Merge pull request #28 from ipqa-research/27-get-rid-of-problematic-s…

…tructures 27 get rid of problematic structures
ipqa-research · Oct 20, 2024 · f93f355 · f93f355
2 parents 7c75a8f + 010886e
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diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,6 @@
 .vscode
+docs/source/tutorial/database
+docs/source/tutorial/figure.svg
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 ![logo](logo.png)
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ipqa-research/ugropy/main)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ipqa-research/ugropy/blob/main/docs/source/tutorial/easy_way.ipynb)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://tldrlegal.com/license/mit-license)
 ![Python 3.10+](https://img.shields.io/badge/Python-3.10%2B-blue)
 [![Docs](https://img.shields.io/badge/docs%20-%20green?style=flat&label=Sphinx&link=https%3A%2F%2Fipqa-research.github.io%2Fugropy%2Findex.html)](https://salvadorbrandolin.github.io/ugropy/)
@@ -22,11 +22,9 @@ molecules that `ugropy` fails solving the subgroups of a model is very helpful.
 OS.
 
 # Try ugropy now
-You can try ugropy from its
-[Binder](https://mybinder.org/v2/gh/ipqa-research/ugropy/main). Open the
-binder.ipynb file to explore the basic features.
+You can try `ugropy` without installing it by clicking on the Colab badge.
 
-# Models supported v2.0.7
+# Models implemented
 - Classic liquid-vapor UNIFAC
 - Predictive Soave-Redlich-Kwong (PSRK)
 - Joback
@@ -93,19 +91,15 @@ print(f"{limonene.joback.vapor_pressure(176 + 273.15)} bar")
 Visualize your results! (The next code creates the `ugropy` logo)
 
 ```Python
-from IPython.display import SVG
-
 mol = Groups("CCCC1=C(COC(C)(C)COC(=O)OCC)C=C(CC2=CC=CC=C2)C=C1", "smiles")
 
-svg = mol.unifac.draw(
+mol.unifac.draw(
     title="ugropy",
     width=800,
     height=450,
     title_font_size=50,
     legend_font_size=14
 )
-
-SVG(svg)
 ```
 
 Write down the [Clapeyron.jl](https://github.com/ClapeyronThermo/Clapeyron.jl)
@@ -132,15 +126,15 @@ Obtain the [Caleb Bell's Thermo](https://github.com/CalebBell/thermo) subgroups
 ```python
 from ugropy import unifac
 
-names = ["hexane", "2-butanone"]
+names = ["hexane", "ethanol"]
 
 grps = [Groups(n) for n in names]
 
 [writers.to_thermo(g.unifac.subgroups, unifac) for g in grps]
 ```
 
 ```
-[{1: 2, 2: 4}, {1: 1, 2: 1, 18: 1}]
+[{1: 2, 2: 4}, {1: 1, 2: 1, 14: 1}]
 ```
 
 ## Installation

diff --git a/binder.ipynb b/binder.ipynb
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -13,5 +13,7 @@ ipython
 
 matplotlib
 
+pytest
+
 thermo >= 0.2.27
 toml
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -44,6 +44,9 @@
 # =============================================================================
 # EXTRA CONF
 # =============================================================================
+# nbsphinx
+nbsphinx_execute = "always"
+
 autodoc_member_order = "bysource"
 
 bibtex_bibfiles = ["refs.bib"]
@@ -72,10 +75,8 @@
 """Configuration Module."""
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-import sphinx_rtd_theme
 
 html_theme = "sphinx_rtd_theme"
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

diff --git a/docs/source/constants.rst b/docs/source/constants.rst
@@ -0,0 +1,7 @@
+constants
+=========
+
+.. automodule:: ugropy.constants
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/checks.rst b/docs/source/core/checks.rst
@@ -0,0 +1,7 @@
+Checks
+======
+
+.. automodule:: ugropy.core.checks
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/base/fragmentation_model.rst b/docs/source/core/frag_classes/base/fragmentation_model.rst
@@ -0,0 +1,7 @@
+FragmentationModel
+==================
+
+.. automodule:: ugropy.core.frag_classes.base.fragmentation_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/base/fragmentation_result.rst b/docs/source/core/frag_classes/base/fragmentation_result.rst
@@ -0,0 +1,7 @@
+FragmentationModelResult
+========================
+
+.. automodule:: ugropy.core.frag_classes.base.fragmentation_result
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/base/init.rst b/docs/source/core/frag_classes/base/init.rst
@@ -0,0 +1,13 @@
+Base fragmentation Class
+========================
+
+.. automodule:: ugropy.core.frag_classes.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 1
+
+   fragmentation_model
+   fragmentation_result
diff --git a/docs/source/core/frag_classes/gibbs_model/gibbs_model.rst b/docs/source/core/frag_classes/gibbs_model/gibbs_model.rst
@@ -0,0 +1,7 @@
+Gibbs Model
+===========
+
+.. automodule:: ugropy.core.frag_classes.gibbs_model.gibbs_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/gibbs_model/gibbs_result.rst b/docs/source/core/frag_classes/gibbs_model/gibbs_result.rst
@@ -0,0 +1,7 @@
+Gibbs Fragmentation Result
+==========================
+
+.. automodule:: ugropy.core.frag_classes.gibbs_model.gibbs_result
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/gibbs_model/init.rst b/docs/source/core/frag_classes/gibbs_model/init.rst
@@ -0,0 +1,13 @@
+Gibbs Fragmentation Model
+=========================
+
+.. automodule:: ugropy.core.frag_classes.gibbs_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 1
+
+   gibbs_model
+   gibbs_result
diff --git a/docs/source/core/frag_classes/init.rst b/docs/source/core/frag_classes/init.rst
@@ -0,0 +1,14 @@
+Fragmentation Classes
+=====================
+
+.. automodule:: ugropy.core.frag_classes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 1
+
+   base/init
+   gibbs_model/init
+   joback_model/init
diff --git a/docs/source/core/frag_classes/joback_model/init.rst b/docs/source/core/frag_classes/joback_model/init.rst
@@ -0,0 +1,14 @@
+Joback Model
+============
+
+.. automodule:: ugropy.core.frag_classes.joback
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. toctree::
+   :maxdepth: 1
+
+   joback_model
+   joback_result
diff --git a/docs/source/core/frag_classes/joback_model/joback_model.rst b/docs/source/core/frag_classes/joback_model/joback_model.rst
@@ -0,0 +1,7 @@
+Joback Fragmentation Model
+==========================
+
+.. automodule:: ugropy.core.frag_classes.joback.joback_model
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/core/frag_classes/joback_model/joback_result.rst b/docs/source/core/frag_classes/joback_model/joback_result.rst
@@ -0,0 +1,7 @@
+Joback Fragmentation Result
+===========================
+
+.. automodule:: ugropy.core.frag_classes.joback.joback_result
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/core/get_rdkit_object.rst b/docs/source/core/get_rdkit_object.rst
@@ -0,0 +1,7 @@
+get rdkit object
+================
+
+.. automodule:: ugropy.core.get_rdkit_object
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/ilp_solvers/default_solver.rst b/docs/source/core/ilp_solvers/default_solver.rst
@@ -0,0 +1,7 @@
+Default solver
+==============
+
+.. automodule:: ugropy.core.ilp_solvers.default_solver
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/ilp_solvers/ilp_solver.rst b/docs/source/core/ilp_solvers/ilp_solver.rst
@@ -0,0 +1,7 @@
+ILP solver
+==========
+
+.. automodule:: ugropy.core.ilp_solvers.ilp_solver
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/ilp_solvers/init.rst b/docs/source/core/ilp_solvers/init.rst
@@ -0,0 +1,13 @@
+ILP solvers
+===========
+
+.. automodule:: ugropy.core.ilp_solvers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 1
+
+   ilp_solver
+   default_solver
diff --git a/docs/source/core/init.rst b/docs/source/core/init.rst
@@ -0,0 +1,16 @@
+Core
+====
+
+.. automodule:: ugropy.core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 1
+
+   checks
+   get_rdkit_object
+   ilp_solvers/init
+   frag_classes/init
+
diff --git a/docs/source/groups.rst b/docs/source/groups.rst
@@ -0,0 +1,7 @@
+Groups
+======
+
+.. automodule:: ugropy.groups
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,23 +1,31 @@
-.. ugropy documentation master file, created by
-   sphinx-quickstart on Mon Nov 27 19:27:24 2023.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 .. include:: ../../README.md
    :parser: myst_parser.sphinx_
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
    tutorial/tutorial
-   modules
+
+.. toctree::
+   :maxdepth: 1
+
+   tests_book/index
 
 .. toctree::
    :maxdepth: 1
 
    references.rst
 
+.. toctree::
+   :maxdepth: 1
+   :caption: API documentation
+
+   constants
+   groups
+   models/init
+   writers/init
+   core/init
+
 
 Indices and tables
 ==================

diff --git a/docs/source/logo.png b/docs/source/logo.png
diff --git a/docs/source/models/init.rst b/docs/source/models/init.rst
@@ -0,0 +1,14 @@
+Models
+======
+
+.. automodule:: ugropy.models
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 1
+
+   jobackmod
+   psrkmod
+   unifacmod
diff --git a/docs/source/models/jobackmod.rst b/docs/source/models/jobackmod.rst
@@ -0,0 +1,7 @@
+Joback
+======
+
+.. automodule:: ugropy.models.jobackmod
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/models/psrkmod.rst b/docs/source/models/psrkmod.rst
@@ -0,0 +1,7 @@
+PSRK
+====
+
+.. automodule:: ugropy.models.psrkmod
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/models/unifacmod.rst b/docs/source/models/unifacmod.rst
@@ -0,0 +1,7 @@
+UNIFAC
+======
+
+.. automodule:: ugropy.models.unifacmod
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/modules.rst b/docs/source/modules.rst