add functionality to constrain parameters to a range (#56)

- The curve fitting parameters (top, bottom, slope) can now be constrained to a range in addition to being completely free or fixed. This can help with fitting some curves more sensibly (see [this issue](#53)). Specifically:
  - ``fixtop`` and ``fixbottom`` parameters to ``HillCurve`` can be 2-tuples of bounds
  - added ``fixslope`` parameter to ``HillCurve`` and ``CurveFits``
  - New ``constrain_params_range`` notebook tests and documents this functionality.

- Add ``no_curve_fit_first`` argument to ``HillCurve`` to aid debugging/development.

.github/workflows/test.yml

@@ -28,9 +28,6 @@ jobs:
       - name: lint code with ruff
         run: ruff check .
 
-      - name: lint Jupyter notebooks with ruff
-        run: nbqa ruff .
-
       - name: check code format with black
         run: black --check .
 

CHANGELOG.rst

@@ -6,6 +6,15 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
+2.0.0
+-----
+- The curve fitting parameters (top, bottom, slope) can now be constrained to a range in addition to being completely free or fixed. This can help with fitting some curves more sensibly (see [this issue](https://github.com/jbloomlab/neutcurve/issues/53)). Specifically:
+  - ``fixtop`` and ``fixbottom`` parameters to ``HillCurve`` can be 2-tuples of bounds
+  - added ``fixslope`` parameter to ``HillCurve`` and ``CurveFits``
+  - New ``constrain_params_range`` notebook tests and documents this functionality.
+
+- Add ``no_curve_fit_first`` argument to ``HillCurve`` to aid debugging/development.
+
 1.1.2
 -----
 

README.rst

@@ -4,13 +4,10 @@ neutcurve
 
 .. image:: https://img.shields.io/pypi/v/neutcurve.svg
         :target: https://pypi.python.org/pypi/neutcurve
-
 .. image:: https://github.com/jbloomlab/neutcurve/actions/workflows/test.yml/badge.svg
         :target: https://github.com/jbloomlab/neutcurve/actions/workflows/test.yml
-
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
         :target: https://github.com/psf/black
-
 .. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json
         :target: https://github.com/astral-sh/ruff
 

docs/constrain_params_range.nblink

@@ -0,0 +1,3 @@
+{
+    "path": "../notebooks/constrain_params_range.ipynb"
+}

docs/index.rst

@@ -20,6 +20,7 @@ Contents
    installation
    hillcurve_example
    curvefits_example
+   constrain_params_range
    combine_curvefits
    test_curves
    neutcurve

neutcurve/__init__.py

@@ -16,7 +16,7 @@
 
 __author__ = "Jesse Bloom"
 __email__ = "[email protected]"
-__version__ = "1.1.2"
+__version__ = "2.0.0"
 __url__ = "https://github.com/jbloomlab/neutcurve"
 
 from neutcurve.curvefits import CurveFits  # noqa: F401

neutcurve/curvefits.py

@@ -36,9 +36,11 @@ class CurveFits:
         `replicate_col` (str`)
             Column in data with name of replicate of this measurement. Replicates can
             **not** be named 'average' as we compute the average from the replicates.
-        `fixbottom` (`False` or float)
+        `fixbottom` (`False` or float or 2-tuple)
             Same meaning as for :class:`neutcurve.hillcurve.HillCurve`.
-        `fixtop` (`False` or float)
+        `fixtop` (`False` or float or 2-tuple)
+            Same meaning as for :class:`neutcurve.hillcurve.HillCurve`.
+        `fixslope` (`False` or float or 2-tuple)
             Same meaning as for :class:`neutcurve.hillcurve.HillCurve`.
         `infectivity_or_neutralized` ({'infectivity', 'neutralized'})
             Same meaning as for :class:`neutcurve.hillcurve.HillCurve`.
@@ -121,6 +123,7 @@ def combineCurveFits(
         attrs_can_differ = [  # attributes that can differ among objects
             "fixbottom",
             "fixtop",
+            "fixslope",
             "df",
             "sera",
             "allviruses",
@@ -142,8 +145,8 @@ def combineCurveFits(
         for attr in attrs_can_differ:
             delattr(combined_fits, attr)
 
-        # fixtop and fixbottom are kept at shared value or None
-        for attr in ["fixtop", "fixbottom"]:
+        # fixtop, fixbottom, fixslope are kept at shared value or None
+        for attr in ["fixtop", "fixbottom", "fixslope"]:
             if any(
                 getattr(curvefits_list[0], attr) != getattr(c, attr)
                 for c in curvefits_list
@@ -293,6 +296,7 @@ def __init__(
         init_slope=1.5,
         fixbottom=0,
         fixtop=1,
+        fixslope=False,
         allow_reps_unequal_conc=False,
     ):
         """See main class docstring."""
@@ -304,6 +308,7 @@ def __init__(
         self.replicate_col = replicate_col
         self.fixbottom = fixbottom
         self.fixtop = fixtop
+        self.fixslope = fixslope
         self._infectivity_or_neutralized = infectivity_or_neutralized
         self._fix_slope_first = fix_slope_first
         self._init_slope = init_slope
@@ -462,6 +467,7 @@ def getCurve(self, *, serum, virus, replicate):
                     fs_stderr=fs_stderr,
                     fixbottom=self.fixbottom,
                     fixtop=self.fixtop,
+                    fixslope=self.fixslope,
                     infectivity_or_neutralized=self._infectivity_or_neutralized,
                     fix_slope_first=self._fix_slope_first,
                     init_slope=self._init_slope,