ethoscopy 2.0__tar.gz → 2.0.1__tar.gz

ethoscopy-2.0.1/.claude/settings.local.json

@@ -0,0 +1,16 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(paplay:*)",
+      "Bash(rg:*)",
+      "Bash(sqlite3:*)",
+      "Bash(python test:*)",
+      "Bash(source:*)",
+      "Bash(python:*)",
+      "Bash(rm:*)",
+      "Bash(git add:*)",
+      "Bash(git push:*)"
+    ],
+    "deny": []
+  }
+}

ethoscopy-2.0.1/.gitignore

@@ -0,0 +1,10 @@
+*.txt
+*.pyc
+*venv
+dist/
+*vscode
+__pycache__/
+ethoscopy.egg-info/
+.gitignore
+*.pkl
+.python-version

ethoscopy-2.0.1/CLAUDE.md

@@ -0,0 +1,111 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+Ethoscopy is a Python data analysis toolbox for behavioral time series data from Ethoscope (Drosophila monitoring system). It's built as a specialized pandas DataFrame subclass that maintains linked metadata and provides analysis/visualization tools for circadian rhythms, sleep patterns, and behavioral states using HMM.
+
+## Development Environment
+
+### Python Environment
+- **Use Python 3.10+** (project requires >=3.10,<4.0)
+- **Always use virtual environment** (`venv_linux` as mentioned in user's global instructions)
+- **Install in development mode**: `pip install -e .`
+
+### Package Management
+- Uses **pyproject.toml** for modern Python packaging (not setup.py for production)
+- **Hatchling** as build backend
+- **Rye** for dependency management (managed = true in pyproject.toml)
+
+### Key Dependencies
+- Core: pandas >=2.2.2, numpy >=2.0.0
+- Visualization: plotly >=5.22.0, seaborn >=0.13.2
+- Analysis: hmmlearn >=0.3.2, astropy >=6.1, pywavelets >=1.6.0
+- Dev: ipykernel for Jupyter notebook support
+
+## Build and Development Commands
+
+### Installation
+```bash
+# Install in development mode
+pip install -e .
+
+# For Jupyter notebook development
+pip install -e ".[dev]"
+```
+
+### Testing
+- **No formal test suite found** - project relies on Jupyter notebooks for validation
+- Use the tutorial notebooks in `tutorial_notebook/` for testing functionality
+- Run notebooks: `jupyter notebook tutorial_notebook/`
+
+### Docker Environment
+- **Docker available** for JupyterHub deployment
+- Build: `JUPYTER_HUB_TAG=5.3.0 ETHOSCOPE_LAB_TAG=1.0 docker compose build`
+- Run: `docker compose up -d` (from Docker/ directory)
+
+## Architecture and Code Structure
+
+### Core Architecture
+- **behavpy_core**: Base DataFrame subclass with core functionality (xmv, curate, summary)
+- **behavpy**: Main user-facing class for backward compatibility
+- **Canvas System**: Supports both 'plotly' and 'seaborn' for visualization backends
+
+### Key Components
+1. **Data Loading** (`load.py`): FTP download, ethoscope database loading, metadata linking
+2. **Analysis** (`analyse.py`): Sleep annotation, velocity detection, stimulus response
+3. **Visualization**: Split between plotly (`behavpy_plotly.py`) and seaborn (`behavpy_seaborn.py`)
+4. **Specialized Classes**:
+   - `behavpy_HMM_class.py`: Hidden Markov Model analysis
+   - `behavpy_periodogram_class.py`: Circadian rhythm analysis
+5. **Utilities** (`misc/`): General functions, validation, tutorial data
+
+### Data Structure
+- **Dual DataFrame design**: Main data + linked metadata via shared 'id' column
+- **Metadata cleaning**: Automatically removes columns like 'path', 'file_name', 'file_size', 'machine_id'
+- **Index requirement**: Data must have 'id' as index name
+
+### Import Pattern
+```python
+import ethoscopy as etho
+df = etho.behavpy(data, metadata, check=True, canvas='plotly', palette='Set2')
+```
+
+## Key Design Patterns
+
+### Version 2.0 Migration
+- **Backward compatible** with pre-2.0 pickled data
+- **Unified class structure**: All analysis under single `behavpy()` class
+- **Canvas selection**: Choose between plotly/seaborn at initialization
+- **New concat function**: Use `etho.concat()` instead of `behavpy_object.concat()`
+
+### Plotting Architecture
+- **Dual backend support**: Plotly (interactive) vs Seaborn (static)
+- **Built-in statistical processing**: Z-score normalization, bootstrapping for plotly
+- **Seaborn backend**: Uses seaborn's internal statistics
+- **Performance consideration**: Plotly can create large notebook files
+
+### Analysis Capabilities
+- **Sleep detection**: Movement-based sleep annotation
+- **Circadian analysis**: Periodograms (Lomb-Scargle, Fourier, Wavelet)
+- **HMM behavioral states**: Using hmmlearn with visualization tools
+- **Data curation**: Dead specimen removal, interpolation, filtering
+
+## Development Guidelines
+
+### Code Organization
+- **src/ethoscopy/**: Main package code
+- **tutorial_notebook/**: Jupyter notebooks for testing and examples
+- **Docker/**: JupyterHub deployment configuration
+- **Keep files under 500 lines** (per user's global instructions)
+
+### Testing Approach
+- **Use Jupyter notebooks** for validation and testing
+- **Tutorial notebooks serve as integration tests**
+- **Always test with both canvas options** (plotly/seaborn)
+
+### Documentation
+- **Docstrings**: Google style required for all functions
+- **Tutorial notebooks**: Primary documentation method
+- **README.md**: Keep updated with installation and basic usage

ethoscopy-2.0.1/Docker/Dockerfile

@@ -0,0 +1,108 @@
+# Dockerfile for jupyter-rethomics
+ARG JUPYTER_HUB_TAG=5.3.0
+FROM jupyterhub/jupyterhub:${JUPYTER_HUB_TAG}
+
+# ============================================================================
+# SYSTEM DEPENDENCIES AND TOOLS
+# ============================================================================
+
+# Install system prerequisites and build tools
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        fonts-dejavu \
+        apt-utils \
+        nano \
+        jq \
+        git \
+        gfortran \
+        file \
+        gcc \
+        cmake \
+        libcurl4-openssl-dev \
+        libfontconfig1-dev \
+        libharfbuzz-dev \
+        libfribidi-dev \
+        libtiff-dev \
+        libxml2-dev \
+        libpam0g-dev \
+        wget \
+        lsb-release \
+        software-properties-common \
+        dirmngr \
+        jupyter && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# ============================================================================
+# R INSTALLATION AND SETUP
+# ============================================================================
+
+# Add CRAN repository for latest R version
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc && \
+    add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" -y
+
+# Install R from CRAN repository
+RUN apt-get update && \
+    apt-get install -y r-base r-base-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install R packages and rethomics
+COPY install_r_packages.r /root/install_r_packages.r
+RUN ln -s /bin/tar /bin/gtar && \
+    Rscript /root/install_r_packages.r
+
+# ============================================================================
+# JUPYTER INSTALLATION AND CONFIGURATION
+# ============================================================================
+
+# Install JupyterLab (version 3.6.4)
+RUN pip3 install jupyterlab --ignore-installed
+
+# To upgrade to version 4.0.2 (commented out)
+# RUN pip3 install jupyterlab --upgrade
+
+# Install Jupyter extensions (compatible with 3.x only)
+RUN pip3 install jupyterlab-spreadsheet-editor
+
+# ============================================================================
+# PYTHON PACKAGES AND ETHOSCOPE SETUP
+# ============================================================================
+
+# Install Python data science packages
+RUN pip3 install \
+        pandas \
+        seaborn \
+        bokeh \
+        lifelines \
+        opencv-python \
+        mysql-connector \
+        ethoscopy 
+       # pycatch22
+
+# Install Ethoscope from source
+RUN git clone https://github.com/gilestrolab/ethoscope.git /opt/ethoscope && \
+    cd /opt/ethoscope/ && git checkout dev && \
+    cd /opt/ethoscope/src/ethoscope && pip install . 
+
+# ============================================================================
+# USER SETUP
+# ============================================================================
+
+# Add default user ethoscopelab with password ethoscopelab
+RUN useradd -m ethoscopelab && \
+    echo 'ethoscopelab:ethoscope' | chpasswd
+
+# ============================================================================
+# FINAL CONFIGURATION
+# ============================================================================
+
+WORKDIR /srv/jupyterhub/
+# JupyterHub config will be mounted via docker-compose
+
+EXPOSE 8000
+
+LABEL maintainer="Giorgio Gilestro <giorgio@gilest.ro>" \
+      org.jupyter.service="ethoscope-lab"
+
+CMD ["jupyterhub"]

ethoscopy-2.0.1/Docker/README.md

@@ -0,0 +1,87 @@
+# Ethoscopelab docker instance
+
+Note: Most users will **not** need to recreate this image. These instructions are just provided as reference.
+The ethoscopelab docker instance lives on dockerhub at the following address: [https://hub.docker.com/r/ggilestro/ethoscope-lab](https://hub.docker.com/r/ggilestro/ethoscope-lab) and this is what regular users should download and run. Follow instructions there and on the [ethoscopy manual](https://bookstack.lab.gilest.ro/books/ethoscopy/page/getting-started).
+
+
+## Docker files that were used to create the ethoscope-lab docker instance
+
+The files in this folder can be used to recreate the image as uploaded on dockerhub. 
+
+The command to use to recreate that image is `JUPYTER_HUB_TAG=5.3.0 ETHOSCOPE_LAB_TAG=1.0 docker compose build`. This creates the image with the specified tag. For Docker Hub deployment, push the image: `docker push ggilestro/ethoscope-lab:1.0`. To also create a latest tag: `docker tag ggilestro/ethoscope-lab:1.0 ggilestro/ethoscope-lab:latest && docker push ggilestro/ethoscope-lab:latest`. You can verify your local images with `docker images | grep ethoscope-lab`.
+
+After creation, the image can be run using the enclosed `docker-compose.yml` file, replacing values as fit.
+
+## Add new users to the JupyterHub
+
+To add new users to the JupyterHub instance:
+
+### 1. Modify the jupyterhub_config.py file
+
+Edit the `allowed_users` set on lines 14-19 to include your new usernames:
+
+```python
+c.Authenticator.allowed_users = {
+    'amadabhushi', 'ggilestro', 'mjoyce', 'lguo',
+    'labguest1', 'labguest2', 'labguest3', 'labguest4',
+    'labguest5', 'labguest6', 'labguest7', 'labguest8',
+    'ethoscopelab', 'newuser1', 'newuser2'  # Add your new users here
+}
+```
+
+To make a user an admin, add them to the `admin_users` set on line 22:
+
+```python
+c.Authenticator.admin_users = {'ggilestro', 'newadmin'}
+```
+
+### 2. Restart the Docker container
+
+After modifying the config file:
+
+```bash
+docker compose down
+docker compose up -d
+```
+
+**Notes:**
+- All users share the same password: `ethoscope` (line 11)
+- The system uses DummyAuthenticator for simple shared-password authentication
+- Each user gets their own home directory at `/home/{username}`
+- Home directories are created automatically when users first log in
+
+## Mounting Home Directories as Volumes
+
+To persist user data and notebooks across container restarts, you should mount user home directories as Docker volumes. This is done by modifying the `docker-compose.yml` file.
+
+### Benefits of mounting home directories:
+
+1. **Data Persistence**: User notebooks, data files, and configurations survive container restarts and updates
+2. **Backup and Recovery**: Easy to backup user data by copying the mounted directories
+3. **Performance**: Direct access to host filesystem, avoiding container storage overhead
+4. **Sharing**: Users can access their files from the host system if needed
+
+### Example volume configuration:
+
+Add volumes to your `docker-compose.yml`:
+
+```yaml
+services:
+  jupyterhub:
+    volumes:
+      - ./user_data:/home  # Maps host ./user_data to container /home
+      - ./jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py
+```
+
+Or for individual user directories:
+
+```yaml
+volumes:
+  - ./users/ggilestro:/home/ggilestro
+  - ./users/amadabhushi:/home/amadabhushi
+  - ./users/shared:/home/shared  # Shared directory for all users
+```
+
+This ensures all user work is preserved even when containers are recreated or updated.
+
+

ethoscopy-2.0.1/Docker/docker-compose.yml

@@ -0,0 +1,25 @@
+---
+services:
+  ethoscope-lab:
+    build:
+      context: .
+      dockerfile: Dockerfile
+      args:
+        JUPYTER_HUB_TAG: ${JUPYTER_HUB_TAG:-5.3.0}
+    image: ggilestro/ethoscope-lab:${ETHOSCOPE_LAB_TAG:-1.0}
+    container_name: ethoscope-lab
+    ports:
+      - 8082:8000
+    volumes:
+      - /mnt/ethoscope_data/results:/mnt/ethoscope_results:ro
+      - /mnt/ethoscope_data/ethoscope_metadata:/opt/ethoscope_metadata
+      - /mnt/ethoscopy/homes:/home
+      - /mnt/ethoscopy/cache:/home/cache
+      - ./jupyterhub_data:/srv/jupyterhub/
+    user: "${UID:-1000}:${GID:-1000}" # Adjust to your own user. Make sure this matches the permissions of your /mnt/{homes,cache} folder
+    restart: always
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - capabilities: ["gpu"]

ethoscopy-2.0.1/Docker/install_r_packages.r

@@ -0,0 +1,75 @@
+#!/bin/Rscript
+
+install.packages(
+c(
+    'BiocManager',
+    'caTools',
+    'callr',
+    'caret',
+    'cowplot',
+    'crayon',
+    'curl',
+    'DescTools',
+    'devtools',
+    'digest',
+    'dplyr',
+    'EnvStats',
+    'forecast',
+    'formatR',
+    'ggplot2',
+    'ggpubr',
+    'ggtern',
+    'ggthemes',
+    'ggrepel',
+    'ggseas',
+    'gh',
+    'git2r',
+    'httr',
+    'Hmisc',
+    'IRkernel',
+    'nycflights13',
+    'openssl',
+    'plotly',
+    'r-plyr',
+    'randomforest',
+    'rcurl',
+    'remotes',
+    'reshape2',
+    'rlang',
+    'rmarkdown',
+    'rsqlite',
+    'Rtsne',
+    'selectr',
+    'shiny',
+    'svglite',
+    'stringi',
+    'stringr',
+    'survminer',
+    'tictoc',
+    'tidyr',
+    'tidyverse',
+    'usethis',
+    'uuid',
+    'wesanderson',
+    'xgboost'
+  ),
+  repos='http://cran.uk.r-project.org'
+)
+
+# Install rethomics
+install.packages(
+c('behavr', 
+  'ggetho', 
+  'damr',
+#  'scopr', 
+  'sleepr', 
+  'zeitgebr'
+  ),
+  repos= 'http://cran.uk.r-project.org'
+)
+
+#As of Jan 2024 scopr does not seem to be on CRAN for whatever reason so we need to install from github
+library(devtools)
+devtools::install_github("rethomics/scopr")
+
+IRkernel::installspec(user = FALSE)

ethoscopy-2.0.1/Docker/jupyterhub_data/jupyterhub_config.py

@@ -0,0 +1,54 @@
+#  Some spawners allow shell-style expansion here, allowing you to use
+#  environment variables. Most, including the default, do not. Consult the
+#  documentation for your spawner to verify!
+#  Default: ['jupyterhub-singleuser']
+
+#c.Spawner.cmd = ['jupyterhub-singleuser'] #Default would be single user
+c.Spawner.cmd = ['jupyter-labhub', '--allow-root']
+
+# Simple authentication with shared password
+c.JupyterHub.authenticator_class = 'jupyterhub.auth.DummyAuthenticator'
+c.DummyAuthenticator.password = 'ethoscope'
+
+# Allowed users - add as many users as you need, they will all share the same password
+c.Authenticator.allowed_users = {
+    'amadabhushi', 'ggilestro', 'mjoyce', 'lguo',
+    'labguest1', 'labguest2', 'labguest3', 'labguest4',
+    'labguest5', 'labguest6', 'labguest7', 'labguest8',
+    'ethoscopelab'
+}
+
+# Admin users
+c.Authenticator.admin_users = {'ggilestro'}
+
+# Custom spawner that doesn't require system users
+from jupyterhub.spawner import LocalProcessSpawner
+import os
+
+class ConfigUserSpawner(LocalProcessSpawner):
+    def make_preexec_fn(self, name):
+        """Don't try to switch users - run everything as current user"""
+        return None
+    
+    def user_env(self, env):
+        """Set user environment without system user lookup"""
+        env = env.copy()
+        home_dir = f'/home/{self.user.name}'
+        
+        # Ensure home directory exists with proper permissions
+        os.makedirs(home_dir, mode=0o755, exist_ok=True)
+        
+        # Set environment variables
+        env['USER'] = self.user.name
+        env['HOME'] = home_dir
+        env['SHELL'] = '/bin/bash'
+        env['LOGNAME'] = self.user.name
+        
+        return env
+
+c.JupyterHub.spawner_class = ConfigUserSpawner
+c.Spawner.notebook_dir = '/home/{username}'
+
+# Timeouts
+c.Spawner.http_timeout = 60
+c.Spawner.start_timeout = 60

{ethoscopy-2.0 → ethoscopy-2.0.1}/PKG-INFO

@@ -1,27 +1,20 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: ethoscopy
-Version: 2.0
+Version: 2.0.1
 Summary: "A python based toolkit to download and anlyse data from the Ethoscope hardware system."
-License: "GNU GPLv3"
-Author: Lblackhurst29
-Author-email: l.blackhurst19@imperial.ac.uk
-Requires-Python: >=3.10,<4.0
-Classifier: License :: Other/Proprietary License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: astropy (>=6.1,<7.0)
-Requires-Dist: colour (>=0.1.5,<0.2.0)
-Requires-Dist: hmmlearn (>=0.3.2,<0.4.0)
-Requires-Dist: nbformat (>=5.10.4,<6.0.0)
-Requires-Dist: numpy (>=2.0.0,<3.0.0)
-Requires-Dist: pandas (>=2.2.2,<3.0.0)
-Requires-Dist: plotly (>=5.22.0,<6.0.0)
-Requires-Dist: pywavelets (>=1.6.0,<2.0.0)
-Requires-Dist: seaborn (>=0.13.2,<0.14.0)
-Requires-Dist: tabulate (>=0.9.0,<0.10.0)
+Author-email: Lblackhurst29 <lblackhurst29@gmail.com>
+License-File: LICENSE
+Requires-Python: <4.0,>=3.10
+Requires-Dist: astropy<7.0,>=6.1
+Requires-Dist: colour<0.2.0,>=0.1.5
+Requires-Dist: hmmlearn<0.4.0,>=0.3.2
+Requires-Dist: nbformat<6.0.0,>=5.10.4
+Requires-Dist: numpy<3.0.0,>=2.0.0
+Requires-Dist: pandas<3.0.0,>=2.2.2
+Requires-Dist: plotly<6.0.0,>=5.22.0
+Requires-Dist: pywavelets<2.0.0,>=1.6.0
+Requires-Dist: seaborn<0.14.0,>=0.13.2
+Requires-Dist: tabulate<0.10.0,>=0.9.0
 Description-Content-Type: text/markdown
 
 # ethoscopy 
@@ -43,7 +36,7 @@ Ethoscopy contains methods to perform common analytical techniques per specimen
 
 This new update sees a whole refactoring of the code base to make everything more streamline and keep the package up to date with the new versions of pandas and numpy. Gone are seperate classes for periodograms and HMM based analysis, all are under one class behavpy(). Addtioanlly, now the user can choose between plotter packages, Seaborn and Plotly, and choose a desired colour pallete. The previous used package Plotly can balloon the size of jupyter notebooks, putting a strain on storage, despite being great for data exploration. If you just want static plots, use Seaborn. But be wary of comparison, the backend for Plotly plots is all calculated in ethoscopy applying z-score and bootstrapping to quantification plots, whereas Seaborn based plots will use the Seaborn internal tools for errors and averaging.
 
-The latest update is backwards compatible with all previously saved behavpy dataframes. However, post loading they should be re-initiated as the new behavpy class. 
+The latest update is backwards compatible with all previously saved behavpy dataframes. However, post loading they should be re-initiated as the new behavpy class. See in the getting started a demonstration of what to do.
 
 Addtionally, the concat method ( behavpy_object.concat() ) for combining dataframes has been shifted to a function that is imported automatically. Call etho.concat(df1, df2) or etho.concat(*[df1, df2]) instead. There are other minor changes to method and argument names, which are reflected in their docstrings and in the tutorial. 
 
@@ -77,6 +70,14 @@ df = etho.behavpy(data, metadata, check = True, canvas = 'plotly', palette = 'Se
 filtered_df = df.xmv('experimental_column', 'group_2')
 ```
 
+Loading and re-initialising old data (saved pre 2.0)
+```bash
+import ethoscopy as etho
+import pandas as pd
+
+df = pd.read_pickle('path/to/your/file.pkl')
+df = etho.behavpy(df, df.meta, check = True, canvas = 'plotly', palette = 'Set2')
+```
 ## License
 
-This project is licensed under the [GNU-3 license](LICENSE)
+This project is licensed under the [GNU-3 license](LICENSE)

{ethoscopy-2.0 → ethoscopy-2.0.1}/README.md

@@ -17,7 +17,7 @@ Ethoscopy contains methods to perform common analytical techniques per specimen
 
 This new update sees a whole refactoring of the code base to make everything more streamline and keep the package up to date with the new versions of pandas and numpy. Gone are seperate classes for periodograms and HMM based analysis, all are under one class behavpy(). Addtioanlly, now the user can choose between plotter packages, Seaborn and Plotly, and choose a desired colour pallete. The previous used package Plotly can balloon the size of jupyter notebooks, putting a strain on storage, despite being great for data exploration. If you just want static plots, use Seaborn. But be wary of comparison, the backend for Plotly plots is all calculated in ethoscopy applying z-score and bootstrapping to quantification plots, whereas Seaborn based plots will use the Seaborn internal tools for errors and averaging.
 
-The latest update is backwards compatible with all previously saved behavpy dataframes. However, post loading they should be re-initiated as the new behavpy class. 
+The latest update is backwards compatible with all previously saved behavpy dataframes. However, post loading they should be re-initiated as the new behavpy class. See in the getting started a demonstration of what to do.
 
 Addtionally, the concat method ( behavpy_object.concat() ) for combining dataframes has been shifted to a function that is imported automatically. Call etho.concat(df1, df2) or etho.concat(*[df1, df2]) instead. There are other minor changes to method and argument names, which are reflected in their docstrings and in the tutorial. 
 
@@ -51,6 +51,14 @@ df = etho.behavpy(data, metadata, check = True, canvas = 'plotly', palette = 'Se
 filtered_df = df.xmv('experimental_column', 'group_2')
 ```
 
+Loading and re-initialising old data (saved pre 2.0)
+```bash
+import ethoscopy as etho
+import pandas as pd
+
+df = pd.read_pickle('path/to/your/file.pkl')
+df = etho.behavpy(df, df.meta, check = True, canvas = 'plotly', palette = 'Set2')
+```
 ## License
 
 This project is licensed under the [GNU-3 license](LICENSE)

ethoscopy-2.0.1/_config.yml

@@ -0,0 +1 @@
+theme: jekyll-theme-minimal

ethoscopy-2.0.1/pyproject.toml

@@ -0,0 +1,38 @@
+[project]
+name = "ethoscopy"
+version = "2.0.1"
+description = "\"A python based toolkit to download and anlyse data from the Ethoscope hardware system.\""
+authors = [{name = "Lblackhurst29",email = "lblackhurst29@gmail.com"}]
+readme = "README.md"
+dependencies = [
+    "numpy>=2.0.0,<3.0.0",
+    "pandas>=2.2.2,<3.0.0",
+    "plotly>=5.22.0,<6.0.0",
+    "seaborn>=0.13.2,<0.14.0",
+    "tabulate>=0.9.0,<0.10.0",
+    "colour>=0.1.5,<0.2.0",
+    "hmmlearn>=0.3.2,<0.4.0",
+    "pywavelets>=1.6.0,<2.0.0",
+    "astropy>=6.1,<7.0",
+    "nbformat>=5.10.4,<6.0.0",
+]
+requires-python = ">=3.10,<4.0"
+
+[tool]
+[tool.rye]
+managed = true
+virtual = false
+dev-dependencies = [
+    "ipykernel>=6.29.5,<7.0.0",
+]
+
+[tool.hatch]
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/ethoscopy"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

ethoscopy-2.0.1/setup.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+
+import sys
+from setuptools import setup, find_packages
+
+if sys.version_info >= (3, 8):
+    from importlib import metadata
+else:
+    from importlib_metadata import metadata
+
+# This is the setup.py for a developmental version. The Officially tagged versions will have an overwritten 
+# setup.py as generated by poetry https://pypi.org/project/poetry/
+VERSION = 'dev'
+DESCRIPTION = 'A python based toolkit to download and analyse data from the Ethoscope hardware system.'
+
+with open("README.md", "r", encoding="utf-8") as fh:
+    LONG_DESCRIPTION = fh.read()
+
+setup(
+        name = "ethoscopy", 
+        version = VERSION,
+        author = "Laurence Blackhurst",
+        author_email = "l.blackhurst19@imperial.ac.uk",
+        description = DESCRIPTION,
+        long_description = LONG_DESCRIPTION,
+        packages = find_packages('src'),
+        package_dir = {'' : 'src'},
+        install_requires=['pandas >= 1.4', 'numpy >= 1.22',],
+        keywords=['python', 'ethomics', 'ethoscope', 'sleep'],
+        classifiers= [
+            "Development Status :: 3 - Alpha",
+            "Intended Audience :: Education",
+            "Programming Language :: Python :: 3",
+            "Operating System :: Microsoft :: Windows",
+            "Operating System :: POSIX",
+            "Operating System :: MacOS :: MacOS X"
+        ],
+        python_requires = ">=3.8"
+)