Micromamba install (#604)

Added Micromamba installation check
ReactionMechanismGenerator · Mar 12, 2023 · a6af8f9 · a6af8f9
2 parents 9f02dd3 + 93c8b5a
commit a6af8f9
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Showing 8 changed files with 230 additions and 69 deletions.
diff --git a/devtools/install_autotst.sh b/devtools/install_autotst.sh
@@ -1,17 +1,35 @@
-# Properly configure the shell to use 'conda activate'.
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+#!/bin/bash -l
 
-# Check for package manager
-if command -v mamba 2>/dev/null; then
+# Check if Micromamba is installed
+if [ -x "$(command -v micromamba)" ]; then
+    echo "Micromamba is installed."
+    COMMAND_PKG=micromamba
+# Check if Mamba is installed
+elif [ -x "$(command -v mamba)" ]; then
+    echo "Mamba is installed."
     COMMAND_PKG=mamba
-elif command -v conda >/dev/null 2>&1; then
+# Check if Conda is installed
+elif [ -x "$(command -v conda)" ]; then
+    echo "Conda is installed."
     COMMAND_PKG=conda
 else
-    echo "Error: mamba or conda is not installed. Please download and install mamba or conda - we strongly recommend mamba"
+    echo "Micromamba, Mamba, and Conda are not installed. Please download and install one of them - we strongly recommend Micromamba or Mamba."
     exit 1
 fi
 
+# Set up Conda/Micromamba environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    eval "$(micromamba shell hook --shell=bash)"
+    micromamba activate base
+    BASE=$MAMBA_ROOT_PREFIX
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/micromamba.sh"
+else
+    BASE=$(conda info --base)
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/conda.sh"
+fi
+
 # temporarily change directory to install software, and move one directory up in the tree
 pushd .
 cd ..
@@ -37,7 +55,13 @@ echo $PYTHONPATH
 # create the environment
 echo "Creating the AutoTST environment..."
 $COMMAND_PKG env create -f environment.yml
-conda activate tst_env
+# Activate the environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    micromamba activate tst_env
+else
+    conda activate tst_env
+fi
+
 $COMMAND_PKG install -c anaconda yaml -y
 
 # Restore the original directory

diff --git a/devtools/install_gcn_cpu.sh b/devtools/install_gcn_cpu.sh
@@ -1,17 +1,35 @@
-# Properly configure the shell to use 'conda activate'.
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+#!/bin/bash -l
 
-# Check for package manager
-if command -v mamba 2>/dev/null; then
+# Check if Micromamba is installed
+if [ -x "$(command -v micromamba)" ]; then
+    echo "Micromamba is installed."
+    COMMAND_PKG=micromamba
+# Check if Mamba is installed
+elif [ -x "$(command -v mamba)" ]; then
+    echo "Mamba is installed."
     COMMAND_PKG=mamba
-elif command -v conda >/dev/null 2>&1; then
+# Check if Conda is installed
+elif [ -x "$(command -v conda)" ]; then
+    echo "Conda is installed."
     COMMAND_PKG=conda
 else
-    echo "Error: mamba or conda is not installed. Please download and install mamba or conda - we strongly recommend mamba"
+    echo "Micromamba, Mamba, and Conda are not installed. Please download and install one of them - we strongly recommend Micromamba or Mamba."
     exit 1
 fi
 
+# Set up Conda/Micromamba environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    eval "$(micromamba shell hook --shell=bash)"
+    micromamba activate base
+    BASE=$MAMBA_ROOT_PREFIX
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/micromamba.sh"
+else
+    BASE=$(conda info --base)
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/conda.sh"
+fi
+
 # temporarily change directory to install software
 pushd .
 cd ..
@@ -37,8 +55,16 @@ echo $PYTHONPATH
 # create the environment
 echo "Creating the GCN-cpu environment..."
 source ~/.bashrc
+
 bash devtools/create_env_cpu.sh
-conda activate ts_gcn
+
+# Activate the environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    micromamba activate ts_gcn
+else
+    conda activate ts_gcn
+fi
+
 $COMMAND_PKG env update -f devtools/cpu_environment.yml
 
 # Restore the original directory

diff --git a/devtools/install_kinbot.sh b/devtools/install_kinbot.sh
@@ -1,6 +1,34 @@
-# Properly configure the shell to use 'conda activate'.
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+#!/bin/bash -l
+
+# Check if Micromamba is installed
+if [ -x "$(command -v micromamba)" ]; then
+    echo "Micromamba is installed."
+    COMMAND_PKG=micromamba
+# Check if Mamba is installed
+elif [ -x "$(command -v mamba)" ]; then
+    echo "Mamba is installed."
+    COMMAND_PKG=mamba
+# Check if Conda is installed
+elif [ -x "$(command -v conda)" ]; then
+    echo "Conda is installed."
+    COMMAND_PKG=conda
+else
+    echo "Micromamba, Mamba, and Conda are not installed. Please download and install one of them - we strongly recommend Micromamba or Mamba."
+    exit 1
+fi
+
+# Set up Conda/Micromamba environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    eval "$(micromamba shell hook --shell=bash)"
+    micromamba activate base
+    BASE=$MAMBA_ROOT_PREFIX
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/micromamba.sh"
+else
+    BASE=$(conda info --base)
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/conda.sh"
+fi
 
 # temporarily change directory to install software, and move one directory up in the tree
 pushd .
@@ -11,7 +39,12 @@ echo "Cloning/Updating KinBot..."
 wget https://github.com/zadorlab/KinBot/archive/refs/tags/v2.0.6.tar.gz
 tar -xvf "v2.0.6.tar.gz"
 cd KinBot-2.0.6 || exit
-conda activate arc_env
+# Activate the environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    micromamba activate arc_env
+else
+    conda activate arc_env
+fi
 python setup.py build
 python setup.py install
 

diff --git a/devtools/install_ob.sh b/devtools/install_ob.sh
@@ -1,18 +1,30 @@
-# Properly configure the shell to use 'conda activate'.
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+#!/bin/bash -l
 
-# Check for package manager
-if command -v mamba 2>/dev/null; then
+# Check if Micromamba is installed
+if [ -x "$(command -v micromamba)" ]; then
+    echo "Micromamba is installed."
+    COMMAND_PKG=micromamba
+# Check if Mamba is installed
+elif [ -x "$(command -v mamba)" ]; then
+    echo "Mamba is installed."
     COMMAND_PKG=mamba
-elif command -v conda >/dev/null 2>&1; then
+# Check if Conda is installed
+elif [ -x "$(command -v conda)" ]; then
+    echo "Conda is installed."
     COMMAND_PKG=conda
 else
-    echo "Error: mamba or conda is not installed. Please download and install mamba or conda - we strongly recommend mamba"
+    echo "Micromamba, Mamba, and Conda are not installed. Please download and install one of them - we strongly recommend Micromamba or Mamba."
     exit 1
 fi
+
 $COMMAND_PKG clean -a -y
 $COMMAND_PKG env create -n ob_env conda-forge::openbabel
-conda activate ob_env
+# Activate the environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    micromamba activate ob_env
+else
+    conda activate ob_env
+fi
+
 $COMMAND_PKG install -c conda-forge pyyaml
-conda deactivate
+$COMMAND_PKG deactivate
diff --git a/devtools/install_sella.sh b/devtools/install_sella.sh
@@ -1,42 +1,65 @@
-# Properly configure the shell to use 'conda activate'.
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+#!/bin/bash -l
 
-# Check if mamba or conda is installed
-if command -v mamba > /dev/null; then
-  COMMAND_PKG=mamba
-elif command -v conda > /dev/null; then
-  COMMAND_PKG=conda
+# Check if Micromamba is installed
+if [ -x "$(command -v micromamba)" ]; then
+    echo "Micromamba is installed."
+    COMMAND_PKG=micromamba
+# Check if Mamba is installed
+elif [ -x "$(command -v mamba)" ]; then
+    echo "Mamba is installed."
+    COMMAND_PKG=mamba
+# Check if Conda is installed
+elif [ -x "$(command -v conda)" ]; then
+    echo "Conda is installed."
+    COMMAND_PKG=conda
 else
-  echo "mamba and conda are not installed. Please download and install mamba or conda - we strongly recommend mamba"
-  exit 1
+    echo "Micromamba, Mamba, and Conda are not installed. Please download and install one of them - we strongly recommend Micromamba or Mamba."
+    exit 1
+fi
+
+# Set up Conda/Micromamba environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    eval "$(micromamba shell hook --shell=bash)"
+    micromamba activate base
+    BASE=$MAMBA_ROOT_PREFIX
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/micromamba.sh"
+else
+    BASE=$(conda info --base)
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/conda.sh"
 fi
 
 # clone the repo in the parent directory
 echo "Creating the Sella environment..."
-source ~/.bashrc
-$COMMAND_PKG create -n sella_env python=3.7 -y
-conda activate sella_env
+$COMMAND_PKG create -n sella_env python=3.7 -c conda-forge -y
+# Activate the environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    micromamba activate sella_env
+else
+    conda activate sella_env
+fi
+
 $COMMAND_PKG  install -c conda-forge xtb-python -y
 $COMMAND_PKG  install -c conda-forge pyyaml -y
 $COMMAND_PKG  install -c anaconda pandas -y
 $COMMAND_PKG  install -c conda-forge ase -y
 $COMMAND_PKG  install -c conda-forge ncurses
 $COMMAND_PKG  install -c anaconda pip -y
-$CONDA_BASE/envs/sella_env/bin/pip install sella
+$BASE/envs/sella_env/bin/pip install sella
 
-cd $CONDA_BASE/envs/sella_env
+cd $BASE/envs/sella_env || exit
 mkdir -p ./etc/conda/activate.d
 mkdir -p ./etc/conda/deactivate.d
 touch ./etc/conda/activate.d/env_vars.sh
 touch ./etc/conda/deactivate.d/env_vars.sh
 
 #This sets up the LD_LIBRARY_PATH to include Sella_Env, but only when the environment is active
-echo 'export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}' >> $CONDA_BASE/envs/sella_env/etc/conda/activate.d/env_vars.sh
-echo 'export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:'"$CONDA_BASE"'/envs/sella_env/lib' >> $CONDA_BASE/envs/sella_env/etc/conda/activate.d/env_vars.sh
+echo 'export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}' >> $BASE/envs/sella_env/etc/conda/activate.d/env_vars.sh
+echo 'export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:'"$BASE"'/envs/sella_env/lib' >> $BASE/envs/sella_env/etc/conda/activate.d/env_vars.sh
 #This will reset the LD_LIBRARY_PATH back to the original LD_LIBRARY_PATH when the environment is deactivated
-echo 'export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}' >> $CONDA_BASE/envs/sella_env/etc/conda/deactivate.d/env_vars.sh
-echo 'unset OLD_LD_LIBRARY_PATH' >> $CONDA_BASE/envs/sella_env/etc/conda/deactivate.d/env_vars.sh
+echo 'export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}' >> $BASE/envs/sella_env/etc/conda/deactivate.d/env_vars.sh
+echo 'unset OLD_LD_LIBRARY_PATH' >> $BASE/envs/sella_env/etc/conda/deactivate.d/env_vars.sh
 
 source ~/.bashrc
 echo "Done installing Sella."
diff --git a/devtools/install_torchani.sh b/devtools/install_torchani.sh
@@ -1,16 +1,35 @@
-# Properly configure the shell to use 'conda activate'.
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+#!/bin/bash -l
 
-# Check for package manager
-if command -v mamba 2>/dev/null; then
+# Check if Micromamba is installed
+if [ -x "$(command -v micromamba)" ]; then
+    echo "Micromamba is installed."
+    COMMAND_PKG=micromamba
+# Check if Mamba is installed
+elif [ -x "$(command -v mamba)" ]; then
+    echo "Mamba is installed."
     COMMAND_PKG=mamba
-elif command -v conda >/dev/null 2>&1; then
+# Check if Conda is installed
+elif [ -x "$(command -v conda)" ]; then
+    echo "Conda is installed."
     COMMAND_PKG=conda
 else
-    echo "Error: mamba or conda is not installed. Please download and install mamba or conda - we strongly recommend mamba"
+    echo "Micromamba, Mamba, and Conda are not installed. Please download and install one of them - we strongly recommend Micromamba or Mamba."
     exit 1
 fi
+
+# Set up Conda/Micromamba environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    eval "$(micromamba shell hook --shell=bash)"
+    micromamba activate base
+    BASE=$MAMBA_ROOT_PREFIX
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/micromamba.sh"
+else
+    CONDA_BASE=$(conda info --base)
+    # shellcheck source=/dev/null
+    source "$CONDA_BASE/etc/profile.d/conda.sh"
+fi
+
 $COMMAND_PKG clean -a -y
 echo creating tani_env
 $COMMAND_PKG env create -f devtools/tani.yml
diff --git a/devtools/install_xtb.sh b/devtools/install_xtb.sh
@@ -1,19 +1,43 @@
-# Properly configure the shell to use 'conda activate'.
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+#!/bin/bash -l
 
-# Check if mamba or conda is installed
-if command -v mamba > /dev/null; then
-  COMMAND_PKG=mamba
-elif command -v conda > /dev/null; then
-  COMMAND_PKG=conda
+# Check if Micromamba is installed
+if [ -x "$(command -v micromamba)" ]; then
+    echo "Micromamba is installed."
+    COMMAND_PKG=micromamba
+# Check if Mamba is installed
+elif [ -x "$(command -v mamba)" ]; then
+    echo "Mamba is installed."
+    COMMAND_PKG=mamba
+# Check if Conda is installed
+elif [ -x "$(command -v conda)" ]; then
+    echo "Conda is installed."
+    COMMAND_PKG=conda
 else
-  echo "mamba and conda are not installed. Please download and install mamba or conda - we strongly recommend mamba"
-  exit 1
+    echo "Micromamba, Mamba, and Conda are not installed. Please download and install one of them - we strongly recommend Micromamba or Mamba."
+    exit 1
+fi
+
+# Set up Conda/Micromamba environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    eval "$(micromamba shell hook --shell=bash)"
+    micromamba activate base
+    BASE=$MAMBA_ROOT_PREFIX
+    # shellcheck source=/dev/null
+    source "$BASE/etc/profile.d/micromamba.sh"
+else
+    CONDA_BASE=$(conda info --base)
+    # shellcheck source=/dev/null
+    source "$CONDA_BASE/etc/profile.d/conda.sh"
+fi
+
+$COMMAND_PKG create -n xtb_env python=3.7  -c conda-forge -y
+# Activate the environment
+if [ "$COMMAND_PKG" == "micromamba" ]; then
+    micromamba activate xtb_env
+else
+    conda activate xtb_env
 fi
 
-$COMMAND_PKG create -n xtb_env python=3.7 -y
-conda activate xtb_env
 $COMMAND_PKG install -c conda-forge xtb -y
 $COMMAND_PKG install -c anaconda pyyaml -y
-conda deactivate
+$COMMAND_PKG activate base