resutil 0.1.8

Resutil is a utility to manage experimental result data obtained from Python projects. It also manages dependency such as codes and input data with result data. Data is synced to the cloud for team sharing and collaboration.

Resutil

What is Resutil

Resutil is a utility to manage experimental result data obtained from Python projects. It also manages dependency such as codes and input data with result data. Data is synced to the cloud for team sharing and collaboration.

Why choose Resutil?

• Simple: Easy to install and can be quickly integrated into your project.
• High Reproducibility: Tracks programs, input data, and experimental results.
• Open-source and free: Join development to future release of Resutil.

Features

• Sync experimental data saved in a specific directory to the cloud (currently only for Box) after the program execution finished.
• Save information necessary to reproduce the experiment in a YAML file.
• Execution command
• Input files given as arguments (only files within folders managed by resutil)
• Git commit hash
• Uncommitted files
• Upload experimental data that hasn’t been uploaded yet.
• Download experimental data from the cloud using commands.

Installation

Open terminal and run

pip install resutil

Get JWT (JSON Web Tokens) key from Box, and saved as key.json:

{
  "boxAppSettings": {
    "clientID": "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",
    "clientSecret": "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",
    "appAuth": {
      "publicKeyID": "xxxxxxxx",
      "privateKey": "-----BEGIN ENCRYPTED PRIVATE KEY-----\nxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx\n-----END ENCRYPTED PRIVATE KEY-----\n",
      "passphrase": "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
    }
  },
  "enterpriseID": "796607301"
}

Initialize resutil

$ cd your-project-root-directory
$ resutil init
Input project name (resutil): MyProj
Input directory name to store results (results): results
Do you want to add .gitignore to results? (Y/n): Y
Input storage_type (box): box
Input key file_path (key.json): key.json
Do you want to add key.json to .gitignore? (Y/n): Y
Input folder id of base dir: 123456789012
✅ Initialized.

The folder id is the Box folder ID, which is the numeric part of the URL when viewing the folder on Box (e.g., https://xxxx.app.box.com/folder/123456789012).

A file named resutil-conf.yaml will be created.

Modify main function in your project like:

# Import resutil
import resutil

# Add decorator before the main function
@resutil.main()
def main_func(params):
    # A directory is automatically created, and its path is stored in params.ex_dir
    ex_dir = params.ex_dir 

    # Execute the program HERE🚀
    # Resutil will handle the rest

if __name__ == "__main__":
    main_func()

How to setup cloud storage for Resutil

Resutil supports Google Cloud Storage, Google Drive, and Box for a cloud storage to store result files. To connect these cloud services following setup will be required.

Google Cloud Storage

1. Create a Project:
   • If you don't already have a project, go to the Google Cloud Console and create a new project.
2. Enable the Cloud Storage API:
   • Go to the API Library in the Google Cloud Console.
   • Search for "Cloud Storage" and enable the API for your project.
3. Create a Storage Bucket:
   • In the Google Cloud Console, go to the Cloud Storage Browser.
   • Click on "Create Bucket."
   • Follow the prompts to name your bucket, select a storage class, and set the location for your bucket.
4. Create a Service Account:
   • In the Google Cloud Console, go to the IAM & Admin section.
   • Click on "Create Service Account."
   • Provide a name and description for the service account, and click "Create."
5. Grant Permissions to the Service Account:
   • Select the "Storage Object User" roles that grant the necessary permissions to the service account.
   • Click "Continue," and then "Done."
6. Create and Download a Key for the Service Account:
   • Click on the service account you just created.
   • Go to the "Keys" tab.
   • Click "Add Key," then "Create New Key."
   • Choose "JSON" as the key type, and click "Create." The key file will be downloaded to your computer.

Google Drive

1. Create a Folder in Google Drive:
   • Open Google Drive.
   • Click on "New" and select "Folder."
   • Name the folder and click "Create."
2. Get the Folder ID:
   • Navigate to the folder you just created.
   • The folder ID is the part of the URL after folders/. For example, in the URL https://drive.google.com/drive/folders/1a2b3c4d5e6f, the folder ID is 1a2b3c4d5e6f.
3. Create a Service Account:
   • Go to the Google Cloud Console.
   • Select your project or create a new one.
   • Navigate to the IAM & Admin section.
   • Click "Create Service Account."
   • Provide a name and description for the service account, and click "Create."
4. Create and Download a Key for the Service Account:
   • Click on the service account you just created.
   • Go to the "Keys" tab.
   • Click "Add Key," then "Create New Key."
   • Choose "JSON" as the key type, and click "Create." The key file will be downloaded to your computer.
5. Enable the Google Drive API:
   • Go to the API Library in the Google Cloud Console.
   • Search for "Google Drive API" and enable it for your project.
6. Share the Folder:
   • In Google Drive, right-click on the folder you created.
   • Select "Share."
   • In the "Share with people and groups" field, enter the email address of the service account (you can find this in the JSON key file under client_email).
   • Give the service account Editor access.
   • Click "Send."

Box

Sure, I can guide you through the process of obtaining a JWT (JSON Web Token) from Box's developer console. Follow these steps:

1. Create a Box Application

   • Go to the Box Developer Console and log in with your Box account.
   • Click on "Create New App".
   • Give your app a name and click "Next".
   • Choose "Custom App" and select "Server Authentication (with JWT)".

2. Configure Your Application

   • In your app's settings, go to the "Configuration" tab.
   • Under "Application Scopes", choose two access levels, "Read/Write all files and folders stored in Box".
   • Scroll down to the "Add and Manage Public Keys" section and click "Generate a Public/Private Keypair". This will download a .json file containing your app's credentials.

3. Create a Service Account

   • In the "Authorization" tab, click on "Create Service Account".
   • Follow the prompts to create the service account. This account will be used to authenticate your app.

4. Grant permissions to the service account

   • Grant the service account “[e-mail]” editor permissions for the folder you want to use.

Commands

resutil init

resutil init creates resutil-conf.yaml in your project folder such as:

project_name: MyProj
results_dir: results/
storage_type: box
storage_config:
  base_folder_id: xxxx
  key_file: key.json

resutil push

The resutil push command is used to upload experimental data to the cloud that does not exist in the cloud result directory.

resutil push [exp_name] uploads experiment a specific directory to the cloud. Depending directorys included in exp-config.yaml are automtically uploaded. --no-dependency option restrain automatic dependency upload.

resutil pull --all will upload all experimental data to the cloud.

This is useful for keeping your local data up-to-date with the data stored in the cloud, especially when multiple people are working on the same project and updating the experimental data.

resutil pull

The resutil pull command is used to download a specific experimental data from the cloud that does not exist in the local result directory.

resutil pull [exp_name] downloads experiment directory from cloud. Depending directorys included in exp-config.yaml are automtically downlowded. --no-dependency option restrain automatic dependency download.

resutil pull --all will download all experimental data from the cloud that is not currently in your local result directory.

This is useful for keeping your local data up-to-date with the data stored in the cloud, especially when multiple people are working on the same project and updating the experimental data.

resutil add

The resutil add command is used to add an experiment directory without executing any code.

You can use it as follows: resutil add [comment] -d [DEPENDENCY1] [DEPENDENCY2].... This command adds an experiment directory named "comment" and sets its dependencies. The dependencies are other experiments that this experiment depends on.

For example, if you have two experiments exp1 and exp2 and a new experiment depends on them, you can add the new experiment with the following command: resutil add "new experiment" -d exp1 exp2. This will create a new experiment directory named "new experiment" and set exp1 and exp2 as its dependencies.

resutil list

The resutil list command list experiments in the cloud storage.

resutil rm

The resutil rm command removes experiments. You can use it as follows: resutil resutil rm [-l] [-r] EXPERIMENT1 [EXPERIMENT2].... --local or -l option removes only local experiment directory, whereas --remote or -r option for experiment data in cloud. Specifying neither options removes both experiments.

resutil comment EXPERIMENTAL

resutil comment [EXPERIMENT] [COMMENT] add or modify a comment following timestamp in the experiment name. Both local and cloud experiment name will change if existing. It should be noted that Resutil regards a differnt experimental name as a different experiment, and this does not affect the name of the same experiment other users have already pull.

Directory structure in the cloud storage

BaseDir    # Base directory specified base_dir_id
├──MyProj  # Project directory
│   ├── aakuqj_20240511T174522_ex1  # Experiment directory
│   │   ├── resutil-exp.yaml       # Experiment information
│   │   └── data.txt               # Data (example)
│   ├── aamxrp_20240606T135747_ex2
│   │   ├── resutil-exp.yaml
│   │   ├── data.txt
│   │   └── uncommited_files       # Uncommitted files
│   │       └── main.py
│   ...
│   
├──OtherProj
│
...

Experiment directories are formatted as xxxxxx_yyyymmddTHHMMSS_comment, where xxxxxx is timestamped for easy ordering and tab completion in shells.

resutil-exp.yaml [WIP]

Each experiment directory has resutil-exp.yaml, which contains information to reproduce experimental results.

cmd: Execution command
params: Options at runtime
  hoo: xxx
  bar: 123
dependency: Dependencies (automatically extracted from directories in the command)
  - ex1
  - ex2

how to publish

rye build --wheel rye publish