Multi-Task Context-Dependent Decision Making

• Description
• Authors
• Acknowledgments
• Installation
• Usage
• Contributing

Description

Full Documentation: multitask-context-dependent-behavior

Authors

Esther Poniatowski | @esther-poniatowski | esther.poniatowski@ens.psl.eu

Acknowledgments

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Installation

Important

Prerequisites
Ensure that the following tools are available on the local machine:

• git
• conda
• Visual Studio Code (recommended)

To set up this project on a local machine, follow the steps below:

Initialize a local copy of the repository

1. Navigate to the local directory where the root folder of the repository should reside.

2. Clone the repository:

git clone git@github.com:esther-poniatowski/multitask-context-dependent-behavior.git

Note

The repository files are installed into a new directory named multitask-context-dependent-behavior.

Create a virtual environment

1. Create an dedicated conda environment including all the dependencies for using the project:

conda env create -f environment.yml

Note

The new conda environment is named mtcdb.

2. Register the current packages in the environment:

a. Check and copy the path to the site-packages directory of the environment:

conda activate mtcdb
python -c "import site; print(site.getsitepackages()[0])"

Usually: ∼/miniconda3/envs/mtcdb/lib/pythonX.Y/site-packages

b. Register the source directory of the project in a mtcdb.pth file:

echo "/path/to/mtcdb/src" > "path/to/conda/site-packages/mtcbd.pth"

Replace "/path/to/mtcdb" and "path/to/conda/site-packages" by the actual paths.

Usage

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Contributing

Important

To contribute effectively, please conform to those guidelines and use the provided templates.
To suggest improvements, use issues. To actively implement improvements, commit in the local version and push changes to the remote branches.

Sumbitting Issues

To submit an issue on the GitHub page of the repository:

1. Navigate to the "Issues" tab and click on "New Issue".
2. Select and fill the issue template.
3. Add relevant labels, assignees, and milestone if applicable.

Committing changes

Configure the repository

1. Navigate to the root directory of the local repository.

2. Specify the user profile (recorded in commits' metadata):

git config user.name "Example Name"
git config user.email "exampleemail@domain.com"

Replace "Example Name" and "exampleemail@domain.com" by the actual name and email corresponding to the GitHub user.

3. Configure the commit template (.gitmessage file):

git config commit.template .gitmessage

Tip

Format of the Commit Message

• Limit the subject line to 50 characters and the body at 72 characters per line, indicated by the delimiters in the template (####).
• Separate the subject from the body with a blank line.

Contents

• Subject: Indicate a prefix (see the options in the comments of the template), a scope (in parentheses) and a title after a colon (: character).
• Title: Use the imperative mood and capitablize.
• Body: Explain what and why (not how).
• References: Mention issues or other commits using GitHub keywords

Set up credentials

1. Ask the author to share the Personal Access Token of the repository.

2. Create a plaintext file located at .git/credentials:

3. Add authentication data in this file under the form of a URL address:

https://<username>:<personal-access-token>@github.com

Replace <username> and <personal-access-token> by the actual user name indicated before for the Git repository and the personal access token provided by the author.

4. Configure the credential helper to use the credentials file:

git config credential.helper 'store --file=.git/credentials'

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Directory Structure

    multitask-context-dependent-behavior/
    ├── README.md                   # Overall description and instructions
    ├── ROADMAP.md                  # Roadmap to track progress (goals, tasks, open questions)
    ├── mtcdb.code-workspace        # VS Code workspace settings
    ├── meta.env                    # Workspace metadata (environment variables)
    ├── paths.env                   # Central path manager (environment variables)
    ├── setup/                      # Setup scripts and utilities
    │   ├── init.sh                 # Initialization script for Conda environment
    │   ├── post_activate.sh        # Post-activation script for Conda environment
    │   ├── environment.yml         # Conda environment configuration
    │   ├── python.pth              # Paths to Python packages to add to PYTHONPATH (editable mode)
    │   └── bin.pth                 # Paths to binary directories to add to system PATH
    ├── config/                     # Configuration files
    │   ├── dictionaries/           # Dictionaries for spell checking
    │   ├── credentials/            # Credentials for servers
    │   └── tools/                  # Settings for tools and extensions
    ├── src/                        # Source code for Logic/Functionalities/"How" (imported)
    │   ├── core/                   # Main package for analysis, modeling, visualization
    │   ├── ingest/                 # Data ingestion and preprocessing (to perform on the remote hub)
    │   ├── tasks/                  # Administration tasks
    │   │   ├── network/            # Networking tasks (connections, deployment, transfer...)
    │   │   └── ...
    │   └── utils/                  # Helper utilities
    │       ├── io/                 # Input/output functionalities, path management
    │       └── misc/               # Miscellaneous (handling data structures, collections...)
    ├── ops/                        # Entry points for Operations/Execution/"What"-"When"
    │   ├── analysis/               # (organized by types of tasks)
    │   │   ├── preprocess.sh
    │   │   ├── validate.py
    │   │   ├── model.py
    │   │   └── ...
    │   ├── testing/
    │   │   ├── run.sh
    │   │   └── ...
    │   ├── documentation/
    │   │   ├── build.sh
    │   │   └── ...
    │   ├── transfer/
    │   │   ├── connect.sh
    │   │   ├── deploy.sh
    │   │   ├── fetch.sh
    │   │   └── ...
    │   └── maintenance/
    │       ├── inspect.sh
    │       ├── clean.sh
    │       ├── update.sh
    │       └── ...
    ├── tests/                      # Unit tests
    │   └── ...                     # (mirror the structure of the `src/` directory)
    ├── docs/                       # Documentation
    │   ├── build/                  # Output files
    │   ├── source/                 # Source files and configuration
    │   └── reports/                # Reports and summaries
    ├── notebooks/                  # Jupyter notebooks for exploration and visualization
    │   └── ...
    ├── data/                       # Datasets (input and output)
    │   └── ...
    ├── .git/                       # Git workspace
    ├── .gitignore                  # Git ignore file
    ├── .github/                    # GitHub settings and workflows
    ├── archive/                    # Old files kept for reference
    └── ...

This structure separates the functionality/logic ("how") from the execution/task runners ("what" and "when"). For chore tasks, if these are complex or involve multiple steps, they can be encapsulated in separate modules/classes within the tasks/ directory. This way, the ops/ scripts can import and execute these tasks without mingling the concerns of task execution and task definition.

Data Storage

    data/
    ├── samples/                    # Sample data for tests and examples
    ├── raw/                        # Raw data (immutable)
    │   ├── ath011b-c1/             # Data from one unit (neuron)
    │   └── ...
    ├── meta/                       # Metadata about experimental events, trials, units
    ├── interim/                    # Intermediate data which has been transformed
    └── processed/                  # Final data sets for modeling