labplan 0.1.0__tar.gz

labplan-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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labplan-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: labplan
+Version: 0.1.0
+Summary: Plan the measurement, fit the model, keep the record - exact measurement planning, calibration and audit trails for any lab model
+Author: Tanvir Mahmud Mahim
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/TaN-MM-Org/labplan
+Project-URL: Issues, https://github.com/TaN-MM-Org/labplan/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.22
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == "test"
+Dynamic: license-file
+
+# labplan
+
+[![tests](https://github.com/TaN-MM-Org/labplan/actions/workflows/ci.yml/badge.svg)](https://github.com/TaN-MM-Org/labplan/actions)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+
+Every measurement campaign asks the same four questions. Can the
+measurements I am about to take determine the numbers I care about --
+and how well? Which settings are worth the instrument time? Once the
+data exist, what are the numbers, with error bars that mean it? And a
+year from now, can anyone trace exactly what was fitted, to which
+data, by what? `labplan` answers all four for ANY instrument or
+experiment you can describe with a Python function -- and refuses,
+with an explanation, whenever the honest answer is "this design
+cannot tell".
+
+Nine research packages in this organization -- covering colour-centre
+spins, squeezed light, spin-squeezed clocks, Raman maps,
+single-photon emitters, superconducting detectors, band structure,
+semiconductor heterostructures and photonic fabrication -- each grew
+the same planning-and-calibration loop for its own physics. `labplan`
+is that loop extracted, generalized, and hardened into a single
+dependency-light package (NumPy only, Python 3.9-3.14): the tenth
+package is the pattern itself.
+
+## Install
+
+```
+pip install labplan        # NumPy only
+```
+
+## The loop in one example
+
+```python
+import numpy as np
+from labplan import (Model, information, design, fit,
+                     repeats_for, audit_record, report_text)
+
+# 1. Your model: anything that predicts a reading from parameters
+#    and settings. Here, a sensor line y = gain * x + offset.
+m = Model("sensor line",
+          lambda th, x: th[0] * x[:, 0] + th[1],
+          param_names=("gain", "offset"),
+          reference="sensor manual rev. 3, eq. (2)")
+
+# 2. Before measuring: would 12 planned settings determine the
+#    parameters, and how well, at 0.05 units of reading noise?
+x_planned = np.linspace(0.5, 5.0, 12)[:, None]
+plan = information(m, theta=[2.0, 0.0], x=x_planned, sigmas=0.05)
+print(plan["identifiable"], plan["sigma"])
+
+# ... or let labplan pick the best 5 of the settings you can reach,
+#     and price a target error bar in repeats (a closed form):
+pick = design(m, [2.0, 0.0], x_planned, n_pick=5, sigmas=0.05)
+r, predicted = repeats_for({"gain": 0.01}, plan)
+
+# 3. After measuring: fit, with the SAME matrix the plan promised.
+res = fit(m, x_planned, y_measured, theta0=[1.0, 0.0], sigmas=0.05)
+print(res.values, res.sigma, res.chi2)
+
+# 4. Keep the record: what, to which data (sha256), by what, when.
+rec = audit_record(res, operator="T. Mahim", note="bench 2, warm-up ok")
+print(report_text(rec))
+```
+
+The central promise: the planner's error bars and the fit's error
+bars are the same matrix, so what is promised before the measurement
+is what is reported after -- exactly, whenever the model describes
+the data. The tests assert that equality to machine precision.
+
+## When the model might be wrong
+
+Model-based error bars assume the model is right. For the day it is
+not, `conformal_quantile` supplies distribution-free prediction
+intervals from held-out calibration data, with an exact finite-sample
+guarantee that holds whatever the model and whatever the noise (split
+conformal prediction; Vovk, Gammerman and Shafer, Algorithmic
+Learning in a Random World, Springer (2005); Lei et al., J. Am.
+Stat. Assoc. 113, 1094 (2018); Angelopoulos and Bates,
+arXiv:2107.07511):
+
+```python
+from labplan import conformal_quantile, conformal_interval
+
+q = conformal_quantile(abs_errors_heldout, alpha=0.1)   # 90% level
+lo, hi = conformal_interval(new_predictions, q)
+```
+
+Its honest limits are stated in the docstring rather than hidden:
+the guarantee is marginal, and it needs the calibration data to be
+exchangeable with the new measurement -- last month's instrument
+state does not certify next month's drift.
+
+## What is inside
+
+- **`Model`**: your forward function with named parameters and a
+  mandatory `reference` -- provenance travels with every prediction,
+  the same rule every package in this organization applies.
+- **`information` / `design` / `repeats_for`**: predicted error bars
+  from the design alone (the Fisher information of independent
+  Gaussian measurements; any statistics text, under "Cramer-Rao
+  bound"); greedy D-optimal selection of the most informative
+  settings (Pukelsheim, Optimal Design of Experiments, SIAM (2006));
+  and the exact 1/sqrt(repeats) law, inverted in closed form.
+- **`fit`**: Levenberg-Marquardt weighted least squares in pure
+  NumPy, with exact known-noise covariance and a chi-squared check
+  when measurement errors are supplied, and residual-scaled error
+  bars (stated as such) when they are not.
+- **`conformal_quantile` / `conformal_interval` / `coverage_exact`**:
+  distribution-free intervals with the exact finite-sample coverage
+  formula exposed for checking.
+- **`audit_record` / `report_text`**: a JSON-serializable statement
+  of record -- model, source, values, error bars, goodness of fit,
+  identifiability, the sha256 of the exact data arrays, software
+  versions, UTC timestamp, operator -- and its human-readable
+  rendering.
+- **`save_measurements_csv` / `load_measurements_csv`**: a plain,
+  checked file contract whose round trip is bit-exact.
+
+## Refusals, not guesses
+
+A design that cannot tell the parameters apart is refused with an
+explanation, in the planner, the fit and the design tool alike --
+judged on a unit-free (correlation-scaled) information matrix, so
+mixed units can never fake or hide a degeneracy. Too few points, a
+non-converging fit, an uncertifiable conformal level, a malformed
+data file: each refuses with the reason and, where one exists, the
+remedy.
+
+## How it is checked
+
+14 tests (Python 3.9-3.14, run in CI on every push), every
+statistical claim pinned to a closed form, an exact identity, or
+seeded simulation against an exact formula -- never a stored number.
+Highlights: on a linear model the fit covariance equals the textbook
+closed form sigma^2 (X^T X)^-1 exactly, and the planner promises the
+same matrix; 400 seeded Monte-Carlo experiments match the reported
+error bars; an exactly degenerate model is refused via an exact rank
+argument; the greedy design obeys the rank-one determinant identity,
+reproduces its own rule, never loses to a random subset, and -- for
+the two-point line design -- matches the classical optimum found by
+exhaustion; the repeat law is asserted by tiling the design; the
+conformal quantile is the exact rank formula and seeded simulation
+matches the exact closed-form coverage inside the published
+two-sided guarantee; the audit record survives JSON round trip
+exactly and its digest pins the exact data; file round trips are
+bit-exact.
+
+## Honest limits
+
+Deliberate scope, designed out with reasons: the Gaussian
+error-bar machinery is exact for independent Gaussian measurement
+errors and first-order-accurate otherwise (the conformal tools are
+the assumption-free complement, and their own limits are stated);
+the greedy design is a transparent heuristic, not a proof of global
+optimality; no physics ships in this package at all -- your model
+and its `reference` carry the physics, and the nine physics packages
+of this organization remain the place where specific instruments'
+models live, each already wired into this same loop.
+
+## Support and governance
+
+Written and maintained by Tanvir Mahmud Mahim (Department of
+Electrical and Electronic Engineering, BRAC University), who reviews
+every change and takes the final decision on scope and releases.
+Design questions are discussed in the open in issues and pull
+requests, and the standing rule of
+[CONTRIBUTING.md](CONTRIBUTING.md) binds the maintainer exactly as it
+binds contributors: a change that touches the statistics arrives with
+a test, and a claim arrives with its source.
+
+Support runs through the
+[issue tracker](https://github.com/TaN-MM-Org/labplan/issues). Usage
+questions are welcome alongside bug reports; a docstring that left a
+unit or a convention unclear is treated as a documentation bug, not
+user error. While the version is below 1.0 the API may still move
+between minor versions; such changes are called out in the release
+notes.
+
+## License
+
+Apache-2.0.

labplan-0.1.0/README.md

@@ -0,0 +1,181 @@
+# labplan
+
+[![tests](https://github.com/TaN-MM-Org/labplan/actions/workflows/ci.yml/badge.svg)](https://github.com/TaN-MM-Org/labplan/actions)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+
+Every measurement campaign asks the same four questions. Can the
+measurements I am about to take determine the numbers I care about --
+and how well? Which settings are worth the instrument time? Once the
+data exist, what are the numbers, with error bars that mean it? And a
+year from now, can anyone trace exactly what was fitted, to which
+data, by what? `labplan` answers all four for ANY instrument or
+experiment you can describe with a Python function -- and refuses,
+with an explanation, whenever the honest answer is "this design
+cannot tell".
+
+Nine research packages in this organization -- covering colour-centre
+spins, squeezed light, spin-squeezed clocks, Raman maps,
+single-photon emitters, superconducting detectors, band structure,
+semiconductor heterostructures and photonic fabrication -- each grew
+the same planning-and-calibration loop for its own physics. `labplan`
+is that loop extracted, generalized, and hardened into a single
+dependency-light package (NumPy only, Python 3.9-3.14): the tenth
+package is the pattern itself.
+
+## Install
+
+```
+pip install labplan        # NumPy only
+```
+
+## The loop in one example
+
+```python
+import numpy as np
+from labplan import (Model, information, design, fit,
+                     repeats_for, audit_record, report_text)
+
+# 1. Your model: anything that predicts a reading from parameters
+#    and settings. Here, a sensor line y = gain * x + offset.
+m = Model("sensor line",
+          lambda th, x: th[0] * x[:, 0] + th[1],
+          param_names=("gain", "offset"),
+          reference="sensor manual rev. 3, eq. (2)")
+
+# 2. Before measuring: would 12 planned settings determine the
+#    parameters, and how well, at 0.05 units of reading noise?
+x_planned = np.linspace(0.5, 5.0, 12)[:, None]
+plan = information(m, theta=[2.0, 0.0], x=x_planned, sigmas=0.05)
+print(plan["identifiable"], plan["sigma"])
+
+# ... or let labplan pick the best 5 of the settings you can reach,
+#     and price a target error bar in repeats (a closed form):
+pick = design(m, [2.0, 0.0], x_planned, n_pick=5, sigmas=0.05)
+r, predicted = repeats_for({"gain": 0.01}, plan)
+
+# 3. After measuring: fit, with the SAME matrix the plan promised.
+res = fit(m, x_planned, y_measured, theta0=[1.0, 0.0], sigmas=0.05)
+print(res.values, res.sigma, res.chi2)
+
+# 4. Keep the record: what, to which data (sha256), by what, when.
+rec = audit_record(res, operator="T. Mahim", note="bench 2, warm-up ok")
+print(report_text(rec))
+```
+
+The central promise: the planner's error bars and the fit's error
+bars are the same matrix, so what is promised before the measurement
+is what is reported after -- exactly, whenever the model describes
+the data. The tests assert that equality to machine precision.
+
+## When the model might be wrong
+
+Model-based error bars assume the model is right. For the day it is
+not, `conformal_quantile` supplies distribution-free prediction
+intervals from held-out calibration data, with an exact finite-sample
+guarantee that holds whatever the model and whatever the noise (split
+conformal prediction; Vovk, Gammerman and Shafer, Algorithmic
+Learning in a Random World, Springer (2005); Lei et al., J. Am.
+Stat. Assoc. 113, 1094 (2018); Angelopoulos and Bates,
+arXiv:2107.07511):
+
+```python
+from labplan import conformal_quantile, conformal_interval
+
+q = conformal_quantile(abs_errors_heldout, alpha=0.1)   # 90% level
+lo, hi = conformal_interval(new_predictions, q)
+```
+
+Its honest limits are stated in the docstring rather than hidden:
+the guarantee is marginal, and it needs the calibration data to be
+exchangeable with the new measurement -- last month's instrument
+state does not certify next month's drift.
+
+## What is inside
+
+- **`Model`**: your forward function with named parameters and a
+  mandatory `reference` -- provenance travels with every prediction,
+  the same rule every package in this organization applies.
+- **`information` / `design` / `repeats_for`**: predicted error bars
+  from the design alone (the Fisher information of independent
+  Gaussian measurements; any statistics text, under "Cramer-Rao
+  bound"); greedy D-optimal selection of the most informative
+  settings (Pukelsheim, Optimal Design of Experiments, SIAM (2006));
+  and the exact 1/sqrt(repeats) law, inverted in closed form.
+- **`fit`**: Levenberg-Marquardt weighted least squares in pure
+  NumPy, with exact known-noise covariance and a chi-squared check
+  when measurement errors are supplied, and residual-scaled error
+  bars (stated as such) when they are not.
+- **`conformal_quantile` / `conformal_interval` / `coverage_exact`**:
+  distribution-free intervals with the exact finite-sample coverage
+  formula exposed for checking.
+- **`audit_record` / `report_text`**: a JSON-serializable statement
+  of record -- model, source, values, error bars, goodness of fit,
+  identifiability, the sha256 of the exact data arrays, software
+  versions, UTC timestamp, operator -- and its human-readable
+  rendering.
+- **`save_measurements_csv` / `load_measurements_csv`**: a plain,
+  checked file contract whose round trip is bit-exact.
+
+## Refusals, not guesses
+
+A design that cannot tell the parameters apart is refused with an
+explanation, in the planner, the fit and the design tool alike --
+judged on a unit-free (correlation-scaled) information matrix, so
+mixed units can never fake or hide a degeneracy. Too few points, a
+non-converging fit, an uncertifiable conformal level, a malformed
+data file: each refuses with the reason and, where one exists, the
+remedy.
+
+## How it is checked
+
+14 tests (Python 3.9-3.14, run in CI on every push), every
+statistical claim pinned to a closed form, an exact identity, or
+seeded simulation against an exact formula -- never a stored number.
+Highlights: on a linear model the fit covariance equals the textbook
+closed form sigma^2 (X^T X)^-1 exactly, and the planner promises the
+same matrix; 400 seeded Monte-Carlo experiments match the reported
+error bars; an exactly degenerate model is refused via an exact rank
+argument; the greedy design obeys the rank-one determinant identity,
+reproduces its own rule, never loses to a random subset, and -- for
+the two-point line design -- matches the classical optimum found by
+exhaustion; the repeat law is asserted by tiling the design; the
+conformal quantile is the exact rank formula and seeded simulation
+matches the exact closed-form coverage inside the published
+two-sided guarantee; the audit record survives JSON round trip
+exactly and its digest pins the exact data; file round trips are
+bit-exact.
+
+## Honest limits
+
+Deliberate scope, designed out with reasons: the Gaussian
+error-bar machinery is exact for independent Gaussian measurement
+errors and first-order-accurate otherwise (the conformal tools are
+the assumption-free complement, and their own limits are stated);
+the greedy design is a transparent heuristic, not a proof of global
+optimality; no physics ships in this package at all -- your model
+and its `reference` carry the physics, and the nine physics packages
+of this organization remain the place where specific instruments'
+models live, each already wired into this same loop.
+
+## Support and governance
+
+Written and maintained by Tanvir Mahmud Mahim (Department of
+Electrical and Electronic Engineering, BRAC University), who reviews
+every change and takes the final decision on scope and releases.
+Design questions are discussed in the open in issues and pull
+requests, and the standing rule of
+[CONTRIBUTING.md](CONTRIBUTING.md) binds the maintainer exactly as it
+binds contributors: a change that touches the statistics arrives with
+a test, and a claim arrives with its source.
+
+Support runs through the
+[issue tracker](https://github.com/TaN-MM-Org/labplan/issues). Usage
+questions are welcome alongside bug reports; a docstring that left a
+unit or a convention unclear is treated as a documentation bug, not
+user error. While the version is below 1.0 the API may still move
+between minor versions; such changes are called out in the release
+notes.
+
+## License
+
+Apache-2.0.

labplan-0.1.0/pyproject.toml

@@ -0,0 +1,36 @@
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "labplan"
+version = "0.1.0"
+description = "Plan the measurement, fit the model, keep the record - exact measurement planning, calibration and audit trails for any lab model"
+readme = "README.md"
+requires-python = ">=3.9"
+license = {text = "Apache-2.0"}
+authors = [{name = "Tanvir Mahmud Mahim"}]
+dependencies = ["numpy>=1.22"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+
+[project.urls]
+Homepage = "https://github.com/TaN-MM-Org/labplan"
+Issues = "https://github.com/TaN-MM-Org/labplan/issues"
+
+[project.optional-dependencies]
+test = ["pytest>=7"]
+
+[tool.setuptools.packages.find]
+where = ["src"]

labplan-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+