From f12a5386363c93ad69e06b40f0c64a7ef480a169 Mon Sep 17 00:00:00 2001
From: Ryan Tock <ryan@tocks.org>
Date: Thu, 29 May 2025 01:30:52 -0700
Subject: [PATCH] improved bash scripting for conda setup

---
 .gitignore                      |  3 ++
 setup/activate_conda.sh         |  7 ++++
 setup/checks/check_for_conda.sh |  7 ++--
 setup/export_versions.sh        |  3 ++
 setup/setup.sh                  |  5 +--
 setup/setup_conda.sh            | 63 +++++++++++++++++++++++----------
 setup/teardown.sh               |  3 +-
 setup/teardown_conda.sh         |  8 ++---
 8 files changed, 66 insertions(+), 33 deletions(-)
 create mode 100644 setup/activate_conda.sh
 create mode 100644 setup/export_versions.sh

diff --git a/.gitignore b/.gitignore
index ad8685f1..3d040f3c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -73,6 +73,9 @@ docs/_build/
 # PyBuilder
 target/
 
+# Conda
+miniconda.sh
+
 # Jupyter Notebook
 .ipynb_checkpoints
 
diff --git a/setup/activate_conda.sh b/setup/activate_conda.sh
new file mode 100644
index 00000000..e796cb11
--- /dev/null
+++ b/setup/activate_conda.sh
@@ -0,0 +1,7 @@
+source setup/export_versions.sh
+
+INSTALL_PREFIX=$HOME/miniconda-$EXP_CONDA_VER
+SOURCE_SCRIPT="$HOME/miniconda-$EXP_CONDA_VER/etc/profile.d/conda.sh"
+
+source $SOURCE_SCRIPT
+conda activate emissioneval
\ No newline at end of file
diff --git a/setup/checks/check_for_conda.sh b/setup/checks/check_for_conda.sh
index 722e6053..1bf8f12d 100644
--- a/setup/checks/check_for_conda.sh
+++ b/setup/checks/check_for_conda.sh
@@ -1,9 +1,10 @@
+source setup/export_versions.sh
 CURR_CONDA_VER=`conda --version | cut -d " " -f 2`
-EXP_CONDA_VER=23.1.0
 
-if [ $CURR_CONDA_VER == $EXP_CONDA_VER ]; then
+if [[ $CURR_CONDA_VER == $EXP_CONDA_VER ]]; then
     echo "For conda, found $CURR_CONDA_VER, expected $EXP_CONDA_VER, all is good!"
 else
-    echo "For conda, found $CURR_CONDA_VER, expected $EXP_CONDA_VER, run 'bash setup/setup_conda.sh $EXP_CONDA_VER <platform>' to get the correct version"
+    echo "For conda, found $CURR_CONDA_VER, expected $EXP_CONDA_VER, run 'bash setup/setup_conda.sh <platform>' to get the correct version"
     echo "Or install manually after downloading from https://repo.anaconda.com/miniconda/"
 fi
+
diff --git a/setup/export_versions.sh b/setup/export_versions.sh
new file mode 100644
index 00000000..dfc4557d
--- /dev/null
+++ b/setup/export_versions.sh
@@ -0,0 +1,3 @@
+export EXP_CONDA_VER=23.1.0
+export EXP_CONDA_VER_SUFFIX=1
+export EXP_LIBMAMBA_VER=1.0.0
\ No newline at end of file
diff --git a/setup/setup.sh b/setup/setup.sh
index a0d3af9d..893432c9 100755
--- a/setup/setup.sh
+++ b/setup/setup.sh
@@ -5,10 +5,7 @@
 # - on OSX: /Users/<user>/miniconda3/bin/conda
 # - on Windows: C:/Users/<user>/Miniconda3/Scripts/conda
 
-set -e
-
 source setup/checks/check_for_conda.sh
 
-conda create -n emissioneval
+echo "Installing using conda now"
 conda env update --name emissioneval --file setup/environment.yml
-conda activate emissioneval
diff --git a/setup/setup_conda.sh b/setup/setup_conda.sh
index de6b0179..b67f05d8 100644
--- a/setup/setup_conda.sh
+++ b/setup/setup_conda.sh
@@ -1,21 +1,48 @@
-EXP_CONDA_VER=$1
-PLATFORM=$2
-echo "Installing for version $EXP_CONDA_VER and platform $PLATFORM"
+if [[ ! -f setup/export_versions.sh ]]; then
+    echo "Error: setup/export_versions.sh file is missing. Please ensure it exists before running this script."
+    exit 1
+fi
+
+source setup/export_versions.sh
+if [[ $? -ne 0 ]]; then
+    echo "Error: Failed to source setup/export_versions.sh. Please check the file for errors."
+    exit 1
+fi
+
+if [[ -z $EXP_CONDA_VER ]]; then
+    echo "Error: Requires the EXP_CONDA_VER variable to be set"
+    echo "Please check the 'export_versions.sh' script and ensure that it works"
+    exit 1
+fi
 
-if [[ -z $EXP_CONDA_VER || -z $PLATFORM ]]; then
-    echo "Usage: setup_conda.sh <version> <platform>"
-    echo "   Platform options are Linux-x86_64, MacOSX-x86_64"
-    echo "   For Windows, manually download and install https://repo.anaconda.com/miniconda/Miniconda3-$EXP_CONDA_VER-Windows-x86_64.exe"
-else
+PLATFORM=$1
+INSTALL_PREFIX=$2
+
+if [[ -z $PLATFORM ]]; then
+    echo "Usage: setup_conda.sh <platform> [install_prefix]"
+    echo "   Platform options are Linux-x86_64, MacOSX-x86_64, MacOSX-arm64"
+    WINDOWS_INSTALLER_URL="https://repo.anaconda.com/miniconda/Miniconda3-py39_$EXP_CONDA_VER-$EXP_CONDA_VER_SUFFIX-Windows-x86_64.exe"
+    echo "   For Windows, manually download and install $WINDOWS_INSTALLER_URL"
+    exit 2
+fi
+
+if [[ -z $INSTALL_PREFIX ]]; then
     INSTALL_PREFIX=$HOME/miniconda-$EXP_CONDA_VER
-    SOURCE_SCRIPT="$HOME/miniconda-$EXP_CONDA_VER/etc/profile.d/conda.sh"
-    
-    curl -o miniconda.sh -L https://repo.continuum.io/miniconda/Miniconda3-py39_$EXP_CONDA_VER-1-$PLATFORM.sh;
-    bash miniconda.sh -b -p $INSTALL_PREFIX
-    source $SOURCE_SCRIPT
-    hash -r
-    conda config --set always_yes yes --set changeps1 no
-    # Useful for debugging any issues with conda
-    conda info -a
-    echo "Successfully installed at $INSTALL_PREFIX. Please run 'source $SOURCE_SCRIPT' in every terminal where you want to use conda" 
 fi
+SOURCE_SCRIPT="$INSTALL_PREFIX/etc/profile.d/conda.sh"
+
+echo "Installing for version $EXP_CONDA_VER and platform $PLATFORM at $INSTALL_PREFIX"
+curl -o miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-py39_$EXP_CONDA_VER-$EXP_CONDA_VER_SUFFIX-$PLATFORM.sh
+bash miniconda.sh -b -p $INSTALL_PREFIX
+source $SOURCE_SCRIPT
+hash -r
+conda config --set auto_update_conda false
+conda install conda-libmamba-solver=$EXP_CONDA_VER libmamba=$EXP_LIBMAMBA_VER
+conda config --set solver libmamba
+conda config --set always_yes yes
+# Useful for debugging any issues with conda
+conda info -a
+echo "Successfully installed at $INSTALL_PREFIX"
+echo "Please initalize with '$HOME/miniconda-23.1.0/bin/conda init <shell-name>' (bash, zsh, etc.) and restart your terminal"
+echo "Please run 'source setup/setup.sh' to set up the necessary conda environment"
+echo "Please activate with 'source setup/activate_conda.sh' in every terminal where you want to use conda" 
diff --git a/setup/teardown.sh b/setup/teardown.sh
index c0ed9860..00bd812c 100644
--- a/setup/teardown.sh
+++ b/setup/teardown.sh
@@ -1,2 +1 @@
-conda activate base
-conda env remove --name emissioneval
+conda deactivate && conda env remove --name emissioneval
diff --git a/setup/teardown_conda.sh b/setup/teardown_conda.sh
index af303207..4bce35f3 100644
--- a/setup/teardown_conda.sh
+++ b/setup/teardown_conda.sh
@@ -1,8 +1,4 @@
 EXP_CONDA_VER=$1
+INSTALL_PREFIX=$HOME/miniconda-$EXP_CONDA_VER
 
-if [ -z $EXP_CONDA_VER ]; then
-    echo "Usage: teardown_conda.sh <version>"
-else
-    INSTALL_PREFIX=$HOME/miniconda-$EXP_CONDA_VER
-    rm -rf $INSTALL_PREFIX
-fi
+rm -rf $INSTALL_PREFIX