From 4f96cd102f189bc5b5ba624e8494593dd4d3d57a Mon Sep 17 00:00:00 2001
From: jmtcsngr <jmtc@sanger.ac.uk>
Date: Thu, 28 Nov 2024 17:17:40 +0000
Subject: [PATCH] switch default conda for miniforge

---
 .github/workflows/testing.yml | 34 +++++++++++++++++++---------------
 scripts/install_miniforge.sh  | 26 ++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 15 deletions(-)
 create mode 100755 scripts/install_miniforge.sh

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index aa980b6..45f0758 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -16,36 +16,40 @@ jobs:
 
     env:
       NPM_CONFIG_PREFIX: "$HOME/.npm-global"
+      CONDA_HOME: "$HOME/conda"
+      CONDA_TEST_ENV: test-environment
 
     name: Node ${{ matrix.node }} on ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: '0'
 
-    - name: Initialize Miniconda
+    - name: "Install Miniforge"
       run: |
-          echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile"
-    - name: Cache conda
-      id: minicondaCache
+        CONDA_HOME=${{ env.CONDA_HOME }} ./scripts/install_miniforge.sh
+        echo 'source "${{ env.CONDA_HOME }}/etc/profile.d/conda.sh"' >> "$HOME/.bash_profile"
+
+    - name: "Cache Conda"
+      id: miniforgeCache
       uses: actions/cache@v4
       with:
         path: |
           ~/conda/pkgs
           ~/conda/envs
-        key: ${{ matrix.os }}-build-miniconda
+        key: ${{ runner.os }}-build-miniforge
 
-    - name: install conda client and set up conda environment
+    - name: "Install Conda packages"
       run: |
-          conda config --prepend pkgs_dirs ~/conda/pkgs
-          conda config --prepend envs_dirs ~/conda/envs
-          conda config --set auto_update_conda False
-          conda info
-          conda create -y -n "$CONDA_TEST_ENV"
-          conda install -y -n "$CONDA_TEST_ENV" nodejs=="${{ matrix.node }}"
-      env:
-        CONDA_TEST_ENV: test-environment
+        conda config --prepend pkgs_dirs ${{ env.CONDA_HOME }}/pkgs
+        conda config --prepend envs_dirs ${{ env.CONDA_HOME }}/envs
+        conda info
+        conda create  -y -n "${{ env.CONDA_TEST_ENV }}"
+        conda install -y -n "${{ env.CONDA_TEST_ENV }}" nodejs=="${{ matrix.node }}"
 
     - name: Run install scripts
       run: |
+          conda activate "${{ env.CONDA_TEST_ENV }}"
           mkdir -p "$NPM_CONFIG_PREFIX"
           npm install -g bower grunt-cli node-qunit-phantomjs
           npm install
@@ -54,7 +58,7 @@ jobs:
 
     - name: run script
       run: |
+          conda activate "${{ env.CONDA_TEST_ENV }}"
           export PATH="$NPM_CONFIG_PREFIX/bin:$PATH"
-          conda activate "$CONDA_TEST_ENV"
           conda info --envs
           ${GITHUB_WORKSPACE}/scripts/script.sh
diff --git a/scripts/install_miniforge.sh b/scripts/install_miniforge.sh
new file mode 100755
index 0000000..1e19a3c
--- /dev/null
+++ b/scripts/install_miniforge.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+#
+# Once installed, the Conda environment can be activated by running:
+#
+# source $CONDA_HOME/etc/profile.d/conda.sh
+#
+# conda activate
+set -ex
+MINIFORGE_VERSION="24.9.0-0"
+MINIFORGE_SHA256="77fb505f6266ffa1b5d59604cf6ba25948627e908928cbff148813957b1c28af"
+CONDA_HOME=${CONDA_HOME:="$HOME/conda"}
+export CONDA_HOME
+CONDARC="$HOME/.condarc"
+export CONDARC
+cat <<EOF > "$CONDARC"
+auto_update_conda: false
+always_yes: true
+ssl_verify: true
+show_channel_urls: true
+channels:
+  - conda-forge
+EOF
+curl -sSL "https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Mambaforge-${MINIFORGE_VERSION}-Linux-x86_64.sh" -o ./miniforge.sh
+sha256sum ./miniforge.sh | grep "$MINIFORGE_SHA256"
+/bin/bash ./miniforge.sh -b -p "$CONDA_HOME"
+rm ./miniforge.sh