(HP-1728) re-order imports

README.md

@@ -23,7 +23,7 @@ The [VLMD docs](heal/vlmd/README.md) describe how to use the SDK for extracting
 
 ### Run tests
 
-```
+```bash
 poetry run pytest -vv tests
 ```
 
@@ -35,20 +35,20 @@ reference the git repo.
 As an example, `pip install` can be called from the command line for getting
 the master branch of the `heal-platform-sdk`,
 
-```
+```bash
 pip install -e git+https://github.com/uc-cdis/heal-platform-sdk.git#egg=heal
 ```
 
 or a particular branch, eg,
 
-```
+```bash
 pip install -e git+https://github.com/uc-cdis/heal-platform-sdk.git@my-branch#egg=heal
 ```
 
 The specification can also be listed in requirements.txt file
 (with, say, a tag specification of 0.1.0)
 
-```
+```bash
 pip install -e git+https://github.com/uc-cdis/[email protected]#egg=heal
 ```
 

heal/cli/extract.py

@@ -1,5 +1,4 @@
 import click
-
 from cdislogging import get_logger
 
 from heal.vlmd.extract.extract import vlmd_extract

heal/cli/heal_cli.py

@@ -1,7 +1,8 @@
-import click
 import logging
 
 import cdislogging
+import click
+
 import heal.cli.vlmd as vlmd
 
 

heal/cli/validate.py

@@ -1,5 +1,4 @@
 import click
-
 from cdislogging import get_logger
 
 from heal.vlmd.validate.validate import vlmd_validate

tests/conftest.py

@@ -1,4 +1,5 @@
 import json
+
 import pytest
 
 from heal.vlmd.config import (

tests/test_cli.py

@@ -1,13 +1,13 @@
 import os
 
 from click.testing import CliRunner
-import pytest
 
-import heal.vlmd.file_utils as file_utils
 import heal.cli.heal_cli as cli_module
+import heal.vlmd.file_utils as file_utils
 
 
 def test_help():
+    """Test the help menu"""
     runner = CliRunner()
     expected_text = "HEAL-Platform SDK Command Line Interface"
     expected_commands = ["vlmd  Commands for VLMD"]
@@ -19,6 +19,7 @@ def test_help():
 
 
 def test_vlmd_help():
+    """Test the VLMD submenu"""
     runner = CliRunner()
     expected_text = "Commands for VLMD"
     expected_commands = [
@@ -33,6 +34,7 @@ def test_vlmd_help():
 
 
 def test_extract_help():
+    """Test the extract submenu"""
     runner = CliRunner()
     expected_text = "Extract HEAL-compliant VLMD file from input file"
     expected_commands = [
@@ -47,6 +49,7 @@ def test_extract_help():
 
 
 def test_extract(tmp_path):
+    """Test the cli extract"""
     runner = CliRunner()
     input_file = "tests/test_data/vlmd/valid/vlmd_valid.csv"
     expected_output_file = file_utils.get_output_filepath(
@@ -62,6 +65,7 @@ def test_extract(tmp_path):
 
 
 def test_validate_help():
+    """Test the validate submenu"""
     runner = CliRunner()
     expected_text = "Validate VLMD input file"
     expected_commands = [
@@ -75,6 +79,7 @@ def test_validate_help():
 
 
 def test_validate(tmp_path):
+    """Test the cli validation"""
     runner = CliRunner()
     input_file = "tests/test_data/vlmd/valid/vlmd_valid.json"
     result = runner.invoke(