cleanup

.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"

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
 

pyproject.toml

@@ -4,4 +4,3 @@ line-length = 99
 [tool.isort]
 profile = "black"
 multi_line_output = 3
-src_paths = ["src/ingest-validation-tests"]

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 = """\