Model Checking (#167)

Author: JoshLoecker

.github/workflows/container_build.yml

@@ -11,11 +11,17 @@ env:
 
 jobs:
   build-and-push-image:
+    name: Build and Push Docker Image
     runs-on: ubuntu-20.04
     permissions:
       contents: read
       packages: write
-    name: Build and Push Docker Image
+
+    # A matrix platform is used here to expand functionality for building for additional architectures
+    # For example, intel/amd (linux/amd64) or Apple Silicon (arm64)
+    strategy:
+      matrix:
+        platform: [ linux/amd64 ]
 
     steps:
       # Checkout the repository
@@ -38,21 +44,21 @@ jobs:
             type=semver,pattern={{version}}
             type=raw,value=latest,enable=${{ startsWith(github.ref, 'refs/tags/') && endsWith(github.ref, 'master') }}
 
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-        with:
-          platforms: linux/amd64
-
       - name: Set up Docker Buildx
         id: buildx
         uses: docker/setup-buildx-action@v3
 
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: ${{ matrix.platform }}
 
-      - name: Clean Jupyter Notebook Outputs
+      - name: Set up Jupyter Notebook Cleaner
         uses: actions/setup-python@v4
         with:
           python-version: "3.10"
-      - name: Clean Notebook Output
+
+      - name: Clean Jupyter Notebook Outputs
         run: |
           python -m pip install --upgrade nbstripout --no-cache-dir
           find $GITHUB_WORKSPACE -name "*.ipynb" -exec nbstripout "{}" \;
@@ -74,5 +80,5 @@ jobs:
           tags: ${{ steps.metadata.outputs.tags }}
           labels: ${{ steps.metadata.outputs.labels }}
           builder: ${{ steps.buildx.outputs.name }}
-          platforms: linux/amd64
+          platforms: ${{ matrix.platform }}
 

.github/workflows/unit_tests.yml

@@ -22,24 +22,19 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install Conda environment
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: main/src/tests/environment.yaml
+          environment-file: main/tests/environment.yaml
           environment-name: como_tests
-          extra-specs: |
+          micromamba-version: "latest"
+          init-shell: bash
+          cache-environment: true
+          cache-downloads: true
+          post-cleanup: "none"
+          create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Lint with flake8
-        run: |
-          # Initialize micromamba and activate como_tests environment
-          eval "$(micromamba shell hook --shell=bash)" && micromamba activate como_tests
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
       - name: Run tests
-        run: |
-          # Initialize micromamba and activate como_tests environment
-          eval "$(micromamba shell hook --shell=bash)" && micromamba activate como_tests
-          python -m pytest
+        run: python -m pytest
+        shell: micromamba-shell {0}
+

.gitignore

@@ -16,3 +16,4 @@
 /main/data/gene_info.csv
 /main/data/Repurposing_Hub_Preproc.tsv
 /main/microarray.db
+/main/data/config_sheets/*

Dockerfile

@@ -1,27 +1,35 @@
-FROM jupyter/r-notebook:latest
+FROM jupyter/r-notebook:latest as builder
 
-COPY /environment.yaml "${HOME}/environment.yaml"
-COPY --chown=1000:100 main "${HOME}"/main
+COPY environment.yaml "${HOME}/environment.yaml"
+COPY --chown=1000:100 main "${HOME}/main"
 
 # Install python-related items
 # Remove "python" from the pinned file so we can install our own version
 RUN sed -i '/^python/d' /opt/conda/conda-meta/pinned && \
     echo "auto_activate_base: true" >> "${HOME}/.condarc" && \
-    conda config --quiet --add channels conda-forge && \
-    conda config --quiet --add channels bioconda && \
-    conda config --quiet --add channels r && \
-    # Update base environment
-    mamba env update --name=base --file="${HOME}/environment.yaml" && \
-    R -e "devtools::install_github('babessell1/zFPKM')" && \
-    # Trust the jupyter notebook
     jupyter trust "${HOME}/main/COMO.ipynb" && \
     echo "c.ServerApp.ip = '0.0.0.0'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
     echo "c.ServerApp.root_dir = '${HOME}/main'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
     echo "c.ServerApp.token = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
     echo "c.ServerApp.password = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
-    # Purge cache information, reducing image size
+    conda config --quiet --add channels conda-forge && \
+    conda config --quiet --add channels bioconda && \
+    conda config --quiet --add channels r && \
+    rm -rf "${HOME}/main/tests"  # Remove tests, they are not required for running COMO
+
+# Update base environment
+RUN ls "${HOME}" && \
+    mamba env update --name=base --file="${HOME}/environment.yaml" && \
+    R -e "devtools::install_github('babessell1/zFPKM')" && \
     pip cache purge && \
-    conda clean --all --yes --force-pkgs-dirs && \
-    rm -f "${HOME}/environment.yaml"
+    mamba clean --all --yes
+
+FROM jupyter/r-notebook:latest
+
+COPY --from=builder ${HOME} ${HOME}
+
+RUN pip cache purge && \
+    conda clean --all --yes
 
+EXPOSE 8888
 VOLUME /home/joyvan/main/data/local_files

environment.yaml

@@ -1,9 +1,12 @@
 name: como
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - gurobi
   - anaconda
+
+# Use the ~= specifier to allow any minor updates
+# For example, "~=4.0" requires version 4.0, but does not allow version 5.0
 dependencies:
   - anaconda::lxml~=4.9.1
   - bioconda::bioconductor-affyio~=1.64.0
@@ -16,25 +19,21 @@ dependencies:
   - bioconda::bioconductor-hgu133acdf~=2.18.0
   - bioconda::bioconductor-limma~=3.50.1
   - bioconda::crux-toolkit~=4.1
-  - bioconda::escher==1.7.*
   - bioconda::thermorawfileparser~=1.4.0
   - conda-forge::aioftp~=0.21.2
-  - conda-forge::bioservices~=1.11.2
-  - conda-forge::cobra<=1.0.0
+  # - conda-forge::bioservices~=1.11.2
+  - conda-forge::cobra~=0.29.0
   - conda-forge::geoparse~=2.0.3
-  - conda-forge::git~=2.37.0
-  #  - conda-forge::jupyterlab-spreadsheet-editor==0.6.*
+  # - conda-forge::git~=2.37.0
   - conda-forge::jupyterlab~=4.0.0
-  - conda-forge::markupsafe~=2.0.1
   - conda-forge::numpy~=1.23.0
   - conda-forge::openpyxl~=3.0.10
-  - conda-forge::optlang~=1.5.2
+  # - conda-forge::optlang~=1.5.2
   - conda-forge::pandas<=3.0.0
-  - conda-forge::pip~=22.1.2
+  - conda-forge::pip
   - conda-forge::python-libsbml~=5.19.2
   - conda-forge::python~=3.10
-  # - conda-forge::r-base~=4
-  # - conda-forge::r-base
+  - conda-forge::r-base
   - conda-forge::r-biocmanager~=1.30.18
   - conda-forge::r-devtools~=2.4.3
   - conda-forge::r-factominer~=2.8
@@ -50,18 +49,20 @@ dependencies:
   - conda-forge::r-tidyverse~=1.3.1
   - conda-forge::r-uwot~=0.1.11
   - conda-forge::r-zoo~=1.8_10
-  - conda-forge::requests~=2.28.1
+  # - conda-forge::requests~=2.28.1
   - conda-forge::rpy2~=3.5.1
-  - conda-forge::scipy~=1.8.1
+  # - conda-forge::scipy~=1.8.1
   - conda-forge::sqlalchemy~=1.4.39
   - conda-forge::tqdm~=4.64.1
-  - conda-forge::unidecode~=1.3.4
-  - conda-forge::wget~=1.20.3
-  - conda-forge::xlrd~=2.0.1
-  - gurobi::gurobi~=10.0
+  # - conda-forge::unidecode~=1.3.4
+  # - conda-forge::wget~=1.20.3
+  # - conda-forge::xlrd~=2.0.1
+  - gurobi::gurobi
   - pip:
       - async_bioservices
+      # - escher==1.7.3
+      - git+https://github.com/JoshLoecker/escher.git@python38#subdirectory=py
       - framed==0.5.*
-      - memote==0.13.*
+      - memote<=1.0
       - git+https://github.com/JoshLoecker/cobamp.git
       - git+https://github.com/JoshLoecker/troppo.git

main/COMO.ipynb

@@ -786,7 +786,7 @@
     "import cobra\n",
     "import os\n",
     "from pathlib import Path\n",
-    "from project import configs\n",
+    "from src.project import configs\n",
     "\n",
     "user_map_dir = Path(f\"{configs.datadir}/local_files/maps/\")\n",
     "map_dict = {\n",
@@ -818,7 +818,8 @@
     "                                  \"results\",\n",
     "                                  context,\n",
     "                                  f\"{context}_SpecificModel_{recon_algorithm}.json\")\n",
-    "        \n",
+    "\n",
+    "        print(f\"Loading '{context}', this may take some time...\")\n",
     "        model = cobra.io.load_json_model(model_json)\n",
     "        for key in map_dict.keys():\n",
     "            print(f\"Running with: {key}\")\n",
@@ -1049,7 +1050,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.11.6"
   },
   "toc-autonumbering": true,
   "toc-showcode": true

main/data/config_sheets/mrnaseq_data_inputs_auto.xlsx

@@ -0,0 +1,92 @@
+Abbreviation
+D_LACtm
+HEX1
+FBP
+PFK
+FBA2
+GAPD
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+PGK
+ENO
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+PGMT
+TPI
+PYK
+LDH_L
+PDHm
+PEPCK
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+r0354
+r0355
+G6PPer
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+CSm
+ACONTm
+ICDHxm
+ICDH_m
+AKGDm
+SUCD1m
+FUMm
+MDHm
+SUCOAS1m
+SUCOASm
+ACITL
+ACCOAC
+ADRNCPT1
+C160CPT1
+C161CPT1
+C161CPT12
+CLPNDCPT1
+DCSPTN1CPT1
+DLNLCGCPT1
+EICOSTETCPT1
+ELAIDCPT1
+LNELDCCPT1
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+LNLNCACPT1
+LNLNCGCPT1
+STRDNCCPT1
+TETPENT3CPT1
+TETPENT6CPT1
+TETTET6CPT1
+TMNDNCCPT1
+CATC140_c
+HMR_2602
+HMR_2608
+HMR_2611
+HMR_2620
+HMR_2633
+HMR_2648
+HMR_2651
+HMR_2657
+HMR_2660
+HMR_2666
+HMR_2669
+HMR_2675
+HMR_2681
+HMR_2684
+HMR_2687
+HMR_2690
+HMR_2693
+HMR_2699
+HMR_2702
+HMR_2705
+HMR_2708
+HMR_2711
+HMR_2733
+HMR_2736
+HMR_2739
+HMR_2768
+HMR_2771
+HMR_2774
+ATPS4mi
+CYOOm2i
+CYOR_u10mi
+NADH2_u10mi
+CYOOm3i
+FADH2ETC
+GLYC3PFADm
+PGL
+GNDc
+G6PDH2c
+r0249