circadian-workbench 0.5.0__tar.gz

circadian_workbench-0.5.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Brancaccio Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+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.

circadian_workbench-0.5.0/MANIFEST.in

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+prune deploy
+prune docs
+prune presets
+prune scripts
+prune scripted
+prune tests
+prune graphify-out
+prune .circadian-agent
+exclude README.md
+global-exclude __pycache__ *.py[cod]

circadian_workbench-0.5.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: circadian-workbench
+Version: 0.5.0
+Summary: Local-first, reproducible circadian activity analysis
+Author: Brancaccio Lab
+Maintainer: Jay2owe
+License-Expression: MIT
+Project-URL: Homepage, https://pypi.org/project/circadian-workbench/
+Keywords: circadian rhythms,actogram,activity analysis,chronobiology
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: analysis-kit>=0.1.0
+Requires-Dist: fastapi>=0.115
+Requires-Dist: uvicorn>=0.34
+Requires-Dist: python-multipart>=0.0.20
+Requires-Dist: numpy>=2.0
+Requires-Dist: pandas>=2.2
+Requires-Dist: scipy>=1.14
+Requires-Dist: statsmodels>=0.14
+Requires-Dist: PyWavelets>=1.6
+Requires-Dist: plotly>=6.0
+Requires-Dist: SQLAlchemy>=2.0
+Requires-Dist: alembic>=1.13
+Requires-Dist: argon2-cffi>=23.1
+Provides-Extra: test
+Requires-Dist: pytest>=8.0; extra == "test"
+Requires-Dist: httpx>=0.27; extra == "test"
+Provides-Extra: release
+Requires-Dist: build>=1.0; extra == "release"
+Dynamic: license-file
+
+# Circadian Workbench
+
+Circadian Workbench is a local-first application for transparent analysis of
+activity rhythms. It imports ClockLab `.AWD` files and timestamped CSV files,
+including metadata-prefixed MotionWatch exports, and provides actograms,
+activity profiles, period analysis, cosinor fitting, bout analysis,
+non-parametric measures, group statistics and reproducible exports.
+
+The web interface and analysis service run on the same host. Uploaded data are
+stored under a configurable local data root and are not sent to an external
+service.
+
+## Install and run
+
+Circadian Workbench requires Python 3.10 or newer.
+
+```powershell
+pip install circadian-workbench
+circadian-workbench
+```
+
+The interface opens at <http://127.0.0.1:8765>. Choose **Load demo** to explore
+the workflow without an input file.
+
+The default data root is home-relative at `~/.circadian-workbench`. Set the
+application's documented environment variables before launch when a different
+durable location is required.
+
+## Command-line entry points
+
+- `circadian-workbench` starts the local application.
+- `circadian-workbench-service` runs the service without opening a browser.
+- `circadian-workbench-admin` exposes administrative maintenance commands.
+
+## Reproducibility
+
+Imports retain source checksums and original bytes. Analysis actions record
+their parameters and software version, and figure exports retain the values
+used to draw them. Invalid or incomplete time series are reported rather than
+silently regularised.
+
+## Support status
+
+Circadian Workbench is pre-1.0 research software. Validate exported results for
+the intended scientific use and retain the original activity records.
+
+## License
+
+Released under the MIT License; the license text is included in every source
+and wheel distribution.

circadian_workbench-0.5.0/PYPI_README.md

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+# Circadian Workbench
+
+Circadian Workbench is a local-first application for transparent analysis of
+activity rhythms. It imports ClockLab `.AWD` files and timestamped CSV files,
+including metadata-prefixed MotionWatch exports, and provides actograms,
+activity profiles, period analysis, cosinor fitting, bout analysis,
+non-parametric measures, group statistics and reproducible exports.
+
+The web interface and analysis service run on the same host. Uploaded data are
+stored under a configurable local data root and are not sent to an external
+service.
+
+## Install and run
+
+Circadian Workbench requires Python 3.10 or newer.
+
+```powershell
+pip install circadian-workbench
+circadian-workbench
+```
+
+The interface opens at <http://127.0.0.1:8765>. Choose **Load demo** to explore
+the workflow without an input file.
+
+The default data root is home-relative at `~/.circadian-workbench`. Set the
+application's documented environment variables before launch when a different
+durable location is required.
+
+## Command-line entry points
+
+- `circadian-workbench` starts the local application.
+- `circadian-workbench-service` runs the service without opening a browser.
+- `circadian-workbench-admin` exposes administrative maintenance commands.
+
+## Reproducibility
+
+Imports retain source checksums and original bytes. Analysis actions record
+their parameters and software version, and figure exports retain the values
+used to draw them. Invalid or incomplete time series are reported rather than
+silently regularised.
+
+## Support status
+
+Circadian Workbench is pre-1.0 research software. Validate exported results for
+the intended scientific use and retain the original activity records.
+
+## License
+
+Released under the MIT License; the license text is included in every source
+and wheel distribution.

circadian_workbench-0.5.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "circadian-workbench"
+version = "0.5.0"
+description = "Local-first, reproducible circadian activity analysis"
+readme = "PYPI_README.md"
+requires-python = ">=3.10"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{name = "Brancaccio Lab"}]
+maintainers = [{name = "Jay2owe"}]
+keywords = ["circadian rhythms", "actogram", "activity analysis", "chronobiology"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    # The shared house style and agent chassis. export_figures.py draws from its
+    # themes and palette, so the figures are wrong without it — this is what
+    # replaced the hand-kept plot_style.py mirror of PyFLASH/aesthetics.py.
+    "analysis-kit>=0.1.0",
+    "fastapi>=0.115",
+    "uvicorn>=0.34",
+    "python-multipart>=0.0.20",
+    "numpy>=2.0",
+    "pandas>=2.2",
+    "scipy>=1.14",
+    # Stage 04 group statistics: MixedLM REML fallback for missing bins in the
+    # two-way mixed RM ANOVA. Declared here because the RM ANOVA, GG and HF are
+    # hand-rolled in numpy — statsmodels is used ONLY for the variance-component
+    # optimiser (no closed-form check exists for a REML fit, so it is delegated).
+    # statsmodels.stats.anova.AnovaRM cannot express a between factor and has no
+    # sphericity correction; pingouin implements GG but is GPL-3.0, which would
+    # force a relicense of this MIT project. See docs/group-analysis/04.
+    "statsmodels>=0.14",
+    "PyWavelets>=1.6",
+    "plotly>=6.0",
+    # Persistence foundation (Stage 01): database-neutral access + versioned
+    # migrations. Both SQLAlchemy and Alembic support SQLite now and PostgreSQL
+    # later, keeping the promised database migration route open.
+    "SQLAlchemy>=2.0",
+    "alembic>=1.13",
+    # Authentication (Stage 02): Argon2id password hashing. argon2-cffi's
+    # PasswordHasher uses the Argon2id variant by default.
+    "argon2-cffi>=23.1",
+]
+
+[project.optional-dependencies]
+test = ["pytest>=8.0", "httpx>=0.27"]
+# Tooling to BUILD a release set (not needed to run the service).
+release = ["build>=1.0"]
+
+[project.urls]
+Homepage = "https://pypi.org/project/circadian-workbench/"
+
+[project.scripts]
+circadian-workbench = "circadian_workbench.launcher:main"
+circadian-workbench-service = "circadian_workbench.launcher:serve"
+circadian-workbench-admin = "circadian_workbench.cli:main"
+circadian-workbench-release = "circadian_workbench.release.build:main"
+circadian-workbench-host = "circadian_workbench.release.host:main"
+circadian-workbench-distribute = "circadian_workbench.release.distribute:main"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+circadian_workbench = ["static/*", "persistence/migrations/*.mako"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+pythonpath = ["src"]

circadian_workbench-0.5.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

circadian_workbench-0.5.0/src/circadian_workbench/__init__.py

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+"""Circadian Workbench analysis package."""
+
+__version__ = "0.5.0"