Merge pull request #7 from acceleratescience/6-update-setting-up

6 update setting up

docs/1_setting_up.md

@@ -1,7 +1,33 @@
 ## Setting up Codespaces
-The first step is to create a new repository in your GitHub called `cancer-prediction`. Now head over to the `accelerate/packaging-publishing` repo, switch to the basic branch, and download a zip of the code.
+The first step is to fork this repository to your own GitHub account. This will allow you to make changes to the code without affecting the original repository.
 
-Now head back over to your newly created repo and open Codespaces:
+Now head back over to your newly created repo. Everything in the `main` repo is not needed, so we do a few things:
+
+**Change the default branch**
+
+- Head to the Repo Settings
+- There is a heading called "Default Branch"
+- Click on the pencil icon and change the default branch to `basic`
+
+**Delete the `main` branch**
+
+- Head back to the Code tab
+- Locate the branch dropdown and click on the thing to the right of it
+- Find the `main` branch and delete it
+
+**Rename the `basic` branch to `main`**
+
+- In the same page, next to the trash can, click on the three dots
+- Click on "Rename branch"
+- Change the name to `main`
+
+**Rename the repo**
+
+- Head back over to the Settings tab
+- At the top, you can change the name of the repo to whatever you want
+- Rename it to `cancer-prediction-<your-crsid>`
+
+Now open Codespaces on `main`:
 
 ![](imgs/createcodespace.png)
 
@@ -18,7 +44,7 @@ It is good practice to do development work on a new branch, but first we should
 
 Set up the new virtual environment with,
 ```bash
-python3.10 -m venv venv
+python -m venv venv
 . venv/bin/activate
 ``` 
 
@@ -53,6 +79,14 @@ This will automatically create and move over to a new branch called `dev`. The e
 
 In the source control tab, hit "Publish Branch".
 
+When you see this symbol:
+
+<br>
+![Dark Souls Bonfire](../imgs/dark-souls-bonfire.gif "Commit your changes and rest, weary traveller"){ width="50" .center }
+<br>
+
+it means that you should commit and push your changes to the repository. They indicate key checkpoints in the workshop.
+
 ## Further reading
 <div class="grid cards" markdown>
 

docs/2_project_overview.md

@@ -299,19 +299,16 @@ if app_mode == "Load model and predict" or app_mode == "Manual data entry for pr
     elif app_mode == "Manual data entry for prediction":
         st.header("Manual data entry for prediction")
 
-        # Define your features names here based on the model's training dataset
-        feature_names = model.feature_names  # Replace these with actual feature names
+        feature_names = model.feature_names
 
         # Create a dictionary to store user inputs
         input_data = {}
 
         # Dynamically generate input fields for each feature
         for feature in feature_names:
-            # You might want to customize the `step` parameter based on the feature's data type and expected range
             input_data[feature] = st.number_input(f"Enter {feature}:", step=0.01)
 
         if st.button('Predict'):
-            # Prepare the data for prediction (ensure it matches the model's expected input format)
             input_df = pd.DataFrame([input_data])
 
             # Perform the prediction

docs/4_Testing.md

@@ -95,6 +95,13 @@ OK
 
 You can try changing part of the test code to force them to fail, and check the output. Now that the tests have run succesfully, it's time to commit and push the changes.
 
+<br>
+![Dark Souls Bonfire](../imgs/dark-souls-bonfire.gif "Commit your changes and rest, weary traveller"){ width="50" .center }
+<br>
+
+!!! note
+
+    For some reason Codespaces is not discovering the tests. Just run them in the terminal for now. But VSCode run locally should work fine.
 
 ## Further reading
 <div class="grid cards" markdown>
@@ -105,8 +112,3 @@ You can try changing part of the test code to force them to fail, and check the
     Information on `unittest`, Pytest, and testing in VSCode
 
 </div>
-
-
-!!! note
-
-    For some reason Codespaces is not discovering the tests. Just run them in the terminal for now. But VSCode run locally should work fine.

docs/CICD/documentation.md

@@ -5,31 +5,61 @@ Here is the workflow for this:
 name: documentation
 on:
   push:
-    branches:
-    - main
+    tags:
+      - 'v*'
 
 jobs:
   build-docs:
     needs: tests
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     runs-on: ubuntu-latest
+
     steps:
-      # Set up dependencies
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Verify tag is on main
+        run: |
+          # Get the branch containing this tag
+          BRANCH=$(git branch -r --contains ${{ github.ref }} | grep 'main' || true)
+          
+          # Check if the tag is on main
+          if [ -z "$BRANCH" ]; then
+            echo "Error: Tag must be created on main branch"
+            exit 1
+          fi
+
+      - name: Install Poetry
+        run: pipx install poetry
+
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-          cache: 'pip'
-      - run: python3 -m pip install mkdocs==1.4.2 mkdocstrings==0.21.2 "mkdocstrings[python]>=0.18"
+          python-version: '3.12'
+          cache: 'poetry'
+
+      - name: Install dependencies with dev group
+        run: poetry install --with dev
 
       # Deploy docs
       - name: Deploy documentation
-        run: mkdocs gh-deploy --force
+        run: |
+          poetry run mkdocs gh-deploy --force
 ```
 
-This simply says: when a push is made to main, publish the documentation.
+Most of this is the same as for publishing the package to PyPi. The main difference is that we are running `mkdocs gh-deploy --force` to deploy the documentation to GitHub Pages. This will create a new branch called `gh-pages` which will contain the documentation.
+
+You should now be able to navigate to `https://<username>.github.io/<repo-name>` and see your documentation!
+
+!!! tip
+
+    This is a great tool to make personal websites for your work. You can add images, links, and even videos to your documentation. It is a great way to showcase your research.
+
+    This website was made using MkDocs and the Material theme! Check out the Material website [here](https://squidfunk.github.io/mkdocs-material/).
+
+    For more details on how our websites are made, then you can browse through the folders in the github repo by clicking the GitHub icon at the top left of the page.
 
-In addition, since we are using some tools, we should let everyone know! So we can add the following to our `README.md` file:
+In addition, since we are using some tools, we should let everyone know! So we can add the following to our `README.md` file (just be sure to replace the links with the correct ones):
 ```html
 <div align="center">
 

docs/CICD/precommit.md

@@ -152,6 +152,10 @@ Found 4 errors in 1 file (checked 7 source files)
 isort....................................................................Passed
 ```
 
+<br>
+![Dark Souls Bonfire](../imgs/dark-souls-bonfire.gif "Commit your changes and rest, weary traveller"){ width="50" .center }
+<br>
+
 ## Further reading
 <div class="grid cards" markdown>