Add codespell support: config, action (to detect new) + get some typo…

…s fixed (#671) * Add github action to codespell main on push and PRs * Add rudimentary codespell config * codespell ignore some words etc * ignore infarctions * Ignore all input files * [DATALAD RUNCMD] run codespell throughout fixing typo automagically === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --------- Co-authored-by: Chris Mungall <cjm@berkeleybop.org>
INCATools · Jan 20, 2024 · d139e99 · d139e99
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diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/docs/datamodels/cross-ontology-diff/Objectidentifier.md b/docs/datamodels/cross-ontology-diff/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/lexical-index/Objectidentifier.md b/docs/datamodels/lexical-index/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/mapping-rules/Objectidentifier.md b/docs/datamodels/mapping-rules/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/obograph/Graph.md b/docs/datamodels/obograph/Graph.md
@@ -266,7 +266,7 @@ attributes:
     name: nodes
     description: All nodes present in a graph. This includes class nodes as well as
       supporting nodes, including nodes representing relationship types, subsets,
-      annotation proeprties, etc
+      annotation properties, etc
     from_schema: https://github.com/geneontology/obographs
     rank: 1000
     multivalued: true

diff --git a/docs/datamodels/obograph/Objectidentifier.md b/docs/datamodels/obograph/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/obograph/nodes.md b/docs/datamodels/obograph/nodes.md
@@ -1,5 +1,5 @@
 # Slot: nodes
-_All nodes present in a graph. This includes class nodes as well as supporting nodes, including nodes representing relationship types, subsets, annotation proeprties, etc_
+_All nodes present in a graph. This includes class nodes as well as supporting nodes, including nodes representing relationship types, subsets, annotation properties, etc_
 
 
 URI: [obographs:nodes](https://github.com/geneontology/obographs/nodes)
@@ -56,7 +56,7 @@ URI: [obographs:nodes](https://github.com/geneontology/obographs/nodes)
 ```yaml
 name: nodes
 description: All nodes present in a graph. This includes class nodes as well as supporting
-  nodes, including nodes representing relationship types, subsets, annotation proeprties,
+  nodes, including nodes representing relationship types, subsets, annotation properties,
   etc
 from_schema: https://github.com/geneontology/obographs
 rank: 1000

diff --git a/docs/datamodels/ontology-metadata/Objectidentifier.md b/docs/datamodels/ontology-metadata/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/search/Objectidentifier.md b/docs/datamodels/search/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/search/SearchBaseConfiguration.md b/docs/datamodels/search/SearchBaseConfiguration.md
@@ -132,7 +132,7 @@ attributes:
     description: An individual search term. The syntax is determined by the syntax
       slot
     comments:
-    - This slot is optional when the configuration is used to paramterize multiple
+    - This slot is optional when the configuration is used to parameterize multiple
       searches
     - If multiple terms are provided this is treated as a union query
     from_schema: https://w3id.org/oak/search-datamodel
@@ -222,7 +222,7 @@ attributes:
     description: An individual search term. The syntax is determined by the syntax
       slot
     comments:
-    - This slot is optional when the configuration is used to paramterize multiple
+    - This slot is optional when the configuration is used to parameterize multiple
       searches
     - If multiple terms are provided this is treated as a union query
     from_schema: https://w3id.org/oak/search-datamodel

diff --git a/docs/datamodels/search/search_terms.md b/docs/datamodels/search/search_terms.md
@@ -36,7 +36,7 @@ URI: [ontosearch:search_terms](https://w3id.org/oak/search-datamodel/search_term
 
 ## Comments
 
-* This slot is optional when the configuration is used to paramterize multiple searches
+* This slot is optional when the configuration is used to parameterize multiple searches
 * If multiple terms are provided this is treated as a union query
 
 ## Identifier and Mapping Information
@@ -62,7 +62,7 @@ URI: [ontosearch:search_terms](https://w3id.org/oak/search-datamodel/search_term
 name: search_terms
 description: An individual search term. The syntax is determined by the syntax slot
 comments:
-- This slot is optional when the configuration is used to paramterize multiple searches
+- This slot is optional when the configuration is used to parameterize multiple searches
 - If multiple terms are provided this is treated as a union query
 from_schema: https://w3id.org/oak/search-datamodel
 rank: 1000

diff --git a/docs/datamodels/summary-statistics/Objectidentifier.md b/docs/datamodels/summary-statistics/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/text-annotator/Objectidentifier.md b/docs/datamodels/text-annotator/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/datamodels/validation/Objectidentifier.md b/docs/datamodels/validation/Objectidentifier.md
@@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)
 
 ## Comments
 
-* Used for inheritence and type checking
+* Used for inheritance and type checking
 
 ## Identifier and Mapping Information
 

diff --git a/docs/faq/architecture.rst b/docs/faq/architecture.rst
@@ -67,7 +67,7 @@ OAK uses a mixture of native an external data models.
 
 Native data models have the OAK w3id namespace - for example, `<https://w3id.org/oak/class-enrichment>`_.
 
-What is an interator and why does OAK use them so much?
+What is an iterator and why does OAK use them so much?
 ---------------------
 
 OAK uses iterators in place of lists in a lot of places, in order to make the

diff --git a/docs/glossary.rst b/docs/glossary.rst
@@ -195,7 +195,7 @@ For a deeper dive into some of these concepts, see the :ref:`guide`.
    Ancestor
     The :term:`Ancestor` of an entity is the set of all entities that are reachable by following
     all :term:`Relationship`s, from :term:`subject` or :term:`object`. Ancestor traversal is frequently
-    paramaterized by a set of :term:`Predicates<Predicate>`. The concept of :term:`Ancestor` and
+    parameterized by a set of :term:`Predicates<Predicate>`. The concept of :term:`Ancestor` and
     graph traversal is closely related to the concept of :term:`Entailment<Entailed Axiom>` in :term:`OWL`.
 
     - See also :ref:`relationships_and_graphs` in the Guide.

diff --git a/docs/guide/curies-and-uris.rst b/docs/guide/curies-and-uris.rst
@@ -117,7 +117,7 @@ can understand. These can be used in the same way:
     subject	subject_label	predicate	predicate_label	object	object_label
     schema:Person	Person	rdfs:subClassOf	None	schema:Thing	Thing
 
-Futher reading
+Further reading
 --------------
 
 * `OBO Foundry Identifiers <https://obofoundry.org/id-policy>`_
diff --git a/docs/howtos/fhir-conversions.rst b/docs/howtos/fhir-conversions.rst
@@ -67,7 +67,7 @@ concepts that are not native to that CodeSystem. In cases where they do appear,
 references, unless this flag is present, in which case the converter will attempt to construct CURIEs.
 
 predicate_period_replacement (default=False): _Predicates URIs populated into `CodeSystem.
-concept.property.code` and `CodeSystem.concept.property.code`, but the popular FHIR server "HAPI" has a bug in whih
+concept.property.code` and `CodeSystem.concept.property.code`, but the popular FHIR server "HAPI" has a bug in which
 periods '.' cause errors. If this flag is present, periods will be replaced with underscores '_'.
 
 Example:

diff --git a/docs/intro/tutorial07.rst b/docs/intro/tutorial07.rst
@@ -14,7 +14,7 @@ The :ref:`sql_implementation` wraps SQLite or any relational database.
 Download a SQLite file
 ----------------
 
-You can download ready made SQLite files for any :term:`OBO` Libray ontology
+You can download ready made SQLite files for any :term:`OBO` Library ontology
 
 For example: the Cell Ontology (CL) is available from https://s3.amazonaws.com/bbop-sqlite/cl.db.gz
 

diff --git a/notebooks/Commands/DiffViaMappings.ipynb b/notebooks/Commands/DiffViaMappings.ipynb
@@ -690,7 +690,7 @@
     "\n",
     "### Non-entailed relationships\n",
     "\n",
-    "i.e. this is an edge in UBERON that corresonds to a different kind of edge in ZFA (or vice versa), where the former\n",
+    "i.e. this is an edge in UBERON that corresponds to a different kind of edge in ZFA (or vice versa), where the former\n",
     "doesn't subsume the latter.\n",
     "\n",
     "For example, in UBERON PNS *part_of* NS; in ZFA PNS *is_a* NS"

diff --git a/notebooks/Commands/Enrichment.ipynb b/notebooks/Commands/Enrichment.ipynb
@@ -889,7 +889,7 @@
    "id": "b37993c2-f9b3-47a5-bd09-156eab378f49",
    "metadata": {},
    "source": [
-    "This is identical to the gene list in the original examle, and can be used in the same way"
+    "This is identical to the gene list in the original example, and can be used in the same way"
    ]
   },
   {

diff --git a/notebooks/Commands/TaxonConstraints.ipynb b/notebooks/Commands/TaxonConstraints.ipynb
@@ -311,7 +311,7 @@
    "source": [
     "## Evaluating Candidate taxon constraints\n",
     "\n",
-    "The related `apply-taxon-constraints` commmand can be used to test taxon constraints\n",
+    "The related `apply-taxon-constraints` command can be used to test taxon constraints\n",
     "\n"
    ]
   },

diff --git a/notebooks/Developers-Tutorial.ipynb b/notebooks/Developers-Tutorial.ipynb
@@ -125,7 +125,7 @@
     "![images/oak-docs-code.png](images/oak-docs-code.png)\n",
     "\n",
     "If you click the \"copy\" button it will copy the code only (no `>>>`s, and no output) such that you\n",
-    "can paste directly into a Pythin REPL or a notebook (provided the paths are preserved).\n",
+    "can paste directly into a Python REPL or a notebook (provided the paths are preserved).\n",
     "\n",
     "E.g. try copying this section from the docs\n",
     "\n",
@@ -256,7 +256,7 @@
     "The [BasicOntologyInterface](https://incatools.github.io/ontology-access-kit/packages/interfaces/basic) provides basic methods that encompass the majority of what most people need to do when\n",
     "working with ontologies - lookups of various kinds as well as simple graph operations.\n",
     "\n",
-    "OAK has the architectural concept of separating interfaces from implementatations. It helps to read about this concept, but for now you don't need to worry about it. We are using the sql adapter which fully *implements* almost all the existing OAK interfaces"
+    "OAK has the architectural concept of separating interfaces from implementations. It helps to read about this concept, but for now you don't need to worry about it. We are using the sql adapter which fully *implements* almost all the existing OAK interfaces"
    ]
   },
   {
@@ -313,7 +313,7 @@
     "\n",
     "Let's try working with descendants.\n",
     "\n",
-    "This time we are going to demonstate how OAK deals with collections.\n",
+    "This time we are going to demonstrate how OAK deals with collections.\n",
     "\n",
     "__note__ _we expect the following code **not** to work_"
    ]

diff --git a/notebooks/Lessons/PrefixMaps.ipynb b/notebooks/Lessons/PrefixMaps.ipynb
@@ -869,7 +869,7 @@
       "ERROR:root:Multiple labels for OAE:0000352 = ['a pain AE that occurs in shoulder', 'shoulder pain is a pain iin or around the shoulder joint']\n",
       "WARNING:root:Multiple labels for OAE:0001610 = abdomen crushing AE != blood folate level abnormal AE\n",
       "\n",
-      "ERROR:root:Multiple labels for OAE:0001610 = ['a metabolic and nutritional investigation result abnormal AE that is charaterized by an abnormal blood folate level', 'This is an AE which is a symptom associated with both non-serious and serious medical issues.']\n",
+      "ERROR:root:Multiple labels for OAE:0001610 = ['a metabolic and nutritional investigation result abnormal AE that is characterized by an abnormal blood folate level', 'This is an AE which is a symptom associated with both non-serious and serious medical issues.']\n",
       "WARNING:root:Multiple labels for OAE:0001628 = blood pH decreased AE\n",
       " != hernial eventration AE\n",
       "ERROR:root:Multiple labels for OAE:0001628 = ['This is an AE which is the protrusion of contents of the abdomen through a defect or weakness in the abdominal wall.', 'a blood pH abnormal AE that is characterized by a decreased blood pH']\n",

diff --git a/notebooks/Lessons/Why-predicates-are-important.ipynb b/notebooks/Lessons/Why-predicates-are-important.ipynb
@@ -563,7 +563,7 @@
     "\n",
     "## So how do we handle these?\n",
     "\n",
-    "At this point you might be thinking it makes no sense to use measures like semantic similarity over cyclic graphs. Or that it may be necessary to include ad-hoc measures like maximim distance. _But this isn't the case_\n",
+    "At this point you might be thinking it makes no sense to use measures like semantic similarity over cyclic graphs. Or that it may be necessary to include ad-hoc measures like maximum distance. _But this isn't the case_\n",
     "\n",
     "Because ontology graphs are _existential graphs_ over concepts, where the existence of the subject depends on the existence of the object, you can still use algorithms designed with concepts of \"ancestors\" and \"descendants\". The overall structure of the relation graph will still (in general) follow a pattern of narrowing down to more general concepts.\n",
     "\n",

diff --git a/notebooks/Monarch/PhenIO-Tutorial.ipynb b/notebooks/Monarch/PhenIO-Tutorial.ipynb
@@ -289,7 +289,7 @@
     "\n",
     "#### siblings\n",
     "\n",
-    "Next we will explore siblings. Again, we paramaterize the predicate list to avoid flooding results:"
+    "Next we will explore siblings. Again, we parameterize the predicate list to avoid flooding results:"
    ]
   },
   {

diff --git a/notebooks/Neuro/CL-Neuro-Tutorial.ipynb b/notebooks/Neuro/CL-Neuro-Tutorial.ipynb
@@ -1379,7 +1379,7 @@
    "source": [
     "### Complex queries\n",
     "\n",
-    "We can also make use of entailed egdes in complex boolean queries.\n",
+    "We can also make use of entailed edges in complex boolean queries.\n",
     "\n",
     "The following query is an *intersection* (using `and`) syntax of\n",
     "\n",

diff --git a/pyproject.toml b/pyproject.toml
@@ -79,3 +79,8 @@ profile = "black"
 multi_line_output = 3
 include_trailing_comma = true
 reverse_relative = true
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,poetry.lock,*.obo,*.ttl,*.ofn,*.gaf,*.tsv,*.json,input'
+ignore-regex = '(^\s*"image/\S+": ".*|[a-z]*\.\.\.)'
+ignore-words-list = 'ptd,ot,nd,ser,oger,gard,te,fo,fof,bu,ue,ois,processus,infarction,infarctions'
diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py
@@ -1258,7 +1258,7 @@ def statistics(
     For bundled ontologies, we recommend some kind of partitioning, such as via
     defined roots, or via the CURIE prefix, using the ``--group-by-prefix`` option.
 
-    Ouput formats:
+    Output formats:
 
     The recommended output types for this command are yaml, json, or csv.
     The default output type is yaml, following the SummaryStatistics data model.
@@ -2027,7 +2027,7 @@ def ancestors(
 
     This will show ancestry over the full relationship graph. Like any relational
     OAK command, this can be filtered by relationship type (predicate), using --predicate (-p).
-    For exampple, constrained to is-a and part-of:
+    For example, constrained to is-a and part-of:
 
         runoak -i cl.owl ancestors CL:4023094 -p i,BFO:0000050
 

diff --git a/src/oaklib/converters/obo_graph_to_fhir_converter.py b/src/oaklib/converters/obo_graph_to_fhir_converter.py
@@ -158,7 +158,7 @@ def convert(
                                             will attempt to construct CURIEs. (not implemented)
         :param predicate_period_replacement: Predicates URIs populated into `CodeSystem.concept.property.packages`
                                              and `CodeSystem.concept.property.packages`, but the HAPI FHIR server
-                                             has a bug in whih periods '.' cause errors. If this flag is present,
+                                             has a bug in which periods '.' cause errors. If this flag is present,
                                              periods will be replaced with underscores '_'.
         :return: FHIR CodeSystem object
         """

diff --git a/src/oaklib/datamodels/obograph.yaml b/src/oaklib/datamodels/obograph.yaml
@@ -228,7 +228,7 @@ slots:
     inlined_as_list: true
     description: >-
       All nodes present in a graph. This includes class nodes as well as supporting nodes, including
-      nodes representing relationship types, subsets, annotation proeprties, etc
+      nodes representing relationship types, subsets, annotation properties, etc
   edges:
     multivalued: true
     range: Edge

diff --git a/src/oaklib/datamodels/search_datamodel.yaml b/src/oaklib/datamodels/search_datamodel.yaml
@@ -56,7 +56,7 @@ classes:
         description: >-
           An individual search term. The syntax is determined by the syntax slot
         comments:
-          - This slot is optional when the configuration is used to paramterize multiple searches
+          - This slot is optional when the configuration is used to parameterize multiple searches
           - If multiple terms are provided this is treated as a union query
       syntax:
         range: SearchTermSyntax

diff --git a/src/oaklib/datamodels/taxon_constraints.yaml b/src/oaklib/datamodels/taxon_constraints.yaml
@@ -113,7 +113,7 @@ classes:
       predicate:
         slot_uri: rdf:predicate
         range: PredicateTerm
-        description: The relationship type for the contraint (e.g. in_taxon, never_in taxon)
+        description: The relationship type for the constraint (e.g. in_taxon, never_in taxon)
         todos:
           - define a value set of this
       asserted:

diff --git a/src/oaklib/interfaces/association_provider_interface.py b/src/oaklib/interfaces/association_provider_interface.py
@@ -170,7 +170,7 @@ def associations(
         PomBase:SPAC1142.02c sgt2
         ...
 
-        When determinining a match on `objects`, the predicates in ``object_closure_predicates`` is used.
+        When determining a match on `objects`, the predicates in ``object_closure_predicates`` is used.
         We recommend you always explicitly provide this. A good choice is typically IS_A and PART_OF for
         ontologies like GO, Uberon, CL, ENVO.
 

diff --git a/src/oaklib/interfaces/basic_ontology_interface.py b/src/oaklib/interfaces/basic_ontology_interface.py
@@ -91,7 +91,7 @@ class BasicOntologyInterface(OntologyInterface, ABC):
     horsetail nucleus
     nucleus
 
-    This omits metdata about the synonym, such as the predicate, source, and type.
+    This omits metadata about the synonym, such as the predicate, source, and type.
     For this more granular view, the :ref:`obograph_interface` can be used.
 
     Basic concepts:

diff --git a/src/oaklib/interfaces/mapping_provider_interface.py b/src/oaklib/interfaces/mapping_provider_interface.py
@@ -223,7 +223,7 @@ def normalize_prefix(
         """
         Normalize a CURIE to a target prefix.
 
-        If a prefix alias map is supplied, this is takes precendence:
+        If a prefix alias map is supplied, this is takes precedence:
 
         >>> from oaklib import get_adapter
         >>> adapter = get_adapter("tests/input/go-nucleus.obo")

diff --git a/src/oaklib/interfaces/taxon_constraint_interface.py b/src/oaklib/interfaces/taxon_constraint_interface.py
@@ -321,7 +321,7 @@ def filter_nr_never(self, taxa: Collection[TAXON_CURIE]) -> List[TAXON_CURIE]:
         return list(include)
 
     def _fill_missing(self, st: SubjectTerm):
-        # fills in trivial inferrable information
+        # fills in trivial inferable information
         for tc in st.only_in:
             if not tc.subject:
                 tc.subject = st.id
-Original file line number
+Diff line change
@@ Expand Up / @@ -289,7 +289,7 @@ @@
         "\n",
         "#### siblings\n",
         "\n",
-        "Next we will explore siblings. Again, we paramaterize the predicate list to avoid flooding results:"
+        "Next we will explore siblings. Again, we parameterize the predicate list to avoid flooding results:"
        ]
       },
       {
@@ Expand Down @@