Fix conflicts and add jsonschema to conda deps list

README.md

@@ -4,21 +4,24 @@ Introduction
 Consult the documentation to learn more about the CLI: [introduction](doc/introduction.md)
 
 This repository contains:
-* an abstract CLI to implement on the `master` branch 
-* an implementation example on the branch `baseline_system_master`. 
+
+* an abstract CLI to implement on the `master` branch.
+* an implementation example on the branch `baseline_system_master`.
 
 You should fork the project and use the `master` branch in order to implement the entry point methods and get the updates.
 
 Test it
+
 ============
 
 Get the CLI
 -----------
 
-**Requirements: python3.X**
+**Requirements:** python > 3.7
 
 Clone the repository:
-```
+
+```bash
 git clone https://gitlab.kitware.com/actev/diva_evaluation_cli.git
 ```
 
@@ -27,29 +30,33 @@ Install it
 
 * Go into the clone of this repository:
 
-```
-$ cd diva_evaluation_cli
+```bash
+cd diva_evaluation_cli
 ```
 
 * Execute the following script:
 
+```bash
+diva_evaluation_cli/bin/install.sh
 ```
-$ diva_evaluation_cli/bin/install.sh
-```
+
+See `diva_evaluation_cli/bin/install.sh -h` for more options. If using `--all`, make sure to install the submodules before.
+
+N.B.: We recommend to set the `-c` and `-s` options to what will be used as `system_cache_dir` by the entry_points ; otherwise, some operations like `validate-execution` will likely fail.
 
 Test the installation
 ---------------------
 
 Run the following command:
 
-```
-$ actev
+```bash
+actev
 ```
 
 You should be able to see the available subcommands.
 
-
 Usage
+
 =====
 
 Command line
@@ -57,8 +64,8 @@ Command line
 
 Run the following command to obtain help with the CLI:
 
-```
-$ actev -h
+```bash
+actev -h
 ```
 
 Documentation
@@ -66,8 +73,8 @@ Documentation
 
 Consult the documentation to have information: [CLI](doc/cli_commands/index.md)
 
-
 Fork it and develop your own implementation
+
 ===========================================
 
 Fork it
@@ -75,8 +82,8 @@ Fork it
 
 Click on the “Fork” button to make a copy of the repository in your own space and add this repository as a remote upstream to get the latest updates
 
-```
-$ git remote add upstream https://gitlab.kitware.com/actev/diva_evaluation_cli.git
+```bash
+git remote add upstream https://gitlab.kitware.com/actev/diva_evaluation_cli.git
 ```
 
 Update it
@@ -84,10 +91,10 @@ Update it
 
 Execute the following commands to update it:
 
-```
-$ git fetch upstream
-$ git checkout master
-$ git rebase upstream/master
+```bash
+git fetch upstream
+git checkout master
+git rebase upstream/master
 ```
 
 Develop it
@@ -100,6 +107,7 @@ We suggest you to call your scripts in the entry point methods and store them in
 More information about the development and the update of the CLI here: [development](doc/development.md)
 
 Contact
+
 =======
 
 * diva-nist@nist.gov

diva_evaluation_cli/bin/install.sh

@@ -4,54 +4,95 @@
 # Command Line Interface actev: installation script #
 #####################################################
 
+usage() {
+  echo "usage: install.sh [-h | --help] [--cli-env | -c CLI_ENV_PATH] [--scorer-env | -s SCORER_ENV_PATH] [--force-conda | -f] [--all]"
+}
+
 CURRENT_DIR=`pwd`
 cd "$(dirname "$0")"
 
-# Make sure we are using python3.7
-source update_python.sh
+# Requirements
+python3 -h &> /dev/null
+if [[ $? -ne "0" ]]; then
+  echo "Python3 is required to install and run the CLI."
+  echo "Please install Python3.X >= 3.7 and make sure \`python3 -h\` is working."
+  exit 1
+fi
+conda -h &> /dev/null
+if [[ $? -ne "0" ]]; then
+  echo "conda is required to install and run the CLI."
+  echo "Please install conda and make sure \`conda -h\` is working."
+  exit 1
+fi
 
-# Determine if python3.7 is running in a virtual environment
-python3.7 private_src/implementation/utils/is_virtual_env.py
+cd "${CURRENT_DIR}"
+# Check that .local/bin path is in $PATH
+echo $PATH | grep /.local/bin > /dev/null
 EXIT_STATUS=$?
 
-cd "${CURRENT_DIR}"
 if [ $EXIT_STATUS -ne 0 ];then
-
-  # Check that .local/bin path is in $PATH
-  echo $PATH | grep /.local/bin > /dev/null
-  EXIT_STATUS=$?
-
-  if [ $EXIT_STATUS -ne 0 ];then
-    echo "Please add ~/.local/bin to your PATH  before running the script:"
-    echo "export PATH=\"${PATH}:${HOME}/.local/bin\""
-    exit 1
-  fi
-
-  # Install using python3
-  options='--user'
-else
-  # Install using venv python
-  options=''
+  echo "Please add ~/.local/bin to your PATH  before running the script:"
+  echo "export PATH=\"${PATH}:${HOME}/.local/bin\""
+  exit 1
 fi
 
 cd "$(dirname "$0")"
 
-sudo apt-get install python3-pip -y
-sudo apt-get install python3.7-dev -y
-
-python3.7 -m pip install pip --upgrade
-python3.7 -m pip install setuptools $options
-python3.7 -m pip install -r ../../requirements.txt $options
-python3.7 -m pip install -e ../../. -U $options
-
 # Install dependencies (e.g. ActEV scorer) contained in `install.sh` scripts
 # if '--all' is passed as an argument
-if [ ! -z "$1" ] && [ "$1" == "--all" ];then
-    installation_scripts=`find private_src | grep "install.sh"`
-    for install_script in $installation_scripts; do
-        echo "Installation in progress: $install_script"
-        ./$install_script
-	echo "Installation done: $install_script"
-    done
+envs="~/.conda_envs"
+cli_env="$envs/cli.env"
+scorer_env="$envs/scorer.env"
+all=0
+force_env=0
+while [ "$1" != "" ]; do
+  case $1 in
+    -c | --cli-env )      shift
+                          cli_env=$1
+                          ;;
+    -s | --scorer-env )   shift
+                          scorer_env=$1
+                          ;;
+    -f | --force-conda )  force_env=1
+                          ;;
+    -h | --help )         usage
+                          exit
+                          ;;
+    --all )               all=1
+                          ;;
+    * )                   usage
+                          exit 1
+  esac
+  shift
+done
+
+# back to ./, creating CLI conda env
+cd ../..
+conda env create -f environment.yml -p $cli_env
+conda_script="$(conda shell.bash hook)"
+# Adding it to bashrc for execution flow
+if [[ $force_env -eq 1 ]]; then
+  echo "# Activate ActEV-CLI conda environment" >> ~/.bashrc
+  echo $conda_script >> ~/.bashrc
+  echo "conda activate $cli_env" >> ~/.bashrc
+  echo '' >> ~/.bashrc
+fi
+# Activating it and installing the CLI
+eval "$conda_script"
+conda activate $cli_env
+python3 setup.py develop --prefix $cli_env
+conda deactivate
+
+# Exporting scorer env directory to the CLI shell env
+cd "$(dirname "$0")"
+echo "SCORER_CONDA_ENV=$scorer_env" >> ./private_src/implementation/utils/actev_cli_environment.env
+
+# TODO replace ca par juste lui du scorer
+# conda le scorer etc
+if [[ $all -eq 1 ]]; then
+  cd "$(dirname "$0")"
+  echo "Installation in progress: ActEV_Scorer"
+  ./private_src/implementation/validate_execution/install.sh $scorer_env
+  echo "Installation done: ActEV_Scorer"
 fi
 

diva_evaluation_cli/bin/private_src/entry_points/actev_validate_execution.py

@@ -12,6 +12,9 @@ import sys
 
 from collections import Counter
 
+from diva_evaluation_cli.bin.private_src.implementation.utils.\
+    actev_cli_environment import activate_environment
+
 logger = logging.getLogger(__name__)
 
 
@@ -38,7 +41,7 @@ def entry_point(output, reference, activity_index, file_index, result, score,
         current_path, '../implementation/validate_execution')
     """
     installation_script = os.path.join(execution_validation_dir, 'install.sh')
-    scoring_cmd = 'python3.7 ' + os.path.join(
+    scoring_cmd = 'python3 ' + os.path.join(
         execution_validation_dir, 'ActEV_Scorer',
         'ActEV_Scorer.py ActEV18_AD -v ')
 
@@ -52,11 +55,12 @@ def entry_point(output, reference, activity_index, file_index, result, score,
     if not result and score:
         raise Exception("Please provide a -R option when using --score")
 
+    """
     # status is a 16-bit long integer
     # The 8 strongest bits are exit_code
     # The 8 weakest bits are signal_number
     cmd = 'cd ' + execution_validation_dir + '; '
-    cmd += '. ' + installation_script + ';' + scoring_cmd
+    cmd += 'bash ' + installation_script + ';' + scoring_cmd
     status = os.system(cmd)
     exit_code = status >> 8
     signal_number = status & (2**8 - 1)
@@ -65,6 +69,11 @@ def entry_point(output, reference, activity_index, file_index, result, score,
             raise KeyboardInterrupt
         else:
             raise Exception("Error occured in install.sh or score.sh")
+    """
+    # Loading dotenv and running scorer
+    activate_environment()
+    os.system('eval "$(conda shell.bash hook)"; conda activate %s; %s; \
+        conda deactivate' % (os.getenv('SCORER_CONDA_ENV'), scoring_cmd))
 
     # If the system output is scored, make it also check the alignments
     # Produced by the scorer. This is a reproducibility check made to compare

diva_evaluation_cli/bin/private_src/implementation/utils/actev_cli_environment.env

+
+ACTEV_GET_SYSTEM_URL="https://gitlab.kitware.com/actev/diva_evaluation_cli.git"
\ No newline at end of file

diva_evaluation_cli/bin/private_src/implementation/utils/is_virtual_env.py

-"""Utils module
-
-Can be used by any other module of the CLI
-Determine if python3 is running in a virtual environment
-"""
-import sys
-
-if __name__ == "__main__":
-    if hasattr(sys, 'real_prefix'):
-        sys.exit(0)
-    else:
-        sys.exit(1)

diva_evaluation_cli/bin/private_src/implementation/validate_execution/install.sh

 #!/bin/bash
-env_dir="python_env"
-current_path=`realpath $(dirname $0)`
-path_to_env_dir="$current_path/$env_dir"
 
-sudo apt-get install -y python3-dev python3-pip
-python3.7 -m pip install virtualenv
-if [ -d $path_to_env_dir ];then
-  . $path_to_env_dir/bin/activate
-else
-  virtualenv $path_to_env_dir
-  . $path_to_env_dir/bin/activate
-  python3.7 -m pip --no-cache-dir install -r $current_path/ActEV_Scorer/requirements.txt
+if [[ $# -ne 1 ]]; then
+  echo "usage: install.sh <scorer_conda_env_path>"
+  exit 1
 fi
+
+current_path=`realpath $(dirname $0)`
+conda env create -f $current_path/ActEV_Scorer/environment.yml -p $1
+eval "$(conda shell.bash hook)"
+conda activate $1
+conda deactivate

diva_evaluation_cli/bin/update_python.sh

-#!/bin/bash
-
-bin_dir="/usr/bin"
-if [ ! -f $bin_dir/python3.7 ];then
-  sudo apt install -y python3.7
-fi
-if [ -f $bin_dir/python3 ];then
-  sudo rm -rf $bin_dir/python3
-fi
-sudo ln -s $bin_dir/python3.7 $bin_dir/python3

environment.yml

+name: CLI
+channels:
+- conda-forge
+- defaults
+- fastai
+dependencies:
+- python=3.8
+- psutil=5.7.2
+- python-dotenv=0.13.0
+- nvidia-ml-py3=7.352.0
+- pycodestyle
+- pyyaml
+- jsonschema=3.2.0

scripts/diva_data_download_cli_execution.sh

@@ -57,18 +57,18 @@ git clone https://gitlab.kitware.com/actev/actev-data-repo $TMP_DIR/actev-data-r
 
 # Create an environment to run the data download script
 pushd $TMP_DIR
-virtualenv envpy3 -p python3.7
+virtualenv envpy3 -p python3
 popd
 source $TMP_DIR/envpy3/bin/activate
-python3.7 -m pip install jsonschema pandas
+python3 -m pip install jsonschema pandas
 
 # Add the credentials to download the videos
-python3.7 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation summary --corpus MEVA --add_credential `echo $ACTEV_DATA_REPO_CREDENTIALS_MEVA | tr -d ' '`
-python3.7 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation summary --corpus VIRAT-V1 --add_credential `echo $ACTEV_DATA_REPO_CREDENTIALS_VIRAT1 | tr -d ' '`
-python3.7 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation summary --corpus VIRAT-V2 --add_credential `echo $ACTEV_DATA_REPO_CREDENTIALS_VIRAT2 | tr -d ' '`
+python3 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation summary --corpus MEVA --add_credential `echo $ACTEV_DATA_REPO_CREDENTIALS_MEVA | tr -d ' '`
+python3 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation summary --corpus VIRAT-V1 --add_credential `echo $ACTEV_DATA_REPO_CREDENTIALS_VIRAT1 | tr -d ' '`
+python3 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation summary --corpus VIRAT-V2 --add_credential `echo $ACTEV_DATA_REPO_CREDENTIALS_VIRAT2 | tr -d ' '`
 
 # Download the video
-python3.7 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation download --partitions $VALIDATION_SET
+python3 $TMP_DIR/actev-data-repo/scripts/actev-corpora-maint.py --operation download --partitions $VALIDATION_SET
 deactivate
 
 ## CLI EXECUTION

setup.py

@@ -12,7 +12,7 @@ import diva_evaluation_cli
 
 setup(name='diva_evaluation_cli',
       version=diva_evaluation_cli.__version__,
-      package=find_packages(),
+      packages=find_packages(),
       include_package_data=True,
       entry_points='''
       [console_scripts]