Add codespell to pre-commit

WMD-group · Aug 19, 2024 · 7366279 · 7366279
1 parent cc1dac9
commit 7366279
Show file tree

Hide file tree

Showing 9 changed files with 165 additions and 384 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,3 +1,9 @@
+ci:
+  autoupdate_schedule: quarterly
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
+  skip: [eslint, pyright]
+
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.5.5
@@ -39,3 +45,11 @@ repos:
     hooks:
       - id: pyright
         args: [--level, error]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+        args: [--toml, pyproject.toml]
+        additional_dependencies:
+          - tomli
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -55,7 +55,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - Fix package name in contributing.md ([075e657](https://github.com/WMD-group/ElementEmbeddings/commit/075e657d260aa72fca91c7f8cc57466235788426) by Anthony Onwuli).
 - Fixed bug with is_standarised attribute ([ebaf773](https://github.com/WMD-group/ElementEmbeddings/commit/ebaf773134c8ab4988f071da9eca2193e4340f60) by Anthony Onwuli).
-- Fixed composistion featuriser test ([3b729c9](https://github.com/WMD-group/ElementEmbeddings/commit/3b729c9584bf7cc4de2fd5c70baff41c8753800b) by Anthony Onwuli).
+- Fixed composition featuriser test ([3b729c9](https://github.com/WMD-group/ElementEmbeddings/commit/3b729c9584bf7cc4de2fd5c70baff41c8753800b) by Anthony Onwuli).
 - Fixed dim for linear/scalar representations ([f6cc681](https://github.com/WMD-group/ElementEmbeddings/commit/f6cc681ee4f343240f5bb4d49cf9dfc5fa89f455) by Anthony Onwuli).
 
 ### Changed

diff --git a/docs/embeddings/species.md b/docs/embeddings/species.md
@@ -1,6 +1,6 @@
 # Species Embeddings
 
-The `ElementEmbeddings` package has been expanded to incoporate representation of ionic species. We provide the literature source for these representations as well as the data source for which the files were obtained.
+The `ElementEmbeddings` package has been expanded to incorporate representation of ionic species. We provide the literature source for these representations as well as the data source for which the files were obtained.
 
 ## SkipSpecies
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -24,7 +24,7 @@ nav:
       - "Simple usage": tutorials.md
       - "Core usage (notebook)": tutorial/usage.ipynb
       - "Composition usage (notebook)": tutorial/composition.ipynb
-      - "Ionic Speices (notebook)": tutorial/species.ipynb
+      - "Ionic Species (notebook)": tutorial/species.ipynb
   - Embedding Schemes:
       - "Element Embeddings": "embeddings/element.md"
       - Species Embeddings: "embeddings/species.md"

diff --git a/pyproject.toml b/pyproject.toml
@@ -76,7 +76,7 @@ ignore = [
     "TRY003",  # Avoid specifying long messages outside the exception class
     "TRY300",  # Check for return statements in try blocks
     "TRY301",  # Check for raise statements within try blocks
-    "E741",    # Ambigous variable
+    "E741",    # Ambiguous variable
 ]
 exclude = ["Publications/*"]
 pydocstyle.convention = "google"
@@ -93,3 +93,106 @@ docstring-code-format = true
 typeCheckingMode = "off"
 reportPossiblyUnboundVariable = true
 reportUnboundVariable = true
+
+[tool.codespell]
+skip = "*.csv,*/site/*,Publication/element_similarity/**,*periodic-table*.json"
+check-filenames = true
+ignore-words-list = [
+            "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",
+        ]
diff --git a/src/elementembeddings/data/element_data/periodic-table-lookup-symbols.json b/src/elementembeddings/data/element_data/periodic-table-lookup-symbols.json
@@ -895,7 +895,7 @@
     ],
     "cpk-hex": "bfc2c7",
     "image": {
-      "title": "Titanium Crystal made with the van Arkel-de Booer Process. 87 grams, Orginial size in cm: 2.5 x 4",
+      "title": "Titanium Crystal made with the van Arkel-de Booer Process. 87 grams, Original size in cm: 2.5 x 4",
       "url": "https://upload.wikimedia.org/wikipedia/commons/e/ec/Titanium.jpg",
       "attribution": "Hi-Res Images ofChemical Elements, CC BY 3.0 <https://creativecommons.org/licenses/by/3.0>, via Wikimedia Commons, source: https://images-of-elements.com/titanium.php"
     },
@@ -1957,7 +1957,7 @@
     "image": {
       "title": "48 Cd Cadmium",
       "url": "https://images-of-elements.com/cadmium-4.jpg",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/cadmium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/cadmium.php"
     },
     "block": "d"
   },
@@ -4024,7 +4024,7 @@
     "image": {
       "title": "This is only an illustration, not mendelevium itself. Chemically similar to Thulium, the highly radioactive heavy metal emits very energetic \u03b1-radiation.",
       "url": "https://images-of-elements.com/s/mendelevium.jpg",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/mendelevium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/mendelevium.php"
     },
     "block": "f"
   },
@@ -4063,7 +4063,7 @@
     "image": {
       "title": "This is only an illustration, not nobelium itself. Nobelium can only be made in very small amounts and emits strong radiation of various kinds.",
       "url": "https://images-of-elements.com/nobelium.jpg",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/nobelium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/nobelium.php"
     },
     "block": "f"
   },
@@ -4102,7 +4102,7 @@
     "image": {
       "title": "This is only an illustration, not lawrencium itself. Lawrencium can only be made in very small amounts and emits strong radiation",
       "url": "https://images-of-elements.com/lawrencium.jpg",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/lawrencium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/lawrencium.php"
     },
     "block": "d"
   },
@@ -4141,7 +4141,7 @@
     "image": {
       "title": "Decay traces in a spark chamber, not of rutherfordium, but of a pion. This is a completely different, unrelated particle, but the decay of rutherfordium would make streaks there, too.",
       "url": "https://images-of-elements.com/s/rutherfordium.jpg",
-      "attribution": "Image \u00a9 CERN, Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/rutherfordium.php"
+      "attribution": "Image \u00a9 CERN, Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/rutherfordium.php"
     },
     "block": "d"
   },
@@ -4180,7 +4180,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/dubnium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/dubnium.php"
     },
     "block": "d"
   },
@@ -4219,7 +4219,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/seaborgium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/seaborgium.php"
     },
     "block": "d"
   },
@@ -4258,7 +4258,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/bohrium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/bohrium.php"
     },
     "block": "d"
   },
@@ -4297,7 +4297,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/hassium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/hassium.php"
     },
     "block": "d"
   },
@@ -4336,7 +4336,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/meitnerium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/meitnerium.php"
     },
     "block": "d"
   },
@@ -4375,7 +4375,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/darmstadtium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/darmstadtium.php"
     },
     "block": "d"
   },
@@ -4414,7 +4414,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/roentgenium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/roentgenium.php"
     },
     "block": "d"
   },
@@ -4453,7 +4453,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/copernicium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/copernicium.php"
     },
     "block": "d"
   },
@@ -4492,7 +4492,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/nihonium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/nihonium.php"
     },
     "block": "p"
   },
@@ -4531,7 +4531,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/flerovium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/flerovium.php"
     },
     "block": "p"
   },
@@ -4570,7 +4570,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/moscovium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/moscovium.php"
     },
     "block": "p"
   },
@@ -4609,7 +4609,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/livermorium.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/livermorium.php"
     },
     "block": "p"
   },
@@ -4648,7 +4648,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/tenessine.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/tenessine.php"
     },
     "block": "p"
   },
@@ -4687,7 +4687,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/oganesson.php"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com/oganesson.php"
     },
     "block": "p"
   },
@@ -4726,7 +4726,7 @@
     "image": {
       "title": "No Image Found",
       "url": "https://images-of-elements.com/s/transactinoid.png",
-      "attribution": "Chemical Elments A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com"
+      "attribution": "Chemical Elements A Virtual Museum under a Creative Commons Attribution 3.0 Unported License, source: https://images-of-elements.com"
     },
     "block": "s"
   }