quantized-lab 0.8.0__tar.gz

quantized_lab-0.8.0/.gitignore

@@ -0,0 +1,58 @@
+# ── Python ────────────────────────────────────────────────────────────
+__pycache__/
+*.py[cod]
+.venv/
+.uv/
+*.egg-info/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+dist/
+build/
+dist-sidecar/
+
+# ── Node / frontend ───────────────────────────────────────────────────
+node_modules/
+frontend/dist/
+*.tsbuildinfo
+
+# ── Tauri / desktop ───────────────────────────────────────────────────
+src-tauri/target/
+
+# ── Local-only research corpus (never commit instrument data) ─────────
+tests/realdata/
+**/*.dat
+**/*.xrdml
+**/*.raw
+# Exception: small committed golden-corpus fixtures (inline comments are
+# NOT supported in .gitignore, so this note must be on its own line).
+!tests/fixtures/**
+
+# ── OS / editor ───────────────────────────────────────────────────────
+.DS_Store
+Thumbs.db
+.idea/
+.vscode/
+
+# ── Claude private working area (per-machine, not shared) ─────────────
+.claude/
+CLAUDE.local.md
+
+# NOTE: plans/ is TRACKED in this repo for now (founding design docs).
+# Once active development starts we may adopt the sibling-repo convention
+# (gitignore plans/, track a BACKLOG.md dashboard) — see CLAUDE.md.
+
+# Built SPA (vite build output, served by FastAPI in prod)
+src/quantized/web/
+
+# Beautiful-defaults audit renders (tools/audit_defaults.py) -- regenerate
+# locally, never commit the PNG grid
+tools/audit_defaults_out/
+
+# OneDrive conflict copies — when two machines edit the same file, OneDrive
+# saves a duplicate named "<file>-<Device>.<ext>". Never commit these.
+*MacBook*
+*-DESKTOP-*
+
+# OneDrive sync-conflict copies ("<name>-<machine>.<ext>") — never commit
+*MacBook Air*

quantized_lab-0.8.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
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+   6. Trademarks. This License does not grant permission to use the trade
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+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
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+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
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+   Copyright 2026 Paige Quarterman
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quantized_lab-0.8.0/NOTICE

@@ -0,0 +1,11 @@
+quantized
+Copyright 2026 Paige Quarterman
+
+This product includes software developed as a clean-architecture port of
+the quantized_matlab toolbox.
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not
+use this file except in compliance with the License. You may obtain a copy
+of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0

quantized_lab-0.8.0/PKG-INFO

@@ -0,0 +1,122 @@
+Metadata-Version: 2.4
+Name: quantized-lab
+Version: 0.8.0
+Summary: Clean-architecture Python + React port of the quantized_matlab scientific toolbox (magnetometry / XRD / lab data).
+Author: Paige Quarterman
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Requires-Python: >=3.11
+Requires-Dist: fastapi>=0.139.0
+Requires-Dist: h5py>=3.10
+Requires-Dist: matplotlib>=3.11.0
+Requires-Dist: numpy>=1.26
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: periodictable>=1.7
+Requires-Dist: platformdirs>=4.10.0
+Requires-Dist: pydantic>=2.7
+Requires-Dist: python-multipart>=0.0.32
+Requires-Dist: scipy>=1.11
+Requires-Dist: uvicorn[standard]>=0.51.0
+Provides-Extra: bumps
+Requires-Dist: bumps>=1.0; extra == 'bumps'
+Provides-Extra: desktop
+Requires-Dist: pywebview>=5.1; extra == 'desktop'
+Provides-Extra: office
+Requires-Dist: python-docx>=1.1; extra == 'office'
+Requires-Dist: python-pptx>=1.0; extra == 'office'
+Provides-Extra: origin-com
+Requires-Dist: pywin32; (sys_platform == 'win32') and extra == 'origin-com'
+Provides-Extra: stats
+Requires-Dist: lifelines>=0.27; extra == 'stats'
+Requires-Dist: statsmodels>=0.14; extra == 'stats'
+Description-Content-Type: text/markdown
+
+# quantized
+
+A clean-architecture Python + React port of the
+[`quantized_matlab`](../quantized_matlab) scientific data toolbox for
+magnetometry, X-ray/neutron diffraction, and generic lab data.
+
+- **Backend parity** with the MATLAB toolbox: parsers, corrections,
+  plotting, peak & curve fitting, materials calculators (DiraCulator),
+  and a spreadsheet workspace (DataWorkspace).
+- **Revamped GUI** built fresh in React, sharing the look-and-feel and
+  component conventions of the sibling [`fermiviewer`](../fermiviewer)
+  Python app.
+- **Architecture that holds the line:** pure `io/` + `calc/` libraries,
+  thin FastAPI `routes/`, a 500-line per-module ceiling, and golden tests
+  that freeze MATLAB outputs as the parity oracle — so this port never
+  grows the god-scripts the MATLAB original accumulated.
+
+> Status: **active development** — backend + GUI are functional; native
+> installers and PyPI packages publish from tagged releases (see
+> [`RELEASE.md`](RELEASE.md)). See [`plans/PORT_PLAN.md`](plans/PORT_PLAN.md)
+> for the detailed workstream plan, and [`CLAUDE.md`](CLAUDE.md) for the
+> architecture hard-rules.
+
+## Scope
+
+Magnetometry / XRD / lab-data analysis (parity with `quantized_matlab`).
+Electron-microscopy tooling (Fermi viewer, EELS/EDS, imaging) is **out of
+scope** and lives in the separate `fermiviewer` project.
+
+## Run it
+
+**Install matrix** — pick whichever fits your workflow:
+
+| Method | Command | Notes |
+|--------|---------|-------|
+| pipx (recommended) | `pipx install quantized-lab && qz` | isolated env, `qz` on PATH, no dev tools needed |
+| uv tool | `uv tool install quantized-lab && qz` | same idea, via `uv` |
+| pip | `pip install quantized-lab && qz` | into whatever env is active |
+| Native installer | download from [Releases](https://github.com/pquarterman17/quantized/releases) | Windows `.exe` (NSIS, auto-updates), macOS `.dmg`, Linux `.deb` — no Python required, see [`RELEASE.md`](RELEASE.md) |
+| From source | see below | for development |
+
+Once installed, `qz` serves the app at `http://127.0.0.1:8000` and opens a
+browser tab. An empty library shows a **"Drop files here, or use ⊞ to import
+/ ✚ for a demo"** hint — click **✚** for an instant synthetic dataset (built
+client-side), or hit `GET /api/samples/demo` for a bundled sample dataset
+parsed server-side through the normal import path — so a fresh install has
+something to plot within seconds, no data file required.
+
+**From source — double-click a launcher** (builds the UI + installs deps on
+first run, then opens the app in your browser):
+
+- **Windows:** double-click [`run.cmd`](run.cmd)
+- **macOS:** double-click [`run.command`](run.command) (first time:
+  right-click → Open)
+
+**Or one command** (after `uv` + Node.js are installed):
+
+```bash
+# first time only: build the UI bundle the app serves
+cd frontend && npm install && npm run build && cd ..
+
+uv run qz                 # serve on :8000 and open a browser tab
+uv run qz --port 9000     # different port
+uv run qz --no-browser    # headless (don't open a tab; never auto-exits)
+uv run qz --desktop       # native window (needs: pip install quantized-lab[desktop])
+uv run qz --dev           # contributor mode: Vite HMR + reloading backend
+```
+
+The default mode behaves like an app: closing the last browser tab shuts
+the server down (a page refresh doesn't). Set `QZ_AUTO_SHUTDOWN=0` to opt
+out, use `--no-browser` for a persistent/headless server, or stop any mode
+with **Ctrl+C** in its window.
+
+Building your own wheel/sdist (e.g. for `pip install .`)? Build the frontend
+**first** — `cd frontend && npm ci && npm run build` — before `uv build` /
+`python -m build`, or the wheel ships without a UI (`qz` still runs; it just
+prints a "UI not built" warning instead of serving one).
+
+## Develop
+
+```bash
+uv sync --group dev          # backend deps
+uv run pytest                # backend tests (+ `-m golden` for MATLAB parity)
+uv run ruff check src tests && uv run mypy src
+cd frontend && npm test && npm run build
+```
+
+License: Apache-2.0.

quantized_lab-0.8.0/README.md

@@ -0,0 +1,88 @@
+# quantized
+
+A clean-architecture Python + React port of the
+[`quantized_matlab`](../quantized_matlab) scientific data toolbox for
+magnetometry, X-ray/neutron diffraction, and generic lab data.
+
+- **Backend parity** with the MATLAB toolbox: parsers, corrections,
+  plotting, peak & curve fitting, materials calculators (DiraCulator),
+  and a spreadsheet workspace (DataWorkspace).
+- **Revamped GUI** built fresh in React, sharing the look-and-feel and
+  component conventions of the sibling [`fermiviewer`](../fermiviewer)
+  Python app.
+- **Architecture that holds the line:** pure `io/` + `calc/` libraries,
+  thin FastAPI `routes/`, a 500-line per-module ceiling, and golden tests
+  that freeze MATLAB outputs as the parity oracle — so this port never
+  grows the god-scripts the MATLAB original accumulated.
+
+> Status: **active development** — backend + GUI are functional; native
+> installers and PyPI packages publish from tagged releases (see
+> [`RELEASE.md`](RELEASE.md)). See [`plans/PORT_PLAN.md`](plans/PORT_PLAN.md)
+> for the detailed workstream plan, and [`CLAUDE.md`](CLAUDE.md) for the
+> architecture hard-rules.
+
+## Scope
+
+Magnetometry / XRD / lab-data analysis (parity with `quantized_matlab`).
+Electron-microscopy tooling (Fermi viewer, EELS/EDS, imaging) is **out of
+scope** and lives in the separate `fermiviewer` project.
+
+## Run it
+
+**Install matrix** — pick whichever fits your workflow:
+
+| Method | Command | Notes |
+|--------|---------|-------|
+| pipx (recommended) | `pipx install quantized-lab && qz` | isolated env, `qz` on PATH, no dev tools needed |
+| uv tool | `uv tool install quantized-lab && qz` | same idea, via `uv` |
+| pip | `pip install quantized-lab && qz` | into whatever env is active |
+| Native installer | download from [Releases](https://github.com/pquarterman17/quantized/releases) | Windows `.exe` (NSIS, auto-updates), macOS `.dmg`, Linux `.deb` — no Python required, see [`RELEASE.md`](RELEASE.md) |
+| From source | see below | for development |
+
+Once installed, `qz` serves the app at `http://127.0.0.1:8000` and opens a
+browser tab. An empty library shows a **"Drop files here, or use ⊞ to import
+/ ✚ for a demo"** hint — click **✚** for an instant synthetic dataset (built
+client-side), or hit `GET /api/samples/demo` for a bundled sample dataset
+parsed server-side through the normal import path — so a fresh install has
+something to plot within seconds, no data file required.
+
+**From source — double-click a launcher** (builds the UI + installs deps on
+first run, then opens the app in your browser):
+
+- **Windows:** double-click [`run.cmd`](run.cmd)
+- **macOS:** double-click [`run.command`](run.command) (first time:
+  right-click → Open)
+
+**Or one command** (after `uv` + Node.js are installed):
+
+```bash
+# first time only: build the UI bundle the app serves
+cd frontend && npm install && npm run build && cd ..
+
+uv run qz                 # serve on :8000 and open a browser tab
+uv run qz --port 9000     # different port
+uv run qz --no-browser    # headless (don't open a tab; never auto-exits)
+uv run qz --desktop       # native window (needs: pip install quantized-lab[desktop])
+uv run qz --dev           # contributor mode: Vite HMR + reloading backend
+```
+
+The default mode behaves like an app: closing the last browser tab shuts
+the server down (a page refresh doesn't). Set `QZ_AUTO_SHUTDOWN=0` to opt
+out, use `--no-browser` for a persistent/headless server, or stop any mode
+with **Ctrl+C** in its window.
+
+Building your own wheel/sdist (e.g. for `pip install .`)? Build the frontend
+**first** — `cd frontend && npm ci && npm run build` — before `uv build` /
+`python -m build`, or the wheel ships without a UI (`qz` still runs; it just
+prints a "UI not built" warning instead of serving one).
+
+## Develop
+
+```bash
+uv sync --group dev          # backend deps
+uv run pytest                # backend tests (+ `-m golden` for MATLAB parity)
+uv run ruff check src tests && uv run mypy src
+cd frontend && npm test && npm run build
+```
+
+License: Apache-2.0.

quantized_lab-0.8.0/pyproject.toml

@@ -0,0 +1,158 @@
+[project]
+name = "quantized-lab"
+version = "0.8.0"
+description = "Clean-architecture Python + React port of the quantized_matlab scientific toolbox (magnetometry / XRD / lab data)."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "Apache-2.0"
+authors = [{ name = "Paige Quarterman" }]
+dependencies = [
+    "fastapi>=0.139.0",
+    "uvicorn[standard]>=0.51.0",
+    "numpy>=1.26",
+    "scipy>=1.11",
+    "pydantic>=2.7",
+    "openpyxl>=3.1",
+    "h5py>=3.10",
+    "python-multipart>=0.0.32",
+    "matplotlib>=3.11.0",
+    "periodictable>=1.7",
+    "platformdirs>=4.10.0",
+]
+
+[project.scripts]
+qz = "quantized.cli:main"
+quantized = "quantized.cli:main"
+diraculator = "quantized.cli:main_calc"
+
+[project.optional-dependencies]
+# Word/PowerPoint report export (#37). MIT-licensed, pure-python. Optional so
+# the core install stays lean — io/report_export.py guards these imports and
+# LaTeX/HTML export always work; `pip install quantized[office]` enables .docx/.pptx.
+office = [
+    "python-docx>=1.1",
+    "python-pptx>=1.0",
+]
+# COM "Send to Origin" (item 25) — Windows-only optional, behind QZ_ORIGIN_COM=1
+# (architecture guard #10: never a hard dependency, never a CI requirement).
+# io/origin_com.py imports win32com lazily and guards its absence; the
+# cross-platform fallback (Origin-ASCII / .ogs, always available) is
+# io/origin.py. `pip install quantized[origin-com]` adds the live COM path.
+origin-com = [
+    "pywin32; sys_platform == 'win32'",
+]
+# `qz --desktop` native window (PORT_PLAN #3): pure-Python pywebview shell for
+# dev/daily use; the Tauri shell (src-tauri/) stays the packaged path (W8).
+# BSD-3 licensed. server_launch.py guards the import — without this extra,
+# `qz --desktop` prints an install hint and every other mode works normally.
+desktop = [
+    "pywebview>=5.1",
+]
+# Advanced statistics: GLM, survival analysis, Cox PH (gap #30). BSD-3 / MIT
+# licensed. Optional so core install stays lean — calc/stats_glm.py and
+# calc/stats_survival.py guard these imports; ROC is pure numpy and always
+# available. `pip install quantized[stats]` enables GLM/survival methods.
+stats = [
+    "statsmodels>=0.14",
+    "lifelines>=0.27",
+]
+# Optional bumps fit engine (GOTO #10). BSD-3 licensed. calc/fit_bumps.py
+# guards the import — the MATLAB-parity fitter (calc/fitting.py, golden-locked)
+# stays the default engine everywhere; bumps adds amoeba/lm/de/dream as an
+# ADDITIONAL engine. `pip install quantized[bumps]` enables it.
+bumps = [
+    "bumps>=1.0",
+]
+
+[dependency-groups]
+dev = [
+    "pytest>=8",
+    "httpx>=0.27",
+    "ruff>=0.15.21",
+    "mypy>=2.2.0",
+    # exercise the optional office exporters (#37) in CI
+    "python-docx>=1.1",
+    "python-pptx>=1.0",
+    # exercise the optional stats methods (GLM/survival/Cox) in CI
+    "statsmodels>=0.14",
+    "lifelines>=0.27",
+    # exercise the optional bumps fit engine (GOTO #10) in CI
+    "bumps>=1.0",
+]
+# Desktop packaging only — used by the release workflow to freeze the server
+# into a self-contained sidecar (tools/bundle/qz-server.spec). Never a runtime
+# dependency; CI installs it with `uv sync --group bundle`.
+bundle = [
+    "pyinstaller>=6.10",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+# Hatchling's default sdist has no include/exclude list, so it sweeps in the
+# whole repo (frontend/node_modules alone is 5000+ files) — scope it to just
+# what a build needs: the package sources (including src/quantized/web/, the
+# gitignored Vite build output, and src/quantized/samples/, the bundled demo
+# dataset — both walked from disk, not from git, so they're picked up when
+# present) plus top-level metadata. Build the SPA BEFORE `uv build` / `python
+# -m build` (`cd frontend && npm ci && npm run build`) or the wheel ships
+# without a UI (qz still runs — see cli.py's "UI not built" warning).
+[tool.hatch.build.targets.sdist]
+include = ["src/quantized", "README.md", "LICENSE", "NOTICE"]
+# Hatchling force-includes LICENSE*/README*-named files project-wide by
+# default (a footgun here: every vendored npm package under
+# frontend/node_modules ships its own LICENSE + README.md) — exclude wins
+# over that default, so this is required even with the include list above.
+exclude = ["frontend/**"]
+# The Vite SPA output (src/quantized/web/**) is gitignored, so hatchling's
+# VCS-aware sdist drops it even though it's under the `include` path above.
+# `uv build`/`python -m build` build the WHEEL FROM THIS SDIST, so if the SPA
+# is missing here it's missing from the wheel too (the wheel target's own
+# artifacts= can't re-add what the sdist never carried). Force-include it in
+# BOTH targets. (Regression fixed 2026-07-08: v0.5.0's wheel shipped UI-less.)
+artifacts = ["src/quantized/web/**"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/quantized"]
+# `packages` alone only reliably ships src/quantized/web/ when hatchling
+# builds directly against a live git checkout; building the wheel FROM an
+# sdist (what `uv build`/`python -m build` do by default, and what the
+# publish workflow does) drops it, since that step can't see this repo's
+# .git and treats the gitignored build output as excluded. `artifacts` is
+# hatchling's explicit "include this even though it looks ignored" escape
+# hatch — force it so the SPA ships in both the direct-build and
+# build-from-sdist paths.
+artifacts = ["src/quantized/web/**"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+src = ["src", "tests"]
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "UP", "B"]
+
+[tool.ruff.lint.per-file-ignores]
+# Miller indices are conventionally named h, k, l — `l` is unavoidable and clear
+# in crystallographic context (E741 "ambiguous variable name").
+"src/quantized/calc/crystallography.py" = ["E741"]
+"src/quantized/routes/crystallography.py" = ["E741"]
+"tests/test_crystallography.py" = ["E741"]
+"tests/test_calc_planespacings.py" = ["E741"]
+
+[tool.mypy]
+python_version = "3.11"
+strict = true
+
+[[tool.mypy.overrides]]
+# Third-party libs without bundled type stubs — skeleton-safe.
+module = ["scipy.*", "uvicorn.*", "openpyxl.*", "h5py.*", "periodictable.*", "docx.*", "pptx.*", "mpl_toolkits.*", "win32com.*", "statsmodels.*", "lifelines.*", "pandas.*", "webview.*", "bumps.*"]
+ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+markers = [
+    "golden: compares output against frozen quantized_matlab reference values",
+    "realdata: needs the local-only instrument corpus (auto-skips when absent)",
+    "perf: wall-time regression tripwires with generous ceilings (not benchmarks)",
+]

quantized_lab-0.8.0/src/quantized/__init__.py

@@ -0,0 +1,11 @@
+"""quantized — Python backend for the quantized toolbox port.
+
+Layered, enforced architecture (see CLAUDE.md):
+  - ``datastruct`` + ``io`` + ``calc`` are pure libraries (no web imports).
+  - ``routes`` are thin FastAPI adapters.
+"""
+
+from __future__ import annotations
+
+__version__ = "0.7.0"
+__all__ = ["__version__"]

quantized_lab-0.8.0/src/quantized/__main__.py

@@ -0,0 +1,14 @@
+"""Enable ``python -m quantized`` → runs the ``qz`` CLI.
+
+The Tauri desktop shell's dev fallback spawns the server as
+``python -m quantized --no-browser`` (so ``kill()`` reaches uvicorn directly,
+not an orphaned launcher). Keeping this module trivial means the entry point
+stays stable regardless of how ``cli.main`` evolves.
+"""
+
+from __future__ import annotations
+
+from quantized.cli import main
+
+if __name__ == "__main__":
+    main()