Merge pull request #15 from kaitj/readme-update

Add contributing to README

.pre-commit-config.yaml

@@ -1,32 +1,23 @@
-default_language_version:
-  python: python3.8
+exclude: "^migrations/"
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
     hooks:
-      - id: check-yaml
-      - id: debug-statements
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-  - repo: local
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.10.1
     hooks:
-      - id: isort
-        entry: poetry run isort
-        name: isort
-        language: system
-        types_or: [cython, pyi, python]
-  - repo: local
+    -   id: isort
+
+-   repo: https://github.com/psf/black
+    rev: 22.8.0
     hooks:
-      - id: flake8
-        entry: poetry run flake8
-        language: system
-        name: flake8
-        types_or: [cython, pyi, python]
-  - repo: local
+    -   id: black
+
+-   repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
     hooks:
-      - id: system
-        name: PyLint
-        entry: poetry run pylint
-        language: system
-        exclude: \._py\}\}$
-        types_or: [cython, pyi, python]
+    -   id: flake8

README.md

@@ -10,6 +10,39 @@ connectome), making use of existing neuroimaging tools like `prepdwi`,
 This workflow was used to process the data for the analysis from 
 [`hcp_subcortical_repo`](https://github.com/kaitj/hcp_subcortical_repro).
 
+### Contributing
+Clone the git repository. DBSC dependencies are managed with Poetry 
+(version 1.2.x), which you'll need installed on your machine. 
+You can find instructions on the Poetry 
+[website](https://python-poetry.org/docs/). 
+
+Then, setup the development environment with the following commands:
+
+```
+poetry install
+poetry run poe setup
+```
+
+DBSC uses poethepoet as a task runner. 
+You can see what commands are available by running:
+
+```
+poetry run poe
+```
+
+If you wish, you can also run poe [command] directly by installing poethepoet 
+on your system. Follow the install instructions at the link above.
+
+DBSC uses pre-commit hooks (installed via the poe setup command above) to lint 
+and format code (we use black, isort, flake8). By default, these hooks are 
+run on every commit. Additionally, please run the following task:
+
+```
+poetry run poe quality
+```
+
+Please be sure they all pass before making a PR.
+
 ### Notes
 
 * Original workflow had worked on HCP data which had transforms readily