simba-uw-tf-dev 5.5.1__tar.gz → 5.5.2__tar.gz

simba_uw_tf_dev-5.5.2/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+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-5.5.2/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+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-5.5.2/.github/workflows/bigquery_download_stats.yml

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+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-5.5.2/.github/workflows/cleaning.yml

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+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-5.5.2/.github/workflows/issue_msg.yml.disabled

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+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-5.5.2/.github/workflows/issue_report.yml

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+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-5.5.2/.github/workflows/tests_py310.yml

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+# 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-5.5.2/.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-5.5.2/.github/workflows/usecase_map.yml

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+name: Update SimBA Use-Case Map
+
+on:
+  schedule:
+    - cron: '30 7 * * *'   # daily at 07:30 UTC (just after the download-stats job)
+  workflow_dispatch:        # "Run workflow" button — click after editing the sheet
+
+permissions:
+  contents: write           # needed to commit the regenerated HTML
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      # No pip install and no secrets needed — the generator uses only the
+      # Python standard library and reads the public Google Sheet as CSV.
+      - name: Regenerate use-case map from the public sheet
+        run: python misc/usecase_map_stats.py
+
+      - name: Configure Git
+        run: |
+          git config user.email "action@github.com"
+          git config user.name "GitHub Actions"
+
+      - name: Commit updated map (if changed)
+        run: |
+          git add docs/_generated/usecase_map.html
+          git commit -m "Update SimBA use-case global-reach map" || echo "Nothing to commit"
+          git push

simba_uw_tf_dev-5.5.2/.gitignore

@@ -0,0 +1,52 @@
+# 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/
+
+# runtime logs written by SimBA into project folders (incl. test fixtures)
+**/logs/project_log.log
+
+# macOS finder metadata
+.DS_Store
+**/.DS_Store

simba_uw_tf_dev-5.5.2/.pytest.ini

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

simba_uw_tf_dev-5.5.2/.readthedocs.yaml

@@ -0,0 +1,33 @@
+
+# .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"
+  jobs:
+    # Read the Docs shallow-clones the repo, which leaves `git log --numstat`
+    # (used by docs/conf.py to compute per-contributor lines-of-code for the
+    # credits chart) with no history. Fetch full history so the line counts
+    # populate. `|| true` keeps the build green if the repo is already complete.
+    post_checkout:
+      - git fetch --unshallow || true
+
+# 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-5.5.2/App.py

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

simba_uw_tf_dev-5.5.2/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-5.5.2/CODE_OF_CONDUCT.md

@@ -0,0 +1,132 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+sronilsson@gmail.com.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations