Fix bug in grep (#89)

artifact_requirements.txt

@@ -0,0 +1,23 @@
+# Note: The lines we will return via grep will look like 'package_name>=#.#.#' or will be of the format 
+# 'package_name @ git+https://github.com/ihmeuw/package_name@SOME_BRANCH'
+vivarium>=3.0.0
+vivarium_public_health>=3.0.0
+gbd_mapping>=4.0.0
+click
+jinja2
+loguru
+numpy
+pandas
+pyyaml
+scipy
+tables
+vivarium_inputs>=5.0.0
+# Note viv_in is not install with [data] extra because we might need to specify the branch
+# for viv_in for the data requirements
+vivarium_gbd_access>=4.0.0
+core-maths
+vivarium_cluster_tools>=2.0.0
+black==22.3.0
+isort
+jupyterlab
+matplotlib

environment.sh

@@ -0,0 +1,146 @@
+#!/bin/bash
+
+# Reset OPTIND so help can be invoked multiple times per shell session.
+OPTIND=1
+Help()
+{ 
+   # Display Help
+   echo "Script to automatically create and validate conda environments."
+   echo
+   echo "Syntax: source environment.sh [-h|t|v]"
+   echo "options:"
+   echo "h     Print this Help."
+   echo "t     Type of conda environment. Either 'simulation' (default) or 'artifact'."
+   echo "f     Force creation of a new environment."
+}
+
+# Define variables
+username=$(whoami)
+env_type="simulation"
+make_new="no"
+
+# Process input options
+while getopts ":hft:" option; do
+   case $option in
+      h) # display help
+         Help
+         return;;
+      t) # Type of conda environment to build
+         env_type=$OPTARG;;
+      f) # Force creation of a new environment
+         make_new="yes";;
+     \?) # Invalid option
+         echo "Error: Invalid option"
+         return;;
+   esac
+done
+
+# Parse environment name
+env_name=$(basename "`pwd`")
+env_name+="_$env_type"
+branch_name=$(git rev-parse --abbrev-ref HEAD)
+# Determine which requirements.txt to install from
+if [ $env_type == 'simulation' ]; then
+  install_file="requirements.txt"
+elif [ $env_type == 'artifact' ]; then
+  install_file="artifact_requirements.txt"
+else
+  echo "Invalid environment type. Valid argument types are 'simulation' and 'artifact'."
+  return 
+fi
+
+# Pull repo to get latest changes from remote if remote exists
+git ls-remote --exit-code --heads origin $branch_name >/dev/null 2>&1
+exit_code=$?
+if [[ $exit_code == '0' ]]; then
+  git fetch --all
+  echo "Git branch '$branch_name' exists in the remote repository, pulling latest changes..."
+  git pull origin $branch_name
+fi
+
+# Check if environment exists already
+create_env=$(conda info --envs | grep $env_name | head -n 1)
+if [[ $create_env == '' ]]; then
+  # No environment exists with this name
+  echo "Environment $env_name does not exist."
+  create_env="yes"
+  env_exists="no"
+elif [[ $make_new == 'yes' ]]; then
+  # User has requested to make a new environment
+  echo "Making a new environment."
+  create_env="yes"
+  env_exists="yes"
+else
+  env_exists="yes"
+  conda activate $env_name
+  # Check if existing environment needs to be recreated
+  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.
+  if [[ $one_week_ago > $creation_time ]] | [[ $creation_time < $requirements_modification_time ]]; then
+    echo "Environment is stale. Deleting and remaking environment..."
+    create_env="yes"
+  else
+    # Install json parser if it is not installed
+    jq_exists=$(conda list | grep -w jq)
+    if [[ $jq_exists == '' ]]; then
+      # Empty string is no return on grep
+      conda install jq -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
+    # 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'
+    # echo $(grep -E 'vivarium|gbd|risk_distribution|layered_config' $install_file)
+    framework_packages=$(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 '.releases | to_entries | max_by(.key) | .value | .[0].upload_time')
+      fi
+      if [[ $creation_time > $last_commit_time ]]; then
+        create_env="yes"
+        echo "Last update time for $repo: $last_update_time. Environment is stale. Remaking environment..."
+        break
+      fi
+    done
+  fi
+fi
+
+if [[ $create_env == 'yes' ]]; then
+  if [[ $env_exists == 'yes' ]]; then
+    if [[ $env_name == $CONDA_DEFAULT_ENV ]]; then
+      conda deactivate
+    fi
+    conda remove -n $env_name --all -y
+  fi
+  # Create conda environment
+  conda create -n $env_name python=3.11 -y
+  conda activate $env_name
+  # 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
+  fi
+else
+  echo "Existing environment validated"
+fi

requirements.txt

@@ -0,0 +1,18 @@
+# Note: The lines we will return via grep will look like 'package_name>=#.#.#' or will be of the format 
+# 'package_name @ git+https://github.com/ihmeuw/package_name@SOME_BRANCH'
+vivarium>=3.0.0
+vivarium_public_health>=3.0.0
+click
+jinja2
+loguru
+numpy
+pandas
+pyyaml
+scipy
+tables
+vivarium_cluster_tools>=2.0.0
+pytest
+black==22.3.0
+isort
+jupyterlab
+matplotlib