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‎.github/workflows/docker-publish.yml‎

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

‎.gitignore‎

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**.ipynb_checkpoints
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**.DS_Store
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**.cache/
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**.ipython/
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**.jupyter/
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**.local/
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**.npm/

‎Dockerfile‎

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

‎LICENSE‎

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## Non-software content
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Copyright: Jordan Bourak & Tiffany Timbers
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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/)).
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This is a human-readable summary of (and not a substitute for) the [license](https://creativecommons.org/licenses/by/4.0/legalcode).
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You are free:
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* to **Share**---copy and redistribute the material in any medium or format
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* to **Adapt**---remix, transform, and build upon the material
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for any purpose, even commercially.
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The licensor cannot revoke these freedoms as long as you follow the
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license terms.
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Under the following terms:
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* **Attribution**---You must give appropriate credit (mentioning that
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your work is derived from work that is Copyright © Software
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Carpentry and, where practical, linking to
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http://software-carpentry.org/), provide a [link to the
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license][cc-by-human], and indicate if changes were made. You may do
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so in any reasonable manner, but not in any way that suggests the
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licensor endorses you or your use.
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**No additional restrictions**---You may not apply legal terms or
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technological measures that legally restrict others from doing
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anything the license permits. With the understanding that:
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Notices:
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* You do not have to comply with the license for elements of the
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material in the public domain or where your use is permitted by an
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applicable exception or limitation.
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* No warranties are given. The license may not give you all of the
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permissions necessary for your intended use. For example, other
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rights such as publicity, privacy, or moral rights may limit how you
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use the material.
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## Software
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Copyright: Jordan Bourak & Tiffany Timbers
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Except where otherwise noted, the software
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provided in the DSCI 310 individual assignment on reproducible reports
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is available under the
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[OSI][osi]-approved
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[MIT license][mit-license].
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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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
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This is a template repository
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for the individual assignment on Quarto reproducible reports using Python
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from the DSCI 522 (Workflows for data science) course.
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Instructions for this assignment can be found on the DSCI 522 course website.
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### Dependencies
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- [Docker](https://www.docker.com/)
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### Usage
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#### Setup
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> If you are using Windows or Mac, make sure Docker Desktop is running.
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1. Clone this GitHub repository.
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#### Running the analysis
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1. Navigate to the root of this project on your computer using the
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command line and enter the following command:
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```
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docker compose up
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```
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2. In the terminal, look for a URL that starts with
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`http://127.0.0.1:8888/lab?token=`
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(for an example, see the highlighted text in the terminal below).
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Copy and paste that URL into your browser.
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<img src="img/jupyter-container-web-app-launch-url.png" width=400>
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3. To run the analysis,
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open a terminal (in the docker jupyter lab) and run the following commands:
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```
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python scripts/generate_figures.py --input_dir="data/00030067-eng.csv" \
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--out_dir="results"
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quarto render reports/qmd_example.qmd --to html
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quarto render reports/qmd_example.qmd --to pdf
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```
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#### Clean up
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1. To shut down the container and clean up the resources,
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type `Cntrl` + `C` in the terminal
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where you launched the container, and then type `docker compose rm`
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## Developer notes
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### Developer dependencies
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- `conda` (version 23.9.0 or higher)
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- `conda-lock` (version 2.5.7 or higher)
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### Adding a new dependency
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1. Add the dependency to the `environment.yml` file on a new branch.
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2. Run `conda-lock -k explicit --file environment.yml -p linux-64` to update the `conda-linux-64.lock` file.
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2. Re-build the Docker image locally to ensure it builds and runs properly.
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3. Push the changes to GitHub. A new Docker
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image will be built and pushed to Docker Hub automatically.
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It will be tagged with the SHA for the commit that changed the file.
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4. Update the `docker-compose.yml` file on your branch to use the new
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container image (make sure to update the tag specifically).
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5. Send a pull request to merge the changes into the `main` branch.
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### License:
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The non-software content of this template repository is licensed under the
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[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License](https://creativecommons.org/licenses/by-nc-sa/4.0/).
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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

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# Generated by conda-lock.
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# platform: linux-64
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# input_hash: c741a250b9198dde712edc9f15753e8f58d55f89739bd81714ba4fee7c615367
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@EXPLICIT
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https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
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https://conda.anaconda.org/conda-forge/linux-64/dart-sass-1.58.3-ha770c72_1.conda#d54982a58cd9be3d00a7efe76ba6f60c
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