simba-uw-tf-dev 5.3.7__tar.gz → 5.3.9__tar.gz

simba_uw_tf_dev-5.3.9/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Python Version [e.g. 3.6.0]
+ - Are you using anaconda?
+ 
+
+**Additional context**
+Add any other context about the problem here.

simba_uw_tf_dev-5.3.9/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

simba_uw_tf_dev-5.3.9/.github/workflows/bigquery_download_stats.yml

@@ -0,0 +1,47 @@
+name: Get BigQuery Download Stats
+
+on:
+  schedule:
+    - cron: '0 7 * * *'  # Runs at 7 AM UTC, which is 2 AM EST
+  workflow_dispatch:  # Allows manual trigger
+
+jobs:
+  query:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Needed to push to existing branches
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install google-cloud-bigquery pandas
+
+      - name: Run BigQuery query
+        env:
+          GOOGLE_APPLICATION_CREDENTIALS_CONTENT: ${{ secrets.GCP_CREDENTIALS }}
+        run: python misc/bigquery_download_stats.py
+
+      - name: Configure Git
+        run: |
+          git config user.email "action@github.com"
+          git config user.name "GitHub Actions"
+
+      - name: Commit and force push CSV to 'download_stats' branch
+        run: |
+          git fetch origin download_stats || true
+          git checkout -B download_stats origin/download_stats || git checkout -b download_stats
+
+          git add misc/bigquery_download_stats.csv
+          git commit -m "Update BigQuery download stats CSV" || echo "Nothing to commit"
+
+          git push origin download_stats --force
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

simba_uw_tf_dev-5.3.9/.github/workflows/cleaning.yml

@@ -0,0 +1,24 @@
+name: Format code
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Format code with black
+        run: |
+          pip install black isort
+          cd simba
+          isort .
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v4
+        with:
+          author_name: ${{ github.actor }}
+          author_email: ${{ github.actor }}@users.noreply.github.com
+          message: "cleaned"
+          add: "."
+          branch: ${{ github.ref }}

simba_uw_tf_dev-5.3.9/.github/workflows/issue_msg.yml.disabled

@@ -0,0 +1,20 @@
+name: Auto Comment on New Issue
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  comment:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Comment on the new issue
+        uses: actions/github-script@v7
+        with:
+          script: |
+            github.rest.issues.createComment({
+              issue_number: context.issue.number,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: `Hi y’all - I'm Simon.\n\nI write and maintain the code for SimBA and have been answering a lot of questions and requests around here :wrench:\n\nI'm stepping away from the keyboard and plan to be BACK AROUND MAY 24TH.\n\nI will have limited internet access during this time. I may get back to you, if it is some quick general advice, or some crazy bug that has a quick fix. But otherwise, it will have to wait.\n\nBetween this forum, and the GitHub issues, there are nearly 15k posts at last count – you can search some of them by searching the issues here for keywords, or clicking the info button at the top right on Gitter and entering some keywords – fingers crossed it could have been covered previously!\n\nThanks for your patience, everyone! :v::tent::desert:`
+            })

simba_uw_tf_dev-5.3.9/.github/workflows/issue_report.yml

@@ -0,0 +1,70 @@
+name: Daily GitHub Issue Report
+
+on:
+  schedule:
+  workflow_dispatch:  # Allows manual trigger
+
+jobs:
+  report:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout master branch
+      uses: actions/checkout@v3
+      with:
+        ref: 'master'  # Checkout the master branch where the workflow is located
+
+    - name: Verify current branch
+      run: |
+        git branch
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pandas requests  # Install required dependencies
+
+    - name: List files in the repository
+      run: |
+        ls -R /home/runner/work/simba/simba/  # Confirm repo structure
+
+    - name: Fetch GitHub issues and generate report
+      run: |
+        python /home/runner/work/simba/simba/scripts/create_issues_report.py  # Ensure the path is correct
+
+    - name: Verify if the report file exists
+      run: |
+        ls -l /home/runner/work/simba/simba/misc/github_issues_report.csv
+
+    - name: Commit CSV file to master branch
+      run: |
+        mkdir -p misc  # Create misc directory if it doesn't exist
+
+        # Ensure the report is placed in the correct location
+        output_path='misc/github_issues_report.csv'
+
+        # Check if the file exists before attempting to remove it
+        if [ -f "$output_path" ]; then
+          rm -f "$output_path"  # Remove the existing CSV report if it exists
+        fi
+
+        # Move the new CSV file to the misc directory (if it's not already there)
+        cp /home/runner/work/simba/simba/misc/github_issues_report.csv $output_path
+
+        # Add the file to Git
+        git add $output_path
+
+        # Configure Git with authentication using GITHUB_TOKEN
+        git config user.name "github-actions"
+        git config user.email "github-actions@github.com"
+
+        # Use the built-in GITHUB_TOKEN for authentication
+        git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}.git
+
+        # Commit and push changes to master branch
+        git commit -m "Update daily issues report"
+        git push origin master  # Push changes to the master branch

simba_uw_tf_dev-5.3.9/.github/workflows/tests_py310.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: py3.10 tests
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: FedericoCarboni/setup-ffmpeg@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+        architecture: "x64"
+    - name: Install dependencies
+      run: |
+        python -m pip install pip==21.2.2
+        pip install --upgrade setuptools
+        pip install flake8 pytest black pytest-cov
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install simba-uw-tf-dev --no-deps
+    # - name: Install ffmpeg
+    #   id: setup-ffmpeg
+    #   run: ffmpeg -version
+    # - name: Test with pytest
+    #   run: |
+    #     pytest -cov

simba_uw_tf_dev-5.3.9/.github/workflows/tests_py36.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: py3.6 tests
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: FedericoCarboni/setup-ffmpeg@v2
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.6.13"
+        architecture: "x64"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --upgrade setuptools
+        pip install flake8 pytest black pytest-cov
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install simba-uw-tf-dev --no-deps
+    - name: Install ffmpeg
+      id: setup-ffmpeg
+      run: ffmpeg -version
+    - name: Test with pytest
+      run: |
+        pytest -cov

simba_uw_tf_dev-5.3.9/.gitignore

@@ -0,0 +1,45 @@
+# Byte-compiled / optimized Python files
+__pycache__/
+*.py[cod]
+
+# Virtual environment
+venv/
+env/
+ENV/
+
+# IDE or editor specific files
+.idea/
+*.o
+*.pyc
+*.class
+.ipynb_checkpoints/
+.pytest_cache/
+simba/pose_configurations_archive/
+
+# Ignore PyPI build artifacts
+dist/
+build/
+runs/
+*.egg-info/
+*.egg
+*.tar.gz
+*.whl
+*.pt
+*.cursorrules
+
+# dev
+simba/sandbox
+
+#local docs build
+_build/html/
+docs/_build
+/docs/_build/
+/simba/sandbox/
+
+
+# ignore recent projects file anywhere
+**/.recent_projects.txt
+
+# Claude Code
+simba/.claude/
+.claude/

simba_uw_tf_dev-5.3.9/.pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+
+addopts = -ra -q
+testpaths = tests

simba_uw_tf_dev-5.3.9/.readthedocs.yaml

@@ -0,0 +1,26 @@
+
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+conda:
+  environment: docs/environment.yml
+  
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-4.10"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+#formats:
+#  - pdf
+
+

simba_uw_tf_dev-5.3.9/App.py

@@ -0,0 +1,5 @@
+from simba.SimBA import main as App
+
+if __name__ == '__main__':
+    App()
+

simba_uw_tf_dev-5.3.9/CITATION.cff

@@ -0,0 +1,66 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+message: "If you use this research or software, please cite the following publication."
+title: "Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience"
+authors:
+  - family-names: "Goodwin"
+    given-names: "Nastacia L."
+  - family-names: "Choong"
+    given-names: "Jia J."
+  - family-names: "Hwang"
+    given-names: "Sophia"
+  - family-names: "Pitts"
+    given-names: "Kayla"
+  - family-names: "Bloom"
+    given-names: "Liana"
+  - family-names: "Islam"
+    given-names: "Aasiya"
+  - family-names: "Zhang"
+    given-names: "Yizhe Y."
+  - family-names: "Szelenyi"
+    given-names: "Eric R."
+  - family-names: "Tong"
+    given-names: "Xiaoyu"
+  - family-names: "Newman"
+    given-names: "Emily L."
+  - family-names: "Miczek"
+    given-names: "Klaus"
+  - family-names: "Wright"
+    given-names: "Hayden R."
+  - family-names: "McLaughlin"
+    given-names: "Ryan J."
+  - family-nnames: "Norville"
+    given-names: "Zane C."
+  - family-names: "Eshel"
+    given-names: "Neir"
+  - family-names: "Heshmati"
+    given-names: "Mitra"
+  - family-names: "Nilsson"
+    given-names: "Simon R. O."
+  - family-names: "Golden"
+    given-names: "Sam A."
+contact:
+  - family-names: "Golden"
+    given-names: "Sam A."
+    email: "sgolden@uw.edu"
+  - family-names: "Nilsson"
+    given-names: "Simon R. O."
+    email: "sronilsson@gmail.com"
+date-released: "2024-05-22"
+url: "https://simba-uw-tf-dev.readthedocs.io/"
+repository-code: "https://github.com/sgoldenlab/simba"
+repository: "https://osf.io/tmu6y/"
+identifiers:
+  - type: doi
+    value: "10.1038/s41593-024-01649-9"
+    description: "DOI for the published article"
+abstract: >-
+  The study of complex behaviors is often challenging when using manual annotation due to the absence of quantifiable behavioral definitions and the subjective nature of behavioral annotation. Integration of supervised machine learning approaches mitigates some of these issues through accessible and explainable model interpretation. To decrease barriers to access, we developed Simple Behavioral Analysis (SimBA) for behavioral neuroscientists. SimBA introduces machine learning interpretability tools, including SHapley Additive exPlanation (SHAP) scores, for explainable classifiers, enabling comparisons across species and providing a sharable framework.
+license: GPL-3.0
+keywords:
+  - behavioral neuroscience
+  - machine learning
+  - animal behavior analysis
+  - explainable AI

simba_uw_tf_dev-5.3.9/CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at goldenneurolab@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

{simba_uw_tf_dev-5.3.7 → simba_uw_tf_dev-5.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: simba_uw_tf_dev
-Version: 5.3.7
+Version: 5.3.9
 Summary: Toolkit for computer classification and analysis of behaviors in experimental animals
 Home-page: https://github.com/sgoldenlab/simba
 Author: Simon Nilsson, Jia Jie Choong, Sophia Hwang
@@ -57,7 +57,7 @@ If you use the code, please cite:
 ```
 
 ### Licence
-SimBA is licensed under GNU Lesser General Public License v3.0.
+SimBA is licensed under a modified BSD 3-Clause License, permitting use for academic and research purposes only. For commercial licensing inquiries, contact sronilsson@gmail.com.
 
 ### Contributors
 Contributers on Github https://github.com/sgoldenlab/simba#contributors

{simba_uw_tf_dev-5.3.7 → simba_uw_tf_dev-5.3.9}/README.md

@@ -4,7 +4,7 @@
 [![py3.10 tests](https://github.com/sgoldenlab/simba/actions/workflows/tests_py310.yml/badge.svg)](https://github.com/sgoldenlab/simba/actions/workflows/tests_py310.yml)
 [![py3.6 tests](https://github.com/sgoldenlab/simba/actions/workflows/tests_py36.yml/badge.svg)](https://github.com/sgoldenlab/simba/actions/workflows/tests_py36.yml)
 ![Docs](https://readthedocs.org/projects/simba-uw-tf-dev/badge/?version=latest&style=flat)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+[![License: Modified BSD 3-Clause](https://img.shields.io/badge/License-Modified%20BSD%203--Clause%20(Academic%2FResearch)-blue.svg)](LICENSE)
 [![Gitter chat](https://badges.gitter.im/USER/REPO.png)](https://gitter.im/SimBA-Resource/community)
 [![Download: Weights](https://img.shields.io/badge/Download-Weights-orange.svg)](https://osf.io/5t4y9/)
 [![SimBA: listserv](https://img.shields.io/static/v1?label=SimBA&message=listserv&color=blue)](https://docs.google.com/forms/d/e/1FAIpQLSfjbjae0XqNcl7GYOxmqvRsCveG-cmf4p4hBNNJ8gu5vPLHng/viewform)

simba_uw_tf_dev-5.3.9/requirements.txt

@@ -0,0 +1,77 @@
+cefpython3 == 66.0
+dash == 1.14.0
+dash_color_picker == 0.0.1
+dash_colorscales == 0.0.4
+dash_core_components==1.10.2
+dash_html_components == 1.0.3
+dtreeviz == 0.8.1; python_version=="3.6"
+dtreeviz == 1.3.0; python_version>="3.9"
+eli5 == 0.10.1
+ffmpeg-python==0.2.0
+geos==0.2.3
+graphviz==0.11
+h5py==2.9.0;python_version=="3.6"
+h5py==3.11.0;python_version>="3.9"
+imbalanced-learn==0.6.2; python_version=="3.6"
+imbalanced-learn==0.12.2; python_version>="3.9"
+imgaug == 0.4.0
+imutils == 0.5.2
+joblib == 1.1.1; python_version=="3.6"
+joblib == 1.4.2; python_version>="3.9"
+kaleido == 0.1.0; python_version=="3.6"
+kaleido; python_version>="3.9"
+matplotlib==3.3.4; python_version == "3.6"
+matplotlib==3.5.0; python_version >= "3.9" and python_version <= "3.11"
+matplotlib==3.8.*; python_version >= "3.12"
+numba==0.53.1;python_version=="3.6"
+numba==0.63.1;python_version>="3.9"
+numexpr==2.6.9;python_version=="3.6"
+numexpr==2.10.0;python_version>="3.9"
+numpy==1.19.1; python_version=="3.6"
+numpy==1.26.4; python_version >= "3.9" and python_version <= "3.11"
+numpy==1.26.1; python_version >= "3.12"
+opencv-python == 3.4.5.20; python_version=="3.6"
+opencv-python == 4.8.1.78; python_version>="3.9"
+openpyxl==3.1.2;python_version=="3.6"
+openpyxl==3.1.5;python_version >= "3.9" and python_version <= "3.11"
+osfclient == 0.0.5
+packaging==21.3; python_version=="3.6"
+pandas==0.25.3;python_version=="3.6"
+pandas==2.2.2;python_version>="3.9"
+Pillow==8.3.2; python_version=="3.6"
+Pillow==10.3.0; python_version>="3.9"
+plotly == 4.9.0
+psutil == 5.9.8; python_version=="3.6"
+psutil; python_version>="3.9"
+pyarrow==6.0.1; python_version < "3.12"
+pyarrow==21.0.0; sys_platform == "win32" and python_version >= "3.12"
+pyarrow>=13.0.0; sys_platform != "win32" and python_version >= "3.12"
+pyglet==1.5.27; python_version=="3.6"
+pyglet==2.0.10; python_version>="3.9"
+python-dotenv==0.20.0; python_version=="3.6"
+python-dotenv==1.0.1; python_version>="3.9"
+pyvis==0.3.2; python_version=="3.6"
+pyyaml==5.3.1; python_version=="3.6"
+pyyaml==6.0.2; python_version>="3.9"
+scikit-image == 0.17.2;python_version=="3.6"
+scikit-image == 0.23.2; python_version>="3.9"
+scikit-learn == 0.22.2; python_version=="3.6"
+scikit-learn == 1.4.2; python_version>="3.9"
+scipy== 1.5.4; python_version=="3.6"
+scipy== 1.13.0; python_version>="3.9"
+seaborn == 0.11.0
+shap == 0.35.0;python_version=="3.6"
+shap == 0.42.0;python_version>="3.9"
+shapely == 1.8.0; python_version=="3.6"
+shapely == 2.0.2; python_version>="3.9"
+statsmodels==0.12.0;python_version=="3.6"
+statsmodels==0.14.2;python_version>="3.9"
+tables==3.6.1;python_version=="3.6"
+tables==3.9.2;python_version>="3.9"
+tabulate == 0.8.3; python_version=="3.6"
+tabulate == 0.9.0; python_version>="3.9"
+tqdm == 4.30.0; python_version=="3.6"
+tqdm == 4.67.0; python_version>="3.9"
+trafaret==2.1.1
+xgboost == 0.90
+xlrd==1.2.0