Configure pre-commit https://pre-commit.com/ and some documentation on tools (#761)

* Add basic https://pre-commit.com/ config

* Move Black config up to a -dev requirements

* Some documentation on Black
adapted from RLO equivalent, by Vitaly Kurin

* We now use the Black default line length

* Use requirements-dev.txt

.github/workflows/pythonchecks.yml

@@ -23,7 +23,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install black==19.10b0 flake8 
+        python -m pip install -r requirements-dev.txt
 #        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
 #     - name: Lint with flake8

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+# -   repo: https://github.com/pre-commit/pre-commit-hooks
+#     rev: v3.2.0
+#     hooks:
+#     -   id: trailing-whitespace
+#     -   id: end-of-file-fixer
+#     -   id: check-yaml
+#     -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 19.10b0
+    hooks:
+    -   id: black

requirements-dev.txt

@@ -0,0 +1,2 @@
+pre-commit==2.12.1
+black==19.10b0

src/python/requirements.txt

@@ -3,4 +3,3 @@ sexpdata==0.0.3
 numpy==1.20.2
 jax==0.1.57
 editdistance==0.5.3
-black==19.10b0

tools.md

@@ -0,0 +1,31 @@
+# Tools
+
+`knossos` has various continuous-integration (CI) tests in place to ensure code quality and correctness, including formatting. The following tools may make it easier to comply with these checks locally before checking in code and failing the various CI tests. They are not automatically integrated into the workflow.
+
+## VSCode
+
+`knossos` uses [black](https://github.com/psf/black) for formatting. Note we currently use the default black line length of `88`. You may find the following settings useful. To use, copy them into `.vscode/settings.json` (don't commit them, they are covered by .gitignored) or your user settings:
+
+```json
+    "python.formatting.provider": "black",
+    "editor.formatOnSave": true,
+```
+
+## [Pre-commit](https://github.com/pre-commit)
+
+Pre-commit is a package manager for various git hooks that process files and can help with consistency and correctness. It is configured in [.pre-commit-config.yaml](.pre-commit-config.yaml) . If any changes are made, you will need to re-stage the relevant files and try again.
+
+Per-user, to setup, run
+
+```bash
+pip install --requirement .\requirements-dev.txt
+pre-commit install
+```
+
+Usually pre-commit will only be run on staged files. The first run will take a bit of time, but subsequent runs should be relatively fast.
+
+You can apply pre-commit and hooks to all files using
+
+```bash
+pre-commit run --all-files
+```