Merge pull request #288 from WMD-group/develop

Merge develop branch changes into the master branch

Author: AntObi

README.md

@@ -68,7 +68,7 @@ List of modules
   *  **properties.py** A collection of tools for estimating useful properties based on composition.
   * **lattice.py** Given the sites, multiplicities and possible oxidation states
     at those sites, this reads from the database and generates all possible
-    stoichiometeries.
+    stoichiometries.
   * **builder.py** Builds some common lattice structures, given the chemical
     composition.
   * **lattice_parameters.py** Estimation of lattice parameters for various lattice types using covalent/ionic radii.
@@ -82,11 +82,11 @@ Requirements
 ------------
 The main language is Python 3 and has been tested using Python 3.9+.
 Basic requirements are Numpy and Scipy.
-The [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE),  [spglib](http://atztogo.github.io/spglib), and [pymatgen](www.pymatgen.org) are also required for many components.
+The [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE),  [spglib](http://atztogo.github.io/spglib), and [pymatgen](https://pymatgen.org) are also required for many components.
 
 Installation
 ------------
-The latest stable release can be installed via pip which will automatically setup other Python packages as required:
+The latest stable release can be installed via pip which will automatically set up other Python packages as required:
 
     pip install smact  
 
@@ -98,12 +98,12 @@ conda install -c conda-forge smact
 
 Alternatively, the very latest version can be installed using:
 
-    pip install git+git://github.com/WMD-group/SMACT.git
+    pip install git+https://github.com/WMD-group/SMACT.git
 
 For developer installation SMACT can be installed from a copy of the source
 repository (https://github.com/wmd-group/smact); this will be preferred if using experimental code branches.
 
-To clone the project from Github and make a local installation:
+To clone the project from GitHub and make a local installation:
 
     git clone https://github.com/wmd-group/smact.git
     cd smact
@@ -136,21 +136,21 @@ Testing modules should be pass/fail and wrapped into **tests/test_core.py** or a
 Run the tests using `python -m pytest -v`.
 (The final `-v` is optional and adds more detail to the output.)
 
-We also use integrated testing on Github via [GitHub Actions](hhttps://github.com/features/actions).
+We also use integrated testing on GitHub via [GitHub Actions](hhttps://github.com/features/actions).
 
 References
 ----------
 
-[H. Park et al,
+[H. Park et al.,
 "Mapping inorganic crystal chemical space" *Faraday Discuss.* (2024)](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00063c)
 
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "SMACT: Semiconducting Materials by Analogy and Chemical Theory" *JOSS* **4**, 1361 (2019)](https://joss.theoj.org/papers/7efd2f2ad60d25bdccee3fbd3fc11448)
 
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Materials discovery by chemical analogy: role of oxidation states in structure prediction" *Faraday Discuss.* **211**, 553 (2018)](https://pubs.rsc.org/en/Content/ArticleLanding/2018/FD/C8FD00032H)
 
-[D. W. Davies et al,
+[D. W. Davies et al.,
 "Computational screening of all stoichiometric inorganic materials" *Chem* **1**, 617 (2016)](http://www.cell.com/chem/abstract/S2451-9294(16)30155-3)
 
 [B. R. Pamplin, "A systematic method of deriving new semiconducting

docs/conf.py

@@ -52,17 +52,17 @@
 
 # General information about the project.
 project = "Smact"
-copyright = "2016, Materials Design Group"
+copyright = "2024, Materials Design Group"
 author = "Materials Design Group"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = "2.5"
+version = "2.6"
 # The full version, including alpha/beta/rc tags.
-release = "2.5.5"
+release = "2.6.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -382,5 +382,6 @@ def __getattr__(cls, name):
     "pymatgen.util.plotting",
     "pymatgen.analysis.structure_prediction",
     "pymatgen.transformations.standard_transformations",
+    "tabulate",
 ]
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

examples/Dopant_Prediction/doper_example.ipynb

@@ -5,10 +5,10 @@
 __copyright__ = (
     "Copyright Daniel W. Davies, Adam J. Jackson, Keith T. Butler (2019)"
 )
-__version__ = "2.5.5"
+__version__ = "2.6"
 __maintainer__ = "Anthony O. Onwuli"
 __maintaier_email__ = "[email protected]"
-__date__ = "December 7 2023"
+__date__ = "July 10 2024"
 
 import os
 import unittest
@@ -43,6 +43,7 @@
                 "data/*.data",
                 "data/*.xlsx",
                 "data/*.json",
+                "data/species_rep/*.json",
             ]
         },
         zip_safe=False,