From b667a52535b01736083371b20cbcc4b7e5ef036c Mon Sep 17 00:00:00 2001
From: Gesina Phillips <gesina@psc.edu>
Date: Thu, 1 Feb 2024 14:24:17 -0500
Subject: [PATCH] cleanup

---
 .github/workflows/isort.yml         |  4 ++--
 README.md                           | 17 +++++++++++------
 pyproject.toml                      |  1 -
 tests/test_fastq_validator_logic.py |  1 +
 4 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/isort.yml b/.github/workflows/isort.yml
index db105a8..8802cf3 100644
--- a/.github/workflows/isort.yml
+++ b/.github/workflows/isort.yml
@@ -11,5 +11,5 @@ jobs:
           python-version: 3.9
       - uses: isort/isort-action@master
         with:
-            configuration: "--check-only --diff --profile black"
-            requirementsFiles: "requirements.txt requirements-test.txt"
+          configuration: "--check-only --diff --profile black --multi-line 3"
+          requirementsFiles: "requirements.txt requirements-test.txt"
diff --git a/README.md b/README.md
index 5ff0ca9..81be8dc 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,12 @@ This repository contains plug-in tests for use during validation of submissions.
 - Make new feature branches from `devel`.
 - Before submitting a PR, make sure your code is black and isort compliant. Run the following from the base `ingest-validation-tests` directory:
 
-  - `black --line-length 99 .` (you can integrate black with your editor to skip this step, see Setup section below)
-  - `isort .`
+  ```
+  black --line-length 99 .
+  isort --profile black --multi-line 3 .
+  ```
+
+  (You can integrate black and potentially isort with your editor to skip this step, see Setup section below)
 
 - Make PRs to `devel`. (This is the default branch.)
 - The last reviewer to approve a PR should merge it.
@@ -19,14 +23,15 @@ This repository contains plug-in tests for use during validation of submissions.
 
 - Creating and activating a virtual environment is recommended. These instructions assume you are using a virtual environment. Example using venv:
 
-```
-python3.9 -m venv hm-ingest-validation-tests
-source hm-ingest-validation-tests/bin/activate
-```
+  ```
+  python3.9 -m venv hm-ingest-validation-tests
+  source hm-ingest-validation-tests/bin/activate
+  ```
 
 - Run `pip install -r requirements-dev.txt`
 - (optional) Integrate black with your editor.
   - [Instructions for black.](https://black.readthedocs.io/en/stable/integrations/editors.html)
+- (optional) Integrate isort with your editor.
 
 ### Testing
 
diff --git a/pyproject.toml b/pyproject.toml
index 72dd8d9..93863fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,4 +4,3 @@ line-length = 99
 [tool.isort]
 profile = "black"
 multi_line_output = 3
-src_paths = ["src/ingest-validation-tests"]
diff --git a/tests/test_fastq_validator_logic.py b/tests/test_fastq_validator_logic.py
index c554d6f..31bd68a 100644
--- a/tests/test_fastq_validator_logic.py
+++ b/tests/test_fastq_validator_logic.py
@@ -3,6 +3,7 @@
 from typing import TextIO
 
 import pytest
+
 from src.ingest_validation_tests.fastq_validator_logic import FASTQValidatorLogic
 
 _GOOD_RECORDS = """\