Fix root directory calculation

HelikarLab · Oct 9, 2024 · b7e2c53 · b7e2c53
1 parent 2314bac
commit b7e2c53
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Showing 3 changed files with 11 additions and 12 deletions.
diff --git a/.github/workflows/container_build.yml b/.github/workflows/container_build.yml
@@ -80,5 +80,5 @@ jobs:
           tags: ${{ steps.metadata.outputs.tags }}
           labels: ${{ steps.metadata.outputs.labels }}
           builder: ${{ steps.buildx.outputs.name }}
-          platforms: ${{ matrix.platform }}
+          `platforms: ${{ matrix.platform }}
 
diff --git a/Dockerfile b/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

diff --git a/main/tests/test_project.py b/main/tests/test_project.py
@@ -9,9 +9,9 @@
 
 def test_config():
     configs = project.Config()
-    current_dir = Path(__file__).parent
+    root_dir = Path(__file__).parent.parent
 
-    assert configs.data_dir == current_dir / "data"
-    assert configs.config_dir == current_dir / "data" / "config_sheets"
-    assert configs.result_dir == current_dir / "data" / "results"
-    assert configs.code_dir == current_dir / "como"
+    assert configs.data_dir == root_dir / "data"
+    assert configs.config_dir == root_dir / "data" / "config_sheets"
+    assert configs.result_dir == root_dir / "data" / "results"
+    assert configs.code_dir == root_dir / "como"