hsolbrig · yarikoptic · Nov 22, 2024 · Nov 22, 2024 · Nov 22, 2024 · Nov 22, 2024
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,25 @@
+# Codespell configuration is within setup.cfg
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/README.md b/README.md
@@ -141,7 +141,7 @@ At the moment, there are 1088 tests, of which:
 1) (52) sht:LexicalBNode, sht:ToldBNode and sht:BNodeShapeLabel test non-blank blank nodes (`rdflib` does not preserve bnode "identity")
 2) (18) sht:Import Uses ShEx 2.1 IMPORT feature -- not yet implemented (three aren't tagged)
 3) (3) Uses manifest shapemap feature -- not yet implemented
-4) (2) sht:relativeIRI -- this isn't a real problem, but we havent taken time to deal with this in the test harness
+4) (2) sht:relativeIRI -- this isn't a real problem, but we haven't taken time to deal with this in the test harness
 5) (6) `rdflib` has a parsing error when escaping single quotes. (Issue submitted, awaiting release)
 
 As mentioned above, at the moment this is as literal an implementation of the specification as was sensible.  This means, in particular, that we are less than clever when it comes to partition management.

diff --git a/ancilliary/__init__.py → ancillary/__init__.py b/ancilliary/__init__.py → ancillary/__init__.py
diff --git a/ancilliary/earlreport.py → ancillary/earlreport.py b/ancilliary/earlreport.py → ancillary/earlreport.py
@@ -42,7 +42,7 @@
 
 <https://github.com/hsolbrig> a foaf:Person, earl:Assertor;
   foaf:name "Harold Solbrig";
-  foaf:title "Implementor";
+  foaf:title "Implementer";
   foaf:homepage <https://github.com/hsolbrig> ."""
 
 EARL = Namespace("http://www.w3.org/ns/earl#")

diff --git a/notebooks/PrefixLib.ipynb b/notebooks/PrefixLib.ipynb
@@ -47,7 +47,7 @@
     "\"\"\"\n",
     "p = PrefixLibrary(shex, rdf=str(RDF))\n",
     "\n",
-    "# Gives us acces to the PROV, GW and RDF namespaces\n",
+    "# Gives us access to the PROV, GW and RDF namespaces\n",
     "print(p.PROV)\n",
     "print(p.PROV.source)\n",
     "print(p.GW.g117)\n",
@@ -280,7 +280,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## We didn't overrite RDF because it was already defined on the import statement at the top of this document.\n",
+    "## We didn't overwrite RDF because it was already defined on the import statement at the top of this document.\n",
     "### This warning can be omitted:"
    ]
   },

diff --git a/notebooks/SPARQLEndpoints.ipynb b/notebooks/SPARQLEndpoints.ipynb
@@ -137,7 +137,7 @@
     "START=@:S1\n",
     "\n",
     ":S1 {foaf:page IRI{3} ;                     # one or more foaf pages\n",
-    "     drugbank:limsDrugId xsd:string       # ane exactly one drug id\n",
+    "     drugbank:limsDrugId xsd:string       # and exactly one drug id\n",
     "}\"\"\"\n",
     "\n",
     "\n",

diff --git a/notebooks/WikiSlurper.ipynb b/notebooks/WikiSlurper.ipynb
@@ -176,7 +176,7 @@
       "        \"erhebliche krankhafte Abweichung von der Norm im Erleben oder Verhalten\",\n",
       "        \"lidské onemocnění\",\n",
       "        \"mielen toiminnan poikkeama, joka aiheuttaa merkittävää kärsimystä ja toimintakyvyn laskua\",\n",
-      "        \"ohälsa i psyket, det vill säga i personligheten, emotionerna eller kognitionen, vilka primärt har psykiska orsaker\",\n",
+      "        \"ohälsa i psyket, det will säga i personligheten, emotionerna eller kognitionen, vilka primärt har psykiska orsaker\",\n",
       "        \"označenie pre výrazný odklon od spôsobu vnímania a správania psychicky zdravého jedinca\",\n",
       "        \"psigiese aandoening\",\n",
       "        \"psihološki poremećaj ili anomalija\",\n",

diff --git a/pyshex/shape_expressions_language/p5_3_shape_expressions.py b/pyshex/shape_expressions_language/p5_3_shape_expressions.py
@@ -25,7 +25,7 @@ def satisfies(cntxt: Context, n: Node, se: ShExJ.shapeExpr) -> bool:
             satisfies(n, se2, G, m).
             * Se is a ShapeAnd and for every shape expression se2 in shapeExprs, satisfies(n, se2, G, m).
             * Se is a ShapeNot and for the shape expression se2 at shapeExpr, notSatisfies(n, se2, G, m).
-            * Se is a ShapeExternal and implementation-specific mechansims not defined in this specification
+            * Se is a ShapeExternal and implementation-specific mechanisms not defined in this specification
             indicate success.
             * Se is a shapeExprRef and there exists in the schema a shape expression se2 with that id and
                       satisfies(n, se2, G, m).
@@ -77,7 +77,7 @@ def satisfiesShapeNot(cntxt: Context, n: Node, se: ShExJ.ShapeNot, _: DebugConte
 
 @trace_satisfies(True)
 def satisfiesExternal(cntxt: Context, n: Node, se: ShExJ.ShapeExternal, c: DebugContext) -> bool:
-    """ Se is a ShapeExternal and implementation-specific mechansims not defined in this specification indicate
+    """ Se is a ShapeExternal and implementation-specific mechanisms not defined in this specification indicate
      success.
      """
     if c.debug:

diff --git a/pyshex/shape_expressions_language/p5_6_schema_requirements.py b/pyshex/shape_expressions_language/p5_6_schema_requirements.py
@@ -1,4 +1,4 @@
-""" Implemention of `5.6 Schema Requirements <http://shex.io/shex-semantics/#schema-requirements>`_
+""" Implementation of `5.6 Schema Requirements <http://shex.io/shex-semantics/#schema-requirements>`_
 
 The semantics defined above assume two structural requirements beyond those imposed by the grammar of the
 abstract syntax. These ensure referential integrity and eliminate logical paradoxes such as those that arrise

diff --git a/pyshex/shape_expressions_language/p5_context.py b/pyshex/shape_expressions_language/p5_context.py
@@ -199,7 +199,7 @@ def __init__(self, g: Optional[Graph], s: Schema,
 
     def reset(self) -> None:
         """
-        Reset the context preceeding an evaluation
+        Reset the context preceding an evaluation
         """
         self.evaluating = set()
         self.assumptions = {}
@@ -363,7 +363,7 @@ def start_evaluating(self, n: Node, s: ShExJ.shapeExpr) -> Optional[bool]:
         :return: Assumed evaluation result.  If None, evaluation must be performed
         """
         if not s.id:
-            s.id = str(BNode())                 # Random permanant id
+            s.id = str(BNode())                 # Random permanent id
         key = (n, s.id)
 
         # We only evaluate a node once

diff --git a/pyshex/shex_evaluator.py b/pyshex/shex_evaluator.py
@@ -107,7 +107,7 @@ def rdf(self) -> str:
 
     @rdf.setter
     def rdf(self, rdf: Optional[Union[str, Graph]]) -> None:
-        """ Set the RDF DataSet to be evaulated.  If ``rdf`` is a string, the presence of a return is the
+        """ Set the RDF DataSet to be evaluated.  If ``rdf`` is a string, the presence of a return is the
         indicator that it is text instead of a location.
 
         :param rdf: File name, URL, representation of rdflib Graph

diff --git a/pyshex/utils/datatype_utils.py b/pyshex/utils/datatype_utils.py
@@ -20,7 +20,7 @@ def can_cast_to(v: Literal, dt: str) -> bool:
 
 
 def total_digits(n: Literal) -> Optional[int]:
-    """ 5.4.5 XML Schema Numberic Facet Constraints
+    """ 5.4.5 XML Schema Numeric Facet Constraints
 
      totaldigits and fractiondigits constraints on values not derived from xsd:decimal fail.
      """

diff --git a/pyshex/utils/deprecated.py b/pyshex/utils/deprecated.py
@@ -3,7 +3,7 @@
 
 def deprecated(func):
     """This is a decorator which can be used to mark functions
-    as deprecated. It will result in a warning being emmitted
+    as deprecated. It will result in a warning being emitted
     when the function is used."""
     # Note: copied from https://code.activestate.com/recipes/391367-deprecated/
     def newFunc(*args, **kwargs):

diff --git a/pyshex/utils/matchesEachOfEvaluator.py b/pyshex/utils/matchesEachOfEvaluator.py
@@ -19,7 +19,7 @@ def __init__(self, cntxt: Context, T: RDFGraph, expr: ShExJ.EachOf) -> None:
         """
         # tripleExpr = Union["EachOf", "OneOf", "TripleConstraint", tripleExprLabel]
         #
-        # For each tripleExpr in expressions deteremine the set of applicable predicates and their
+        # For each tripleExpr in expressions determine the set of applicable predicates and their
         # corresponding triples.
         #
         #       Case 1: predicate occurs in exactly one expression and expression references exactly one predicate

diff --git a/setup.cfg b/setup.cfg
@@ -28,3 +28,11 @@ packages =
 console_scripts =
     shexeval = pyshex.shex_evaluator:evaluate_cli
 
+
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+# TODO: data/ actually might benefit from some typos fixed
+skip = .git*,data,WikiSlurper.ipynb
+check-hidden = true
+ignore-regex = ^\s*"image/\S+": ".*
+ignore-words-list = te
diff --git a/tests/test_primer/SPARQLEndpoints.py b/tests/test_primer/SPARQLEndpoints.py
@@ -26,7 +26,7 @@
 START=@:S1
 
 :S1 {foaf:page IRI+ ;                     # one or more foaf pages
-     drugbank:limsDrugId xsd:string       # ane exactly one drug id
+     drugbank:limsDrugId xsd:string       # and exactly one drug id
 }"""
 
 

diff --git a/tests/test_pyshex_utils/test_partitions.py b/tests/test_pyshex_utils/test_partitions.py
@@ -209,7 +209,7 @@ def test_large_integer_partition(self):
 
     def test_large_filtered_integer(self):
         """ The purpose of this test is to make sure that the generators work all the way through. If there
-        is something in the pipeline that requires complet resolution, this test will never finish. """
+        is something in the pipeline that requires complete resolution, this test will never finish. """
         x = filtered_integer_partition(25, 20)
         [next(x) for _ in range(100)]
         self.assertEqual((

diff --git a/tests/test_shextest_validation/test_manifest_shex_shexc.py b/tests/test_shextest_validation/test_manifest_shex_shexc.py
@@ -3,7 +3,7 @@
 
 from rdflib import URIRef
 
-from ancilliary.earlreport import EARLPage
+from ancillary.earlreport import EARLPage
 from tests.utils.manifest_tester import ManifestEntryTestCase
 
 

diff --git a/tests/test_support_libraries/local_context.py b/tests/test_support_libraries/local_context.py
@@ -2,7 +2,7 @@
 from rdflib import URIRef, XSD
 from pyshex import PrefixLibrary
 
-""" This module is used to test the PrefixLibrary's ability to inject namespaces directoy into the containing module 
+""" This module is used to test the PrefixLibrary's ability to inject namespaces directory into the containing module 
 It is used in conjunction with test_prefixlib.test_add_to_module """
 
 pl = PrefixLibrary("""

diff --git a/tests/utils/manifest_tester.py b/tests/utils/manifest_tester.py
@@ -9,7 +9,7 @@
 import rdflib_shim
 shimin = rdflib_shim.RDFLIB_SHIM
 
-from ancilliary.earlreport import EARLPage
+from ancillary.earlreport import EARLPage
 from pyshex.shape_expressions_language.p5_2_validation_definition import isValid
 from pyshex.shape_expressions_language.p5_context import Context
 from pyshex.shapemap_structure_and_language.p3_shapemap_structure import ShapeAssociation, FixedShapeMap, START