add isort workflow

.github/CONTRIBUTING.md

@@ -33,7 +33,9 @@ Then install your local fork of nf-core/tools:
 pip install -e .
 ```
 
-## Code formatting with Black
+## Code formatting
+
+### Black
 
 All Python code in nf-core/tools must be passed through the [Black Python code formatter](https://black.readthedocs.io/en/stable/).
 This ensures a harmonised code formatting style throughout the package, from all contributors.
@@ -51,6 +53,24 @@ You can also set it up to run when you [make a commit](https://black.readthedocs
 There is an automated CI check that runs when you open a pull-request to nf-core/tools that will fail if
 any code does not adhere to Black formatting.
 
+### isort
+
+All Python code must also be passed through [isort](https://pycqa.github.io/isort/index.html).
+This ensures a harmonised imports throughout the package, from all contributors.
+
+To run isort on the command line recursively on the whole repository you can use:
+
+```bash
+isort .
+```
+
+isort also has [plugins for most common editors](https://github.com/pycqa/isort/wiki/isort-Plugins)
+to automatically format code when you hit save.
+Or [version control integration](https://pycqa.github.io/isort/docs/configuration/pre-commit.html) to set it up to run when you make a commit.
+
+There is an automated CI check that runs when you open a pull-request to nf-core/tools that will fail if
+any code does not adhere to isort formatting.
+
 ## API Documentation
 
 We aim to write function docstrings according to the [Google Python style-guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings). These are used to automatically generate package documentation on the nf-core website using Sphinx.

.github/workflows/fix-linting.yml

@@ -38,6 +38,16 @@ jobs:
           # Override to remove the default --check flag so that we make changes
           options: "--color"
 
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: python-isort
+        uses: isort/isort-action@v0.1.0
+        with:
+          isortVersion: "latest"
+          requirementsFiles: "requirements.txt requirements-dev.txt"
+
       - name: Commit & push changes
         run: |
           git config user.email "core@nf-co.re"

.github/workflows/lint-code.yml

@@ -58,3 +58,19 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
+
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out source-code repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: python-isort
+        uses: isort/isort-action@v0.1.0
+        with:
+          isortVersion: "latest"
+          requirementsFiles: "requirements.txt requirements-dev.txt"

CHANGELOG.md

@@ -16,6 +16,10 @@
 
 - Fix a bug in the regex extracting the version from biocontainers URLs [#1596](https://github.com/nf-core/tools/pull/1596)
 
+### Linting
+
+- Add isort configuration and GitHub workflow ([#1538](https://github.com/nf-core/tools/pull/1538))
+
 ## [v2.4.1 - Cobolt Koala Patch](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
 
 - Patch release to try to fix the template sync ([#1585](https://github.com/nf-core/tools/pull/1585))

README.md

@@ -3,6 +3,7 @@
 [![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster)
 [![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 
 [![install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/recipes/nf-core/README.html)
 [![install with PyPI](https://img.shields.io/badge/install%20with-PyPI-blue.svg)](https://pypi.org/project/nf-core/)

docs/api/make_lint_md.py

@@ -2,6 +2,7 @@
 
 import fnmatch
 import os
+
 import nf_core.lint
 import nf_core.modules.lint
 

nf_core/__main__.py

@@ -1,14 +1,15 @@
 #!/usr/bin/env python
 """ nf-core: Helper tools for use with nf-core Nextflow pipelines. """
-from rich import print
 import logging
 import os
 import re
+import sys
+
 import rich.console
 import rich.logging
 import rich.traceback
 import rich_click as click
-import sys
+from rich import print
 
 import nf_core
 import nf_core.bump_version

nf_core/bump_version.py

@@ -6,8 +6,10 @@
 import logging
 import os
 import re
-import rich.console
 import sys
+
+import rich.console
+
 import nf_core.utils
 
 log = logging.getLogger(__name__)

nf_core/create.py

@@ -2,19 +2,20 @@
 """Creates a nf-core pipeline matching the current
 organization's specification based on a template.
 """
-from genericpath import exists
-import git
 import imghdr
-import jinja2
 import logging
 import os
 import pathlib
 import random
-import requests
 import shutil
 import sys
 import time
 
+import git
+import jinja2
+import requests
+from genericpath import exists
+
 import nf_core
 
 log = logging.getLogger(__name__)

nf_core/download.py

@@ -3,22 +3,23 @@
 
 from __future__ import print_function
 
-from io import BytesIO
-import logging
+import concurrent.futures
 import hashlib
+import logging
 import os
-import questionary
 import re
-import requests
-import requests_cache
 import shutil
 import subprocess
 import sys
 import tarfile
-import concurrent.futures
+from io import BytesIO
+from zipfile import ZipFile
+
+import questionary
+import requests
+import requests_cache
 import rich
 import rich.progress
-from zipfile import ZipFile
 
 import nf_core
 import nf_core.list

nf_core/launch.py

@@ -2,21 +2,23 @@
 """ Launch a pipeline, interactively collecting params """
 
 from __future__ import print_function
-from rich.console import Console
-from rich.markdown import Markdown
-from rich.prompt import Confirm
 
 import copy
 import json
 import logging
 import os
-import questionary
 import re
 import subprocess
 import webbrowser
+
+import questionary
 import requests
+from rich.console import Console
+from rich.markdown import Markdown
+from rich.prompt import Confirm
 
-import nf_core.schema, nf_core.utils
+import nf_core.schema
+import nf_core.utils
 
 log = logging.getLogger(__name__)
 

nf_core/licences.py

@@ -3,14 +3,15 @@
 
 from __future__ import print_function
 
-import logging
 import json
+import logging
 import os
 import re
+
 import requests
-import yaml
 import rich.console
 import rich.table
+import yaml
 
 import nf_core.utils
 

nf_core/lint/__init__.py

@@ -5,21 +5,22 @@
 the nf-core community guidelines.
 """
 
-from rich.markdown import Markdown
-from rich.table import Table
-from rich.panel import Panel
-from rich.console import group
 import datetime
-import git
 import json
 import logging
 import re
+
+import git
 import rich
 import rich.progress
+from rich.console import group
+from rich.markdown import Markdown
+from rich.panel import Panel
+from rich.table import Table
 
-import nf_core.utils
 import nf_core.lint_utils
 import nf_core.modules.lint
+import nf_core.utils
 from nf_core import __version__
 from nf_core.lint_utils import console
 from nf_core.utils import plural_s as _s
@@ -160,9 +161,9 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .pipeline_name_conventions import pipeline_name_conventions
     from .pipeline_todos import pipeline_todos
     from .readme import readme
+    from .schema_description import schema_description
     from .schema_lint import schema_lint
     from .schema_params import schema_params
-    from .schema_description import schema_description
     from .template_strings import template_strings
     from .version_consistency import version_consistency
 

nf_core/lint/actions_awsfulltest.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import os
+
 import yaml
 
 

nf_core/lint/actions_awstest.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import os
+
 import yaml
 
 

nf_core/lint/actions_ci.py

@@ -2,6 +2,7 @@
 
 import os
 import re
+
 import yaml
 
 

nf_core/lint/actions_schema_validation.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python
 
-import logging
-import yaml
+import glob
 import json
-import jsonschema
+import logging
 import os
-import glob
+
+import jsonschema
 import requests
+import yaml
 
 
 def actions_schema_validation(self):

nf_core/lint/merge_markers.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 
+import fnmatch
+import io
 import logging
 import os
-import io
-import fnmatch
 
 import nf_core.utils
 

nf_core/lint/modules_json.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 from logging import warn
+
 from nf_core.modules.modules_command import ModuleCommand
 
 

nf_core/lint/multiqc_config.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import os
+
 import yaml
 
 

nf_core/lint/nextflow_config.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 
-import re
-import os
 import logging
+import os
+import re
 
 log = logging.getLogger(__name__)
 

nf_core/lint/pipeline_todos.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 
+import fnmatch
+import io
 import logging
 import os
-import io
-import fnmatch
 
 log = logging.getLogger(__name__)
 

nf_core/lint/schema_description.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 from logging import warn
+
 import nf_core.schema
 
 

nf_core/lint/schema_lint.py

@@ -1,9 +1,11 @@
 #!/usr/bin/env python
 
 import logging
-import nf_core.schema
+
 import jsonschema
 
+import nf_core.schema
+
 
 def schema_lint(self):
     """Pipeline schema syntax

nf_core/lint_utils.py

@@ -1,7 +1,8 @@
+import logging
+
 import rich
 from rich.console import Console
 from rich.table import Table
-import logging
 
 import nf_core.utils
 from nf_core.utils import plural_s as _s