From dfe2d63135d6921ecc2bd5f256cc0e3771c1ae20 Mon Sep 17 00:00:00 2001
From: Anthony Gitter <gitter@biostat.wisc.edu>
Date: Wed, 10 Jul 2024 19:30:01 -0500
Subject: [PATCH 1/3] Restore Docker build tests

---
 .github/workflows/install-test.yml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/install-test.yml b/.github/workflows/install-test.yml
index 443b581..64016b4 100644
--- a/.github/workflows/install-test.yml
+++ b/.github/workflows/install-test.yml
@@ -17,19 +17,19 @@ jobs:
       run: docker pull agitter/singe:tmp
 #    Docker image build fails
 #    The repository 'http://deb.debian.org/debian stretch Release' does no longer have a Release file.
-#    - name: Build Docker image
-#      uses: docker/build-push-action@v1
-#      with:
-#        username: ${{ secrets.DOCKER_USERNAME }}
-#        password: ${{ secrets.DOCKER_PASSWORD }}
-#        path: .
-#        dockerfile: docker/Dockerfile
-#        repository: agitter/singe
-#        tags: tmp
-#        cache_froms: agitter/singe:tmp
-#        add_git_labels: true
-#        # Only push when running on the master branch
-#        push: ${{ github.ref == 'refs/heads/master' }}
+    - name: Build Docker image
+      uses: docker/build-push-action@v1
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        path: .
+        dockerfile: docker/Dockerfile
+        repository: agitter/singe
+        tags: tmp
+        cache_froms: agitter/singe:tmp
+        add_git_labels: true
+        # Only push when running on the master branch
+        push: ${{ github.ref == 'refs/heads/master' }}
     - name: Test SINGE
       run: |
         # Store the md5sums of the tracked source files before running tests in the Docker image

From b1d6b0dafb4a593e1c64c82d6d12680378211471 Mon Sep 17 00:00:00 2001
From: Anthony Gitter <gitter@biostat.wisc.edu>
Date: Wed, 10 Jul 2024 19:32:37 -0500
Subject: [PATCH 2/3] Update apt sources in Dockerfile Per
 https://github.com/Murali-group/Beeline/commit/e38d7d8a2a51a852981d491bd01dc98b08ce3edc

---
 docker/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 7548331..10ac738 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,6 +1,7 @@
 # MATLAB R2018a in a Debian environment
 FROM amarburg/matlab-runtime:R2018a
 
+RUN echo "deb http://archive.debian.org/debian stretch main contrib non-free" > /etc/apt/sources.list
 RUN apt-get update && \
     apt-get -y install libxt6 bzip2 && \
     rm -rf /var/lib/apt/lists/*

From 2fb2deea1a45da7bb7193a01388539079c040368 Mon Sep 17 00:00:00 2001
From: Anthony Gitter <gitter@biostat.wisc.edu>
Date: Wed, 10 Jul 2024 20:29:12 -0500
Subject: [PATCH 3/3] Update conda environment so Docker image builds

---
 docker/Dockerfile     | 2 +-
 tests/environment.yml | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 10ac738..8de1e1e 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -10,7 +10,7 @@ RUN apt-get update && \
 # Python is only needed for testing SINGE and could be removed from the base
 # to reduce the image size
 ENV PATH /opt/conda/bin:$PATH
-RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O ~/miniconda.sh && \
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh --no-check-certificate -O ~/miniconda.sh && \
     /bin/bash ~/miniconda.sh -b -p /opt/conda && \
     rm ~/miniconda.sh && \
     /opt/conda/bin/conda clean --all && \
diff --git a/tests/environment.yml b/tests/environment.yml
index e3136b0..10ba296 100644
--- a/tests/environment.yml
+++ b/tests/environment.yml
@@ -1,7 +1,9 @@
 name: singe-test
 dependencies:
+  - h5py=2.10.0
   - numpy=1.16.3
-  - pip=19.1
+  - pip=19.1.1
+  - python=3.7.11
   - scipy=1.2.1
   - pip:
     - csvdiff==0.3.3