Set up GitHub Actions to run code checks

For:
https://github.com/ClinGen/stanford-hci/issues/8

.github/workflows/check.yml

@@ -0,0 +1,23 @@
+name: Run affils code checks
+on: [push, pull_request]
+permissions:
+    contents: read
+jobs:
+    check:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - name: Set up Python 3.12
+              uses: actions/setup-python@v5
+              with:
+                  python-version: "3.12"
+            - name: Set up Node.js 20
+              uses: actions/setup-node@v4
+              with:
+                node-version: 20
+            - name: Install front end and back end dependencies
+              run: |
+                npm install
+                pip install -r requirements.txt
+            - name: Run all code checks
+              run: invoke check

doc/tutorial.md

@@ -18,3 +18,12 @@
 - Look at the `tasks.py` script in the root of the `stanford-hci` repo. This
   script contains all the command line tasks available to you for this repo.
 - List the commands available to you on the command line: `inv --list`
+- Create a `pre-commit` hook in `.git/hooks/pre-commit`. Add the following
+  content:
+  ```
+  #!/usr/bin/env bash
+  inv check
+  inv reqs
+  ```
+- Make sure the `pre-commit` hook is executable:
+  `chmod +x .git/hooks/pre-commit`

requirements.txt

@@ -0,0 +1,31 @@
+# Do not edit directly. This file is generated.
+
+astroid==3.1.0
+black==24.4.1
+blinker==1.7.0
+click==8.1.7
+coverage==7.5.0
+dill==0.3.8
+Flask==3.0.3
+iniconfig==2.0.0
+invoke==2.2.0
+isort==5.13.2
+itsdangerous==2.2.0
+Jinja2==3.1.3
+markdown-it-py==3.0.0
+MarkupSafe==2.1.5
+mccabe==0.7.0
+mdformat==0.7.17
+mdurl==0.1.2
+mypy==1.10.0
+mypy-extensions==1.0.0
+packaging==24.0
+pathspec==0.12.1
+platformdirs==4.2.1
+pluggy==1.5.0
+pylint==3.1.0
+pytest==8.1.1
+python-dotenv==1.0.1
+tomlkit==0.12.4
+typing_extensions==4.11.0
+Werkzeug==3.0.2

tasks.py

@@ -27,6 +27,7 @@ def lint(c):
     """Lint front end and back end code."""
     c.run("npm run lint")
     c.run("pylint src/api")
+    c.run("pylint tasks.py")
 
 
 @task
@@ -61,7 +62,7 @@ def mdfmt(c):
 
 
 @task(pre=[fmt, lint, types, test, mdfmt])
-def check(c):
+def check(c):  # pylint: disable=unused-argument
     """Run all front end and back end code checks."""
 
 
@@ -75,3 +76,21 @@ def frontend(c):
 def backend(c):
     """Run the back end for development."""
     c.run(f"flask --app {os.environ.get('HCI_BACK_END_ENTRYPOINT')} run")
+
+
+@task
+def reqs(c):
+    """Generate requirements.txt file.
+
+    The GitHub Actions workflow runners don't seem to play nicely with
+    Pipenv. We generate a requirements.txt file and use it to install
+    dependencies in GitHub Actions.
+    """
+    add_warning = (
+        "echo '# Do not edit directly. This file is generated.\n' > requirements.txt"
+    )
+    # The PIPENV_VERBOSITY variable suppresses a warning issued Pipenv
+    # if you use the run command when you've already activated the
+    # virtual environment.
+    add_reqs = "PIPENV_VERBOSITY=-1 pipenv run pip freeze >> requirements.txt"
+    c.run(f"{add_warning} && {add_reqs}")