bindtools 0.3.2__tar.gz → 0.3.4__tar.gz

{bindtools-0.3.2 → bindtools-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bindtools
-Version: 0.3.2
+Version: 0.3.4
 Keywords: chemistry,analytical chemistry,binding constants,supramolecular
 Author: Martin Peeks
 Author-email: Martin Peeks <martinp23@googlemail.com>, m.peeks@unsw.edu.au
@@ -9,22 +9,23 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Dist: corner==2.2.3
+Requires-Dist: corner==2.3.0
 Requires-Dist: emcee==3.1.6
 Requires-Dist: h5py>=3.14.0
 Requires-Dist: latex2mathml>=3.81.0
 Requires-Dist: lmfit==1.3.4
-Requires-Dist: matplotlib==3.11.0
-Requires-Dist: numba>=0.66
+Requires-Dist: matplotlib==3.11.2
+Requires-Dist: numba>=0.68
 Requires-Dist: numpy>=2.3.4
 Requires-Dist: openpyxl>=3.1.5
 Requires-Dist: pandas>=2.3.3
-Requires-Dist: scipy==1.18.0
-Requires-Dist: tqdm==4.68.3
+Requires-Dist: scipy==1.18.1
+Requires-Dist: tqdm==4.70.1
 Requires-Dist: uncertainties==3.2.3
-Requires-Python: >=3.12
+Requires-Python: >=3.12, <3.16
 Project-URL: Homepage, https://github.com/martinp23/bindtools
 Project-URL: Documentation, https://readthedocs.org
 Project-URL: Repository, https://github.com/martinp23/bindtools.git
@@ -36,6 +37,9 @@ Description-Content-Type: text/markdown
 [![PyPI version](https://badge.fury.io/py/bindtools.svg)](https://badge.fury.io/py/bindtools)
 [![Python Version](https://img.shields.io/pypi/pyversions/bindtools.svg)](https://pypi.org/project/bindtools/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23651650.svg)](https://doi.org/10.5281/zenodo.23651650)
+
+
 
 `bindtools` is a Python library for supramolecular chemistry designed for modeling, fitting, and analyzing binding equilibria. It provides numerical and analytical solvers for complex chemical systems, robust parameter optimization, and Bayesian parameter estimation.
 

{bindtools-0.3.2 → bindtools-0.3.4}/README.md

@@ -3,6 +3,9 @@
 [![PyPI version](https://badge.fury.io/py/bindtools.svg)](https://badge.fury.io/py/bindtools)
 [![Python Version](https://img.shields.io/pypi/pyversions/bindtools.svg)](https://pypi.org/project/bindtools/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23651650.svg)](https://doi.org/10.5281/zenodo.23651650)
+
+
 
 `bindtools` is a Python library for supramolecular chemistry designed for modeling, fitting, and analyzing binding equilibria. It provides numerical and analytical solvers for complex chemical systems, robust parameter optimization, and Bayesian parameter estimation.
 

{bindtools-0.3.2 → bindtools-0.3.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bindtools"
-version = "0.3.2"
+version = "0.3.4"
 readme = "README.md"
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -12,10 +12,11 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
     "Topic :: Scientific/Engineering :: Chemistry",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-requires-python = ">=3.12"
+requires-python = ">=3.12,<3.16"
 keywords = [
     "chemistry",
     "analytical chemistry",
@@ -23,18 +24,18 @@ keywords = [
     "supramolecular",
 ]
 dependencies = [
-    "corner==2.2.3",
+    "corner==2.3.0",
     "emcee==3.1.6",
     "h5py>=3.14.0",
     "latex2mathml>=3.81.0",
     "lmfit==1.3.4",
-    "matplotlib==3.11.0",
-    "numba>=0.66",
+    "matplotlib==3.11.2",
+    "numba>=0.68",
     "numpy>=2.3.4",
     "openpyxl>=3.1.5",
     "pandas>=2.3.3",
-    "scipy==1.18.0",
-    "tqdm==4.68.3",
+    "scipy==1.18.1",
+    "tqdm==4.70.1",
     "uncertainties==3.2.3",
 ]
 

{bindtools-0.3.2 → bindtools-0.3.4}/pyproject.toml.orig

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bindtools"
-version = "0.3.2"
+version = "0.3.4"
 readme = "README.md"
 classifiers = [
   # How mature is this project? Common values are
@@ -20,25 +20,25 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
-
+  "Programming Language :: Python :: 3.15",
   "Topic :: Scientific/Engineering :: Chemistry",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-requires-python = ">=3.12"
+requires-python = ">=3.12,<3.16"
 keywords = ["chemistry", "analytical chemistry", "binding constants", "supramolecular"]
 dependencies = [
-    "corner==2.2.3",
+    "corner==2.3.0",
     "emcee==3.1.6",
     "h5py>=3.14.0",
     "latex2mathml>=3.81.0",
     "lmfit==1.3.4",
-    "matplotlib==3.11.0",
-    "numba>=0.66",
+    "matplotlib==3.11.2",
+    "numba>=0.68",
     "numpy>=2.3.4",
     "openpyxl>=3.1.5",
     "pandas>=2.3.3",
-    "scipy==1.18.0",
-    "tqdm==4.68.3",
+    "scipy==1.18.1",
+    "tqdm==4.70.1",
     "uncertainties==3.2.3",
 ]
 authors = [

{bindtools-0.3.2 → bindtools-0.3.4}/src/bindtools/models/binding_model.py

@@ -48,7 +48,7 @@ class bindingModel:
             self.nConcs = np.shape(compConcs)[0]
 
         self.concUnits = None  # mM #TODO
-        self.specToDd = specToDd
+        self.specToDd = specToDd  # (n_species, n_obs) object array for NMR chemical shifts
         self.specToLinear: Optional[List] = specToLinear  # (n_species, n_obs) object array for UV-vis / fluorescence
         self.analytical_fast_exchange: bool = False
         self.analytical_topology: Optional[str] = None
@@ -169,14 +169,32 @@ class bindingModel:
                 elif isinstance(x, lmfit.Parameter):
                     self._addExistingParam(x)
 
-        # add chemical shift fitting params
         if self.specToDd is not None:
+            if not isinstance(self.specToDd, np.ndarray) or self.specToDd.dtype != object:
+                raw_list = list(self.specToDd)
+                if len(raw_list) > 0 and isinstance(raw_list[0], (list, tuple, np.ndarray)):
+                    # Already 2D-like
+                    rows, cols = len(raw_list), len(raw_list[0])
+                    arr = np.empty((rows, cols), dtype=object)
+                    for r in range(rows):
+                        for c in range(cols):
+                            arr[r, c] = raw_list[r][c]
+                else:
+                    # 1D-like -> reshape to (n_species, 1)
+                    arr = np.empty((len(raw_list), 1), dtype=object)
+                    for r, val in enumerate(raw_list):
+                        arr[r, 0] = val
+                self.specToDd = arr
+            elif self.specToDd.ndim == 1:
+                self.specToDd = self.specToDd[:, None]
+
+
             for ii, x in np.ndenumerate(self.specToDd):
                 if isinstance(x, tuple):
                     self._addParam("shift_{}_{}".format(ii[0], ii[1]), x[1], min=x[0], max=x[2])
                 elif isinstance(x, lmfit.Parameter):
                     self._addExistingParam(x)
-
+                
     def runModel(self, sigma=1, skip_col=1, method="least_squares", ret=False, kwargs={}) -> Optional["bindingModel"]:
         exptData = np.copy(self.rawData)
         spec_to_integ = None