Merge pull request #10 from HelikarLab/fix/remove-microarray

Remove microarray references as they are no longer used

.github/workflows/unit_tests.yml

@@ -35,6 +35,6 @@ jobs:
             python=${{ matrix.python-version }}
 
       - name: Run tests
-        run: python -m pytest
+        run: "cd main && python -m pytest"
         shell: micromamba-shell {0}
 

.gitignore

@@ -19,7 +19,6 @@ main/data/results/
 main/data/config_sheets/*_data_inputs_auto.xlsx
 main/data/gene_info.csv
 main/data/Repurposing_Hub_Preproc.tsv
-main/microarray.db
 main/data/config_sheets/*
 main/data/GSE*_RAW
 main/data/gpl*entrez.csv

Dockerfile

@@ -12,14 +12,13 @@ RUN sed -i '/^python/d' /opt/conda/conda-meta/pinned && \
     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" && \
-    conda config --quiet --add channels conda-forge && \
-    conda config --quiet --add channels bioconda && \
-    conda config --quiet --add channels r && \
-    rm -rf "${HOME}/main/tests"  # Remove tests, they are not required for running COMO
+    mamba config --quiet --add channels conda-forge && \
+    mamba config --quiet --add channels bioconda && \
+    mamba config --quiet --add channels r && \
+    rm -rf "${HOME}/main/tests"  # Tests not required for running COMO
 
 # Update base environment
-RUN ls "${HOME}" && \
-    mamba env update --name=base --file="${HOME}/environment.yaml" && \
+RUN mamba env update --name=base --file="${HOME}/environment.yaml" && \
     R -e "devtools::install_github('babessell1/zFPKM')" && \
     pip cache purge && \
     mamba clean --all --yes