axis of the array the aggregation is performed on. If no `axis` is defined, the aggregation will return a scalar. 
+The `kind` field defines the kind of aggregation performed on a numpy array. The optional `axis` field defines the axis of the array the aggregation is performed on. If no `axis` is defined, the aggregation will return a scalar.
 
 ```yaml
 # Aggregation