From c812d61ad3241deeff55b5a511ba48d9f98b6302 Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Mon, 29 Jul 2024 11:19:41 -0400
Subject: [PATCH 1/2] CI: Update Dockerfile

Trying to understand intermittent GHA failures
---
 Dockerfile | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 101c565d..fe563f7a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,7 +30,11 @@ RUN conda update -c defaults conda && \
 
 WORKDIR /usr/local/src
 COPY environment.yml .
-RUN conda env update -n base
+RUN echo "CONDA INFO: " && \
+    conda info && \
+    conda config --show-sources && \
+    echo "Updating conda" && \
+    conda env update -n base
 COPY . .
 
 # number of parallel make jobs

From 56bfccf0c7058c01c7a7e78baa4b1d9f84cc66ba Mon Sep 17 00:00:00 2001
From: Philip A Cook <cookpa@pennmedicine.upenn.edu>
Date: Mon, 29 Jul 2024 14:10:39 -0400
Subject: [PATCH 2/2] ENH: Activate conda env

---
 Dockerfile | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index fe563f7a..6e1d2739 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,7 +2,7 @@
 # Note: QEMU emulated ppc64le build might take ~6 hours
 
 # Use conda to resolve dependencies cross-platform
-FROM debian:bookworm-slim as builder
+FROM debian:bookworm as builder
 
 # install libpng to system for cross-architecture support
 # https://github.com/ANTsX/ANTs/issues/1069#issuecomment-681131938
@@ -22,24 +22,26 @@ RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py310_23.11.0-1-
     && rm Miniconda3-py310_23.11.0-1-Linux-$(uname -m).sh
 ENV PATH=/opt/conda/bin:$PATH
 
-# install cmake binary using conda for multi-arch support
-# apt install fails because libssl1.0.0 is not available for newer Debian
-RUN conda update -c defaults conda && \
-    conda install -c conda-forge cmake && \
-    conda config --set solver classic
-
 WORKDIR /usr/local/src
+
 COPY environment.yml .
-RUN echo "CONDA INFO: " && \
+
+# Activate the base environment and update it
+RUN . /opt/conda/etc/profile.d/conda.sh && \
+    conda activate base && \
     conda info && \
     conda config --show-sources && \
     echo "Updating conda" && \
-    conda env update -n base
+    conda env update -n base && \
+    echo "installing cmake" && \
+    conda install -c conda-forge cmake
+
 COPY . .
 
 # number of parallel make jobs
 ARG j=2
-RUN pip --no-cache-dir -v install .
+RUN . /opt/conda/etc/profile.d/conda.sh && \
+    pip --no-cache-dir -v install .
 
 # run tests
 RUN bash tests/run_tests.sh