https://github.com/esther-poniatowski/multitask-context-dependent-behavior
Data analysis of neuronal recordings in naive and trained animals performing multiple tasks in active and passive attentional states
https://github.com/esther-poniatowski/multitask-context-dependent-behavior
cognitive-neuroscience computational-neuroscience data-analysis data-visualization information-processing
Last synced: 2 months ago
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Data analysis of neuronal recordings in naive and trained animals performing multiple tasks in active and passive attentional states
- Host: GitHub
- URL: https://github.com/esther-poniatowski/multitask-context-dependent-behavior
- Owner: esther-poniatowski
- License: gpl-3.0
- Created: 2024-05-19T18:26:23.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-18T08:14:29.000Z (3 months ago)
- Last Synced: 2025-02-18T09:25:28.674Z (3 months ago)
- Topics: cognitive-neuroscience, computational-neuroscience, data-analysis, data-visualization, information-processing
- Language: Jupyter Notebook
- Homepage: https://esther-poniatowski.github.io/multitask-context-dependent-behavior/
- Size: 42 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 55
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Roadmap: ROADMAP.md
Awesome Lists containing this project
README
# Multi-Task Context-Dependent Decision Making
- [Description](#description)
- [Authors](#authors)
- [Acknowledgments](#acknowledgments)
- [Installation](#installation)
- [Usage](#usage)
- [Contributing](#contributing)
## Description
**Full Documentation**: [multitask-context-dependent-behavior](https://esther-poniatowski.github.io/multitask-context-dependent-behavior/)
## Authors
**Esther Poniatowski** | @esther-poniatowski | [email protected]
## Acknowledgments
...
## 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:
```bash
git clone [email protected]: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:
```bash
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:
```bash
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
...
## 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):
```bash
git config user.name "Example Name"
git config user.email "[email protected]"
```
Replace `"Example Name"` and `"[email protected]"` 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](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/using-keywords-in-issues-and-pull-requests)
#### 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:
```plaintext
https://:@github.com
```
Replace `` and `` 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:
```bash
git config credential.helper 'store --file=.git/credentials'
```
---
## Directory Structure
```plaintext
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
```plaintext
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
```