2.52.20 release; python 3.13 support

Author: yoelcortes

biosteam/__init__.py

@@ -13,7 +13,7 @@
 
 """
 from __future__ import annotations
-__version__ = '2.52.19'
+__version__ = '2.52.20'
 
 #: Chemical engineering plant cost index (defaults to 567.5 at 2017).
 CE: float = 567.5 

biosteam/_system.py

@@ -212,14 +212,15 @@ def solve_material_flows(self, composition_sensitive=False, full_output=False):
                 [(f(j) if callable(f:=bi[j]) else f) for j in delayed_index]
                 for bi in b
             ], float)
-            values = solve(A_delayed, b_delayed.T).T
+            values = np.array([solve(A_delayed[i], b_delayed[:, i]) for i in range(b.shape[1])]).T
             values[values < 0] = 0
             for obj, value in zip(objs, values): 
                 obj._update_material_flows(value, delayed_index)
         else:
             A, objs = dictionaries2array(A)
             if np.isnan(A).any(): raise RuntimeError('invalid number encountered')
-            values = solve(A, np.array(b).T).T
+            b = np.array(b)
+            values = np.array([solve(A[i], b[:, i]) for i in range(b.shape[1])]).T
             if np.isnan(values).any(): raise RuntimeError('invalid number encountered')
             values[(values < 0) & (values > -1e-6)] = 0
             masks = values < 0

biosteam/evaluation/_model.py

@@ -16,7 +16,6 @@
 from scipy.optimize import shgo, differential_evolution
 import numpy as np
 import pandas as pd
-from chaospy import distributions as shape
 from ._indicator import Indicator
 from ._feature import MockFeature
 from ._utils import var_indices, var_columns, indices_to_multiindex
@@ -30,6 +29,12 @@
 from ._parameter import Parameter
 from .evaluation_tools import load_default_parameters
 import pickle
+try:
+    from chaospy import distributions as shape
+    import chaospy as cp
+    Distribution = shape.baseclass.Distribution
+except:
+    Distribution = None
 
 __all__ = ('Model', 'EasyInputModel')
 
@@ -60,35 +65,6 @@ def f(x):
     function = wrapper_fn(code)
     return function
 
-# %% Fix compatibility with new chaospy version
-
-import chaospy as cp
-version_components = cp.__version__.split('.')
-CP_MAJOR, CP_MINOR = int(version_components[0]), int(version_components[1])
-CP4 = (CP_MAJOR, CP_MINOR) >= (4, 0)
-if CP4:
-    from inspect import signature
-    def save_repr_init(f):
-        defaults = list(signature(f).parameters.values())[1:]
-        defaults = {i.name: i.default for i in defaults}
-        def init(self, *args, **kwargs):
-            if not hasattr(self, '_repr'):
-                self._repr = params = defaults.copy()
-                for i, j in zip(params, args): params[i] = j
-                params.update(kwargs)
-            f(self, *args, **kwargs)
-        return init
-    
-    shapes = cp.distributions
-    Distribution = cp.distributions.Distribution
-    baseshapes = set([i for i in cp.distributions.baseclass.__dict__.values()
-                      if isinstance(i, type) and issubclass(i, Distribution)])
-    for i in shapes.__dict__.values():
-        if isinstance(i, type) and issubclass(i, Distribution) and i not in baseshapes:
-            i.__init__ = save_repr_init(i.__init__)
-    del signature, save_repr_init, shapes, baseshapes, Distribution, i
-del version_components, CP_MAJOR, CP_MINOR, CP4
-
 # %% Simulation of process systems
 
 class Model:
@@ -324,7 +300,7 @@ def parameter(self,
             element: Optional[Unit]=None, 
             coupled: Optional[bool]=None,
             name: Optional[str]=None, 
-            distribution: Optional[str|shape.baseclass.Distribution]=None, 
+            distribution: Optional[str|Distribution]=None, 
             units: Optional[str]=None, 
             baseline: Optional[float]=None, 
             bounds: Optional[tuple[float, float]]=None, 

biosteam/evaluation/_parameter.py

@@ -12,9 +12,41 @@
 from ._feature import Feature
 from ..utils import format_title
 import biosteam as bst
-from chaospy import distributions as shape
+from warnings import warn
 from inspect import signature
 
+try:
+    from chaospy import distributions as shape
+except:
+    warn('chaospy not installed; cannot use automation features for uncertainty and optimization', RuntimeWarning, stacklevel=2)
+else:
+    # Fix compatibility with new chaospy version
+    import chaospy as cp
+    version_components = cp.__version__.split('.')
+    CP_MAJOR, CP_MINOR = int(version_components[0]), int(version_components[1])
+    CP4 = (CP_MAJOR, CP_MINOR) >= (4, 0)
+    if CP4:
+        def save_repr_init(f):
+            defaults = list(signature(f).parameters.values())[1:]
+            defaults = {i.name: i.default for i in defaults}
+            def init(self, *args, **kwargs):
+                if not hasattr(self, '_repr'):
+                    self._repr = params = defaults.copy()
+                    for i, j in zip(params, args): params[i] = j
+                    params.update(kwargs)
+                f(self, *args, **kwargs)
+            return init
+        
+        shapes = cp.distributions
+        Distribution = cp.distributions.Distribution
+        baseshapes = set([i for i in cp.distributions.baseclass.__dict__.values()
+                          if isinstance(i, type) and issubclass(i, Distribution)])
+        for i in shapes.__dict__.values():
+            if isinstance(i, type) and issubclass(i, Distribution) and i not in baseshapes:
+                i.__init__ = save_repr_init(i.__init__)
+        del save_repr_init, shapes, baseshapes, Distribution, i
+    del version_components, CP_MAJOR, CP_MINOR, CP4
+
 class Parameter(Feature):
     """
     Create a Parameter object that, when called, runs the setter and

biosteam/evaluation/evaluation_tools/parameter.py

@@ -7,7 +7,8 @@
 # for license details.
 """
 """
-from chaospy import distributions as shape
+try: from chaospy import distributions as shape
+except: pass
 import biosteam as bst
 
 __all__ = ('load_default_parameters',

docs/index.rst

@@ -117,8 +117,13 @@ Installation
    
       $ git clone --depth 10 git://github.com/BioSTEAMDevelopmentGroup/biosteam
 
-#. BioSTEAM uses `Graphviz <http://www.graphviz.org/>`__ to make flowsheet diagrams. 
-   You will need to install Graphviz separately as follows:
+#. BioSTEAM uses `Graphviz <http://www.graphviz.org/>`__ to make flowsheet diagrams. To properly install Graphviz in an anaconda distribution, run the following line:
+
+   .. code-block:: bash
+    
+      $ conda install python-graphviz
+
+#. If you **do not** have an anaconda distribution, you will need to install Graphviz separately as follows:
 
    * Windows: Download the EXE installer and follow the instructions listed `in this link <https://graphviz.org/download/>`__
 
@@ -133,19 +138,20 @@ Installation
      .. code-block:: bash
     
         $ brew install graphviz
-   
-#. To properly install Graphviz in an anaconda distribution, run the following line:
-
-   .. code-block:: bash
-    
-      $ conda install python-graphviz
 
 Common Issues
 -------------
 
+* **Unit and system diagrams are not displaying:**
+
+  Graphviz may not be properly installed or may be missing from your python path. 
+  Please follow the graphviz installation procedure outlined above.
+
 * **Cannot install/update BioSTEAM:**
 
-  If you are having trouble installing or updating BioSTEAM, it may be due to dependency issues. You can bypass these using:
+  If you are having trouble installing or updating BioSTEAM, it may be due to dependency issues. 
+  Some dependencies like chaospy/numpoly require Microsoft C++ Build Tools. Download and install the `C++ build tools here. <https://visualstudio.microsoft.com/visual-cpp-build-tools/>`__
+  You can also bypass dependency issues using:
 
   .. code-block:: bash
 
@@ -157,11 +163,6 @@ Common Issues
 
      $ pip install biosteam==<version>
 
-* **Unit and system diagrams are not displaying:**
-
-  Graphviz may not be properly installed or may be missing from your python path. 
-  Please follow the graphviz installation procedure outlined above.
-
 Scientific Papers
 -----------------
 

setup.py

@@ -11,15 +11,14 @@
     name='biosteam',
     packages=['biosteam'],
     license='MIT',
-    version='2.52.19',
+    version='2.52.20',
     description='The Biorefinery Simulation and Techno-Economic Analysis Modules',
     long_description=open('README.rst', encoding='utf-8').read(),
     author='Yoel Cortes-Pena',
     install_requires=['IPython>=7.9.0',
-                      'thermosteam>=0.52.16', 
+                      'thermosteam>=0.52.18', 
                       'graphviz>=0.17',
-                      'numpoly==1.2.13',
-                      'chaospy==4.3.15',
+                      'chaospy>=4.3.21',
                       'pyyaml'],
     extras_require={ 
         'dev': [