Albrja/mic-5272/miniforge (#90)

* Update creation script

* Remove line

{{cookiecutter.package_name}}/environment.sh

@@ -27,7 +27,7 @@ while getopts ":hft:" option; do
          return;;
       t) # Type of conda environment to build
          env_type=$OPTARG;;
-      f) # Force creation of new environment
+      f) # Force creation of a new environment
          make_new="yes";;
      \?) # Invalid option
          echo "Error: Invalid option"
@@ -77,6 +77,7 @@ else
   echo "Existing environment found for $env_name."
   one_week_ago=$(date -d "7 days ago" '+%Y-%m-%d %H:%M:%S')
   creation_time="$(head -n1 $CONDA_PREFIX/conda-meta/history)"
+  creation_time=$(echo $creation_time | sed -e 's/^==>\ //g' -e 's/\ <==//g')
   requirements_modification_time="$(date -r $install_file '+%Y-%m-%d %H:%M:%S')"
   # Check if existing environment is older than a week or if environment was built 
   # before last modification to requirements file. If so, mark for recreation.
@@ -88,26 +89,36 @@ else
     jq_exists=$(conda list | grep -w jq)
     if [[ $jq_exists == '' ]]; then
       # Empty string is no return on grep
-      conda install jq -y
+      conda install jq -c anaconda -y
     fi
+    echo "Checking framework packages are up to date..."
     # Check if there has been an update to vivarium packages since last modification to requirements file
     # or more reccent than environment creation
-    grep @ $install_file 
-    # TODO: can we make this grep output a variable?
-    while read -r line ; do
-      # Parse each line of grep output
-      repo_info=(${line//@/ })
-      repo=${repo_info[0]}
-      repo_branch=${repo_info[2]}
-      last_commit_time=$(curl -H "Accept: application/vnd.github.v3+json" https://api.github.com/repos/ihmeuw/$repo/commits?sha=$repo_branch | jq '.["0"].commit.committer.date')
-      if [[ $creation_time > $last_commit_time ]]; then
+    # Note: The lines we will return via grep will look like 'vivarium>=#.#.#' or will be of the format 
+    # 'vivarium @ git+https://github.com/ihmeuw/vivarium@SOME_BRANCH'
+    framework_packages=$(grep -E 'vivarium|gbd|risk_distribution|layered_config' $install_file)
+    num_packages=$(grep -E 'vivarium|gbd|risk_distribution|layered_config' -c $install_file)
+
+    # Iterate through each return of the grep output
+    for ((i = 1; i <= $num_packages; i++)); do
+      line=$(echo "$framework_packages" | sed -n "${i}p")
+      # Check if the line contains '@'
+      if [[ "$line" == *"@"* ]]; then
+          repo_info=(${line//@/ })
+          repo=${repo_info[0]}
+          repo_branch=${repo_info[2]}
+          last_update_time=$(curl -H "Accept: application/vnd.github.v3+json" https://api.github.com/repos/ihmeuw/$repo/commits?sha=$repo_branch | jq .[0].commit.committer.date)
+      else
+          repo=$(echo "$line" | cut -d '>' -f1)
+          last_update_time=$(curl -s https://pypi.org/pypi/$repo/json | jq -r '.releases | to_entries | max_by(.key) | .value | .[0].upload_time')
+      fi
+      last_update_time=$(date -d "$last_update_time" '+%Y-%m-%d %H:%M:%S')
+      if [[ $creation_time < $last_update_time ]]; then
         create_env="yes"
+        echo "Last update time for $repo: $last_update_time. Environment is stale. Remaking environment..."
         break
       fi
-    # This way of writing/exiting while loop is a here string so the process runs
-    # in the main shell and not a subshell: https://www.gnu.org/software/bash/manual/bashref.html#Here-Strings
-    # I put an arbitrary empty string here but this is so we can set create_env to yes if we hit that trigger
-    done <<< "$(echo "")"
+    done
   fi
 fi
 
@@ -119,21 +130,17 @@ if [[ $create_env == 'yes' ]]; then
     conda remove -n $env_name --all -y
   fi
   # Create conda environment
-  conda create -n $env_name python=3.11 -y
+  conda create -n $env_name python=3.11 -c anaconda -y
   conda activate $env_name
-else
-  echo "Existing environment validated"
-fi
-
-# Install requirements via Github
-if [[ $create_env == 'yes' ]]; then
   # NOTE: update branch name if you update requirements.txt in a branch
   echo "Installing packages for $env_type environment"
   pip install -r $install_file
   # Editable install of repo
   pip install -e .[dev] 
   # Install redis for simulation environments
   if [ $env_type == 'simulation' ]; then
-    conda install redis -y
+    conda install redis -c anaconda -y
   fi
+else
+  echo "Existing environment validated"
 fi