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| # A list of items to ignore when building the docker image | ||
| /.github | ||
| /doc | ||
| /docs | ||
| /docker_old | ||
| /.gitattributes | ||
| /Dockerfile_test | ||
| /.gitignore | ||
| /README.md | ||
| /pipelines/py/rlogs | ||
| /pipelines/py/.ipynb_checkpoints | ||
| /main/py/tests | ||
| /main/py/.pytest_cache | ||
| /main/py/rlogs | ||
| /main/py/.Rhistory |
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@@ -7,74 +7,64 @@ on: | |
| # - 'bulk_dev' | ||
| # - "master" | ||
| workflow_dispatch: | ||
| schedule: | ||
| # Every day at midnight | ||
| - cron: '0 0 * * *' | ||
| push: | ||
| tags: | ||
| - "*" | ||
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| env: | ||
| REGISTRY: ghcr.io | ||
| IMAGE_NAME: ${{ github.repository }} | ||
| DEBIAN_FRONTEND: noninteractive | ||
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| jobs: | ||
| # This job will check if there has been a push to the master branch within the past day | ||
| # If there has been a push to the master branch, then it will run the build job | ||
| # From: https://github.com/doxygen/doxygen/blob/68b134f1457aa88553665c3bb77b85154436bf4c/.github/workflows/coverity.yml#L16 | ||
| check_build: | ||
| build-and-push-image: | ||
| runs-on: ubuntu-20.04 | ||
| name: Check Latest Commit | ||
| outputs: | ||
| should_run: ${{ steps.should_run.outputs.should_run }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Get Latest Commit Hash | ||
| run: echo ${{ github.sha }} | ||
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| - id: should_run | ||
| continue-on-error: true | ||
| name: Check if commit <24 hours | ||
| if: ${{ github.event_name == 'schedule' }} | ||
| run: test -z $(github rev-list --after="24 hours" %{{ github.sha }}) && echo "::set-output name=should_run::false" | ||
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| dockerhub: | ||
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| # Only run the docker build if we have a commit within the past 24 hours | ||
| needs: check_build | ||
| if: ${{ needs.check_build.outputs.should_run != 'false' }} | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: read | ||
| packages: write | ||
| name: Build Docker Image | ||
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| env: | ||
| DEBIAN_FRONTEND: noninteractive | ||
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| steps: | ||
| # Checkout the repository | ||
| - name: Checkout Repository | ||
| uses: actions/[email protected] | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ github.GITHUB_REF }} | ||
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| - name: Log in to Container Registry | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| registry: ${{ env.REGISTRY }} | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
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| # Get tag/release information for docker tags | ||
| - name: Docker Metadata | ||
| id: metadata | ||
| uses: docker/metadata-action@v4 | ||
| with: | ||
| flavor: | | ||
| latest=false | ||
| prefix= | ||
| suffix= | ||
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | ||
| tags: | | ||
| type=semver,pattern={{version}} | ||
| type=raw,value=latest,enable=${{ startsWith(github.ref, 'refs/tags/master') }} | ||
| - name: Set up QEMU | ||
| uses: docker/setup-qemu-action@v2 | ||
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| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v2 | ||
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| - name: Login to Docker Hub | ||
| uses: docker/[email protected] | ||
| with: | ||
| username: ${{ secrets.DOCKERHUB_USERNAME }} | ||
| password: ${{ secrets.DOCKERHUB_TOKEN }} | ||
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| # Set the tag based on the current branch | ||
| - name: Test if Master Branch | ||
| continue-on-error: true | ||
| if: ${{ github.ref_name == 'master' }} | ||
| run: echo 'DOCKER_TAG=development' >> $GITHUB_ENV | ||
| - name: Set non-Master Branch Tag | ||
| continue-on-error: true | ||
| if: ${{ github.ref_name != 'master' }} | ||
| run: echo 'DOCKER_TAG=${{ github.ref_name }}' >> $GITHUB_ENV | ||
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| - name: Build and push | ||
| uses: docker/build-push-action@v3 | ||
| with: | ||
| context: . | ||
| push: true | ||
| tags: babessell/madrid:${{env.DOCKER_TAG}} | ||
| cache-from: type=gha | ||
| cache-to: type=gha,mode=max | ||
| tags: ${{ steps.metadata.outputs.tags }} | ||
| labels: ${{ steps.metadata.outputs.labels }} | ||
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| @@ -0,0 +1,42 @@ | ||
| name: Unit Tests | ||
| on: | ||
| push: | ||
| tags: | ||
| - "*" | ||
| pull_request: | ||
| workflow_dispatch: | ||
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| jobs: | ||
| unit_tests: | ||
| runs-on: ubuntu-latest | ||
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| # Using a matrix lets us define additional versions of Python to test against | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.10"] | ||
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| steps: | ||
| - name: Checkout Repository | ||
| uses: actions/checkout@v3 | ||
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| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install --requirement main/py/tests/requirements.txt | ||
| - name: Lint with flake8 | ||
| run: | | ||
| # stop the build if there are Python syntax errors or undefined names | ||
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | ||
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | ||
| # Change into the GITHUB_WORKSPACE /home/runner/work/REPO/REPO and execute tests | ||
| - name: Run tests | ||
| run: pytest |
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| Original file line number | Diff line number | Diff line change |
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| Call clustering after merging | ||
| Want to all cluster replicates at replicate level, batch level, and source level | ||
| S1R* (replicate) | ||
| S*R* (sample/batch) | ||
| transcriptomics (source) | ||
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| Follow combine_distributions.R script as template | ||
| Memory usage may be an issue | ||
| Create a dataframe for all samples? | ||
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| 1. Read clustering R script | ||
| 2. Read merging R script | ||
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| -------------- | ||
| Steps | ||
| -------------- | ||
| 1. Add flag to merge_xomics.py that turns on clustering | ||
| - If this flag is ON, require the option to use binarized data or z scores, and clustering parameter arguments | ||
| 2. Modify (or rewrite) combine_distributions.R (which is called from merge_xomics.py) that: | ||
| - reads zFPKMs/TPM/CPM for each replicate | ||
| + binarizes them if given zFPKM argument in #1 | ||
| + Look at the kOverA function in RNAseq.R to see how to binarize zFPKM data | ||
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| 3. Cluster all replicates for all batches/studies across all cell types (contexts) within a single data source | ||
| 4. Cluster all replicates for all batches/studies across all data sources within one cell type | ||
| 5. Cluster all batches/studies across all cell types (contexts) within one data source at a time | ||
| 6. Cluster all batches/studies across all data sources within one cell type | ||
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| [X] So add a flag to merge that turns on clustering. | ||
| [ ] This flag also demands args that tell it whether to use binarzied data or z scores, and clustering parameter args | ||
| [ ] Also take args for which data sources to check. | ||
| [ ] If the args are using binarized data, it should take argument specifying z-transformed, tpm-quantile, or cpm | ||
| [ ] If using proteomics at all, tpm-quantile and cpm should return an error saying that proteomics and transcriptomics can only be compared with z-transform |
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| Lower bound: Uptake of nutrients | ||
| - "-1" = 1 mmol/hour | ||
| Upper bound: Secretion of nutrients | ||
| Forward or Reverse direction (reverse only for reversible directions) | ||
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| For basal metabolites, set -1000/1000 lower/upper bounds | ||
| Glucose is primary carbon source when proliferating | ||
| All amino acids are required | ||
| - Tight constraints: not in abundance in the body, residues can act as limiting factor | ||
| - Set lower bound as -1 to limit uptake | ||
| Fatty Acids | ||
| - Make lower bound 0 if I am positive NK cell does not uptake | ||
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| Table w/ all media conditions |
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@@ -162,5 +162,3 @@ | |
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| # import mapping | ||
| from . import apps | ||
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| # import dev | ||
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| --- | ||
| title: "Page Not Found" | ||
| search: exclude | ||
| --- | ||
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| Sorry, but the page you were trying to view does not exist. Try searching for it or looking at the URL to see if it looks correct. |
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