diff --git a/.github/workflows/test-terra-jupyter-aou.yml b/.github/workflows/test-terra-jupyter-aou.yml index d3412f11..ead1cd53 100644 --- 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 index 2d61c72a..08975a76 100644 --- 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 index d537b728..ff1967fb 100644 --- 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 index cc6c777d..82ab4d03 100644 --- 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 index 1c903ca7..3b88c058 100644 --- 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 index 20437798..8795ddea 100644 --- 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"