gratinglab 0.1.7__tar.gz → 0.1.9__tar.gz

{gratinglab-0.1.7 → gratinglab-0.1.9}/PKG-INFO

@@ -1,17 +1,21 @@
 Metadata-Version: 2.4
 Name: gratinglab
-Version: 0.1.7
+Version: 0.1.9
 Summary: Open platform for diffraction grating groove metrology and efficiency analysis
 Author: Jake McCoy
 License: BSD-3-Clause
 Project-URL: Homepage, https://github.com/jamccoy/gratinglab
-Keywords: diffraction,grating,efficiency,rcwa,x-ray,spectroscopy,afm,metrology,blaze,pcgrate
+Project-URL: Changelog, https://github.com/jamccoy/gratinglab/blob/master/CHANGELOG.md
+Keywords: diffraction,grating,diffraction grating,diffraction efficiency,optics,rcwa,integral method,spectroscopy,afm,metrology,blaze,groove profile,ultraviolet,infrared,x-ray
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
@@ -27,7 +31,8 @@ Requires-Dist: pandas>=2.1; extra == "dev"
 Requires-Dist: ruff>=0.16; extra == "dev"
 Provides-Extra: gui
 Requires-Dist: matplotlib>=3.8; extra == "gui"
-Requires-Dist: PySide6-Essentials>=6.7; extra == "gui"
+Requires-Dist: PySide6-Essentials!=6.12.0,>=6.7; python_version < "3.12" and extra == "gui"
+Requires-Dist: PySide6-Essentials>=6.7; python_version >= "3.12" and extra == "gui"
 Requires-Dist: endstation[qt]>=0.2.2; extra == "gui"
 Provides-Extra: metrology
 Requires-Dist: matplotlib>=3.9; extra == "metrology"
@@ -44,7 +49,7 @@ Dynamic: license-file
 [![tests](https://github.com/jamccoy/gratinglab/actions/workflows/test.yml/badge.svg)](https://github.com/jamccoy/gratinglab/actions/workflows/test.yml)
 [![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD--3--Clause-blue)](https://github.com/jamccoy/gratinglab/blob/master/LICENSE)
 
-**[PyPI](https://pypi.org/project/gratinglab/)** · **[Documentation](https://github.com/jamccoy/gratinglab/wiki)** · **[Releases](https://github.com/jamccoy/gratinglab/releases)** · **[Issues](https://github.com/jamccoy/gratinglab/issues)**
+**[PyPI](https://pypi.org/project/gratinglab/)** · **[Documentation](https://github.com/jamccoy/gratinglab/wiki)** · **[Changelog](https://github.com/jamccoy/gratinglab/blob/master/CHANGELOG.md)** · **[Releases](https://github.com/jamccoy/gratinglab/releases)** · **[Issues](https://github.com/jamccoy/gratinglab/issues)**
 
 gratinglab is a Python package for measuring the groove profiles of diffraction
 gratings from atomic force microscope (AFM) scans and for computing the diffraction
@@ -225,12 +230,14 @@ does not install one. A subpackage that needs an optional extra names it when it
 missing, instead of failing with a bare `ModuleNotFoundError`.
 
 Apart from numpy, scipy and pydantic, the only dependency is
-[endstation](https://github.com/jamccoy/endstation), a library of shared components for
-desktop scientific applications by the same author. gratinglab uses its guards for
-optional extras (the messages described above), form validation, Qt layout sizing,
-test helpers, and the tools that build the icon and the macOS application and publish
-the wiki. The core of endstation has no dependencies of its own, so it adds nothing to
-a solver-only install; its Qt components are installed only with the `gui` extra.
+**[endstation](https://pypi.org/project/endstation/)**
+([source](https://github.com/jamccoy/endstation)), a library of shared components for
+desktop scientific applications by the same author, which gratinglab is built on.
+gratinglab uses its guards for optional extras (the messages described above), form
+validation, Qt layout sizing, test helpers, and the tools that build the icon and the
+macOS application and publish the wiki. The core of endstation has no dependencies of
+its own, so it adds nothing to a solver-only install; its Qt components are installed
+only with the `gui` extra.
 
 ### Where the measurement data lives
 
@@ -293,9 +300,14 @@ contributed backend appears in the window once it is registered.
 
 The Help menu contains the theory pages, rendered with typeset equations and tables.
 
-A macOS `.app` can be built with `python tools/make_app.py` (macOS 13 or later, the
-minimum supported by the PySide6 wheels), and the icon is regenerated with
-`python tools/make_icon.py`.
+A macOS `.app` can be built for either window with `python tools/apps.py bundle --app
+gratinglab` (or `--app metrology`), on macOS 13 or later, the minimum supported by the
+PySide6 wheels. `--dest ~/Applications` puts it where Finder will list it. The bundle
+is a stub that execs the console script in this checkout's virtualenv rather than a
+frozen application, so it is not portable to another machine; `python tools/apps.py
+check --app gratinglab` reports when that virtualenv has moved, which is the one
+failure a bundle cannot show from the outside. `python tools/apps.py icon --app
+gratinglab` regenerates the icon from the artwork in `gratinglab.gui.icon`.
 
 ## Documentation
 
@@ -367,6 +379,75 @@ The test suite relies on three practices in particular:
   .venv/bin/mutmut run
   ```
 
-## License
+## License, copyright and reuse
 
-BSD-3-Clause.
+gratinglab is released under the
+[BSD 3-Clause License](https://github.com/jamccoy/gratinglab/blob/master/LICENSE),
+copyright (c) 2026 Jake McCoy. What follows is a plain summary for convenience; the
+`LICENSE` file is what governs, and nothing here is legal advice.
+
+**What you may do.** Use, modify and redistribute the code, in source or binary form,
+for any purpose, including commercial use and inside closed-source work. There is no
+copyleft obligation: software that imports gratinglab does not become BSD-licensed,
+and you are not required to publish your modifications.
+
+**What you must do.** Retain the copyright notice, the list of conditions and the
+disclaimer when you redistribute — in the source for a source distribution, and in the
+documentation or other accompanying materials for a binary one. The third clause
+separately forbids using the author's or contributors' names to endorse or promote a
+derived product without prior written permission.
+
+**What you do not get.** The software is provided as is, without warranty of any kind,
+and the author is not liable for any use of it. That disclaimer carries more weight
+here than it does for most packages, because the efficiency solvers are experimental
+(see Status): a number this software produces is evidence to be checked against
+another method, not a result to be relied on because a computer printed it.
+
+Contributions are accepted under the same licence. A pull request is taken as agreement
+that the contribution may be distributed under BSD-3-Clause.
+
+### Citing it
+
+[`CITATION.cff`](https://github.com/jamccoy/gratinglab/blob/master/CITATION.cff) is
+the citation of record, and GitHub's "Cite this repository" renders it as BibTeX or
+APA. It names the version, which is checked against `gratinglab.__version__` on every
+release, so a citation generated from it points at the code that produced the number
+rather than at whatever is current. If a result depends on a solver backend or on an
+optical constant table, cite those too: the method's own reference is in
+[`docs/references.md`](https://github.com/jamccoy/gratinglab/blob/master/docs/references.md),
+and `Provenance` records what a run actually used.
+
+### The licences you inherit by installing it
+
+| Installed with | Package | Licence |
+|---|---|---|
+| core | numpy, scipy | BSD-3-Clause |
+| core | pydantic | MIT |
+| core | [endstation](https://pypi.org/project/endstation/) | BSD-3-Clause |
+| `[gui]`, `[metrology]` | matplotlib | PSF-based, BSD-compatible |
+| `[gui]` | PySide6-Essentials | LGPL-3.0 |
+| `[refractiveindex]` | PyYAML | MIT |
+
+A solver-only install is permissive throughout. The `gui` extra is the one worth
+knowing about: Qt for Python is LGPL-3.0, which is the reason this project depends on
+PySide6 and not on PyQt6, whose licence is GPL and would reach your own code.
+Importing an LGPL library dynamically does not change the licence of what you write,
+but redistributing a bundled application that ships Qt inside it brings LGPL
+obligations for that component — chiefly your users' right to substitute their own
+build of it. Running the window yourself, or installing either extra from PyPI, raises
+no such question.
+
+### What this licence does not cover
+
+**Optical constant tables.** None are distributed with the package, and a table you
+add is governed by the terms of whoever published it, not by this licence. CXRO and
+refractiveindex.info each state their own, and a table exported from another program
+carries whatever that program's terms attach to it.
+[`SOURCES.md`](https://github.com/jamccoy/gratinglab/blob/master/src/gratinglab/materials/data/SOURCES.md)
+records where each kind comes from and why none ships here.
+
+**Measurement data.** AFM scans and the reference efficiency corpus are the research
+group's data and are deliberately absent from the repository, as described above under
+Install. The code is open; the measurements it was validated against are not ours to
+publish, and the documentation says which results are therefore not reproducible from
+a bare clone.

gratinglab-0.1.7/src/gratinglab.egg-info/PKG-INFO → gratinglab-0.1.9/README.md

@@ -1,42 +1,3 @@
-Metadata-Version: 2.4
-Name: gratinglab
-Version: 0.1.7
-Summary: Open platform for diffraction grating groove metrology and efficiency analysis
-Author: Jake McCoy
-License: BSD-3-Clause
-Project-URL: Homepage, https://github.com/jamccoy/gratinglab
-Keywords: diffraction,grating,efficiency,rcwa,x-ray,spectroscopy,afm,metrology,blaze,pcgrate
-Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy>=1.26
-Requires-Dist: scipy>=1.11
-Requires-Dist: pydantic>=2.6
-Requires-Dist: endstation>=0.2.2
-Provides-Extra: dev
-Requires-Dist: pytest>=7; extra == "dev"
-Requires-Dist: pytest-qt>=4.5; extra == "dev"
-Requires-Dist: matplotlib>=3.8; extra == "dev"
-Requires-Dist: pandas>=2.1; extra == "dev"
-Requires-Dist: ruff>=0.16; extra == "dev"
-Provides-Extra: gui
-Requires-Dist: matplotlib>=3.8; extra == "gui"
-Requires-Dist: PySide6-Essentials>=6.7; extra == "gui"
-Requires-Dist: endstation[qt]>=0.2.2; extra == "gui"
-Provides-Extra: metrology
-Requires-Dist: matplotlib>=3.9; extra == "metrology"
-Provides-Extra: refractiveindex
-Requires-Dist: pyyaml>=6; extra == "refractiveindex"
-Provides-Extra: mut
-Requires-Dist: mutmut<3.3,>=3.2; extra == "mut"
-Dynamic: license-file
-
 # gratinglab
 
 [![PyPI](https://img.shields.io/pypi/v/gratinglab?cacheSeconds=3600)](https://pypi.org/project/gratinglab/)
@@ -44,7 +5,7 @@ Dynamic: license-file
 [![tests](https://github.com/jamccoy/gratinglab/actions/workflows/test.yml/badge.svg)](https://github.com/jamccoy/gratinglab/actions/workflows/test.yml)
 [![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD--3--Clause-blue)](https://github.com/jamccoy/gratinglab/blob/master/LICENSE)
 
-**[PyPI](https://pypi.org/project/gratinglab/)** · **[Documentation](https://github.com/jamccoy/gratinglab/wiki)** · **[Releases](https://github.com/jamccoy/gratinglab/releases)** · **[Issues](https://github.com/jamccoy/gratinglab/issues)**
+**[PyPI](https://pypi.org/project/gratinglab/)** · **[Documentation](https://github.com/jamccoy/gratinglab/wiki)** · **[Changelog](https://github.com/jamccoy/gratinglab/blob/master/CHANGELOG.md)** · **[Releases](https://github.com/jamccoy/gratinglab/releases)** · **[Issues](https://github.com/jamccoy/gratinglab/issues)**
 
 gratinglab is a Python package for measuring the groove profiles of diffraction
 gratings from atomic force microscope (AFM) scans and for computing the diffraction
@@ -225,12 +186,14 @@ does not install one. A subpackage that needs an optional extra names it when it
 missing, instead of failing with a bare `ModuleNotFoundError`.
 
 Apart from numpy, scipy and pydantic, the only dependency is
-[endstation](https://github.com/jamccoy/endstation), a library of shared components for
-desktop scientific applications by the same author. gratinglab uses its guards for
-optional extras (the messages described above), form validation, Qt layout sizing,
-test helpers, and the tools that build the icon and the macOS application and publish
-the wiki. The core of endstation has no dependencies of its own, so it adds nothing to
-a solver-only install; its Qt components are installed only with the `gui` extra.
+**[endstation](https://pypi.org/project/endstation/)**
+([source](https://github.com/jamccoy/endstation)), a library of shared components for
+desktop scientific applications by the same author, which gratinglab is built on.
+gratinglab uses its guards for optional extras (the messages described above), form
+validation, Qt layout sizing, test helpers, and the tools that build the icon and the
+macOS application and publish the wiki. The core of endstation has no dependencies of
+its own, so it adds nothing to a solver-only install; its Qt components are installed
+only with the `gui` extra.
 
 ### Where the measurement data lives
 
@@ -293,9 +256,14 @@ contributed backend appears in the window once it is registered.
 
 The Help menu contains the theory pages, rendered with typeset equations and tables.
 
-A macOS `.app` can be built with `python tools/make_app.py` (macOS 13 or later, the
-minimum supported by the PySide6 wheels), and the icon is regenerated with
-`python tools/make_icon.py`.
+A macOS `.app` can be built for either window with `python tools/apps.py bundle --app
+gratinglab` (or `--app metrology`), on macOS 13 or later, the minimum supported by the
+PySide6 wheels. `--dest ~/Applications` puts it where Finder will list it. The bundle
+is a stub that execs the console script in this checkout's virtualenv rather than a
+frozen application, so it is not portable to another machine; `python tools/apps.py
+check --app gratinglab` reports when that virtualenv has moved, which is the one
+failure a bundle cannot show from the outside. `python tools/apps.py icon --app
+gratinglab` regenerates the icon from the artwork in `gratinglab.gui.icon`.
 
 ## Documentation
 
@@ -367,6 +335,75 @@ The test suite relies on three practices in particular:
   .venv/bin/mutmut run
   ```
 
-## License
+## License, copyright and reuse
+
+gratinglab is released under the
+[BSD 3-Clause License](https://github.com/jamccoy/gratinglab/blob/master/LICENSE),
+copyright (c) 2026 Jake McCoy. What follows is a plain summary for convenience; the
+`LICENSE` file is what governs, and nothing here is legal advice.
+
+**What you may do.** Use, modify and redistribute the code, in source or binary form,
+for any purpose, including commercial use and inside closed-source work. There is no
+copyleft obligation: software that imports gratinglab does not become BSD-licensed,
+and you are not required to publish your modifications.
+
+**What you must do.** Retain the copyright notice, the list of conditions and the
+disclaimer when you redistribute — in the source for a source distribution, and in the
+documentation or other accompanying materials for a binary one. The third clause
+separately forbids using the author's or contributors' names to endorse or promote a
+derived product without prior written permission.
+
+**What you do not get.** The software is provided as is, without warranty of any kind,
+and the author is not liable for any use of it. That disclaimer carries more weight
+here than it does for most packages, because the efficiency solvers are experimental
+(see Status): a number this software produces is evidence to be checked against
+another method, not a result to be relied on because a computer printed it.
+
+Contributions are accepted under the same licence. A pull request is taken as agreement
+that the contribution may be distributed under BSD-3-Clause.
+
+### Citing it
+
+[`CITATION.cff`](https://github.com/jamccoy/gratinglab/blob/master/CITATION.cff) is
+the citation of record, and GitHub's "Cite this repository" renders it as BibTeX or
+APA. It names the version, which is checked against `gratinglab.__version__` on every
+release, so a citation generated from it points at the code that produced the number
+rather than at whatever is current. If a result depends on a solver backend or on an
+optical constant table, cite those too: the method's own reference is in
+[`docs/references.md`](https://github.com/jamccoy/gratinglab/blob/master/docs/references.md),
+and `Provenance` records what a run actually used.
+
+### The licences you inherit by installing it
+
+| Installed with | Package | Licence |
+|---|---|---|
+| core | numpy, scipy | BSD-3-Clause |
+| core | pydantic | MIT |
+| core | [endstation](https://pypi.org/project/endstation/) | BSD-3-Clause |
+| `[gui]`, `[metrology]` | matplotlib | PSF-based, BSD-compatible |
+| `[gui]` | PySide6-Essentials | LGPL-3.0 |
+| `[refractiveindex]` | PyYAML | MIT |
+
+A solver-only install is permissive throughout. The `gui` extra is the one worth
+knowing about: Qt for Python is LGPL-3.0, which is the reason this project depends on
+PySide6 and not on PyQt6, whose licence is GPL and would reach your own code.
+Importing an LGPL library dynamically does not change the licence of what you write,
+but redistributing a bundled application that ships Qt inside it brings LGPL
+obligations for that component — chiefly your users' right to substitute their own
+build of it. Running the window yourself, or installing either extra from PyPI, raises
+no such question.
+
+### What this licence does not cover
+
+**Optical constant tables.** None are distributed with the package, and a table you
+add is governed by the terms of whoever published it, not by this licence. CXRO and
+refractiveindex.info each state their own, and a table exported from another program
+carries whatever that program's terms attach to it.
+[`SOURCES.md`](https://github.com/jamccoy/gratinglab/blob/master/src/gratinglab/materials/data/SOURCES.md)
+records where each kind comes from and why none ships here.
 
-BSD-3-Clause.
+**Measurement data.** AFM scans and the reference efficiency corpus are the research
+group's data and are deliberately absent from the repository, as described above under
+Install. The code is open; the measurements it was validated against are not ours to
+publish, and the documentation says which results are therefore not reproducible from
+a bare clone.

{gratinglab-0.1.7 → gratinglab-0.1.9}/pyproject.toml

@@ -14,15 +14,33 @@ readme = "README.md"
 requires-python = ">=3.11"
 license = { text = "BSD-3-Clause" }
 authors = [{ name = "Jake McCoy" }]
-keywords = ["diffraction", "grating", "efficiency", "rcwa", "x-ray", "spectroscopy",
-            "afm", "metrology", "blaze", "pcgrate"]
+# Wavelength-neutral on purpose. The off-plane work this package grew out of is
+# soft x-ray, and that band is still named, but nothing in the solvers or the
+# metrology assumes one: the grating equation carries no band, and the
+# materials layer reads CXRO x-ray tables and refractiveindex.info
+# ultraviolet-to-infrared tables alike. Leading with "x-ray" told a reader the
+# in-plane half of the package was not meant for them.
+#
+# "pcgrate" is deliberately absent. It is a program this project validates
+# against, not a feature of this one, and a search for it should not land here.
+keywords = ["diffraction", "grating", "diffraction grating", "diffraction efficiency",
+            "optics", "rcwa", "integral method", "spectroscopy", "afm", "metrology",
+            "blaze", "groove profile", "ultraviolet", "infrared", "x-ray"]
+# Only classifiers from the trove list, which PyPI rejects uploads over. Note
+# that there is no `Topic :: Scientific/Engineering :: Optics`; Physics is the
+# nearest, with Information Analysis for the metrology and Visualization for
+# the windows. No Qt environment classifier: a classifier cannot be made
+# conditional on an extra, and a default install pulls no toolkit at all.
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Scientific/Engineering :: Visualization",
 ]
 dependencies = [
     "numpy>=1.26",
@@ -48,7 +66,20 @@ dev = ["pytest>=7", "pytest-qt>=4.5", "matplotlib>=3.8", "pandas>=2.1", "ruff>=0
 #
 # PySide6 (LGPLv3) rather than PyQt6 (GPL): this package is BSD-3, and an
 # optional dynamically-linked dependency keeps it that way.
-gui = ["matplotlib>=3.8", "PySide6-Essentials>=6.7", "endstation[qt]>=0.2.2"]
+#
+# PySide6 6.12.0 on Python 3.11 aborts the interpreter at exit (Fatal Python
+# error: bool_dealloc) after heavy GUI use: it releases a reference to True or
+# False that it does not own, which on 3.11 eventually frees the object during
+# finalization. On 3.12 and later True and False are immortal and the bug is
+# harmless. Measured in CI on 2026-10-22: 6.9.3, 6.10.3 and 6.11.2 passed twice
+# each and 6.12.0 crashed twice. Only that release is excluded, and only on 3.11,
+# so a fixed 6.12.x is taken as soon as it exists.
+gui = [
+    "matplotlib>=3.8",
+    "PySide6-Essentials>=6.7,!=6.12.0; python_version < '3.12'",
+    "PySide6-Essentials>=6.7; python_version >= '3.12'",
+    "endstation[qt]>=0.2.2",
+]
 # Groove metrology: reading AFM scans and averaging them into a boundary
 # profile. An extra for the same reason the GUI is one -- `pip install
 # gratinglab` must stay numpy/scipy/pydantic, so a solver-only user never
@@ -76,6 +107,7 @@ gratinglab-metrology = "gratinglab.metrology.cli:main"
 
 [project.urls]
 Homepage = "https://github.com/jamccoy/gratinglab"
+Changelog = "https://github.com/jamccoy/gratinglab/blob/master/CHANGELOG.md"
 
 # Solver backends register here. A backend may live in its own distribution.
 [project.entry-points."gratinglab.solvers"]

{gratinglab-0.1.7 → gratinglab-0.1.9}/src/gratinglab/__init__.py

@@ -21,7 +21,7 @@ from .illumination import Illumination, Polarization
 from .resolution import ResolvingPower, resolving_power
 from .result import EfficiencyScan, OrderEfficiency, Provenance
 
-__version__ = "0.1.7"
+__version__ = "0.1.9"
 
 __all__ = [
     "Illumination",

{gratinglab-0.1.7 → gratinglab-0.1.9}/src/gratinglab/gui/app.py

@@ -58,7 +58,7 @@ def _bring_to_front(window) -> None:
     The fallback was therefore a `subprocess.run` on every launch, wrapped in
     a bare `except`, which did nothing in the one case it was written for, and
     it has been removed. The supported way to bring the window forward when
-    starting from a shell is to launch the bundle, which `tools/make_app.py`
+    starting from a shell is to launch the bundle, which `tools/apps.py bundle`
     builds and the README describes.
     """
     window.raise_()

{gratinglab-0.1.7 → gratinglab-0.1.9}/src/gratinglab/gui/icon.py

@@ -9,7 +9,7 @@ is what this software computes. It uses a few thick elements so that it
 remains legible at 16 px, the size at which icons most often become
 unreadable.
 
-``tools/make_icon.py`` turns this into a macOS ``.icns``.
+``tools/apps.py icon`` turns this into a macOS ``.icns``.
 """
 
 from __future__ import annotations

{gratinglab-0.1.7 → gratinglab-0.1.9}/src/gratinglab/metrology/core/processing.py

@@ -186,7 +186,9 @@ def flatten_profile(x, y, method='linear', poly_order=2, exclude_edges=0.0,
     Parameters:
         method: 'linear', 'polynomial', 'groove_peaks', or 'level_grooves'
         poly_order: polynomial order (for 'polynomial' and 'level_grooves' methods)
-        exclude_edges: fraction of data to exclude from edges (0.0 to 0.5)
+        exclude_edges: fraction of data to exclude from edges (0.0 to 0.5).
+            For 'level_grooves' it is skipped, with a warning, when excluding
+            the edges would leave too few features to fit the requested order.
         feature: for 'level_grooves': 'peaks', 'troughs', or 'both'
         period_nm: estimated period for finding grooves (for 'level_grooves')
     
@@ -262,13 +264,29 @@ def flatten_profile(x, y, method='linear', poly_order=2, exclude_edges=0.0,
                 x_min = x[0] + exclude_edges * (x[-1] - x[0])
                 x_max = x[-1] - exclude_edges * (x[-1] - x[0])
                 mask = (feature_x >= x_min) & (feature_x <= x_max)
-                feature_x = feature_x[mask]
-                feature_y = feature_y[mask]
-            
-            if len(feature_x) < 2:
-                print("    Warning: Not enough features after edge exclusion, using all")
-            
-            poly_coeffs = np.polyfit(feature_x, feature_y, poly_order)
+                kept = int(np.count_nonzero(mask))
+                # Edge exclusion is meant to improve the fit, so it must not be
+                # allowed to starve it. This used to keep the remnant and fit
+                # that while printing "using all": with two features left and a
+                # quadratic asked for, the background was rank-deficient and
+                # still looked like a fit.
+                if kept >= poly_order + 1:
+                    feature_x = feature_x[mask]
+                    feature_y = feature_y[mask]
+                else:
+                    print(f"    Warning: edge exclusion leaves {kept} feature(s), "
+                          f"too few for a degree-{poly_order} background; "
+                          "using all of them")
+
+            # A degree-k polynomial needs k+1 points to be determined. Reaching
+            # here guarantees two, so the order is reduced rather than letting
+            # polyfit return a rank-deficient answer behind a RankWarning.
+            order = min(poly_order, len(feature_x) - 1)
+            if order < poly_order:
+                print(f"    Warning: {len(feature_x)} feature(s) support only a "
+                      f"degree-{order} background, not degree-{poly_order}")
+
+            poly_coeffs = np.polyfit(feature_x, feature_y, order)
             background = np.polyval(poly_coeffs, x)
     else:
         raise ValueError(f"Unknown flattening method: {method}")

{gratinglab-0.1.7 → gratinglab-0.1.9}/src/gratinglab/metrology/gui/icon.py

@@ -19,7 +19,7 @@ importing ``gratinglab.metrology.gui`` must stay cheap, since that is what
 raises the friendly "PySide6 is an optional extra" message.
 ``tests/test_gui_boundary.py`` checks it.
 
-``tools/make_icon.py`` turns this into a macOS ``.icns``.
+``tools/apps.py icon`` turns this into a macOS ``.icns``.
 """
 
 from __future__ import annotations