bmcs-utils - pypi Package Compare versions

Comparing version 0.0.32a1 to 0.0.35a0

bmcs_utils.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: bmcs-utils
-Version: 0.0.32a1
+Version: 0.0.35a0
 Summary: Suite of utilities for to implementation of bmcs_utils for brittle-matrix composites.
@@ -5,0 +5,0 @@ Home-page: https://github.com/bmcs-group/bmcs_utils

bmcs_utils.egg-info/SOURCES.txt

@@ -1,17 +0,8 @@
-.gitignore
 README.md
-__init__.py
-bmcs_devel_environment.yml
-environment.yml
-main.py
-meta.yaml
-requirements.txt
 setup.py
 bmcs_utils/__init__.py
 bmcs_utils/api.py
-bmcs_utils/app_window.ipynb
 bmcs_utils/app_window.py
 bmcs_utils/app_window_example.py
 bmcs_utils/controller.py
-bmcs_utils/design.ipynb
 bmcs_utils/i_model.py
@@ -39,22 +30,7 @@ bmcs_utils/item.py
 bmcs_utils/demo/app_window.py
-bmcs_utils/demo/index.ipynb
 bmcs_utils/demo/layout_model.py
-bmcs_utils/demo/model_elementary.ipynb
-bmcs_utils/demo/model_notify_mixin.ipynb
-bmcs_utils/demo/model_raise_exception.ipynb
-bmcs_utils/demo/model_tree.ipynb
-bmcs_utils/demo/model_with_either_type_depends_on.ipynb
-bmcs_utils/demo/model_with_either_type_tree.ipynb
-bmcs_utils/demo/model_with_enum.ipynb
-bmcs_utils/demo/model_with_history_slider.ipynb
 bmcs_utils/demo/model_with_history_slider.py
-bmcs_utils/demo/model_with_instance_property.ipynb
-bmcs_utils/demo/model_with_list_editor.ipynb
-bmcs_utils/demo/model_with_progress_bar.ipynb
 bmcs_utils/demo/model_with_progress_bar.py
-bmcs_utils/demo/model_with_selector_depends_on.ipynb
-bmcs_utils/demo/model_with_volume.ipynb
 bmcs_utils/demo/model_with_volume.py
 bmcs_utils/demo/shape_model.py
-bmcs_utils/demo/tree_extract.ipynb
 bmcs_utils/editors/__init__.py
@@ -75,3 +51,2 @@ bmcs_utils/editors/dict_editor.py
 bmcs_utils/misc/__init__.py
-bmcs_utils/misc/exp_data_tools.py
 bmcs_utils/misc/plot_tools.py
@@ -87,22 +62,2 @@ bmcs_utils/trait_types/__init__.py
 bmcs_utils/trait_types/trait_types.py
-bmcs_utils/trait_types/weakref_type.py
-docs/README.md
-docs/distribution.md
-docs/jupyter_access.md
-docs/python_access.md
-docs/questions_and_answers.md
-docs/state_change_dependencies.md
-docs/webapp_access.md
-docs/images/my_python_packages.png
-docs/images/pycharm_project_interpreter_1.png
-docs/images/pycharm_project_interpreter_2.png
-figures/.~lock.S0602 - Energy dissipation.odp#
-figures/S0602 - Energy dissipation.odp
-notebooks/dynamic_widget_box.ipynb
-notebooks/implementation_of_interactive_model.ipynb
-notebooks/ipytree.ipynb
-notebooks/k3d_plot_test.ipynb
-notebooks/model_development_patterns.ipynb
-notebooks/sinus_interactive_plot_widget.ipynb
-notebooks/test_nbstripout.ipynb
-notebooks/theano_numpy_test.ipynb
+bmcs_utils/trait_types/weakref_type.py

bmcs_utils/__init__.py

@@ -0,0 +0,0 @@

bmcs_utils/api.py

@@ -20,4 +20,3 @@
     HistoryEditor, TextAreaEditor, IntRangeEditor, FloatSliderEditorSelector, FloatSliderEditor
-from bmcs_utils.misc.exp_data_tools import get_fw_curves_avg, get_asc_upper_env_ids, get_exp_fw_asc
-from bmcs_utils.misc.plot_tools import plot_colors, set_latex_mpl_format, get_color
+from bmcs_utils.misc.plot_tools import plot_colors, set_latex_mpl_format
 from bmcs_utils.parametric_study import ParametricStudy
@@ -27,2 +26,3 @@ from bmcs_utils.data_cache import data_cache
 from bmcs_utils.k3d_utils.k3d_utils import K3DUtils
+from bmcs_utils.symbol.cymbol import Cymbol, cymbols, ccode
 

bmcs_utils/app_window_example.py

@@ -0,0 +0,0 @@

bmcs_utils/app_window.py

@@ -64,4 +64,4 @@ '''
         self.plot_fig.layout = ipw.Layout(width="100%",height="100%")
-        with self.plot_widget:
-            self.plot_fig.display()
+        # with self.plot_widget:
+        #     self.plot_fig.display()
         self.plot_fig.outputs.append(self.plot_widget)
@@ -89,5 +89,4 @@ self.objects = {}
     def show_fig(self):
-        # calling self.plot_fig.display() here will add new k3d interface each time a parameter changes
-        pass
-
+        with self.plot_widget:
+            self.plot_fig.display()
     def setup_plot(self, model):
@@ -94,0 +93,0 @@ model.setup_plot(self)

bmcs_utils/controller.py

@@ -0,0 +0,0 @@ import traits.api as tr

bmcs_utils/data_cache/__init__.py

 
 from .data_cache import data_cache

bmcs_utils/data_cache/data_cache.py

@@ -0,0 +0,0 @@ #-------------------------------------------------------------------------

bmcs_utils/demo/app_window.py

@@ -0,0 +0,0 @@ """

bmcs_utils/demo/layout_model.py

@@ -0,0 +0,0 @@ from bmcs_utils.trait_types import \

bmcs_utils/demo/model_with_history_slider.py

@@ -0,0 +0,0 @@ from bmcs_utils.trait_types import \

bmcs_utils/demo/model_with_progress_bar.py

@@ -0,0 +0,0 @@ from bmcs_utils.trait_types import \

bmcs_utils/demo/model_with_volume.py

@@ -0,0 +0,0 @@ from bmcs_utils.trait_types import \

bmcs_utils/demo/shape_model.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/__init__.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/dict_editor.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/editor_factory.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/editors.py

@@ -275,4 +275,3 @@ import traits.api as tr
             tooltip=self.tooltip,
-            icon=self.icon,  # (FontAwesome names without the `fa-` prefix)
-            style=style,
+            icon=self.icon  # (FontAwesome names without the `fa-` prefix)
         )
@@ -279,0 +278,0 @@

bmcs_utils/editors/either_type_editor.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/enum_type_editor.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/float_range_slider_editor.py

@@ -0,0 +0,0 @@ import traits.api as tr

bmcs_utils/editors/history_editor.py

@@ -18,6 +18,6 @@
     max_value = tr.Float(1)
-    step_value = tr.Float(0.01)
+    step = tr.Float(0.01)
     min_var = tr.Str('')
     max_var = tr.Str('')
-    step_var = tr.Str('')
+    step = tr.Str('')
 
@@ -47,6 +47,6 @@ tooltip = tr.Property(depends_on='time_var, time_max_var')
     def _get_step(self):
-        if self.step_var == '':
-            step = self.step_value
+        if self.step == '':
+            step = self.step
         else:
-            step = getattr(self.model, str(self.step_var))
+            step = getattr(self.model, str(self.step))
         return step
@@ -62,8 +62,10 @@
         var = str(self.var).split('.')[-1]
-        eta = (getattr(self.submodel, var) - self.t_min) / (self.t_max - self.t_min)
+        t_span = self.t_max - self.t_min
+        eta = (getattr(self.submodel, var) - self.t_min) / t_span
+        t_value = eta * t_span + self.t_min
         self.history_slider = ipw.FloatSlider(
             value=eta,
-            min=0,
-            max=1,
-            step=self.step,
+            min=self.t_min,
+            max=self.t_max,
+            step=0.01 * t_span,
             tooltip=self.tooltip,
@@ -70,0 +72,0 @@ continuous_update=False,

bmcs_utils/editors/instance_editor.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/list_editor.py

@@ -0,0 +0,0 @@

bmcs_utils/editors/progress_editor.py

@@ -0,0 +0,0 @@

bmcs_utils/i_model.py

@@ -0,0 +0,0 @@

bmcs_utils/item.py

@@ -21,6 +21,5 @@
             editor = self.editor
+        elif trait.trait_type.editor_factory is None:
+            raise TypeError(f'no editor attribute {self.name} in {model}, maybe not declared?')
         else:
-            # create a new edior using the factory provided by the trait type
-            if trait.trait_type.editor_factory is None:
-                raise TypeError('no editor for %s with type %s' % (self.name,trait.trait_type) )
             editor = trait.trait_type.editor_factory()
@@ -31,12 +30,4 @@ # use the editor supplied in the item defintion and set its attributes
         if not editor.label:
-            if self.latex:
-                editor.label = r'\(%s\)' % self.latex
-            else:
-                editor.label = self.name
-
-        desc = trait.desc
-        if desc:
-            editor.tooltip = desc
-        else:
-            editor.tooltip = self.name
+            editor.label = r'\(%s\)' % self.latex if self.latex else self.name
+        editor.tooltip = desc if (desc := trait.desc) else self.name
         editor.value = value
@@ -43,0 +34,0 @@ editor.trait = trait

bmcs_utils/k3d_utils/extrusion_for_3d_curve.py

@@ -0,0 +0,0 @@ """

bmcs_utils/k3d_utils/k3d_utils.py

@@ -0,0 +0,0 @@ import bmcs_utils.api as bu

bmcs_utils/misc/plot_tools.py

 import matplotlib.pyplot as plt
-import numpy as np
 
-plot_colors = ['#000000',
-               '#bc2122',
-               '#1f77b4',
-               '#ff7f0e',
-               '#2ca02c',
-               '#9467bd',
-               '#8c564b',
-               '#e377c2',
-               '#7f7f7f',
-               '#17becf']
-i_color = 0
+plot_colors = ['#000000', '#bc2122', '#55679e', '#69b628', '#dacf2f', '#ff6600']
 
-def set_latex_mpl_format(font_size = 15):
+
+def set_latex_mpl_format():
     plt.rcParams["font.family"] = "Times New Roman"
-    plt.rcParams["font.size"] = font_size
+    plt.rcParams["font.size"] = 15
     # To have math like LaTeX
     plt.rcParams['mathtext.fontset'] = 'cm'
     plt.rcParams['mathtext.rm'] = 'serif'
-
-    # To save svg fonts as fonts and not paths
-    plt.rcParams['svg.fonttype'] = 'none'
-
-def get_color():
-    global i_color
-    color = plot_colors[i_color] if i_color < len(plot_colors) else np.random.rand(3)
-    i_color += 1
-    return color

bmcs_utils/model_dict.py

@@ -12,4 +12,3 @@
     def __setitem__(self, key, value):
-        old_value = self.items.get(key, None)
-        if old_value:
+        if old_value := self.items.get(key, None):
             old_value.parents.remove(self)
@@ -19,3 +18,3 @@ value.name = str(key)
         value.parents.add(self)
-        self.notify_graph_change('Notification from child %s' % 'item')
+        self.notify_graph_change('Notification from child item')
 
@@ -26,3 +25,3 @@ def __delitem__(self, key):
         del self.items[key]
-        self.notify_graph_change('Notification from child %s' % 'item')
+        self.notify_graph_change('Notification from child item')
 
@@ -29,0 +28,0 @@ def __getitem__(self, key):

bmcs_utils/model_list.py

@@ -0,0 +0,0 @@

bmcs_utils/model_notify_mixin.py

@@ -25,5 +25,3 @@
             value = getattr(self, name, None)
-            # print('name', name, self.__class__, trait_type, value)
-            post_setattr = getattr(trait_type, 'post_setattr', None)
-            if post_setattr:
+            if post_setattr := getattr(trait_type, 'post_setattr', None):
                 post_setattr(self, name, value)
@@ -44,3 +42,3 @@ #                trait_type.post_setattr(self, name, value)
 
-    _state_change_debug = tr.Bool(False)
+    x_state_change_debug = tr.Bool(False)
 
@@ -50,3 +48,3 @@ state_change_debug = tr.Property(tr.Bool)
     def _get_state_change_debug(self):
-        if self._state_change_debug == True:
+        if self.x_state_change_debug == True:
             return True
@@ -58,4 +56,15 @@ for parent in self.parents:
     def _set_state_change_debug(self, value=True):
-        self._state_change_debug = value
+        self.x_state_change_debug = value
 
+    # def __getstate__(self):
+    #     """Customized getstate for correct serialization."""
+    #     state = super().__getstate__()
+    #     # Include private attributes explicitly
+    #     return state, self.x_state_change_debug
+
+    # def __setstate__(self, state):
+    #     """Customized setstate for correct deserialization."""
+    #     base_state, self.x_state_change_debug = state
+    #     super().__setstate__(base_state)
+
     @tr.observe('+TIME,+MESH,+MAT,+CS,+BC,+ALG,+FE,+DSC,+GEO,+ITR')
@@ -97,3 +106,3 @@ def notify_value_change(self, event):
             if parent: # ignore if parent is garbage collected
-                parent.notify_graph_change('Notification from child %s' % self)
+                parent.notify_graph_change(f'Notification from child {self}')
 
@@ -103,3 +112,3 @@ def notify_parents_value_changed(self):
             if parent: # ignore if parent is garbage collected
-                parent.notify_value_change('Notification from child %s' % self)
+                parent.notify_value_change(f'Notification from child {self}')
 
@@ -106,0 +115,0 @@ def __del__(self):

bmcs_utils/model_tree_node_mixin.py

@@ -24,2 +24,4 @@
             trait = self.trait(name)
+            if trait is None:
+                raise TypeError(f'trait with {name} not defined in {self}')
             trait_type = trait.trait_type
@@ -29,3 +31,3 @@ name_ = trait_type.get_name_(name)
             if trait_ is None:
-                raise ValueError('trait %s not found in %s' % (name_, self))
+                raise ValueError(f'trait {name_} not found in {self}')
             submodels.append(trait_)
@@ -32,0 +34,0 @@ return submodels

bmcs_utils/model.py

@@ -34,3 +34,3 @@
         else:
-            raise NameError(self.plot_backend + ' is not a valid plot_backend!')
+            raise NameError(f'{self.plot_backend} is not a valid plot_backend!')
 
@@ -37,0 +37,0 @@ def plot(self, axes):

bmcs_utils/mpl_utils.py

@@ -0,0 +0,0 @@ '''

bmcs_utils/parametric_study.py

@@ -0,0 +0,0 @@ import numpy as np

bmcs_utils/symb_expr_quad_example.py

@@ -0,0 +0,0 @@ import sympy as sp

bmcs_utils/symb_expr.py

@@ -39,7 +39,11 @@ '''
 
+    # expression reduction for lambdify 
+    cse = tr.Bool(False)
+
     # @todo [RC]: check if the model can be taken from the reference
     def get_model_params(self):
-        return tuple([
-            getattr(self.model,param_name) for param_name in self.symb_model_params
-        ])
+        return tuple(
+            getattr(self.model, param_name)
+            for param_name in self.symb_model_params
+        )
 
@@ -49,7 +53,9 @@ def __init__(self, *args, **kw):
         # gather the symbols and construct an ordered tuple
-        default_symbols = tuple([getattr(self, sym_name) for sym_name in self.symb_variables])
+        default_symbols = tuple(
+            getattr(self, sym_name) for sym_name in self.symb_variables
+        )
         for expression in self.symb_expressions:
             if isinstance(expression, Iterable):
                 expr_name, sym_names = expression
-                symbols = tuple([getattr(self, sym_name) for sym_name in sym_names])
+                symbols = tuple(getattr(self, sym_name) for sym_name in sym_names)
             elif isinstance(expression, str):
@@ -62,8 +68,10 @@ expr_name = expression
                 )
-            param_symbols = tuple([getattr(self, model_param)
-                                   for model_param in self.symb_model_params])
+            param_symbols = tuple(
+                getattr(self, model_param)
+                for model_param in self.symb_model_params
+            )
             expr = getattr(self, expr_name)
             # print('defining', expr_name, ':', symbols+param_symbols)
-            callable = sp.lambdify(symbols+param_symbols, expr, 'numpy')
-#            callable = sp.lambdify(symbols, expr, 'numpy', dummify=True)
+            callable = sp.lambdify(symbols+param_symbols, expr, 'numpy',
+                                   cse=self.cse)
             def define_callable(callable):
@@ -79,7 +87,5 @@ def on_the_fly(*args):
                 return on_the_fly
-            self.add_trait(
-                'get_' + expr_name, tr.Callable(define_callable(callable))
-#                lambda *args: callable(*(args+self.get_model_params(self.model)))
-            )
 
+            self.add_trait(f'get_{expr_name}', tr.Callable(define_callable(callable)))
+
 class InjectSymbExpr(tr.HasStrictTraits):
@@ -97,5 +103,1 @@ '''
         self.symb = self.symb_class(model = self)
-
-    # def traits_init(self):
-    #     self.symb = self.symb_class(model = self)
-    #

bmcs_utils/trait_types/__init__.py

@@ -0,0 +0,0 @@

bmcs_utils/trait_types/dict_type.py

@@ -0,0 +0,0 @@ #-------------------------------------------------------------------------

bmcs_utils/trait_types/either_type.py

@@ -0,0 +0,0 @@ #-------------------------------------------------------------------------

bmcs_utils/trait_types/either_type2.py

@@ -0,0 +0,0 @@ # -------------------------------------------------------------------------

bmcs_utils/trait_types/enum_type.py

@@ -0,0 +0,0 @@ #-------------------------------------------------------------------------

bmcs_utils/trait_types/instance_type.py

@@ -0,0 +0,0 @@

bmcs_utils/trait_types/list_type.py

@@ -0,0 +0,0 @@ #-------------------------------------------------------------------------

bmcs_utils/trait_types/selector_type.py

@@ -0,0 +0,0 @@ # -------------------------------------------------------------------------

bmcs_utils/trait_types/trait_types.py

@@ -0,0 +0,0 @@ import traits.api as tr

bmcs_utils/trait_types/weakref_type.py

@@ -0,0 +0,0 @@

bmcs_utils/tree_node.py

@@ -0,0 +0,0 @@

bmcs_utils/version.py

@@ -1,1 +0,1 @@
-__version__='0.0.32a1'
+__version__='0.0.35a'

bmcs_utils/view.py

@@ -0,0 +0,0 @@

PKG-INFO

 Metadata-Version: 2.1
 Name: bmcs_utils
-Version: 0.0.32a1
+Version: 0.0.35a0
 Summary: Suite of utilities for to implementation of bmcs_utils for brittle-matrix composites.
@@ -5,0 +5,0 @@ Home-page: https://github.com/bmcs-group/bmcs_utils

README.md

@@ -0,0 +0,0 @@

setup.cfg

@@ -0,0 +0,0 @@ [egg_info]

setup.py

@@ -0,0 +0,0 @@ #!/usr/bin/env python

__init__.py

.gitignore

-MANIFEST
-build
-dist
-_build
-docs/man/*.gz
-docs/source/api/generated
-docs/source/config.rst
-docs/gh-pages
-notebook/i18n/*/LC_MESSAGES/*.mo
-notebook/i18n/*/LC_MESSAGES/nbjs.json
-notebook/static/components
-notebook/static/style/*.min.css*
-notebook/static/*/js/built/
-notebook/static/*/built/
-notebook/static/built/
-notebook/static/*/js/main.min.js*
-notebook/static/lab/*bundle.js
-node_modules
-*.py[co]
-__pycache__
-*.egg-info
-*~
-*.bak
-.ipynb_checkpoints
-.tox
-.DS_Store
-\#*#
-.#*
-.coverage
-.pytest_cache
-src
-
-*.swp
-*.map
-.idea/
-Read the Docs
-config.rst
-*.iml
-/.project
-/.pydevproject
-
-package-lock.json
-geckodriver.log
-*.iml
-

bmcs_devel_environment.yml

-name: bmcs_env
-channels:
-- conda-forge
-dependencies:
-- jupyterlab
-- traits>=6.1.1
-- traitsui==7.1.0
-- matplotlib-base
-- numpy
-- sympy
-- k3d
-- ipywidgets
-- ipympl
-- ipytree
-- ipyregulartable
-- k3d
-- pip
-- pip:
-  - -e ./bmcs_utils
-  - -e ./bmcs_ibvpy
-  - -e ./bmcs_matmod
-  - -e ./bmcs_cross_section
-  - -e ./bmcs_shear_zone
-  - -e ./bmcs_beam
-  - -e ./bmcs_expsim

bmcs_utils/misc/exp_data_tools.py

-import numpy as np
-
-def get_fw_curves_avg(fw_curves_list, ax=None):
-    """
-    fw_curves_list: [fw_numpy_array, fw_numpy_array, ...] where fw_numpy_array has the shape (data_length, 2)
-    """
-    fw_curves_list = [fw.astype(np.float64) for fw in fw_curves_list]
-    w_list = [fw[:, 1] for fw in fw_curves_list]
-    f_list = [fw[:, 0] for fw in fw_curves_list]
-    max_len = np.max([fw.shape[0] for fw in fw_curves_list])
-    w_max_list = np.array([np.nanmax(w) for w in w_list])
-    w_avg_max = np.average(w_max_list)
-    w = np.linspace(0, w_avg_max, max_len)
-    w_scaled_list = [w_ * w_avg_max / w_max for w_, w_max in zip(w_list, w_max_list)]
-    f_scaled_list = np.array([np.interp(w, w_scaled, f) for w_scaled, f in zip(w_scaled_list, f_list)])
-    f = np.average(f_scaled_list, axis=0)
-
-    if ax is not None:
-        ax.plot(w, f, color='gray')
-    return f, w
-
-
-def get_asc_upper_env_ids(arr):
-    """
-    Useful to get the upper envelope of load-displacement curve (representing load-controlled variant)
-    arr: one dimentional numpy array (typically with positive elements)
-    returns: for example, given the array [2, 1, 0, -5, 5, 3, 9, 10], the ids of [2, 5, 9, 10] will be returned
-    """
-    max_ = arr[0]
-    upper_env_ids = [0]
-    for i, value in enumerate(arr):
-        if value > max_:
-            max_ = value
-            upper_env_ids.append(i)
-    return np.array(upper_env_ids)
-
-
-def get_exp_fw_asc(fw):
-    f_upper_env_ids = get_asc_upper_env_ids(fw[0])
-    return fw[0][f_upper_env_ids].astype(np.float_), fw[1][f_upper_env_ids].astype(np.float_)

docs/distribution.md

-
-# Distribution management
-
-To be able to release versions and to upload
-to the pypi and conda repositories 
-following packages are required
-
- - twine - to upload to pypi 
-    ```
-    conda install -c conda-forge twine
-    ```
- - conda-build - to provide tha package on the conda repository
- - anaconda-client - to be able to upload the package to anaconda cloud
-
-
-# Uploading and releasing your package
-
-@todo: this requires an access to the pypi
-account - a bmcs-group pypi account needs to be setup.
-
-# Installation of a pypi package in your environment 
-
-Released package can be installed in the 
- current environment. using the command
-```
-pip install my_bmcs_package
-```
-The old package will be uninstalled 
-from the environment and replaced by the released package.

docs/jupyter_access.md

-
-# Jupyter interface / Researcher's perspective
-
-## Install miniconda
-
-The packages used in the development of the BMCS tool 
-suite can be conveniently accessed from within the 
-miniconda minimal setup. The installation of miniconda for 
-all platforms is provided here:
-
-https://docs.conda.io/en/latest/miniconda.html
-
-## Install BMCS packages 
- 
-Download the package specification file
-`bmcs_env.yml` 
-
-Run the setup of the environment by issuing
-```
-conda env create -f bmcs_env.yml
-```
-If you wish to update your environment later you can issue
-```
-conda env update -f bmcs_env.yml
-```
-
-## Activate `bmcs_env` environment 
-
-The list of available environments can be obtained by issuing
-```
-conda env list
-```
-Activate the new environment using
-```
-conda activate bmcs_env
-```
-
-The package(s) specified in the `environment.yml`
-are now installed locally in the `bmcs_env` and
-can be imported if this environment is active.
-This can be checked by starting the `python` interpreter
-with the `bmcs_env` environment active and testing
-```
-import bmcs_utils.api as bu
-```
-
-## Setup and configure Jupyter
-
-To be able to import them, the runtime configuration in Jupyter and Pycharm
-projects have to be configured with this environment.
-
-1) register the newly created `bmcs_env` environment as
-   a jupyter kernel y ussuing
-   ```shell script
-   pytom -m ipykernel install --user --name=bmcs_env
-   ```
-2) start the jupyter notebook, by issuing
-   ```shell script
-   jupyter notebook
-   ```
-   navigate to
-   the menu `Kernel -> Change kernel` and select 
-   the `bmcs_env` kernel as the active kernel. The 
-   kernel name will be displaed at the top right corner
-   of the notebook
-
-## Enable notebook extensions 
-It is recommended to use the notebook extensions that 
-include useful features. The extensions have 
-already been installed using `environment.yml`.
-The particular choice depends on personal preference
-and the context of usage. Recommended extensions
-are:
-
-- table of contents which is useful for long 
-  noteboks explaining the model derivation
-- RISE: which can convert the notebook to a slide 
-  presentation
-- appmode: that converts the notebook to an interactive
-  web application
-
-# Access jupyter notebooks
-
-It is important to note, that only python files are installed
-in the `bmcs_env`  - no jupyter notebooks. Thus, they
-are provided just like `numpy` or `matplotlib` for
-further use in the development of further packages.
-In this way, the deployment of the webapps
-on jupyterhub or binder is solved - since it is possible
-to define the environment which automatically
-installed all the required packages on demand
-from the global conda and pypi repos.
-
-Packaging of jupyter notebooks is a separate problem.
-We use them for several different purposes: 
-
-- prototyping code (Phase 1)
-- verification code for python modules - that's what (Phase 2)
-- documentation with interactive examples (Phase 3)
-- presentations - RISE package (Phase 3)
-- webapps - appmode (Phase 3)
-
-Thus, in Phases 1 and 2 the notebooks are
-within the development directory. The phase 3
-is the dissemination of the implemented functionality
-in three different ways.
-
-## Plotting using matplotlib
-
-Matplotlib provides a front end that can be 
-combined with the `ipywidgets` to integrate the 
-figures within a layout of widgets. To use this 
-feature, the notebook must start with the magic command
-```
-%matplotlib widget
-```
-This feature is implemented in the `ipympl` package
-which is automatically included in the environment 
-after the setup. Further instructions to this package 
-are included here:
-https://github.com/matplotlib/ipympl
-
-## Version control for jupyter notebooks 
-
-If the jupyter notebooks are pushed to the github
-repository it is necessary to strip out the 
-output cells to avoid uneceesary conflicts of 
-versions.
-
-### How to activate `nbstripout`
-
-Stripping Jupyter output cells and execution 
-count out while pushing to Git
-
-In Anaconda command prompt execute the following commands
-1. Install `nbstripout` tool:\
-`conda install -c conda-forge nbstripout`
-
-2. Activate the tool on global Git configuration so it work on all your local repositories using
-   * **Windows**\
-   ```
-    mkdir %USERPROFILE%\.config\git
-    nbstripout --install --global --attributes=%USERPROFILE%\.config\git\attributes
-    ```
-
-   * **Linux**\
-   ```
-    mkdir -p ~/.config/git
-    nbstripout --install --global --attributes=~/.config/git/attributes
-   ```
-
-Now, when you **push** a Jupyter Notebook file, 
-the `nbstripout` tool will tell Git to ignore 
-the output cells and the execution count numbers, leaving your local Jupyter file unchanged. It will enable you to push a clean Jupyter file to the repository.
-
-### How does `nbstripout` work?
-
-The tool adds a Git filter to these files\
-`USER_HOME_DIRECTORY\.config\git\attributes`\
-`USER_HOME_DIRECTORY\.gitconfig`\
-which strips output cells and execution count out for Jupyter files.
-
-For more info: https://github.com/kynan/nbstripout

docs/python_access.md

-
-# Python interface / Developer perspective
-
-## Git
-
-Install the git package. 
-For linux use:
-
-sudo apt-get install git
-
-For windows use:
-
-@todo: please add  
-
-## PyCharm
-
-register and pickup the professional academic free version
-https://www.jetbrains.com/pycharm/download
-
-Follow the instructions there to install it.
-
-## Clone bmcs repositories 
-
-Start pycharm. In the introductory window select 
-- open from version control system. Register using the github.com
-credentials. Clone the repository
-
-bmcs-group/bmcs_utils
-
-## Setup the development package
-
-Each of the `bmcs` packages contains the  
-`environment.yml` and the `setup.py` file 
-in its root directory
-
-By issuing the command
-```
-pip install -e .
-```
-your local source code package directory will 
-be integrated into the `bmcs_env`
-environment. 
-Check to see that it is the case by issuing
-```
-import sys
-print(sys.path)
-```
-The current package directory should be included in the list. 
-This approach has the advantage that your workspace is 
-treated in the same way as packages comming from pypi 
-repository. This makes the import paths universally 
-valid in differnt usage modes:
-[Research access](jupyter_access.md), 
-[Python access](python_access.md).
-
-Moreover, it is used also in the deployed 
-installation on a remote service like 
-binder launched from the `github` repository.
-This can be seen in the `environment.yml` which 
-specifies the required
-packages. Note the last entry in this dependency:
-specifying `-e .`
-```
-name: bmcs_env
-channels:
-- conda-forge
-dependencies:
-# required conda packages
-- pip:
-  - -e .
-```
-The entry `-e .` means that 
-The `environment.yml` specification is 
-used if the repository is installed in remote services,
-e.g. on `binder`.
-
-
-# Configure Jupyter
-
-To use and modify the jupyter notebooks in your installation
-access setup the jupyter environment as described in 
-[Jupyter access](jupyter_access.md)
-
-# Configure Pycharm
-
-- In PyCharm - the correct interpreter from `bmcs_env` must be taken -
-  in File->Settings->Build->Interpreter
-

docs/questions_and_answers.md

-
-# Lifecycle of a package
-
-In case of development installation, the import 
-path must be set within the current conda environment.
-
-In case of application installation, the pip dependency
-management is used to install the required 
-packages on demand.   
-

docs/README.md

-
-# BMCS development process
-
-The BMCS tool suite consists of a packages
-that are developed in parallel.
-The  `bmcs_utils` is used by any other package.
-
-It provides the following functionality:
-
- - Infrastructure for the definition and composition 
-   of model components to quickly obtain an interactive 
-   jupyter user interface.
-   
- - Systematic mapping from symbolic expressions
-   derived during the model construction using `sympy`
-   to model classes.
-   
- - Infrastructure for persistent data management in 
-   the `db_cache` directory.
-   
-By using the `bmcs_utils` as the platform for the model
-implementation, the BMCS model components provide 
-a transparent mapping between their interactive features
-as they appear in the user interface and their internal 
-structure, implementation and theoretical background.
-
-The developed models are accessible in three perspectives.
-The aim is to provide a seamless transition between the 
-individual perspectives to the code. The first perspective
- provides a simple interaction with the model 
-via the webapp interface. It presents the functionality and 
-features of the model to a (Visitor/Reader/User). 
-
-Deeper explanation of the model features in presented in
-form of jupyter notebooks accompanying every 
-model component. These notebooks demonstrate the model
-functionality and  can be modfied and extended by the 
-user to get deeper insight into the model behavior, into the 
-modeled phenomena. Then, they can be used to interpret
-expermental data and to perform parameteric studies.
-
-To develop own model components the open source code can be
-cloned using the git versioning control system. The repositories
-are available on `github` in the organization 
-named `bmcs-group`. 
-
-# Summary of interfaces and roles:
-
- - [**Webapp interface (student/reader):**](webapp_access.md) via web browser by accessing a remote server.
-   either in a `jupyterhub` or using  `binder` service. This
-   mode is inteded for casual readers and student classes 
-   that do not need to install anything on their local computer 
-   and can directly start to interact with the models via 
-   remote webapps.
-   
- - [**Jupyter interface (researcher)**](jupyter_access.md) To perform intensive studies of the models, 
-   model calibrations based on experimental data and 
-   parametric studies the BMCS packages can be installed locally. Included Jupyter notebooks provide the starting 
-   point for modifications and processing of data.
-   
- - [**Python interface (developer)**](python_access.md) Development of Python code supporting the 
-   Jupyter notebooks requires the developer setup with an access
-   to the `github server` and a development environment. Currently
-   `Pycharm` IDE is being used in the development 
-   of BMCS tool suite.
-
- - [**Packaging interface (administrator)**](distribution.md) 
-   Build and upload packages to repositories 
-   (pypi, conda)

docs/state_change_dependencies.md

-
-# Introduce dependencies between state variables
-
-Assume two model components defined as follows
-
-```python
-import bmcs_utils.api as bu
-import traits.api as tr
-
-
-class M1(bu.Model):
-    length = bu.Float(10, GEO=True)
-
-
-class M2(bu.Model):
-    m1 = tr.Instance(M1, ())
-
-    a = tr.Property(depends_on='+GEO')
-
-    @tr.cached_property
-    def _get_a(self):
-        return self.m1.length ** 2
-
-```
-to ensure a consistent state of the model
-in a running application model traits are 
-categorized using the tags specifying 
-the kind of information that the model parameter
-delivers. Following tags are predefined
-```
-GEO, BC, DSC, ALG, INT, TIME
-```
-When defining derived properties of the model 
-components, these tags are used to handle 
-the changes upwards in the hierarchy.
-
-The model tree structure is extracted by 
-traversing the base classes. Each subclass
-of `InteractiveModel` contains the events 
-`_TAG` which can be included in the local 
-definition of properties and observers 
-in the local class definition. 

docs/webapp_access.md

-
-# Webapp interface / Browser perspective
-
- - bmcs

environment.yml

-name: bmcs_env
-channels:
-- conda-forge
-dependencies:
-- appmode
-- jupyter_contrib_nbextensions
-- traits>=6.1.1
-- matplotlib-base==3.4.3
-- numpy
-- sympy
-- k3d
-- ipywidgets==7.6.6
-- ipympl==0.9.2
-- ipytree==0.2.2
-- ipyregulartable
-- pip
-- pip:
-  - -e .

main.py

meta.yaml

-{% set name = "bmcs_utils" %}
-{% set version = "0.0.15a0" %}
-
-package:
-  name: "{{ name|lower }}"
-  version: "{{ version }}"
-
-source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 0b3d050b0f040d22c43a0dec5a617f8631b858ed4a6a4122b48cd3e77a6837f5
-
-build:
-  number: 0
-  script: "{{ PYTHON }} -m pip install . -vv"
-
-requirements:
-  host:
-    - pip
-    - python
-  run:
-    - python
-
-test:
-  imports:
-    - bmcs_utils
-
-about:
-  home: "https://github.com/bmcs-group/bmcs_utils"
-  license: MIT
-  license_family: MIT
-  license_file: 
-  summary: "Suite of utilities for to implementation of bmcs_utils for brittle-matrix composites."
-  doc_url: 
-  dev_url: 
-
-extra:
-  recipe-maintainers:
-    - your-github-id-here

requirements.txt

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Worsened metrics

Total package byte prevSize

120548

-89.1%

Number of package files

62

-42.06%

Lines of code

2876

-1.64%