From 05ab90f4003ed2512780088804015ee44f6a5ea2 Mon Sep 17 00:00:00 2001
From: Christopher Tomkins-Tinch <tomkinsc@broadinstitute.org>
Date: Wed, 20 Mar 2024 16:19:58 -0400
Subject: [PATCH] disallow actions/setup-python from changing environment
 variables

disallow actions/setup-python from changing environment variables; see:
https://github.com/actions/runner/issues/781
https://github.com/actions/setup-python/pull/411
---
 .github/workflows/build.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 6697202a..ab4c9812 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -175,6 +175,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "${{ env.GITHUB_ACTIONS_PYTHON_VERSION }}"
+          update-environment: false
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
       - name: pull docker image
@@ -184,10 +185,12 @@ jobs:
           echo "DOCKER_TAG=$DOCKER_TAG" >> $GITHUB_ENV
           echo "pulling $DOCKER_TAG"
           docker pull $DOCKER_TAG
+          cat /proc/cpuinfo
+          ls -lah .
           mkdir coverage
       - name: test with docker
         run: |
-          docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test:rw --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; env; python -c "import locale; print(locale.getpreferredencoding(False))"; pytest test/unit; cp .coverage /coverage'
+          docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test:rw --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; env; echo $LD_LIBRARY_PATH; python -c "import locale; print(locale.getpreferredencoding(False))"; pytest test/unit; cp .coverage /coverage'
       - name: run coveralls
         run: |
           mv coverage/.coverage .