ethoscopy 2.0.1__tar.gz → 2.0.3__tar.gz

ethoscopy-2.0.3/.claude/settings.local.json

@@ -0,0 +1,25 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(git add:*)",
+      "Bash(git commit:*)",
+      "Bash(python:*)",
+      "Bash(ls:*)",
+      "Bash(find:*)",
+      "Bash(docker exec ethoscope-lab ls -la \"/mnt/ethoscope_results/26634d78becf48628fe5d9ffc67fae04/ETHOSCOPE_266/2025-07-29_19-12-16/2025-07-29_19-12-16_26634d78becf48628fe5d9ffc67fae04.db\")",
+      "Bash(docker exec:*)",
+      "Bash(source:*)",
+      "Bash(git push:*)",
+      "Bash(mkdir:*)",
+      "Bash(cp:*)",
+      "Bash(sqlite3:*)",
+      "Bash(black:*)",
+      "Bash(grep:*)",
+      "Bash(pip install:*)",
+      "Bash(git stash pop:*)",
+      "Bash(git checkout:*)",
+      "Bash(git tag:*)"
+    ],
+    "deny": []
+  }
+}

ethoscopy-2.0.3/.codecov.yml

@@ -0,0 +1,26 @@
+coverage:
+  range: 50..90
+  round: down
+  precision: 2
+
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        base: auto
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        base: auto
+
+comment:
+  layout: "reach, diff, flags, files"
+  behavior: default
+
+ignore:
+  - "tests/"
+  - "tutorial_notebook/"
+  - "setup.py"
+  - "run_tests.py"

ethoscopy-2.0.3/.github/workflows/ci.yml

@@ -0,0 +1,151 @@
+name: CI/CD Pipeline
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    # Run tests daily at 6 AM UTC
+    - cron: '0 6 * * *'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache pip dependencies
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[dev]"
+        pip install pytest-cov pytest-xdist pytest-mock
+
+    - name: Lint with ruff
+      run: |
+        pip install ruff
+        ruff check src/
+
+    - name: Format check with black
+      run: |
+        pip install black
+        black --check src/ tests/
+
+    - name: Run unit tests
+      run: |
+        python -m pytest tests/ -v --cov=ethoscopy --cov-report=xml --cov-report=term-missing -m "unit"
+
+    - name: Run integration tests
+      run: |
+        python -m pytest tests/ -v -m "integration"
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: gilestrolab/ethoscopy
+
+  test-notebooks:
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[dev]"
+        pip install nbval jupyter
+
+    - name: Test notebooks
+      run: |
+        pytest --nbval-lax tutorial_notebook/*.ipynb -v
+      continue-on-error: true  # Notebooks may fail due to data dependencies
+
+  build:
+    runs-on: ubuntu-latest
+    needs: [test, test-notebooks]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: |
+        python -m build
+
+    - name: Check package
+      run: |
+        twine check dist/*
+
+    - name: Upload build artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: dist-files
+        path: dist/
+
+  security-scan:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install bandit safety
+
+    - name: Run security scan with bandit
+      run: |
+        bandit -r src/ -f json -o bandit-report.json
+      continue-on-error: true
+
+    - name: Run safety check
+      run: |
+        safety check --json --output safety-report.json
+      continue-on-error: true
+
+    - name: Upload security reports
+      uses: actions/upload-artifact@v4
+      with:
+        name: security-reports
+        path: |
+          bandit-report.json
+          safety-report.json

ethoscopy-2.0.3/.github/workflows/release.yml

@@ -0,0 +1,74 @@
+name: Release to PyPI
+
+on:
+  release:
+    types: [published]
+  push:
+    tags:
+      - 'v*.*.*'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[dev]"
+        pip install pytest-cov
+
+    - name: Run tests
+      run: |
+        python -m pytest tests/ -v --cov=ethoscopy -m "not slow"
+
+  build-and-publish:
+    needs: test
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: |
+        python -m build
+
+    - name: Check package
+      run: |
+        twine check dist/*
+
+    - name: Publish to Test PyPI
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+      run: |
+        twine upload --repository testpypi dist/*
+
+    - name: Publish to PyPI
+      if: github.event_name == 'release'
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        twine upload dist/*

{ethoscopy-2.0.1 → ethoscopy-2.0.3}/.gitignore

@@ -7,4 +7,5 @@ __pycache__/
 ethoscopy.egg-info/
 .gitignore
 *.pkl
-.python-version
+.python-version
+tmp

ethoscopy-2.0.3/.pre-commit-config.yaml

@@ -0,0 +1,62 @@
+repos:
+  # General file checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        files: \.(py|yml|yaml|md|txt)$
+      - id: end-of-file-fixer
+        files: \.(py|yml|yaml|md|txt)$
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+      - id: debug-statements
+        files: ^(src/|tests/).*\.py$
+      - id: check-ast
+        files: ^(src/|tests/).*\.py$
+
+  # Black - Code formatting
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+        args: [--line-length=88]
+        files: ^(src/|tests/).*\.py$
+
+  # Ruff - Linting and code analysis
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        files: ^src/.*\.py$
+      - id: ruff-format
+        files: ^(src/|tests/).*\.py$
+
+  # Import sorting
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: [--profile, black, --line-length=88]
+        files: ^(src/|tests/).*\.py$
+
+  - repo: local
+    hooks:
+      - id: pytest-unit
+        name: pytest-unit
+        entry: .venv/bin/python -m pytest tests/ -m "unit" -v
+        language: system
+        pass_filenames: false
+        always_run: true
+        stages: [commit]
+
+      - id: pytest-fast
+        name: pytest-fast
+        entry: .venv/bin/python -m pytest tests/ -m "not slow" -v --tb=short
+        language: system
+        pass_filenames: false
+        always_run: true
+        stages: [push]

{ethoscopy-2.0.1 → ethoscopy-2.0.3}/CLAUDE.md

@@ -10,7 +10,7 @@ Ethoscopy is a Python data analysis toolbox for behavioral time series data from
 
 ### 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)
+- **Always use virtual environment** (`.venv` as mentioned in user's global instructions)
 - **Install in development mode**: `pip install -e .`
 
 ### Package Management
@@ -108,4 +108,4 @@ df = etho.behavpy(data, metadata, check=True, canvas='plotly', palette='Set2')
 ### Documentation
 - **Docstrings**: Google style required for all functions
 - **Tutorial notebooks**: Primary documentation method
-- **README.md**: Keep updated with installation and basic usage
+- **README.md**: Keep updated with installation and basic usage

ethoscopy-2.0.3/Docker/.claude/settings.local.json

@@ -0,0 +1,19 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(ls:*)",
+      "Bash(git checkout:*)",
+      "Bash(docker images:*)",
+      "Read(//tmp/**)",
+      "Bash(JUPYTER_HUB_TAG=5.3.0 ETHOSCOPE_LAB_TAG=1.1 docker compose build:*)",
+      "Bash(tee:*)",
+      "Bash(docker compose:*)",
+      "Bash(find:*)",
+      "Bash(sqlite3:*)",
+      "Bash(python3:*)",
+      "Bash(docker exec:*)",
+      "Bash(docker cp:*)"
+    ],
+    "deny": []
+  }
+}

ethoscopy-2.0.3/Docker/.env

@@ -0,0 +1,39 @@
+# Keycloak OAuth Configuration for JupyterHub
+# To use: cp .env.keycloak .env && docker compose restart
+
+# Image versions
+JUPYTER_HUB_TAG=5.3.0
+ETHOSCOPE_LAB_TAG=1.1
+
+# Authentication
+AUTHENTICATOR_CLASS=generic
+DUMMY_PASSWORD=ethoscope
+
+# User configuration
+ALLOWED_USERS=amadabhushi,ggilestro,mjoyce,lguo,labguest1,labguest2,labguest3,labguest4,labguest5,labguest6,labguest7,ethoscopelab
+ADMIN_USERS=ggilestro
+
+# User/Group IDs (must match your host system)
+UID=1000
+GID=1000
+
+# Keycloak OAuth Settings
+OAUTH_CLIENT_ID=jupyter-lab
+OAUTH_CLIENT_SECRET=pBUaqP6b8bO5IamJ7jw4lD3l5EyKJaKq
+OAUTH_CALLBACK_URL=https://jupyter.lab.gilest.ro/hub/oauth_callback
+
+# Keycloak endpoints (realm: gilestro-lab)
+OAUTH_AUTHORIZE_URL=https://auth.gilest.ro/realms/gilestro-lab/protocol/openid-connect/auth
+OAUTH_TOKEN_URL=https://auth.gilest.ro/realms/gilestro-lab/protocol/openid-connect/token
+OAUTH_USERDATA_URL=https://auth.gilest.ro/realms/gilestro-lab/protocol/openid-connect/userinfo
+
+# Username claim (Keycloak typically uses 'preferred_username')
+OAUTH_USERNAME_CLAIM=preferred_username
+
+# OAuth scopes
+OAUTH_SCOPE=openid profile email
+
+# Provider-specific (not used for Keycloak, but needed for env validation)
+GITHUB_ORG=
+GOOGLE_HOSTED_DOMAIN=
+GITLAB_URL=

ethoscopy-2.0.3/Docker/.env.keycloak

@@ -0,0 +1,39 @@
+# Keycloak OAuth Configuration for JupyterHub
+# To use: cp .env.keycloak .env && docker compose restart
+
+# Image versions
+JUPYTER_HUB_TAG=5.3.0
+ETHOSCOPE_LAB_TAG=1.1
+
+# Authentication
+AUTHENTICATOR_CLASS=generic
+DUMMY_PASSWORD=ethoscope
+
+# User configuration
+ALLOWED_USERS=amadabhushi,ggilestro,mjoyce,lguo,labguest1,labguest2,labguest3,labguest4,labguest5,labguest6,labguest7,ethoscopelab
+ADMIN_USERS=ggilestro
+
+# User/Group IDs (must match your host system)
+UID=1000
+GID=1000
+
+# Keycloak OAuth Settings
+OAUTH_CLIENT_ID=jupyter-lab
+OAUTH_CLIENT_SECRET=pBUaqP6b8bO5IamJ7jw4lD3l5EyKJaKq
+OAUTH_CALLBACK_URL=https://jupyter.lab.gilest.ro/hub/oauth_callback
+
+# Keycloak endpoints (realm: gilestro-lab)
+OAUTH_AUTHORIZE_URL=https://auth.gilest.ro/realms/gilestro-lab/protocol/openid-connect/auth
+OAUTH_TOKEN_URL=https://auth.gilest.ro/realms/gilestro-lab/protocol/openid-connect/token
+OAUTH_USERDATA_URL=https://auth.gilest.ro/realms/gilestro-lab/protocol/openid-connect/userinfo
+
+# Username claim (Keycloak typically uses 'preferred_username')
+OAUTH_USERNAME_CLAIM=preferred_username
+
+# OAuth scopes
+OAUTH_SCOPE=openid profile email
+
+# Provider-specific (not used for Keycloak, but needed for env validation)
+GITHUB_ORG=
+GOOGLE_HOSTED_DOMAIN=
+GITLAB_URL=

{ethoscopy-2.0.1 → ethoscopy-2.0.3}/Docker/README.md

@@ -6,7 +6,7 @@ The ethoscopelab docker instance lives on dockerhub at the following address: [h
 
 ## 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 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`.
 
@@ -83,5 +83,3 @@ volumes:
 ```
 
 This ensures all user work is preserved even when containers are recreated or updated.
-
-

ethoscopy-2.0.3/Docker/config/jupyterhub_cookie_secret

@@ -0,0 +1 @@
+dc4907b418101083a39e9e3f1d9e2cf2014f9a9b17dedaf584f36f3300cc44be

ethoscopy-2.0.3/Docker/jupyterhub_data/jupyterhub-proxy.pid

@@ -0,0 +1 @@
+9

{ethoscopy-2.0.1 → ethoscopy-2.0.3}/Docker/jupyterhub_data/jupyterhub_config.py

@@ -29,21 +29,21 @@ 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

ethoscopy-2.0.3/Docker/jupyterhub_data/jupyterhub_cookie_secret

@@ -0,0 +1 @@
+90911154c749321ff6ebb164e8501c130e62388a387de6b121cc889ef518aa85

ethoscopy-2.0.1/README.md → ethoscopy-2.0.3/PKG-INFO

@@ -1,4 +1,49 @@
-# ethoscopy 
+Metadata-Version: 2.4
+Name: ethoscopy
+Version: 2.0.3
+Summary: "A python based toolkit to download and anlyse data from the Ethoscope hardware system."
+Author-email: Lblackhurst29 <lblackhurst29@gmail.com>
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+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
+Provides-Extra: dev
+Requires-Dist: black<25.0.0,>=24.0.0; extra == 'dev'
+Requires-Dist: ipykernel<7.0.0,>=6.29.5; extra == 'dev'
+Requires-Dist: isort<6.0.0,>=5.13.0; extra == 'dev'
+Requires-Dist: pre-commit<4.0.0,>=3.0.0; extra == 'dev'
+Requires-Dist: pytest-cov<6.0.0,>=5.0.0; extra == 'dev'
+Requires-Dist: pytest-mock<4.0.0,>=3.12.0; extra == 'dev'
+Requires-Dist: pytest-xdist<4.0.0,>=3.5.0; extra == 'dev'
+Requires-Dist: pytest<9.0.0,>=8.0.0; extra == 'dev'
+Requires-Dist: ruff<1.0.0,>=0.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# ethoscopy
+
+[![CI/CD Pipeline](https://github.com/gilestrolab/ethoscopy/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/gilestrolab/ethoscopy/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/gilestrolab/ethoscopy/branch/main/graph/badge.svg)](https://codecov.io/gh/gilestrolab/ethoscopy)
+[![PyPI version](https://img.shields.io/pypi/v/ethoscopy.svg)](https://pypi.org/project/ethoscopy/)
+[![Python versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue.svg)](https://pypi.org/project/ethoscopy/)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 A data-analysis toolbox utilising Pandas, Seaborn, and Plotly to curate, clean, analyse, and visualise behavioural time series data. Whilst the toolbix was created around the data produced from an Ethoscope (a Drosophila monitoring system), if the users data follows the same structure for time series data all methods can be utilised.
 
@@ -19,7 +64,7 @@ This new update sees a whole refactoring of the code base to make everything mor
 
 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. 
+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.
 
 ## Getting Started
 
@@ -59,6 +104,41 @@ 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')
 ```
+
+## Development and Testing
+
+Ethoscopy includes a comprehensive test suite to ensure code reliability and prevent regressions.
+
+### Running Tests
+
+Install development dependencies:
+```bash
+pip install -e ".[dev]"
+```
+
+Run all tests:
+```bash
+pytest
+```
+
+Run tests with coverage:
+```bash
+pytest --cov=ethoscopy --cov-report=term-missing
+```
+
+Or use the convenience script:
+```bash
+python run_tests.py
+```
+
+### Test Categories
+
+- **Unit tests**: Fast tests for individual functions (`pytest -m unit`)
+- **Integration tests**: Workflow testing (`pytest -m integration`)
+- **Performance tests**: Long-running tests (`pytest -m slow`)
+
+For detailed testing information, see [TESTING.md](TESTING.md).
+
 ## License
 
-This project is licensed under the [GNU-3 license](LICENSE)
+This project is licensed under the [GNU-3 license](LICENSE)