Initial commit

.github/workflows/docker-publish.yml

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+# Publishes docker image, pinning actions to a commit SHA,
+# and updating most recently built image with the latest tag.
+# Can be triggered by either pushing a commit that changes the `Dockerfile`, 
+# or manually dispatching the workflow.
+
+name: Publish Docker image
+
+on: 
+  workflow_dispatch:
+  push: 
+    paths: 
+      - 'Dockerfile'
+      - 'conda-linux-64.lock'
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ttimbers/dsci-522-individual-assignment-quarto-python
+          tags: |
+            type=raw, value={{sha}},enable=${{github.ref_type != 'tag' }}
+            type=raw, value=latest
+      
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Update docker-compose.yml with new image tag
+        if: success()
+        run: |
+          sed -i "s|image:  ttimbers/dsci-522-individual-assignment-quarto-python:.*|image:  ttimbers/dsci-522-individual-assignment-quarto-python:${{ steps.meta.outputs.version }}|" docker-compose.yml
+
+      - name: Commit and push updated docker-compose.yml
+        if: success()
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git add docker-compose.yml
+          git commit -m "Update docker-compose.yml with new image tag"
+          git push

.gitignore

@@ -0,0 +1,7 @@
+**.ipynb_checkpoints
+**.DS_Store
+**.cache/
+**.ipython/
+**.jupyter/
+**.local/
+**.npm/

Dockerfile

@@ -0,0 +1,17 @@
+FROM quay.io/jupyter/minimal-notebook:afe30f0c9ad8
+
+COPY conda-linux-64.lock /tmp/conda-linux-64.lock
+
+USER root
+
+# install lmodern for Quarto PDF rendering
+RUN sudo apt update \
+    && sudo apt install -y lmodern
+
+USER $NB_UID
+
+# install packages from conda-linux-64.lock
+RUN mamba update --quiet --file /tmp/conda-linux-64.lock \
+    && mamba clean --all -y -f \
+    && fix-permissions "${CONDA_DIR}" \
+    && fix-permissions "/home/${NB_USER}"

LICENSE

@@ -0,0 +1,71 @@
+## Non-software content
+
+Copyright: Jordan Bourak & Tiffany Timbers
+
+The DSCI 310 individual assignment on reproducible reports is made available under the **Attribution 4.0 International** ([CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)). 
+
+This is a human-readable summary of (and not a substitute for) the [license](https://creativecommons.org/licenses/by/4.0/legalcode).
+
+You are free:
+
+* to **Share**---copy and redistribute the material in any medium or format
+* to **Adapt**---remix, transform, and build upon the material
+
+for any purpose, even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the
+license terms.
+
+Under the following terms:
+
+* **Attribution**---You must give appropriate credit (mentioning that
+  your work is derived from work that is Copyright © Software
+  Carpentry and, where practical, linking to
+  http://software-carpentry.org/), provide a [link to the
+  license][cc-by-human], and indicate if changes were made. You may do
+  so in any reasonable manner, but not in any way that suggests the
+  licensor endorses you or your use.
+
+**No additional restrictions**---You may not apply legal terms or
+technological measures that legally restrict others from doing
+anything the license permits.  With the understanding that:
+
+Notices:
+
+* You do not have to comply with the license for elements of the
+  material in the public domain or where your use is permitted by an
+  applicable exception or limitation.
+* No warranties are given. The license may not give you all of the
+  permissions necessary for your intended use. For example, other
+  rights such as publicity, privacy, or moral rights may limit how you
+  use the material.
+
+
+## Software
+
+Copyright: Jordan Bourak & Tiffany Timbers
+
+Except where otherwise noted, the software
+provided in the DSCI 310 individual assignment on reproducible reports 
+is available under the
+[OSI][osi]-approved
+[MIT license][mit-license].
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+## DSCI 522 individual assignment on Quarto reproducible reports using Python
+
+This is a template repository 
+for the individual assignment on Quarto reproducible reports using Python
+from the DSCI 522 (Workflows for data science) course.
+Instructions for this assignment can be found on the DSCI 522 course website.
+
+### Dependencies
+
+- [Docker](https://www.docker.com/) 
+
+### Usage
+
+#### Setup
+
+> If you are using Windows or Mac, make sure Docker Desktop is running.
+
+1. Clone this GitHub repository.
+
+#### Running the analysis
+
+1. Navigate to the root of this project on your computer using the
+   command line and enter the following command:
+
+``` 
+docker compose up
+```
+
+2. In the terminal, look for a URL that starts with 
+`http://127.0.0.1:8888/lab?token=` 
+(for an example, see the highlighted text in the terminal below). 
+Copy and paste that URL into your browser.
+
+<img src="img/jupyter-container-web-app-launch-url.png" width=400>
+
+3. To run the analysis,
+open a terminal (in the docker jupyter lab) and run the following commands:
+
+```
+python scripts/generate_figures.py --input_dir="data/00030067-eng.csv" \
+    --out_dir="results"
+
+quarto render reports/qmd_example.qmd --to html
+quarto render reports/qmd_example.qmd --to pdf
+```
+
+#### Clean up
+
+1. To shut down the container and clean up the resources, 
+type `Cntrl` + `C` in the terminal
+where you launched the container, and then type `docker compose rm`
+
+## Developer notes
+
+### Developer dependencies
+- `conda` (version 23.9.0 or higher)
+- `conda-lock` (version 2.5.7 or higher)
+
+### Adding a new dependency
+
+1. Add the dependency to the `environment.yml` file on a new branch.
+
+2. Run `conda-lock -k explicit --file environment.yml -p linux-64` to update the `conda-linux-64.lock` file.
+
+2. Re-build the Docker image locally to ensure it builds and runs properly.
+
+3. Push the changes to GitHub. A new Docker
+   image will be built and pushed to Docker Hub automatically.
+   It will be tagged with the SHA for the commit that changed the file.
+
+4. Update the `docker-compose.yml` file on your branch to use the new
+   container image (make sure to update the tag specifically).
+
+5. Send a pull request to merge the changes into the `main` branch. 
+
+### License:
+The non-software content of this template repository is licensed under the 
+[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License](https://creativecommons.org/licenses/by-nc-sa/4.0/). 
+The software content of this template repository licensed under the [MIT License](https://spdx.org/licenses/MIT.html). See the [license file](LICENSE.md) for more information.

conda-linux-64.lock

@@ -0,0 +1,70 @@
+# Generated by conda-lock.
+# platform: linux-64
+# input_hash: c741a250b9198dde712edc9f15753e8f58d55f89739bd81714ba4fee7c615367
+@EXPLICIT
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