Merge branch 'main' into interaction-matrix-of-user

.github/workflows/ci.yml

@@ -23,3 +23,24 @@ jobs:
 
       - name: Run tests
         run: pipenv run pytest
+
+  ruff:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+    
+      # Update output format to enable automatic inline annotations.
+      - name: Run Ruff
+        run: ruff check --output-format=github .
+

.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+	"recommendations": [
+		"charliermarsh.ruff"
+	],
+	"unwantedRecommendations": [
+
+	]
+}

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "charliermarsh.ruff",
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": "explicit"
+    }
+  }
+}

Pipfile

@@ -4,12 +4,14 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-requests = "==2.26.0"
-python-dotenv = "==1.0.1"
-pytest = "==8.3.3"
-pytest-cov = "==5.0.0"
+python-dotenv = "~=1.0"
+requests = "~=2.26"
+ruff = "~=0.7"
+tqdm = "~=4.66"
 
 [dev-packages]
+pytest = "~=8.3"
+pytest-cov = "~=5.0"
 
 [requires]
 python_version = "3.12"

README.md

@@ -8,15 +8,43 @@ Currently, we are only accepting contributions from members of the project who m
 
 ## Development
 
-This code uses Python 3, probably at least 3.9.
+This code uses Python 3. It is tested on Python 3.12, but will probably work on versions back to 3.9.
 
-To install the project dependencies, first install pipenv globally with `pip install pipenv`. Then create a virtual env/install dependencies with `pipenv install`.
+To install the project dependencies, first install pipenv globally with `pip install pipenv`. Then create a virtual env/install dependencies with `pipenv install --dev`.
 
 To run code in the project, prefix your command with `pipenv run`, a la `pipenv run python -m mediabridge.main`.
 
+## Running main
+
+The "main.py" script is part of the `mediabridge` module. Additionally, running it requires `pipenv run` as mentioned above. So the full command to run the main script (or any other script in the `mediabridge` module) is:
+
+```
+pipenv run python -m mediabridge.main
+```
+
+This should be run from the root of the project directory.
+
+### Running from VSCode
+
+To fix import errors and other Intellisense features, make sure you've let VSCode know about your pipenv environment. To do that:
+
+1. Open the VSCode command palette (Control/Command+SHIFT+P)
+2. Search for and select the "Python: Select Interpreter" command
+3. Choose the option that starts with `MediaBridge`
+
 ## Testing
 
 To run unit tests,
 
 1. Ensure `pipenv` is installed
 2. Run `pipenv run pytest`
+
+There is a GitHub actions "check" for passing tests, which must pass for you to be able to merge your PR.
+
+## Code formatting
+
+We use [ruff](https://docs.astral.sh/ruff/) for code formatting, linting, and import sorting. If you've installed the project with the instructions above, you should have access to the `ruff` binary.
+
+The repo comes with a `.vscode` directory that contains a recommended ruff extension, as well as settings to set ruff as your Python formatter and to format code and sort imports on save. If you're not using VSCode, you can run `ruff format` from the project root directory to format all Python code.
+
+There is a GitHub actions "check" for code formatting, which will fail if you have unformatted code in your PR.

mediabridge/config/setting.py

@@ -1 +1 @@
- # Configuration settings (e.g., MongoDB URI, paths)
+# Configuration settings (e.g., MongoDB URI, paths)

mediabridge/data_processing/build_matrices.py

@@ -1 +1 @@
-# Scripts to build interaction and feature matrices
+# Scripts to build interaction and feature matrices

mediabridge/data_processing/preprocess.py

@@ -1 +1 @@
-# Data preprocessing scripts (e.g., feature extraction)
+# Data preprocessing scripts (e.g., feature extraction)