Merge branch 'release/4.1.1'

CHANGELOG.rst

@@ -2,6 +2,15 @@
 Changelog
 =========
 
+4.1.1 (2022-03-10)
+------------------
+
+Fixes:
+
+* AIF file export now more reliable with custom properties
+* Isotherm models correctly instantiate their variables (parameters would
+  otherwise be shared between instances)
+
 4.1.0 (2022-03-02)
 ------------------
 

README.rst

@@ -164,8 +164,8 @@ or `Anaconda/Conda <https://www.anaconda.com/>`__:
 
 If you are just starting out, `Anaconda/Conda <https://www.anaconda.com/>`__ is
 a good bet since it manages virtual environments for you. Check out
-`<https://pygaps.readthedocs.io/en/master/installation.html>`__ for more
-details.
+`Installation <https://pygaps.readthedocs.io/en/master/installation.html>`__ for
+more details.
 
 Development
 ===========
@@ -185,7 +185,7 @@ Then install the package with pip either in regular or developer mode.
 
 If you want to contribute to pyGAPS or develop your own code from the package,
 check out the detailed information in
-`<https://pygaps.readthedocs.io/en/master/contributing.html>`.
+`CONTRIBUTING.rst <https://pygaps.readthedocs.io/en/master/contributing.html>`__.
 
 Bugs or questions?
 ==================

conda_recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "pygaps" %}
-{% set version = "4.1.0" %}
+{% set version = "4.1.1" %}
 
 package:
   name: {{ name|lower }}

pyproject.toml

@@ -10,7 +10,7 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 write_to = "src/pygaps/_version.py"
 local_scheme = 'dirty-tag'
-fallback_version = '4.1.0'
+fallback_version = '4.1.1'
 
 # linting: pylint
 [tool.pylint.basic]

setup.cfg

@@ -1,12 +1,12 @@
 [bumpversion]
-current_version = 4.1.0
+current_version = 4.1.1
 commit = True
 tag = False
 message = '{current_version} → {new_version}'
 
 [metadata]
 name = pygaps
-version = 4.1.0
+version = 4.1.1
 description = A framework for processing adsorption data for porous materials.
 long_description = file: README.rst
 long_description_content_type = text/x-rst

src/pygaps/__init__.py

@@ -9,7 +9,7 @@
     from ._version import version
     __version__ = version
 except ImportError:
-    __version__ = '4.1.0'
+    __version__ = '4.1.1'
 
 import sys
 from .logging import logger

src/pygaps/core/modelisotherm.py

@@ -88,8 +88,6 @@ class ModelIsotherm(BaseIsotherm):
 
     _reserved_params = BaseIsotherm._reserved_params + [
         'model',
-        'param_guess',
-        'param_bounds',
     ]
 
     ##########################################################
@@ -189,45 +187,32 @@ def __init__(
 
             # Name of analytical model to fit to pure-component isotherm data
             # adsorption isotherm.
-            self.model = get_isotherm_model(model)
+            self.model = get_isotherm_model(
+                model,
+                pressure_range=(min(pressure), max(pressure)),
+                loading_range=(min(loading), max(loading)),
+                param_bounds=param_bounds,
+            )
 
             # Pass odd parameters
             self.model.__init_parameters__(other_properties)
 
-            # The pressure range on which the model was built.
-            self.model.pressure_range = [min(pressure), max(pressure)]
-
-            # The loading range on which the model was built.
-            self.model.loading_range = [min(loading), max(loading)]
-
-            # Override defaults if user provides param_bounds dictionary
-            if param_bounds is not None:
-                for param, bound in param_bounds.items():
-                    if param not in self.model.param_bounds.keys():
-                        raise ParameterError(
-                            f"'{param}' is not a valid parameter"
-                            f" in the '{model}' model."
-                        )
-                    self.model.param_bounds[param] = bound
-
             # Dictionary of parameters as a starting point for data fitting.
-            self.param_guess = self.model.initial_guess(pressure, loading)
-
-            # Override defaults if user provides param_guess dictionary
-            if param_guess is not None:
-                for param, guess_val in param_guess.items():
-                    if param not in self.param_guess.keys():
+            if param_guess:
+                for param in param_guess.keys():
+                    if param not in self.model.param_names:
                         raise ParameterError(
                             f"'{param}' is not a valid parameter"
                             f" in the '{model}' model."
                         )
-                    self.param_guess[param] = guess_val
+            else:
+                param_guess = self.model.initial_guess(pressure, loading)
 
             # fit model to isotherm data
             self.model.fit(
                 pressure,
                 loading,
-                self.param_guess,
+                param_guess,
                 optimization_params,
                 verbose,
             )

src/pygaps/graphing/isotherm_graphs.py

@@ -183,7 +183,8 @@ def plot_iso(
 
     # Store which branches will be displayed
     if not branch:
-        raise ParameterError("Specify a branch to display" " e.g. branch=\'ads\'")
+        raise ParameterError("Specify a branch to display"
+                             " e.g. branch=\'ads\'")
     if branch not in _BRANCH_TYPES:
         raise GraphingError(
             "The supplied branch type is not valid."
@@ -279,7 +280,9 @@ def plot_iso(
         y2_ls.update(y2_line_style)
 
         # If there's an adsorption branch, plot it
-        if ads and isotherm.has_branch('ads'):
+        iso_has_ads = isotherm.has_branch('ads')
+        iso_has_des = isotherm.has_branch('des')
+        if ads and iso_has_ads:
             # Points
             x1_p, y1_p, x2_p, y2_p = _get_data(
                 isotherm,
@@ -303,7 +306,7 @@ def plot_iso(
         y2_ls['markerfacecolor'] = 'white'
 
         # If there's a desorption branch, plot it
-        if des and isotherm.has_branch('des'):
+        if des and iso_has_des:
             # Points
             x1_p, y1_p, x2_p, y2_p = _get_data(
                 isotherm,
@@ -313,15 +316,15 @@ def plot_iso(
                 range_params=range_params,
             )
             # Plot line 1
-            if branch == 'all' and 'branch' not in lgd_keys:
+            if branch == 'all' and 'branch' not in lgd_keys and iso_has_ads:
                 y1_lbl = ''
             else:
                 y1_lbl = label_lgd(isotherm, lgd_keys, 'des', y1_data)
             ax1.plot(x1_p, y1_p, label=y1_lbl, **y1_ls)
 
             # Plot line 2
             if y2_data and y2_p is not None:
-                if branch == 'all' and 'branch' not in lgd_keys:
+                if branch == 'all' and 'branch' not in lgd_keys and iso_has_ads:
                     y2_lbl = ''
                 else:
                     y2_lbl = label_lgd(isotherm, lgd_keys, 'des', y2_data)

src/pygaps/modelling/__init__.py

@@ -6,7 +6,7 @@
 
 If adding a custom model, it should be also added below as a string.
 """
-
+import typing as t
 import importlib
 
 from pygaps.utilities.exceptions import ParameterError
@@ -136,7 +136,7 @@ def is_model_class(model):
     return isinstance(model, IsothermBaseModel)
 
 
-def get_isotherm_model(model_name: str, params: dict = None):
+def get_isotherm_model(model_name: str, **params: dict):
     """
     Check whether specified model name exists and return an instance of that model class.
 
@@ -165,22 +165,22 @@ def get_isotherm_model(model_name: str, params: dict = None):
     pg_model_name = _MODELS[index]
     module = importlib.import_module(f"pygaps.modelling.{pg_model_name.lower()}")
     model = getattr(module, pg_model_name)
-    return model(params)
+    return model(**params)
 
 
 def model_from_dict(model_dict):
     """Obtain a model from a dictionary."""
-    return get_isotherm_model(model_dict.pop('name'), model_dict)
+    return get_isotherm_model(model_dict.pop('name'), **model_dict)
 
 
 def model_iso(
     isotherm,
-    branch='ads',
-    model=None,
-    param_guess=None,
-    param_bounds=None,
-    optimization_params=None,
-    verbose=False
+    branch: str = 'ads',
+    model: t.Union[str, t.List[str], t.Any] = None,
+    param_guess: dict = None,
+    param_bounds: dict = None,
+    optimization_params: dict = None,
+    verbose: bool = False,
 ):
     """
     Fits a PointIsotherm with a model.