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Merge pull request #17 from yarikoptic/enh-codespell
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add codespell support and fix typos it found
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cmungall authored Jan 16, 2024
2 parents 0b96a96 + f3aa2d4 commit fe56019
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23 changes: 23 additions & 0 deletions .github/workflows/codespell.yml
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# Codespell configuration is within pyproject.toml
---
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
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -123,7 +123,7 @@ The data model for transformations mirrors the data model for schemas:
- A top level `TransformationSpecification` class contains:
- Zero or more `ClassDerivation` objects, specifying how to map to a class, containing:
- Zero or more `SlotDerivation` objects, specifying how to map to a slot, containing:
- Zero or more `EnumDerivation` objects, specifying how to map permissable values.
- Zero or more `EnumDerivation` objects, specifying how to map permissible values.

See the [generated docs](https://linkml.github.io/linkml-transformer/)

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7 changes: 7 additions & 0 deletions pyproject.toml
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Expand Up @@ -47,3 +47,10 @@ profile = "black"
multi_line_output = 3
include_trailing_comma = true
reverse_relative = true

# Ref: https://github.com/codespell-project/codespell#using-a-config-file
[tool.codespell]
skip = '.git,*.pdf,*.svg,go.sum,*.lock'
check-hidden = true
ignore-regex = '(^\s*"image/\S+": ".*|\b(KEGG.BRITE|mor.nlm.nih.gov)\b)'
ignore-words-list = 'infarction,amination'
2 changes: 1 addition & 1 deletion src/docs/specification/compliance.md
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Expand Up @@ -30,7 +30,7 @@ Each test is designed to demonstrate:
- data mapping (transformation)
- derived schemas
- inversion (reverse transformation) (in some cases)
- compliation to other frameworks (coming soon)
- compilation to other frameworks (coming soon)

Feature Set: test\_map\_types
-----------------------------
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14 changes: 7 additions & 7 deletions tests/input/examples/biolink/source/biolink-model.yaml
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Expand Up @@ -1420,7 +1420,7 @@ slots:
to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read
using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using
the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression,
object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but doesnt make
object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but doesn't make
sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not
what we mean to say here: it causes increased expression of Gene Y)
Expand Down Expand Up @@ -3194,7 +3194,7 @@ slots:
and a condition (a phenotype or disease), where the
presence of the entity reduces or eliminates some or
all aspects of the condition.
# 'biological entity' currently includes 'exposure event' which covers alot of related ground
# 'biological entity' currently includes 'exposure event' which covers a lot of related ground
domain: named thing
range: disease or phenotypic feature
annotations:
Expand All @@ -3216,7 +3216,7 @@ slots:
environmental exposure, or some form of genetic variation)
and a condition (a phenotype or disease), where the presence
of the entity worsens some or all aspects of the condition.
# 'biological entity' currently includes 'exposure event' which covers alot of related ground
# 'biological entity' currently includes 'exposure event' which covers a lot of related ground
domain: biological entity
range: disease or phenotypic feature
annotations:
Expand Down Expand Up @@ -3287,7 +3287,7 @@ slots:
process or chemical entity that is used to treat the condition
domain: disease or phenotypic feature
range: chemical or drug or treatment
# range: chemical or drug or treatement
# range: chemical or drug or treatment
in_subset:
- translator_minimal
inverse: treats
Expand Down Expand Up @@ -5020,7 +5020,7 @@ slots:
The most upstream source of the knowledge expressed in an Association that an
implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort
is made to catalog the most upstream source of data in this property. Only one data source should be declared
primary in any association. "aggregator knowledge source" can be used to caputre non-primary sources.
primary in any association. "aggregator knowledge source" can be used to capture non-primary sources.
range: information resource
notes: >-
For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then
Expand Down Expand Up @@ -5199,7 +5199,7 @@ slots:
supporting documents:
is_a: association slot
description: >-
One or more referencable documents that report the statement expressed in an Association, or provide
One or more referenceable documents that report the statement expressed in an Association, or provide
information used as evidence supporting this statement.
range: uriorcurie
multivalued: true
Expand Down Expand Up @@ -7501,7 +7501,7 @@ classes:
in_subset:
- model_organism_database
narrow_mappings:
- SO:0000104 # polypeptide definde in SO conflates protein and polypeptide
- SO:0000104 # polypeptide defined in SO conflates protein and polypeptide
# Amino Acid, Peptide, or Protein
- STY:T116
# Amino Acid Sequence
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2 changes: 1 addition & 1 deletion tests/test_compliance/test_compliance_suite.py
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Expand Up @@ -60,7 +60,7 @@
- data mapping (transformation)
- derived schemas
- inversion (reverse transformation) (in some cases)
- compliation to other frameworks (coming soon)
- compilation to other frameworks (coming soon)
"""
)
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