cicd: fix hook names (#208)

.github/workflows/checks.yaml

@@ -68,9 +68,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        - cmd: "end-of-file-fixer"
-        - cmd: "trailing-whitespace"
-        - cmd: "mixed-line-ending"
+        hook:
+          - "end-of-file-fixer"
+          - "trailing-whitespace"
+          - "mixed-line-ending"
     steps:
       - uses: actions/checkout@v4
 
@@ -81,7 +82,7 @@ jobs:
 
       - uses: pre-commit/[email protected]
         with:
-          extra_args: ${{ matrix.cmd }} --all-files
+          extra_args: ${{ matrix.hook }} --all-files
   docs:
     runs-on: ubuntu-latest
     env:

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
 popd

tests/data/omim/omim_20240806.tsv

@@ -1,19 +1,19 @@
-# Copyright (c) 1966-2024 Johns Hopkins University. Use of this file adheres to the terms specified at https://omim.org/help/agreement
-# Generated: 2024-08-05
-# Prefix	MIM Number	Preferred Title; symbol	Alternative Title(s); symbol(s)	Included Title(s); symbols
-NULL	247640	LYMPHOBLASTIC LEUKEMIA, ACUTE, WITH LYMPHOMATOUS FEATURES; LALL	LYMPHOMATOUS ALL
-Percent	309200	MAJOR AFFECTIVE DISORDER 2; MAFD2	MANIC-DEPRESSIVE ILLNESS; MDI;; MANIC-DEPRESSIVE PSYCHOSIS, X-LINKED; MDX;; BIPOLAR AFFECTIVE DISORDER; BPAD
-Percent	613065	LEUKEMIA, ACUTE LYMPHOBLASTIC; ALL		LEUKEMIA, ACUTE LYMPHOBLASTIC, SUSCEPTIBILITY TO, 1, INCLUDED;; ALL1, INCLUDED;; LEUKEMIA, ACUTE LYMPHOCYTIC, SUSCEPTIBILITY TO, 1, INCLUDED;; LEUKEMIA, B-CELL ACUTE LYMPHOBLASTIC, SUSCEPTIBILITY TO, INCLUDED;; LEUKEMIA, T-CELL ACUTE LYMPHOBLASTIC, SUSCEPTIBILITY TO, INCLUDED;; LEUKEMIA, ACUTE LYMPHOBLASTIC, B-HYPERDIPLOID, SUSCEPTIBILITY TO, INCLUDED
-#
-#
-#
-#
-# MIM number prefix:
-# ------------------
-# Asterisk (*)  Gene
-# Plus (+)  Gene and phenotype, combined
-# Number Sign (#)  Phenotype, molecular basis known
-# Percent (%)  Phenotype or locus, molecular basis unknown
-# NULL (<null>)  Other, mainly phenotypes with suspected mendelian basis
-# Caret (^)  Entry has been removed from the database or moved to another entry
-#
+# Copyright (c) 1966-2024 Johns Hopkins University. Use of this file adheres to the terms specified at https://omim.org/help/agreement
+# Generated: 2024-08-05
+# Prefix	MIM Number	Preferred Title; symbol	Alternative Title(s); symbol(s)	Included Title(s); symbols
+NULL	247640	LYMPHOBLASTIC LEUKEMIA, ACUTE, WITH LYMPHOMATOUS FEATURES; LALL	LYMPHOMATOUS ALL
+Percent	309200	MAJOR AFFECTIVE DISORDER 2; MAFD2	MANIC-DEPRESSIVE ILLNESS; MDI;; MANIC-DEPRESSIVE PSYCHOSIS, X-LINKED; MDX;; BIPOLAR AFFECTIVE DISORDER; BPAD
+Percent	613065	LEUKEMIA, ACUTE LYMPHOBLASTIC; ALL		LEUKEMIA, ACUTE LYMPHOBLASTIC, SUSCEPTIBILITY TO, 1, INCLUDED;; ALL1, INCLUDED;; LEUKEMIA, ACUTE LYMPHOCYTIC, SUSCEPTIBILITY TO, 1, INCLUDED;; LEUKEMIA, B-CELL ACUTE LYMPHOBLASTIC, SUSCEPTIBILITY TO, INCLUDED;; LEUKEMIA, T-CELL ACUTE LYMPHOBLASTIC, SUSCEPTIBILITY TO, INCLUDED;; LEUKEMIA, ACUTE LYMPHOBLASTIC, B-HYPERDIPLOID, SUSCEPTIBILITY TO, INCLUDED
+#
+#
+#
+#
+# MIM number prefix:
+# ------------------
+# Asterisk (*)  Gene
+# Plus (+)  Gene and phenotype, combined
+# Number Sign (#)  Phenotype, molecular basis known
+# Percent (%)  Phenotype or locus, molecular basis unknown
+# NULL (<null>)  Other, mainly phenotypes with suspected mendelian basis
+# Caret (^)  Entry has been removed from the database or moved to another entry
+#