Merge pull request #26 from SalvadorBrandolin/main

release 2.0.5

Author: SalvadorBrandolin

MANIFEST.in

@@ -11,6 +11,7 @@ exclude requirements-dev.txt
 exclude *.svg
 exclude binder.ipynb
 exclude reminder.md
+exclude _build
 
 recursive-exclude dist *
 recursive-exclude tests *

README.md

@@ -7,9 +7,9 @@
 [![PyPI
 version](https://badge.fury.io/py/ugropy.svg)](https://badge.fury.io/py/ugropy)
 
-`ugropy` is a `Python` library to obtain subgroups from different
-thermodynamic group contribution models using both the name or the SMILES
-representation of a molecule. If the name is given, the library uses the
+`ugropy` is a `Python` library to obtain subgroups from different thermodynamic
+group contribution models using both the name or the SMILES representation of a
+molecule. If the name is given, the library uses the
 [PubChemPy](https://github.com/mcs07/PubChemPy) library to obtain the SMILES
 representation from PubChem. In both cases, `ugropy` uses the
 [RDKit](https://github.com/rdkit/rdkit) library to search the functional groups
@@ -18,17 +18,23 @@ in the molecule.
 `ugropy` is in an early development stage, leaving issues of examples of
 molecules that `ugropy` fails solving the subgroups of a model is very helpful.
 
+`ugropy` is tested for `Python` 3.10, 3.11 and 3.12 on Linux, Windows and Mac
+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.
 
-## Models supported v2.0.0
+## Models supported v2.0.5
 - Classic liquid-vapor UNIFAC
 - Predictive Soave-Redlich-Kwong (PSRK)
 - Joback
 
 ## Writers
+`ugropy` allows you to convert the obtained functional groups or estimated
+properties to the input format required by the following thermodynamic
+libraries:
 
 - [Clapeyron.jl](github.com/ClapeyronThermo/Clapeyron.jl)
 - [Thermo](https://github.com/CalebBell/thermo)
@@ -118,7 +124,7 @@ writers.to_clapeyron(
     unifac_groups=[g.unifac.subgroups for g in grps],
     psrk_groups=[g.psrk.subgroups for g in grps],
     joback_objects=[g.joback for g in grps],
-    path="./database"
+    path="database"
 )
 ```
 Obtain the [Caleb Bell's Thermo](https://github.com/CalebBell/thermo) subgroups
@@ -141,22 +147,3 @@ grps = [Groups(n) for n in names]
 ```
 pip install ugropy
 ```
-
-## Refereces
-
-[1] http://www.ddbst.com/published-parameters-unifac.html
-
-[2] Joback, K. G., & Reid, R. C. (1987). ESTIMATION OF PURE-COMPONENT
-PROPERTIES FROM GROUP-CONTRIBUTIONS. Chemical Engineering Communications,
-57(1–6), 233–243. https://doi.org/10.1080/00986448708960487
-
-[3] Joback, K. G. (1989). Designing molecules possessing desired physical
-property values [Thesis (Ph. D.), Massachusetts Institute of Technology].
-https://dspace.mit.edu/handle/1721.1/14191
-
-[4] Bondi, A. (1966). Estimation of Heat Capacity of Liquids. Industrial &
-Engineering Chemistry Fundamentals, 5(4), 442–449.
-https://doi.org/10.1021/i160020a001
-
-[5] Rowlinson, J. S., & Swinton, F. (2013). Liquids and liquid mixtures:
-Butterworths monographs in chemistry. Butterworth-Heinemann

docs/requirements.txt

@@ -1,13 +1,16 @@
+setuptools
+
 Sphinx
 sphinx_rtd_theme
 
 nbsphinx
 sphinx_copybutton
+sphinxcontrib-bibtex
 
 ipykernel
 ipython
 
 matplotlib
-sphinxcontrib-bibtex
 
-thermo >= 0.2.27
+thermo >= 0.2.27
+toml

docs/source/README.rst

@@ -1,11 +1,8 @@
-.. figure:: ../../logo.svg
+.. figure:: logo.svg
    :alt: logo
 
 |Binder| |License| |Python 3.10+| |Docs| |PyPI version|
 
-ugropy
-======
-
 ``ugropy`` is a ``Python`` library to obtain subgroups from different
 thermodynamic group contribution models using both the name or the
 SMILES representation of a molecule. If the name is given, the library
@@ -18,14 +15,17 @@ the functional groups in the molecule.
 of molecules that ``ugropy`` fails solving the subgroups of a model is
 very helpful.
 
+``ugropy`` is tested for ``Python`` 3.10, 3.11 and 3.12 on Linux,
+Windows and Mac 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.
 
-Models supported v2.0.0
+Models supported v2.0.5
 =======================
 
 -  Classic liquid-vapor UNIFAC
@@ -35,6 +35,10 @@ Models supported v2.0.0
 Writers
 =======
 
+``ugropy`` allows you to convert the obtained functional groups or
+estimated properties to the input format required by the following
+thermodynamic libraries:
+
 -  `Clapeyron.jl <github.com/ClapeyronThermo/Clapeyron.jl>`__
 -  `Thermo <https://github.com/CalebBell/thermo>`__
 
@@ -131,7 +135,7 @@ input files.
        unifac_groups=[g.unifac.subgroups for g in grps],
        psrk_groups=[g.psrk.subgroups for g in grps],
        joback_objects=[g.joback for g in grps],
-       path="./database"
+       path="database"
    )
 
 Obtain the `Caleb Bell’s Thermo <https://github.com/CalebBell/thermo>`__
@@ -158,27 +162,6 @@ Installation
 
    pip install ugropy
 
-Refereces
-=========
-
-[1] http://www.ddbst.com/published-parameters-unifac.html
-
-[2] Joback, K. G., & Reid, R. C. (1987). ESTIMATION OF PURE-COMPONENT
-PROPERTIES FROM GROUP-CONTRIBUTIONS. Chemical Engineering
-Communications, 57(1–6), 233–243.
-https://doi.org/10.1080/00986448708960487
-
-[3] Joback, K. G. (1989). Designing molecules possessing desired
-physical property values [Thesis (Ph. D.), Massachusetts Institute of
-Technology]. https://dspace.mit.edu/handle/1721.1/14191
-
-[4] Bondi, A. (1966). Estimation of Heat Capacity of Liquids. Industrial
-& Engineering Chemistry Fundamentals, 5(4), 442–449.
-https://doi.org/10.1021/i160020a001
-
-[5] Rowlinson, J. S., & Swinton, F. (2013). Liquids and liquid mixtures:
-Butterworths monographs in chemistry. Butterworth-Heinemann
-
 .. |Binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/ipqa-research/ugropy/main
 .. |License| image:: https://img.shields.io/badge/License-MIT-blue.svg

docs/source/conf.py

@@ -8,17 +8,24 @@
 import os
 import pathlib
 import sys
+import toml
 
 CURRENT_PATH = pathlib.Path(os.path.abspath(os.path.dirname(__file__)))
 UGROPY_PATH = CURRENT_PATH.parent.parent
 
 sys.path.insert(0, str(UGROPY_PATH))
 
+# Get release from pyproject
+pyproject_path = UGROPY_PATH / "pyproject.toml"
+with open(pyproject_path, "r") as f:
+    pyproject_toml = toml.load(f)
+
+project_version = pyproject_toml["project"]["version"]
 
 project = "ugropy"
 copyright = "2023, Salvador Eduardo Brandolín"
 author = "Salvador Eduardo Brandolín"
-release = "2.0.0"
+release = project_version
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -33,7 +40,7 @@
     "sphinx.ext.autosummary",
     "nbsphinx",
     "sphinx_copybutton",
-    #    "sphinxcontrib.bibtex",
+    "sphinxcontrib.bibtex",
 ]
 
 templates_path = ["_templates"]
@@ -44,6 +51,8 @@
 # =============================================================================
 autodoc_member_order = "bysource"
 
+bibtex_bibfiles = ["refs.bib"]
+
 # =============================================================================
 # NUMPY DOC
 # =============================================================================

docs/source/index.rst

@@ -12,6 +12,12 @@
    tutorial/tutorial
    modules
 
+References
+==========
+
+.. bibliography::
+   :style: unsrt
+   :cited:
 
 
 Indices and tables