try adding required dependency to test install

DataBiosphere · Jul 6, 2023 · 5cfa711 · 5cfa711
1 parent 59c88e6
commit 5cfa711
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/.github/workflows/test-terra-jupyter-aou.yml b/.github/workflows/test-terra-jupyter-aou.yml
@@ -106,7 +106,7 @@ jobs:
           --workdir=/tests \
           --entrypoint="" \
           terra-jupyter-aou:smoke-test \
-          /bin/bash -c 'pip3 install pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-aou/tests/'
+          /bin/bash -c 'pip3 install --upgrade pip; pip3 install --user pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-aou/tests/'
 
     - name: Test Python code specific to notebooks with nbconvert
       # Simply 'Cell -> Run All` these notebooks and expect no errors in the case of a successful run of the test suite.

diff --git a/.github/workflows/test-terra-jupyter-base.yml b/.github/workflows/test-terra-jupyter-base.yml
@@ -86,4 +86,4 @@ jobs:
           --workdir=/tests \
           --entrypoint="" \
           terra-jupyter-base:smoke-test \
-          /bin/sh -c "pip3 install pytest; pytest"
+          /bin/sh -c "pip3 install --upgrade pip; pip3 install --user pytest; pytest"
diff --git a/.github/workflows/test-terra-jupyter-gatk.yml b/.github/workflows/test-terra-jupyter-gatk.yml
@@ -106,7 +106,7 @@ jobs:
           --workdir=/tests \
           --entrypoint="" \
           terra-jupyter-gatk:smoke-test \
-          /bin/bash -c 'pip3 install pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-gatk/tests/'
+          /bin/bash -c 'pip3 install --upgrade pip; pip3 install --user pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-gatk/tests/'
 
     - name: Test Python code specific to notebooks with nbconvert
       # Simply 'Cell -> Run All` these notebooks and expect no errors in the case of a successful run of the test suite.

diff --git a/.github/workflows/test-terra-jupyter-hail.yml b/.github/workflows/test-terra-jupyter-hail.yml
@@ -106,7 +106,7 @@ jobs:
           --workdir=/tests \
           --entrypoint="" \
           terra-jupyter-hail:smoke-test \
-          /bin/bash -c 'pip3 install pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-hail/tests/'
+          /bin/bash -c 'pip3 install --upgrade pip; pip3 install --user pytest ; pytest terra-jupyter-python/tests/ terra-jupyter-hail/tests/'
 
     - name: Test Python code specific to notebooks with nbconvert
       # Simply 'Cell -> Run All` these notebooks and expect no errors in the case of a successful run of the test suite.

diff --git a/.github/workflows/test-terra-jupyter-python.yml b/.github/workflows/test-terra-jupyter-python.yml
@@ -112,7 +112,7 @@ jobs:
           --workdir=/tests \
           --entrypoint="" \
           terra-jupyter-python:smoke-test \
-          /bin/sh -c "pip3 install pytest ; pytest"
+          /bin/sh -c "pip3 install --upgrade pip; pip3 install --user pytest ; pytest"
           
     - name: Test Python code specific to notebooks with nbconvert
       # Simply 'Cell -> Run All` these notebooks and expect no errors in the case of a successful run of the test suite.

diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile
@@ -264,7 +264,7 @@ RUN echo "alias cromshell='cromshell-beta'" >> ~/.bash_aliases
 
 # Downgrade Jinja2 as the newer version breaks the notebook
 # See https://jinja.palletsprojects.com/en/3.1.x/changes/#version-3-1-0
-RUN pip install --force-reinstall -v "Jinja2==3.0.3"
+RUN pip install -v "Jinja2==3.0.3"
 
 ENV PATH="$PATH:/usr/local/RepeatMasker"