simba-uw-tf-dev 5.4.4__tar.gz → 5.4.6__tar.gz

simba_uw_tf_dev-5.4.6/.github/workflows/usecase_map.yml

@@ -0,0 +1,39 @@
+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-5.4.6/.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-5.4.6/MANIFEST.in

@@ -0,0 +1,20 @@
+include LICENSE NOTICE
+recursive-include simba *
+prune simba/sandbox
+recursive-exclude simba/sandbox *
+prune */__pycache__
+recursive-exclude */__pycache__ *
+global-exclude __pycache__/*
+global-exclude */__pycache__/*
+prune */pose_configurations_archive
+recursive-exclude */pose_configurations_archive *
+global-exclude pose_configurations_archive/*
+global-exclude */pose_configurations_archive/*
+prune simba/.claude
+recursive-exclude simba/.claude *
+prune docs
+prune misc
+prune images
+prune tests
+prune output
+prune lightning_logs

simba_uw_tf_dev-5.4.6/NOTICE

@@ -0,0 +1,590 @@
+THIRD-PARTY NOTICES
+===================
+
+SimBA (Simple Behavioral Analysis) includes, bundles, or derives from the
+third-party materials below. SimBA's own license is in the LICENSE file; these
+notices apply only to the corresponding third-party components. The full text
+of each referenced license appears in the LICENSE TEXTS section at the end.
+
+--------------------------------------------------------------------------------
+BUNDLED / ADAPTED CODE
+--------------------------------------------------------------------------------
+
+pybursts (Kleinberg burst-detection port)
+  Used in:  simba/data_processors/pybursts_calculator.py
+  Source:   https://github.com/romain-fontugne/pybursts  (PyPI: pybursts)
+  License:  MIT   (LICENSE.txt in repo; PyPI metadata omits it)
+
+scikit-learn (cluster-validity / silhouette metric)
+  Used in:  simba/data_processors/cuda/statistics.py
+  Source:   https://github.com/scikit-learn/scikit-learn
+  License:  BSD-3-Clause
+  Copyright (c) 2007-2024 The scikit-learn developers. All rights reserved.
+
+pycircstat (Rayleigh test reference)
+  Referenced by: simba/data_processors/cuda/circular_statistics.py
+  Source:   https://github.com/circstat/pycircstat
+  License:  MIT
+  Note:     SimBA re-implements the standard Rayleigh approximation
+            (Berens, CircStat, 2009); courtesy attribution only.
+
+--------------------------------------------------------------------------------
+BUNDLED CONFIGURATION FILES
+--------------------------------------------------------------------------------
+
+PaddleDetection - PP-YOLOE config
+  File:     simba/assets/ppyoloe_plus_crn_s_80e_coco.yml
+  Source:   https://github.com/PaddlePaddle/PaddleDetection
+  License:  Apache License 2.0
+
+ByteTrack - tracker config
+  File:     simba/assets/tracker_yml/bytetrack.yml
+  Source:   https://github.com/ifzhang/ByteTrack
+  License:  MIT - Copyright (c) 2021 Yifu Zhang
+
+BoT-SORT - tracker config
+  File:     simba/assets/tracker_yml/botsort.yml
+  Source:   https://github.com/NirAharon/BoT-SORT
+  License:  MIT
+
+--------------------------------------------------------------------------------
+FONTS
+--------------------------------------------------------------------------------
+
+Licensed under the SIL Open Font License, Version 1.1:
+  Aldrich           - Copyright (c) Matthew Desmond, 2011
+  BioRhyme          - Copyright 2016 The BioRhyme Project Authors
+  Cossette Titre    - Copyright 2025 The Cossette Titre Project Authors
+  DynaPuff          - Copyright 2021 The DynaPuff Project Authors
+  Elms Sans         - Copyright 2025 The Elms Sans Project Authors
+  Ewert             - Copyright (c) 2011 Johan Kallas & Mihkel Virkus (RFN "Ewert")
+  Federo            - Copyright (c) 2011 Olexa M. Volochay | Cyreal.org (RFN "Federo")
+  Indie Flower      - Copyright 2010 The Indie Flower Authors (Kimberly Geswein)
+  Jersey 10         - Copyright 2023 The Soft Type Project Authors (Sarah Cadigan-Fried)
+  Playwrite ES Deco - Copyright 2023 The Playwrite Project Authors
+  Poppins           - Copyright 2020 The Poppins Project Authors (ITF)
+  Quantico          - Copyright (c) 2011 Matthew Desmond (RFN "Quantico")
+
+Licensed under the Apache License, Version 2.0:
+  Ultra             - Copyright (c) 2010 Brian J. Bonislawsky DBA Astigmatic (AOETI)
+  Walter Turncoat   - Copyright (c) 2010 Font Diner, Inc DBA Sideshow
+
+Licensed under the Ubuntu Font Licence, Version 1.0:
+  Ubuntu, Ubuntu Mono - Copyright 2011 Canonical Ltd. (Dalton Maag Ltd)
+
+Font Awesome 5.0.7 (web dash app only; simba/dash_app/*.py CDN include)
+  Icons: CC BY 4.0 - Fonts: SIL OFL 1.1 - Code: MIT - https://fontawesome.com
+
+--------------------------------------------------------------------------------
+USER-INTERFACE ICONS
+--------------------------------------------------------------------------------
+
+Tabler Icons
+  Used in:  simba/assets/icons/ (GUI menu / button icons). Derived from the
+            Tabler "outline" set, recolored and resized to SimBA's icon sizes.
+            (Third-party tool logos in that folder are NOT from Tabler.)
+  Source:   https://tabler.io/icons  (https://github.com/tabler/tabler-icons)
+  License:  MIT - Copyright (c) 2020-2026 Pawel Kuna
+
+--------------------------------------------------------------------------------
+DOCUMENTATION MEDIA (not part of the installable package)
+--------------------------------------------------------------------------------
+
+"Mouse" 3D model - rendered media only
+  Author:   CharlieCatling
+  Source:   https://sketchfab.com/3d-models/mouse-bf516bd5a93341b194976f6f391d1e30
+  License:  Fab "Free Standard", with NoAI restriction:
+            "This model may not be used in datasets for, in the development of,
+             or as inputs to generative AI programs."
+  Usage:    Used solely to produce hand-posed, pre-rendered illustrations
+            (images/video) for the documentation. NOT used as training data,
+            model input, or in any generative-AI pipeline. The source mesh,
+            rig, and textures are NOT distributed - only rendered media.
+
+--------------------------------------------------------------------------------
+REVIEWED - NO NOTICE REQUIRED
+--------------------------------------------------------------------------------
+
+Convex hull (cuda/geometry.py): independent implementation of the public-domain
+  Jarvis March algorithm (Jarvis, 1973); docstrings cite the algorithm.
+Rayleigh statistic (cuda/circular_statistics.py): independent implementation of
+  a standard published formula (Berens/CircStat, 2009); pingouin not bundled.
+STL assets (simba/assets/stl/): first-party, generated via numpy-stl / PyVista.
+
+
+================================================================================
+LICENSE TEXTS
+================================================================================
+
+
+--------------------------------------------------------------------------------
+MIT License
+  (applies to: pybursts (c) Renzo Poddighe / romain-fontugne;
+   pycircstat; ByteTrack (c) 2021 Yifu Zhang; BoT-SORT; Font Awesome code;
+   Tabler Icons (c) 2020-2026 Pawel Kuna)
+--------------------------------------------------------------------------------
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
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+in the Software without restriction, including without limitation the rights
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+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+
+--------------------------------------------------------------------------------
+BSD 3-Clause License
+  (applies to: scikit-learn)
+--------------------------------------------------------------------------------
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+modifying a private copy. Propagation includes copying, distribution (with
+or without modification and with or without charging a redistribution fee),
+making available to the public, and in some countries other activities as
+well.
+
+PERMISSION & CONDITIONS
+
+This licence does not grant any rights under trademark law and all such
+rights are reserved.
+
+Subject to the below conditions, the Copyright Holder(s) and each
+Contributor hereby grant to any person obtaining a copy of the Font
+Software, a worldwide, non-exclusive, royalty-free, copyright licence to do
+any and all of the following:
+
+(a) refers to any names specified as such after the copyright statement(s).
+    Use, study, copy, merge, embed, modify, redistribute, and sell modified
+    and unmodified copies of the Font Software.
+
+(b) Propagate any modification made to the Font Software.
+
+Redistribution of the Font Software, including any Modified Version(s),
+must be made under the terms of this licence, provided the below conditions
+are met:
+
+1) Each copy of the Font Software must contain the above copyright notice
+and this licence. These can be included either as stand-alone text files,
+human-readable headers or in the appropriate machine-readable metadata
+fields within text or binary files as long as those fields can be easily
+viewed by the user.
+
+2) The font name complies with the following:
+
+(a) The Original Version must retain its name, unmodified.
+
+(b) Modified Versions which are Substantially Changed must be renamed to
+avoid use of the name of the Original Version or similar names entirely.
+
+(c) Modified Versions which are not Substantially Changed must be renamed to
+both (i) retain the name of the Original Version and (ii) add additional
+naming for differentiation, that identifies the individual or organisation
+producing the Modified Version.
+
+3) The name(s) of the Copyright Holder(s) and any Contributor(s) must not
+be used to promote, endorse or advertise any Modified Version, except (i)
+as required by this licence, (ii) to acknowledge the contribution(s) of the
+Copyright Holder(s) or (iii) with their explicit written permission.
+
+4) The Font Software, modified or unmodified, in part or in whole, must be
+distributed entirely under this licence, and must not be distributed under
+any other licence. The requirement for fonts to remain under this licence
+does not affect any document created using the Font Software, except any
+version of the Font Software extracted from a document created using the
+Font Software may only be distributed under this licence.
+
+TERMINATION
+
+This licence becomes null and void if any of the above conditions are not
+met.
+
+DISCLAIMER
+
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF
+COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM OTHER DEALINGS
+IN THE FONT SOFTWARE.