From be34c0c6d187d3882f4c672781910d4e79f7c0b8 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Wed, 5 Jul 2023 17:52:05 +0100
Subject: [PATCH 01/30] Updated CHANGELOG.md

---
 CHANGELOG.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5fcb31c..28c87f8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,9 +6,9 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 <!-- insertion marker -->
-## Unreleased
+## [v0.1.1](https://github.com/WMD-group/ElementEmbeddings/releases/tag/v0.1.1) - 2023-07-05
 
-<small>[Compare with latest](https://github.com/WMD-group/ElementEmbeddings/compare/v0.1...HEAD)</small>
+<small>[Compare with v0.1](https://github.com/WMD-group/ElementEmbeddings/compare/v0.1...v0.1.1)</small>
 
 ### Added
 
@@ -20,7 +20,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - removed pandas, pytest and pytest-subtests in reqs ([cd1bf77](https://github.com/WMD-group/ElementEmbeddings/commit/cd1bf776220250377bb7cd48cca6b08e9a968f1d) by Anthony Onwuli).
 
-<!-- insertion marker -->
 ## [v0.1](https://github.com/WMD-group/ElementEmbeddings/releases/tag/v0.1) - 2023-06-30
 
 <small>[Compare with first commit](https://github.com/WMD-group/ElementEmbeddings/compare/262c7e99a438a3527fb73866093ae8cb1ee85ee6...v0.1)</small>

From 173bcee057173ec1a48cdc7bb3141406236119ce Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Wed, 5 Jul 2023 18:01:44 +0100
Subject: [PATCH 02/30] Added test embedding csv file

---
 src/elementembeddings/tests/files/test_embedding.csv | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 src/elementembeddings/tests/files/test_embedding.csv

diff --git a/src/elementembeddings/tests/files/test_embedding.csv b/src/elementembeddings/tests/files/test_embedding.csv
new file mode 100644
index 0000000..74a2a4c
--- /dev/null
+++ b/src/elementembeddings/tests/files/test_embedding.csv
@@ -0,0 +1,4 @@
+element,0,1,2,3,4,5,6,7,8,9
+H,1,0,0,0,0,0,0,0,0,0
+He,0,1,0,0,0,0,0,0,0,0
+Li,0,0,1,0,0,0,0,0,0,0
\ No newline at end of file

From 188aea48e21b3c3d5a1b9624a9885b94f14b2fcc Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Wed, 5 Jul 2023 18:02:41 +0100
Subject: [PATCH 03/30] Added test embedding json file

---
 src/elementembeddings/tests/files/test_embedding.json | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 src/elementembeddings/tests/files/test_embedding.json

diff --git a/src/elementembeddings/tests/files/test_embedding.json b/src/elementembeddings/tests/files/test_embedding.json
new file mode 100644
index 0000000..abcd5a9
--- /dev/null
+++ b/src/elementembeddings/tests/files/test_embedding.json
@@ -0,0 +1 @@
+{"H":[1,0,0,0,0,0,0,0,0,0], "He":[0,1,0,0,0,0,0,0,0,0],"Li":[0,0,1,0,0,0,0,0,0,0]}
\ No newline at end of file

From 87ba9581c506bc16aa377961da28c0cbe60e80de Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Wed, 5 Jul 2023 18:30:23 +0100
Subject: [PATCH 04/30] Added test functions for loading csv and json

---
 src/elementembeddings/tests/test_core.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index de96d3d..9a63f15 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -6,8 +6,11 @@
 import pandas as pd
 
 from elementembeddings.core import Embedding
+import os
 
-
+test_files_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)),"files")
+TEST_EMBEDDING_CSV = os.path.join(test_files_dir, "test_embedding.csv")
+TEST_EMBEDDING_JSON = os.path.join(test_files_dir, "test_embedding.json")
 class EmbeddingTest(unittest.TestCase):
     """Test the Embedding class."""
 
@@ -23,6 +26,13 @@ def test_Embedding_loading(self):
         assert megnet16.embedding_name == "megnet16"
         assert isinstance(skipatom.citation(), list)
         assert isinstance(megnet16.citation(), list)
+    def test_Embedding_file_input(self):
+        """Test that the Embedding class can load custom data."""
+        embedding_csv = Embedding.from_csv(TEST_EMBEDDING_CSV)
+        embedding_json = Embedding.from_json(TEST_EMBEDDING_JSON)
+        assert embedding_csv.dim == 10
+        assert embedding_json.dim == 10
+
 
     def test_Embeddings_class_magpie(self):
         """Test that the Embedding class can load the magpie data."""

From 7f9f87b987a77f1d4b73cf9fed289a5d9a028417 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 09:28:18 +0100
Subject: [PATCH 05/30] Added more tests to the Embedding loading function

---
 src/elementembeddings/tests/test_core.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 9a63f15..94b26f9 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -20,12 +20,17 @@ def test_Embedding_loading(self):
         """Test that the Embedding class can load the data."""
         skipatom = Embedding.load_data("skipatom")
         megnet16 = Embedding.load_data("megnet16")
+        matscholar = Embedding.load_data("matscholar")
         assert skipatom.dim == 200
         assert skipatom.embedding_name == "skipatom"
         assert megnet16.dim == 16
         assert megnet16.embedding_name == "megnet16"
+        assert matscholar.dim == 200
+        assert matscholar.embedding_name == "matscholar"
         assert isinstance(skipatom.citation(), list)
         assert isinstance(megnet16.citation(), list)
+        assert isinstance(matscholar.citation(), list)
+        
     def test_Embedding_file_input(self):
         """Test that the Embedding class can load custom data."""
         embedding_csv = Embedding.from_csv(TEST_EMBEDDING_CSV)

From c7bc12bc915d22425dc2e4123d1216e75fda0678 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 09:30:04 +0100
Subject: [PATCH 06/30] Updated Embedding loading test

---
 src/elementembeddings/tests/test_core.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 94b26f9..65312a4 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -21,16 +21,20 @@ def test_Embedding_loading(self):
         skipatom = Embedding.load_data("skipatom")
         megnet16 = Embedding.load_data("megnet16")
         matscholar = Embedding.load_data("matscholar")
+        mod_petti = Embedding.load_data("mod_petti")
         assert skipatom.dim == 200
         assert skipatom.embedding_name == "skipatom"
         assert megnet16.dim == 16
         assert megnet16.embedding_name == "megnet16"
         assert matscholar.dim == 200
         assert matscholar.embedding_name == "matscholar"
+        assert mod_petti.dim == 1
+        assert mod_petti.embedding_name == "mod_petti"
         assert isinstance(skipatom.citation(), list)
         assert isinstance(megnet16.citation(), list)
         assert isinstance(matscholar.citation(), list)
-        
+        assert isinstance(mod_petti.citation(), list)
+
     def test_Embedding_file_input(self):
         """Test that the Embedding class can load custom data."""
         embedding_csv = Embedding.from_csv(TEST_EMBEDDING_CSV)

From 5532de6d050580382f0fa9688be96f0e9cd231ec Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 09:33:13 +0100
Subject: [PATCH 07/30] Removed an else block from `load_data`

---
 src/elementembeddings/core.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/elementembeddings/core.py b/src/elementembeddings/core.py
index 5d8c132..d743765 100644
--- a/src/elementembeddings/core.py
+++ b/src/elementembeddings/core.py
@@ -151,11 +151,6 @@ def load_data(embedding_name: Optional[str] = None):
                 _json = path.join(data_directory, _cbfv_files[embedding_name])
                 with open(_json) as f:
                     embedding_data = json.load(f)
-
-            # Load a json file from a file specified in the input
-            else:
-                with open(embedding_name) as f:
-                    embedding_data = json.load(f)
         else:
             raise (
                 ValueError(

From d54205875065b328d678d037f04dc5b4b5646d9f Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 09:33:26 +0100
Subject: [PATCH 08/30] Ran pre-commit

---
 src/elementembeddings/tests/test_core.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 65312a4..26100c0 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -1,4 +1,5 @@
 """Test the core module of AtomicEmbeddings."""
+import os
 import unittest
 
 import matplotlib.pyplot as plt
@@ -6,11 +7,12 @@
 import pandas as pd
 
 from elementembeddings.core import Embedding
-import os
 
-test_files_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)),"files")
+test_files_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "files")
 TEST_EMBEDDING_CSV = os.path.join(test_files_dir, "test_embedding.csv")
 TEST_EMBEDDING_JSON = os.path.join(test_files_dir, "test_embedding.json")
+
+
 class EmbeddingTest(unittest.TestCase):
     """Test the Embedding class."""
 
@@ -42,7 +44,6 @@ def test_Embedding_file_input(self):
         assert embedding_csv.dim == 10
         assert embedding_json.dim == 10
 
-
     def test_Embeddings_class_magpie(self):
         """Test that the Embedding class can load the magpie data."""
         magpie = Embedding.load_data("magpie")

From 7256c23d8d2840b77983424ee9247a90f1caaded Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 09:57:19 +0100
Subject: [PATCH 09/30] Added tests for `as_dataframe` method

---
 src/elementembeddings/tests/test_core.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 26100c0..8a8e257 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -274,6 +274,11 @@ def test_Embeddings_class_magpie(self):
         # TO-DO
         # Create tests for checking dataframes and plotting functions
         assert isinstance(magpie.as_dataframe(), pd.DataFrame)
+        assert "H" in magpie.as_dataframe().index.tolist()
+        assert isinstance(magpie.as_dataframe(columns="elements"), pd.DataFrame)
+        assert "H" in magpie.as_dataframe(columns="elements").columns.tolist()
+        self.assertRaises(ValueError, magpie.as_dataframe, columns="test")
+
         assert isinstance(magpie.to(fmt="json"), str)
         assert isinstance(magpie.to(fmt="csv"), str)
         assert isinstance(

From 7cb8ab6d3b731d04831cdfe83a90b926ab1e2a1b Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 15:37:19 +0100
Subject: [PATCH 10/30] Added setUpClass to test_core.py

---
 src/elementembeddings/tests/test_core.py | 84 +++++++++++++++---------
 1 file changed, 54 insertions(+), 30 deletions(-)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 8a8e257..014c2d8 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -17,25 +17,29 @@ class EmbeddingTest(unittest.TestCase):
     """Test the Embedding class."""
 
     # High Level functions
+    @classmethod
+    def setUpClass(cls):
+        """Set up the test."""
+        cls.test_skipatom = Embedding.load_data("skipatom")
+        cls.test_megnet16 = Embedding.load_data("megnet16")
+        cls.test_matscholar = Embedding.load_data("matscholar")
+        cls.test_mod_petti = Embedding.load_data("mod_petti")
+        cls.test_magpie = Embedding.load_data("magpie")
 
-    def test_Embedding_loading(self):
-        """Test that the Embedding class can load the data."""
-        skipatom = Embedding.load_data("skipatom")
-        megnet16 = Embedding.load_data("megnet16")
-        matscholar = Embedding.load_data("matscholar")
-        mod_petti = Embedding.load_data("mod_petti")
-        assert skipatom.dim == 200
-        assert skipatom.embedding_name == "skipatom"
-        assert megnet16.dim == 16
-        assert megnet16.embedding_name == "megnet16"
-        assert matscholar.dim == 200
-        assert matscholar.embedding_name == "matscholar"
-        assert mod_petti.dim == 1
-        assert mod_petti.embedding_name == "mod_petti"
-        assert isinstance(skipatom.citation(), list)
-        assert isinstance(megnet16.citation(), list)
-        assert isinstance(matscholar.citation(), list)
-        assert isinstance(mod_petti.citation(), list)
+    def test_Embedding_attributes(self):
+        """Test attributes of the loaded embeddings."""
+        assert self.test_skipatom.dim == 200
+        assert self.test_skipatom.embedding_name == "skipatom"
+        assert self.test_megnet16.dim == 16
+        assert self.test_megnet16.embedding_name == "megnet16"
+        assert self.test_matscholar.dim == 200
+        assert self.test_matscholar.embedding_name == "matscholar"
+        assert self.test_mod_petti.dim == 1
+        assert self.test_mod_petti.embedding_name == "mod_petti"
+        assert isinstance(self.test_skipatom.citation(), list)
+        assert isinstance(self.test_megnet16.citation(), list)
+        assert isinstance(self.test_matscholar.citation(), list)
+        assert isinstance(self.test_mod_petti.citation(), list)
 
     def test_Embedding_file_input(self):
         """Test that the Embedding class can load custom data."""
@@ -46,7 +50,7 @@ def test_Embedding_file_input(self):
 
     def test_Embeddings_class_magpie(self):
         """Test that the Embedding class can load the magpie data."""
-        magpie = Embedding.load_data("magpie")
+        magpie = self.test_magpie
         # Check if the embeddings attribute is a dict
         assert isinstance(magpie.embeddings, dict)
         # Check if the embedding vector is a numpy array
@@ -273,31 +277,51 @@ def test_Embeddings_class_magpie(self):
 
         # TO-DO
         # Create tests for checking dataframes and plotting functions
+
+    def test_as_dataframe(self):
+        """Test the as_dataframe method."""
+        magpie = self.test_magpie
         assert isinstance(magpie.as_dataframe(), pd.DataFrame)
         assert "H" in magpie.as_dataframe().index.tolist()
         assert isinstance(magpie.as_dataframe(columns="elements"), pd.DataFrame)
         assert "H" in magpie.as_dataframe(columns="elements").columns.tolist()
         self.assertRaises(ValueError, magpie.as_dataframe, columns="test")
 
-        assert isinstance(magpie.to(fmt="json"), str)
-        assert isinstance(magpie.to(fmt="csv"), str)
+    def test_to(self):
+        """Test the to method."""
+        assert isinstance(self.test_magpie.to(fmt="json"), str)
+        self.test_magpie.to(fmt="json", filename="test.json")
+        assert os.path.isfile("test.json")
+        os.remove("test.json")
+
+        assert isinstance(self.test_magpie.to(fmt="csv"), str)
+        self.test_magpie.to(fmt="csv", filename="test.csv")
+        assert os.path.isfile("test.csv")
+        os.remove("test.csv")
+
+    def test_compute_metric_functions(self):
+        """Test the compute metric functions."""
         assert isinstance(
-            magpie.compute_correlation_metric("H", "O", metric="pearson"),
+            self.test_magpie.compute_correlation_metric("H", "O", metric="pearson"),
             float,
         )
         assert isinstance(
-            magpie.compute_distance_metric(
+            self.test_magpie.compute_distance_metric(
                 "H",
                 "O",
             ),
             float,
         )
-        assert isinstance(magpie.distance_df(), pd.DataFrame)
-        assert magpie.distance_df().shape == (
-            len(list(magpie.create_pairs())) * 2 - len(magpie.embeddings),
+
+    def test_distance_dataframe_functions(self):
+        """Test the distance dataframe functions."""
+        assert isinstance(self.test_magpie.distance_df(), pd.DataFrame)
+        assert self.test_magpie.distance_df().shape == (
+            len(list(self.test_magpie.create_pairs())) * 2
+            - len(self.test_magpie.embeddings),
             7,
         )
-        assert magpie.distance_df().columns.tolist() == [
+        assert self.test_magpie.distance_df().columns.tolist() == [
             "ele_1",
             "ele_2",
             "mend_1",
@@ -306,8 +330,8 @@ def test_Embeddings_class_magpie(self):
             "Z_2",
             "euclidean",
         ]
-        assert isinstance(magpie.distance_pivot_table(), pd.DataFrame)
-        assert isinstance(magpie.plot_distance_correlation(), plt.Axes)
+        assert isinstance(self.test_magpie.distance_pivot_table(), pd.DataFrame)
+        assert isinstance(self.test_magpie.plot_distance_correlation(), plt.Axes)
         assert isinstance(
-            magpie.plot_distance_correlation(metric="euclidean"), plt.Axes
+            self.test_magpie.plot_distance_correlation(metric="euclidean"), plt.Axes
         )

From 664cbbf1846757b7d018c199745b6227465c0268 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 15:53:19 +0100
Subject: [PATCH 11/30] Added test function for removing elements

---
 src/elementembeddings/tests/test_core.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 014c2d8..f42703d 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -335,3 +335,8 @@ def test_distance_dataframe_functions(self):
         assert isinstance(
             self.test_magpie.plot_distance_correlation(metric="euclidean"), plt.Axes
         )
+
+    def test_remove_elements(self):
+        """Test the remove_elements function."""
+        self.assertIsNone(self.test_skipatom.remove_elements("H", inplace=True))
+        assert "H" not in self.test_skipatom.element_list

From b69d80699cad211166ff1b112886d19d387890b5 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 16:14:26 +0100
Subject: [PATCH 12/30] Added test for removing multiple elements

---
 src/elementembeddings/tests/test_core.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index f42703d..ec9a18e 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -338,5 +338,13 @@ def test_distance_dataframe_functions(self):
 
     def test_remove_elements(self):
         """Test the remove_elements function."""
+        assert isinstance(self.test_skipatom.remove_elements("H"), Embedding)
+        assert isinstance(self.test_skipatom.remove_elements(["H", "Li"]), Embedding)
         self.assertIsNone(self.test_skipatom.remove_elements("H", inplace=True))
-        assert "H" not in self.test_skipatom.element_list
+        self.assertFalse(self.test_skipatom._is_el_in_embedding("H"))
+        self.assertIsNone(
+            self.test_skipatom.remove_elements(["Li", "Ti", "Bi"], inplace=True)
+        )
+        assert "Li" not in self.test_skipatom.element_list
+        assert "Ti" not in self.test_skipatom.element_list
+        assert "Bi" not in self.test_skipatom.element_list

From edeeb8714ae80b194159738b562606819ffc3ccb Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 16:22:58 +0100
Subject: [PATCH 13/30] Added more dataframe test functions

---
 src/elementembeddings/tests/test_core.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index ec9a18e..dd29247 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -335,6 +335,7 @@ def test_distance_dataframe_functions(self):
         assert isinstance(
             self.test_magpie.plot_distance_correlation(metric="euclidean"), plt.Axes
         )
+        assert isinstance(self.test_magpie.stats_correlation_df(), pd.DataFrame)
 
     def test_remove_elements(self):
         """Test the remove_elements function."""

From 5f715aaa3ba339b5e01012cb0a40c44652481b55 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 16:29:55 +0100
Subject: [PATCH 14/30] Added test for computing spearman's rank

---
 src/elementembeddings/tests/test_core.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index dd29247..be8ecb5 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -312,6 +312,10 @@ def test_compute_metric_functions(self):
             ),
             float,
         )
+        assert isinstance(
+            self.test_magpie.compute_correlation_metric("H", "O", metric="spearman"),
+            float,
+        )
 
     def test_distance_dataframe_functions(self):
         """Test the distance dataframe functions."""

From c4055bcdad6e5bd7832a8568767ced72cd9cdfd9 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 16:44:06 +0100
Subject: [PATCH 15/30] Added more tests for compute metrics function

---
 src/elementembeddings/tests/test_core.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index be8ecb5..5177984 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -312,11 +312,29 @@ def test_compute_metric_functions(self):
             ),
             float,
         )
+        assert isinstance(
+            self.test_magpie.compute_distance_metric("H", "O", "energy"),
+            float,
+        )
+        assert isinstance(
+            self.test_magpie.compute_distance_metric("H", "O", "cosine_distance"),
+            float,
+        )
         assert isinstance(
             self.test_magpie.compute_correlation_metric("H", "O", metric="spearman"),
             float,
         )
 
+        self.assertRaises(
+            ValueError, self.test_skipatom.compute_distance_metric, "He", "O"
+        )
+        self.assertRaises(
+            ValueError, self.test_skipatom.compute_distance_metric, "O", "He"
+        )
+        self.assertRaises(
+            ValueError, self.test_skipatom.compute_distance_metric, "Li", "O", "euclid"
+        )
+
     def test_distance_dataframe_functions(self):
         """Test the distance dataframe functions."""
         assert isinstance(self.test_magpie.distance_df(), pd.DataFrame)

From 6f821e8856a44fbbcb5ecdb54c3fb815ef05f55b Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 19:34:47 +0100
Subject: [PATCH 16/30] Updated dataframe test functions

---
 src/elementembeddings/tests/test_core.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 5177984..2b84faf 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -353,6 +353,9 @@ def test_distance_dataframe_functions(self):
             "euclidean",
         ]
         assert isinstance(self.test_magpie.distance_pivot_table(), pd.DataFrame)
+        assert isinstance(
+            self.test_magpie.distance_pivot_table(sortby="atomic_number"), pd.DataFrame
+        )
         assert isinstance(self.test_magpie.plot_distance_correlation(), plt.Axes)
         assert isinstance(
             self.test_magpie.plot_distance_correlation(metric="euclidean"), plt.Axes

From aaa147279ba609984482813df2ce9530420da2be Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 19:39:38 +0100
Subject: [PATCH 17/30] Added test function for tSNE for Embedding class

---
 src/elementembeddings/tests/test_core.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 2b84faf..5036b6a 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -374,3 +374,11 @@ def test_remove_elements(self):
         assert "Li" not in self.test_skipatom.element_list
         assert "Ti" not in self.test_skipatom.element_list
         assert "Bi" not in self.test_skipatom.element_list
+
+    def test_tSNE(self):
+        """Test the tSNE function."""
+        assert isinstance(self.test_matscholar.calculate_tSNE(), np.ndarray)
+        assert self.test_matscholar.calculate_tSNE().shape == (
+            len(self.test_matscholar.element_list),
+            2,
+        )

From b7ccc8f41384e5e6095090aa016088279b5a0439 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 19:48:24 +0100
Subject: [PATCH 18/30] Added functions to test PCA and UMAP for Embedding

---
 src/elementembeddings/tests/test_core.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/src/elementembeddings/tests/test_core.py b/src/elementembeddings/tests/test_core.py
index 5036b6a..845b3b0 100644
--- a/src/elementembeddings/tests/test_core.py
+++ b/src/elementembeddings/tests/test_core.py
@@ -375,6 +375,14 @@ def test_remove_elements(self):
         assert "Ti" not in self.test_skipatom.element_list
         assert "Bi" not in self.test_skipatom.element_list
 
+    def test_PCA(self):
+        """Test the PCA function."""
+        assert isinstance(self.test_matscholar.calculate_PC(), np.ndarray)
+        assert self.test_matscholar.calculate_PC().shape == (
+            len(self.test_matscholar.element_list),
+            2,
+        )
+
     def test_tSNE(self):
         """Test the tSNE function."""
         assert isinstance(self.test_matscholar.calculate_tSNE(), np.ndarray)
@@ -382,3 +390,11 @@ def test_tSNE(self):
             len(self.test_matscholar.element_list),
             2,
         )
+
+    def test_UMAP(self):
+        """Test the UMAP function."""
+        assert isinstance(self.test_matscholar.calculate_UMAP(), np.ndarray)
+        assert self.test_matscholar.calculate_UMAP().shape == (
+            len(self.test_matscholar.element_list),
+            2,
+        )

From 542e2f2e6bd96b0f0e1624192cb9a9a98fb3dfcc Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 19:50:01 +0100
Subject: [PATCH 19/30] Added deprecation warning to old plotting function

---
 src/elementembeddings/core.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/elementembeddings/core.py b/src/elementembeddings/core.py
index d743765..21a94a0 100644
--- a/src/elementembeddings/core.py
+++ b/src/elementembeddings/core.py
@@ -848,6 +848,10 @@ def plot_PCA_2D(
             ax (matplotlib.axes.Axes): An Axes object with the PCA plot
 
         """
+        warnings.warn(
+            "This method is deprecated and will be removed in a future release. ",
+            DeprecationWarning,
+        )
         embeddings_array = np.array(list(self.embeddings.values()))
         element_array = np.array(self.element_list)
 
@@ -908,6 +912,10 @@ def plot_tSNE(
 
 
         """
+        warnings.warn(
+            "This method is deprecated and will be removed in a future release. ",
+            DeprecationWarning,
+        )
         embeddings_array = np.array(list(self.embeddings.values()))
         element_array = np.array(self.element_list)
 

From e9cc5ed5508e624420b1330973425572ff5b1628 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 21:43:24 +0100
Subject: [PATCH 20/30] Added test for plotting euclidean heatmap

---
 src/elementembeddings/tests/test_plotter.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/elementembeddings/tests/test_plotter.py b/src/elementembeddings/tests/test_plotter.py
index d34c799..bae2a60 100644
--- a/src/elementembeddings/tests/test_plotter.py
+++ b/src/elementembeddings/tests/test_plotter.py
@@ -8,22 +8,29 @@
 from elementembeddings.plotter import dimension_plotter, heatmap_plotter
 
 
-class heatmapTest(unittest.TestCase):
+class HeatmapTest(unittest.TestCase):
     """Test the heatmap_plotter function."""
 
+    @classmethod
+    def setUpClass(cls):
+        """Set up the test class."""
+        cls.test_skipatom = Embedding.load_data("skipatom")
+
     def test_heatmap_plotter(self):
         """Test that the heatmap_plotter function works."""
-        # Load the data
-        skipatom = Embedding.load_data("skipatom")
         # Get the embeddings
         skipatom_cos_plot = heatmap_plotter(
-            skipatom,
+            self.test_skipatom,
             metric="cosine_similarity",
         )
         assert isinstance(skipatom_cos_plot, plt.Axes)
+        skipatom_euc_plot = heatmap_plotter(
+            self.test_skipatom, metric="euclidean", show_axislabels=False
+        )
+        assert isinstance(skipatom_euc_plot, plt.Axes)
 
 
-class dimensionTest(unittest.TestCase):
+class DimensionTest(unittest.TestCase):
     """Test the dimension_plotter function."""
 
     def test_dimension_plotter(self):

From 5bf9b7f3ac047e4b04aed3f0f2f8da88e4040d40 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 22:00:21 +0100
Subject: [PATCH 21/30] Updated tests for dimension plotter

---
 src/elementembeddings/tests/test_plotter.py | 47 ++++++++++++++++++---
 1 file changed, 42 insertions(+), 5 deletions(-)

diff --git a/src/elementembeddings/tests/test_plotter.py b/src/elementembeddings/tests/test_plotter.py
index bae2a60..e6e666e 100644
--- a/src/elementembeddings/tests/test_plotter.py
+++ b/src/elementembeddings/tests/test_plotter.py
@@ -33,12 +33,49 @@ def test_heatmap_plotter(self):
 class DimensionTest(unittest.TestCase):
     """Test the dimension_plotter function."""
 
-    def test_dimension_plotter(self):
+    @classmethod
+    def setUpClass(cls):
+        """Set up the test class."""
+        cls.test_skipatom = Embedding.load_data("skipatom")
+
+    def test_dimension_2d_plotter(self):
         """Test that the dimension_plotter function works."""
-        # Load the data
-        skipatom = Embedding.load_data("skipatom")
-        # Get the embeddings
         skipatom_pca_plot = dimension_plotter(
-            skipatom, n_components=2, reducer="pca", adjusttext=True
+            self.test_skipatom, n_components=2, reducer="pca", adjusttext=False
+        )
+        assert isinstance(skipatom_pca_plot, plt.Axes)
+        skipatom_tsne_plot = dimension_plotter(
+            self.test_skipatom, n_components=2, reducer="tsne", adjusttext=False
+        )
+        assert isinstance(skipatom_tsne_plot, plt.Axes)
+        skipatom_umap_plot = dimension_plotter(
+            self.test_skipatom, n_components=2, reducer="umap", adjusttext=True
+        )
+        assert isinstance(skipatom_umap_plot, plt.Axes)
+
+        self.assertRaises(
+            ValueError,
+            dimension_plotter,
+            self.test_skipatom,
+            n_components=2,
+            reducer="badreducer",
+        )
+
+    def test_dimension_2d_plotter_preloaded_reduction(self):
+        """Test that the dimension_plotter function works with a preloaded reduction."""
+        self.test_skipatom.calculate_PC()
+        self.test_skipatom.calculate_tSNE()
+        self.test_skipatom.calculate_UMAP()
+
+        skipatom_pca_plot = dimension_plotter(
+            self.test_skipatom, n_components=2, reducer="pca", adjusttext=False
         )
         assert isinstance(skipatom_pca_plot, plt.Axes)
+        skipatom_tsne_plot = dimension_plotter(
+            self.test_skipatom, n_components=2, reducer="tsne", adjusttext=False
+        )
+        assert isinstance(skipatom_tsne_plot, plt.Axes)
+        skipatom_umap_plot = dimension_plotter(
+            self.test_skipatom, n_components=2, reducer="umap", adjusttext=False
+        )
+        assert isinstance(skipatom_umap_plot, plt.Axes)

From ef37daff6aa824c3d9917fa1ba26fc37b95a9951 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Thu, 6 Jul 2023 22:05:02 +0100
Subject: [PATCH 22/30] Added test for dimension plotter in 3D

---
 src/elementembeddings/tests/test_plotter.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/elementembeddings/tests/test_plotter.py b/src/elementembeddings/tests/test_plotter.py
index e6e666e..59f9c81 100644
--- a/src/elementembeddings/tests/test_plotter.py
+++ b/src/elementembeddings/tests/test_plotter.py
@@ -79,3 +79,20 @@ def test_dimension_2d_plotter_preloaded_reduction(self):
             self.test_skipatom, n_components=2, reducer="umap", adjusttext=False
         )
         assert isinstance(skipatom_umap_plot, plt.Axes)
+
+    def test_dimension_3d_plotter(self):
+        """Test that the dimension_plotter function works in 3D."""
+        skipatom_3d_pca_plot = dimension_plotter(
+            self.test_skipatom, n_components=3, reducer="pca", adjusttext=False
+        )
+        assert isinstance(skipatom_3d_pca_plot, plt.Axes)
+
+    def test_dimension_Nd_plotter(self):
+        """Test that the dimension_plotter function will fail in d>3."""
+        self.assertRaises(
+            ValueError,
+            dimension_plotter,
+            self.test_skipatom,
+            n_components=4,
+            reducer="pca",
+        )

From b598e78ef33d4f8b5cde840895aec67b713f84cc Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 16:24:59 +0100
Subject: [PATCH 23/30] Updated composition tests

---
 .../tests/test_composition.py                 | 96 ++++++++++++++-----
 1 file changed, 74 insertions(+), 22 deletions(-)

diff --git a/src/elementembeddings/tests/test_composition.py b/src/elementembeddings/tests/test_composition.py
index 3641c67..6ef635d 100644
--- a/src/elementembeddings/tests/test_composition.py
+++ b/src/elementembeddings/tests/test_composition.py
@@ -11,35 +11,53 @@
 class TestComposition(unittest.TestCase):
     """Test the composition module."""
 
+    def setUp(self):
+        """Set up the test class."""
+        self.formulas = [
+            "Sr3Sc2(GeO4)3",
+            "Fe2O3",
+            "Li7La3ZrO12",
+            "CsPbI3",
+        ]
+
     def test_formula_parser(self):
         """Test the formula_parser function."""
-        LLZO_parsed = composition.formula_parser("Li7La3ZrO12")
+        LLZO_parsed = composition.formula_parser(self.formulas[2])
         assert isinstance(LLZO_parsed, dict)
         assert "Zr" in LLZO_parsed
         assert LLZO_parsed["Li"] == 7
 
+    def test_formula_parser_with_parentheses(self):
+        """Test the formula_parser function with parentheses."""
+        SrScGeO4_parsed = composition.formula_parser(self.formulas[0])
+        assert isinstance(SrScGeO4_parsed, dict)
+        assert "Sr" in SrScGeO4_parsed
+        assert SrScGeO4_parsed["Ge"] == 3
+
+    def test_formula_parser_with_invalid_formula(self):
+        """Test the formula_parser function with an invalid formula."""
+        with self.assertRaises(ValueError):
+            composition.formula_parser("Sr3Sc2(GeO4)3)")
+
     def test__get_fractional_composition(self):
         """Test the _get_fractional_composition function."""
-        CsPbI3_frac = composition._get_fractional_composition("CsPbI3")
+        CsPbI3_frac = composition._get_fractional_composition(self.formulas[3])
         assert isinstance(CsPbI3_frac, dict)
         assert "Pb" in CsPbI3_frac
         assert CsPbI3_frac["I"] == 0.6
 
-    def test_Composition_class(self):
-        """Test the Composition class."""
-        Fe2O3_magpie = composition.CompositionalEmbedding(
-            formula="Fe2O3", embedding="magpie"
-        )
-        assert isinstance(Fe2O3_magpie.embedding, core.Embedding)
-        assert Fe2O3_magpie.formula == "Fe2O3"
-        assert Fe2O3_magpie.embedding_name == "magpie"
-        assert isinstance(Fe2O3_magpie.composition, dict)
-        assert {"Fe": 2, "O": 3} == Fe2O3_magpie.composition
-        assert Fe2O3_magpie._natoms == 5
-        assert Fe2O3_magpie.fractional_composition == {"Fe": 0.4, "O": 0.6}
-        assert isinstance(Fe2O3_magpie._mean_feature_vector(), np.ndarray)
-        # Test that the feature vector function works
-        stats = [
+
+class TestCompositionalEmbedding(unittest.TestCase):
+    """Test the CompositionalEmbedding class."""
+
+    def setUp(self):
+        """Set up the test formulas."""
+        self.formulas = ["Sr3Sc2(GeO4)3", "Fe2O3", "Li7La3ZrO12", "CsPbI3", "CsPbI-3"]
+        self.valid_magpie_compositions = [
+            composition.CompositionalEmbedding(formula=formula, embedding="magpie")
+            for formula in self.formulas[:3]
+        ]
+        self.stats = [
             "mean",
             "variance",
             "minpool",
@@ -49,16 +67,50 @@ def test_Composition_class(self):
             "geometric_mean",
             "harmonic_mean",
         ]
-        assert isinstance(Fe2O3_magpie.feature_vector(stats=stats), np.ndarray)
+
+    def test_CompositionalEmbedding_attributes(self):
+        """Test the Composition class."""
+        Fe2O3_magpie = self.valid_magpie_compositions[1]
+        assert isinstance(Fe2O3_magpie.embedding, core.Embedding)
+        assert Fe2O3_magpie.formula == "Fe2O3"
+        assert Fe2O3_magpie.embedding_name == "magpie"
+        assert isinstance(Fe2O3_magpie.composition, dict)
+        assert {"Fe": 2, "O": 3} == Fe2O3_magpie.composition
+        assert Fe2O3_magpie.num_atoms == 5
+        assert Fe2O3_magpie.fractional_composition == {"Fe": 0.4, "O": 0.6}
+        assert Fe2O3_magpie.embedding.dim == 22
+
+    def test_CompositionalEmbedding_negative_formula(self):
+        """Test the Composition class with a negative formula."""
+        with self.assertRaises(ValueError):
+            composition.CompositionalEmbedding(
+                formula=self.formulas[4], embedding="magpie"
+            )
+
+    def test__mean_feature_vector(self):
+        """Test the _mean_feature_vector function."""
+        assert isinstance(
+            self.valid_magpie_compositions[1]._mean_feature_vector(), np.ndarray
+        )
+        # Test that the feature vector function works
+
+    def test_feature_vector(self):
+        """Test the feature_vector function."""
+        assert isinstance(
+            self.valid_magpie_compositions[0].feature_vector(stats=self.stats),
+            np.ndarray,
+        )
         assert len(
-            Fe2O3_magpie.feature_vector(stats=stats)
-        ) == Fe2O3_magpie.embedding.dim * len(stats)
+            self.valid_magpie_compositions[0].feature_vector(stats=self.stats)
+        ) == self.valid_magpie_compositions[0].embedding.dim * len(self.stats)
         # Test that the feature vector function works with a single stat
-        assert isinstance(Fe2O3_magpie.feature_vector(stats="mean"), np.ndarray)
+        assert isinstance(
+            self.valid_magpie_compositions[0].feature_vector(stats="mean"), np.ndarray
+        )
 
     def test_composition_featuriser(self):
         """Test the composition featuriser function."""
-        formulas = ["Fe2O3", "Li7La3ZrO12", "CsPbI3"]
+        formulas = self.formulas[:3]
         formula_df = pd.DataFrame(formulas, columns=["formula"])
         assert isinstance(composition.composition_featuriser(formula_df), pd.DataFrame)
         assert composition.composition_featuriser(formula_df).shape == (3, 2)

From d59e2f15736cf2d5437abed9c8d4b7abf08ba2b8 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 16:28:41 +0100
Subject: [PATCH 24/30] Updated CHANGELOG.md

---
 CHANGELOG.md | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 28c87f8..3d56a35 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,34 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+<!-- insertion marker -->
+## Unreleased
+
+<small>[Compare with latest](https://github.com/WMD-group/ElementEmbeddings/compare/v0.1.1...HEAD)</small>
+
+### Added
+
+- Added test for dimension plotter in 3D ([ef37daf](https://github.com/WMD-group/ElementEmbeddings/commit/ef37daff6aa824c3d9917fa1ba26fc37b95a9951) by Anthony Onwuli).
+- Added test for plotting euclidean heatmap ([e9cc5ed](https://github.com/WMD-group/ElementEmbeddings/commit/e9cc5ed5508e624420b1330973425572ff5b1628) by Anthony Onwuli).
+- Added deprecation warning to old plotting function ([542e2f2](https://github.com/WMD-group/ElementEmbeddings/commit/542e2f2e6bd96b0f0e1624192cb9a9a98fb3dfcc) by Anthony Onwuli).
+- Added functions to test PCA and UMAP for Embedding ([b7ccc8f](https://github.com/WMD-group/ElementEmbeddings/commit/b7ccc8f41384e5e6095090aa016088279b5a0439) by Anthony Onwuli).
+- Added test function for tSNE for Embedding class ([aaa1472](https://github.com/WMD-group/ElementEmbeddings/commit/aaa147279ba609984482813df2ce9530420da2be) by Anthony Onwuli).
+- Added more tests for compute metrics function ([c4055bc](https://github.com/WMD-group/ElementEmbeddings/commit/c4055bcdad6e5bd7832a8568767ced72cd9cdfd9) by Anthony Onwuli).
+- Added test for computing spearman's rank ([5f715aa](https://github.com/WMD-group/ElementEmbeddings/commit/5f715aaa3ba339b5e01012cb0a40c44652481b55) by Anthony Onwuli).
+- Added more dataframe test functions ([edeeb87](https://github.com/WMD-group/ElementEmbeddings/commit/edeeb8714ae80b194159738b562606819ffc3ccb) by Anthony Onwuli).
+- Added test for removing multiple elements ([b69d806](https://github.com/WMD-group/ElementEmbeddings/commit/b69d80699cad211166ff1b112886d19d387890b5) by Anthony Onwuli).
+- Added test function for removing elements ([664cbbf](https://github.com/WMD-group/ElementEmbeddings/commit/664cbbf1846757b7d018c199745b6227465c0268) by Anthony Onwuli).
+- Added setUpClass to test_core.py ([7cb8ab6](https://github.com/WMD-group/ElementEmbeddings/commit/7cb8ab6d3b731d04831cdfe83a90b926ab1e2a1b) by Anthony Onwuli).
+- Added tests for `as_dataframe` method ([7256c23](https://github.com/WMD-group/ElementEmbeddings/commit/7256c23d8d2840b77983424ee9247a90f1caaded) by Anthony Onwuli).
+- Added more tests to the Embedding loading function ([7f9f87b](https://github.com/WMD-group/ElementEmbeddings/commit/7f9f87b987a77f1d4b73cf9fed289a5d9a028417) by Anthony Onwuli).
+- Added test functions for loading csv and json ([87ba958](https://github.com/WMD-group/ElementEmbeddings/commit/87ba9581c506bc16aa377961da28c0cbe60e80de) by Anthony Onwuli).
+- Added test embedding json file ([188aea4](https://github.com/WMD-group/ElementEmbeddings/commit/188aea48e21b3c3d5a1b9624a9885b94f14b2fcc) by Anthony Onwuli).
+- Added test embedding csv file ([173bcee](https://github.com/WMD-group/ElementEmbeddings/commit/173bcee057173ec1a48cdc7bb3141406236119ce) by Anthony Onwuli).
+
+### Removed
+
+- Removed an else block from `load_data` ([5532de6](https://github.com/WMD-group/ElementEmbeddings/commit/5532de6d050580382f0fa9688be96f0e9cd231ec) by Anthony Onwuli).
+
 <!-- insertion marker -->
 ## [v0.1.1](https://github.com/WMD-group/ElementEmbeddings/releases/tag/v0.1.1) - 2023-07-05
 

From e9278c579a031643576f137196aad34e0f5ea98f Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 16:39:54 +0100
Subject: [PATCH 25/30] Added dev & doc reqs and updated version no.

---
 setup.py | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 6497cd0..21b3b27 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 module_dir = os.path.dirname(os.path.abspath(__file__))
 
-VERSION = "0.1.1"
+VERSION = "0.2.0"
 DESCRIPTION = "Element Embeddings"
 with open(os.path.join(module_dir, "README.md"), encoding="utf-8") as f:
     LONG_DESCRIPTION = f.read()
@@ -37,6 +37,26 @@
         "umap-learn==0.5.3",
         "adjustText==0.8",
     ],
+    extra_requires={
+        "dev": [
+            "pre-commit==2.20.0",
+            "black==23.3.0",
+            "isort==5.12.0",
+            "pytest==7.2.1",
+            "pytest-subtests==0.10.0",
+            "nbqa==1.5.3",
+            "pyupgrade==3.3.1",
+            "flake8==6.0.0",
+            "autopep8==2.0.1",
+            "pytest-cov==4.1.0",
+        ],
+        "docs": [
+            "mkdocs==1.4.3",
+            "mkdocs-material==9.1.17",
+            "mkdocstrings ==0.21.2",
+            "mkdocstrings-python == 1.0.0",
+        ],
+    },
     classifiers=[
         "Programming Language :: Python",
         "Programming Language :: Python :: 3.8",

From 8e28e9a09550bfcaf21ec4d95989cd031d717596 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 17:12:00 +0100
Subject: [PATCH 26/30] Fixed spelling error for extras_require setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 21b3b27..6a71566 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@
         "umap-learn==0.5.3",
         "adjustText==0.8",
     ],
-    extra_requires={
+    extras_require={
         "dev": [
             "pre-commit==2.20.0",
             "black==23.3.0",

From c69817fef331e203fb3861e603c7c0176097e51f Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 17:17:39 +0100
Subject: [PATCH 27/30] Removed outdated installation instructions

---
 README.md | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/README.md b/README.md
index 8cd0fac..c7fa406 100644
--- a/README.md
+++ b/README.md
@@ -41,11 +41,6 @@ The latest stable release can be installed via pip using:
 ```bash
 pip install ElementEmbeddings
 ```
-The latest version can be installed using:
-
-```bash
-pip install git+git://github.com/WMD-group/ElementEmbeddings.git
-```
 
 For development, you can clone the repository and install the package in editable mode.
 To clone the repository and make a local installation, run the following commands:

From 761227c25ed7404d26a64f2814c7fa1b4bf40f1c Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 17:22:15 +0100
Subject: [PATCH 28/30] Updated README.md

---
 README.md | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index c7fa406..e59034c 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,6 @@ ElementEmbeddings
 [![documentation](https://img.shields.io/badge/docs-mkdocs%20material-blue.svg?style=flat)](https://wmd-group.github.io/ElementEmbeddings/)
 ![python version](https://img.shields.io/pypi/pyversions/elementembeddings)
 
-
 The **Element Embeddings** package provides high-level tools for analysing elemental
 embeddings data. This primarily involves visualising the correlation between
 embedding schemes using different statistical measures.
@@ -37,11 +36,20 @@ importing the class.
 
 Installation
 --------
+
 The latest stable release can be installed via pip using:
+
 ```bash
 pip install ElementEmbeddings
 ```
 
+For installing the development or documentation dependencies via pip:
+
+```bash
+pip install "ElementEmbeddings[dev]"
+pip install "ElementEmbeddings[docs]"
+```
+
 For development, you can clone the repository and install the package in editable mode.
 To clone the repository and make a local installation, run the following commands:
 
@@ -75,4 +83,3 @@ We can access some of the properties of the `Embedding` class. For example, we c
 The magpie representation has embeddings of dimension 22
 ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk']
 ```
-

From 6f74f549411c49afa0c4d56a72d8d885479bb953 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 17:22:39 +0100
Subject: [PATCH 29/30] Updated changelog

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3d56a35..13cae96 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### Added
 
+- Added dev & doc reqs and updated version no. ([e9278c5](https://github.com/WMD-group/ElementEmbeddings/commit/e9278c579a031643576f137196aad34e0f5ea98f) by Anthony Onwuli).
 - Added test for dimension plotter in 3D ([ef37daf](https://github.com/WMD-group/ElementEmbeddings/commit/ef37daff6aa824c3d9917fa1ba26fc37b95a9951) by Anthony Onwuli).
 - Added test for plotting euclidean heatmap ([e9cc5ed](https://github.com/WMD-group/ElementEmbeddings/commit/e9cc5ed5508e624420b1330973425572ff5b1628) by Anthony Onwuli).
 - Added deprecation warning to old plotting function ([542e2f2](https://github.com/WMD-group/ElementEmbeddings/commit/542e2f2e6bd96b0f0e1624192cb9a9a98fb3dfcc) by Anthony Onwuli).
@@ -29,8 +30,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Added test embedding json file ([188aea4](https://github.com/WMD-group/ElementEmbeddings/commit/188aea48e21b3c3d5a1b9624a9885b94f14b2fcc) by Anthony Onwuli).
 - Added test embedding csv file ([173bcee](https://github.com/WMD-group/ElementEmbeddings/commit/173bcee057173ec1a48cdc7bb3141406236119ce) by Anthony Onwuli).
 
+### Fixed
+
+- Fixed spelling error for extras_require setup.py ([8e28e9a](https://github.com/WMD-group/ElementEmbeddings/commit/8e28e9a09550bfcaf21ec4d95989cd031d717596) by Anthony Onwuli).
+
 ### Removed
 
+- Removed outdated installation instructions ([c69817f](https://github.com/WMD-group/ElementEmbeddings/commit/c69817fef331e203fb3861e603c7c0176097e51f) by Anthony Onwuli).
 - Removed an else block from `load_data` ([5532de6](https://github.com/WMD-group/ElementEmbeddings/commit/5532de6d050580382f0fa9688be96f0e9cd231ec) by Anthony Onwuli).
 
 <!-- insertion marker -->

From c1d1816f53ed51e009a369ae7f240eb95e2c1265 Mon Sep 17 00:00:00 2001
From: Anthony Onwuli <anthony.onwuli16@imperial.ac.uk>
Date: Fri, 7 Jul 2023 17:28:41 +0100
Subject: [PATCH 30/30] Update CITATION.cff

---
 CITATION.cff | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 6c4b898..d12ab06 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -36,5 +36,5 @@ keywords:
   - element representation
 license: MIT
 commit: d3f30602abf825ba3dcd5f247694a174a358ef49
-version: '0.1'
-date-released: '2023-06-30'
+version: '0.2.0'
+date-released: '2023-07-07'