cicd: precommit updates

.coveragerc

@@ -4,4 +4,4 @@ source =
    tests/
 omit =
    setup.py
-   docs/*
+   docs/*

Dockerfile

@@ -1,6 +1,6 @@
 # A simple container for gene-service.
 # Runs service on port 80.
-# Healthchecks service up every 5m.  
+# Healthchecks service up every 5m.
 
 FROM python:3.7
 RUN pip install pipenv uvicorn[standard]

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
-popd
+@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

docs/source/managing_data/index.rst

@@ -8,4 +8,3 @@ The current iteration of the Gene Normalizer stores millions of symbols, names,
     Loading and updating data<loading_and_updating_data>
     DynamoDB storage backend<dynamodb>
     PostgreSQL storage backend<postgresql>
-

tests/unit/data/etl_data/ncbi_history_20210813.tsv

@@ -16,4 +16,4 @@
 9606	7637	100287429	LOC100287429	20110803
 9606	-	103344718	HOTS	20200620
 9606	-	544580	AASTH23	20190503
-9606	10036	107985297	LOC107985297	20220408
+9606	10036	107985297	LOC107985297	20220408

tests/unit/dynamodb_build.bash

@@ -3,4 +3,4 @@ mkdir ./tests/unit/dynamodb_local
 cd ./tests/unit/dynamodb_local
 curl -O "https://s3-us-west-2.amazonaws.com/dynamodb-local/dynamodb_local_latest.tar.gz"
 tar -xvzf dynamodb_local_latest.tar.gz; rm dynamodb_local_latest.tar.gz
-java -jar DynamoDBLocal.jar &
+java -jar DynamoDBLocal.jar &