Linting and formatting with Ruff

.coveragerc

@@ -1,4 +1,4 @@
 [run]
 source = cotainr
 omit = cotainr/tests/*
-branch = True
+branch = True

.github/workflows/CI_pull_request.yml

@@ -6,6 +6,15 @@ on:
   schedule:
       - cron: '15 2 * * TUE'  # Also run the full test suite for PRs on the main branch every Tuesday night
 jobs:
+  lint-and-format:
+    name: Lint and check formatting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]
   run-full-test-suite:
     name: Run full test suite
     runs-on: ${{ matrix.os }}

.github/workflows/CI_push.yml

@@ -6,6 +6,15 @@ on:
     tags-ignore:
       - "**"
 jobs:
+  lint-and-format:
+    name: Lint and check formatting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]
   run-unittests:
     name: Run unittests
     runs-on: ubuntu-latest

.gitignore

@@ -140,4 +140,4 @@ dmypy.json
 # Sphinx
 _build/
 
-systems.json
+systems.json

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.4
+    hooks:
+      - id: ruff
+        args:
+          - --fix
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: trailing-whitespace

LICENSE

@@ -284,4 +284,4 @@ the rights granted in Article 2 of this Licence and protect the covered Source
 Code from exclusive appropriation.
 
 All other changes or additions to this Appendix require the production of a new
-EUPL version.
+EUPL version.

cotainr/cli.py

@@ -51,7 +51,7 @@
 class CotainrSubcommand(ABC):
     """Abstract base class for `CotainrCLI` subcommands."""
 
-    @classmethod
+    @classmethod  # noqa: B027
     def add_arguments(cls, *, parser):
         """
         Add command line arguments to arguments `parser`.

cotainr/pack.py

@@ -301,9 +301,7 @@ def _download_miniforge_installer(self, *, installer_path):
         # Make up to 3 attempts at downloading the installer
         for retry in range(3):
             try:
-                with urllib.request.urlopen(
-                    miniforge_installer_url
-                ) as url:  # nosec B310
+                with urllib.request.urlopen(miniforge_installer_url) as url:  # nosec B310
                     installer_path.write_bytes(url.read())
 
                 break

cotainr/tests/cli/test_build.py

@@ -190,7 +190,7 @@ def test_specifying_both_system_and_base_image(self, capsys):
         Build.add_arguments(parser=parser)
 
         with pytest.raises(SystemExit):
-            args = parser.parse_args(
+            parser.parse_args(
                 args=shlex.split(
                     f"{image_path} --system {system} --base-image {base_image}"
                 )
@@ -275,7 +275,7 @@ def test_specifying_both_verbose_and_quiet(self, capsys):
         base_image = "some_base_image_6021"
 
         with pytest.raises(SystemExit):
-            args = parser.parse_args(
+            parser.parse_args(
                 args=shlex.split(
                     f"{image_path} --base-image={base_image} --verbose --quiet"
                 )
@@ -377,9 +377,7 @@ def test_include_conda_env(
             conda_env_create_cmd,
             conda_clean_cmd,
             sandbox_build_cmd,
-        ) = (
-            capsys.readouterr().out.strip().split("\n")
-        )
+        ) = capsys.readouterr().out.strip().split("\n")
         assert sandbox_create_cmd.startswith("PATCH: Ran command in sandbox:")
         assert all(
             s in sandbox_create_cmd

cotainr/tests/cli/test_cli_utils.py

@@ -57,8 +57,11 @@ def test_description_whitespace_strip(self):
         Parameters
         ----------
         some_arg : str
-            Much leading and trailing space             
+            Much leading and trailing space
         """
+        # Doctor the docstring a little here, so editors etc. which eagerly
+        # strip whitespace don't mess up the test.
+        docstring = docstring.replace("space", "space" + " " * 10)
         help_msg = _extract_help_from_docstring(arg="some_arg", docstring=docstring)
         assert help_msg == "much leading and trailing space"
 

cotainr/tests/cli/test_cotainr_cli.py

@@ -6,6 +6,7 @@
 - see the LICENSE file for details.
 
 """
+
 import itertools
 import logging
 import re
@@ -138,14 +139,17 @@ def test_missing_subcommand(self, argparse_options_line, capsys):
             argparse_options_line=argparse_options_line
         )
 
+
 class TestVersionMessage:
     def test_main_version(self, capsys):
         from cotainr import __version__ as _cotainr_version
+
         with pytest.raises(SystemExit):
             CotainrCLI(args=["--version"])
         stdout = capsys.readouterr().out
         assert stdout == f"cotainr {_cotainr_version}\n"
 
+
 class Test_SetupCotainrCLILogging:
     @pytest.mark.parametrize("verbosity", [-1, -2, -3, -5, -1000])
     def test_cotainr_critical_logging(
@@ -184,7 +188,8 @@ def test_cotainr_critical_logging(
             assert isinstance(handler, logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         assert stdout.rstrip("\n").split("\n") == stdout_msgs
         assert stderr.rstrip("\n").split("\n") == stderr_msgs
 
@@ -225,7 +230,8 @@ def test_cotainr_debug_logging(
             assert isinstance(handler, logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         actual_stdout_msgs = stdout.rstrip("\n").split("\n")
         actual_stderr_msgs = stderr.rstrip("\n").split("\n")
         assert len(actual_stdout_msgs) == len(expected_stdout_msgs)
@@ -275,7 +281,8 @@ def test_cotainr_info_logging(
             assert isinstance(handler, logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         assert stdout.rstrip("\n").split("\n") == stdout_msgs
         assert stderr.rstrip("\n").split("\n") == stderr_msgs
 
@@ -361,6 +368,7 @@ def test_no_color_on_console(
             assert isinstance(handler, logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         assert stdout.rstrip("\n").split("\n") == stdout_msgs
         assert stderr.rstrip("\n").split("\n") == stderr_msgs

cotainr/tests/container/test_singularity_sandbox.py

@@ -43,7 +43,7 @@ def test_setup_log_dispatcher(self):
 
 class TestContext:
     def test_add_verbosity_arg(self, capsys, patch_disable_stream_subprocess):
-        with SingularitySandbox(base_image="my_base_image_6021") as sandbox:
+        with SingularitySandbox(base_image="my_base_image_6021"):
             pass
         stdout_lines = capsys.readouterr().out.rstrip("\n").split("\n")
         assert "args=['singularity', '-q', " in stdout_lines[0]

cotainr/tests/pack/stubs.py

@@ -11,13 +11,15 @@
 
 
 class StubLicensePopen(ABC):
-    def __init__(self, args, stdin=None, stdout=None, text=None):
+    license_text: str
+
+    def __init__(self, args, stdin=None, stdout=None, text=None):  # noqa: B027
         pass
 
     def __enter__(self):
         return self
 
-    def __exit__(self, exc_type, exc_value, traceback):
+    def __exit__(self, exc_type, exc_value, traceback):  # noqa: B027
         pass
 
     def communicate(self, input=None):

cotainr/tests/pack/test_conda_install.py

@@ -58,9 +58,7 @@ def test_beforehand_license_acceptance(
             miniforge_license_accept_cmd,
             _conda_bootstrap_cmd,
             _conda_bootstrap_clean_cmd,
-        ) = (
-            capsys.readouterr().out.strip().split("\n")
-        )
+        ) = capsys.readouterr().out.strip().split("\n")
         assert miniforge_license_accept_cmd == (
             "You have accepted the Miniforge installer license via the command line option "
             "'--accept-licenses'."
@@ -395,7 +393,7 @@ def test_miniforge_still_showing_license(
     ):
         monkeypatch.setattr("builtins.input", factory_mock_input("yes"))
         with SingularitySandbox(base_image="my_base_image_6021") as sandbox:
-            conda_install = CondaInstall(sandbox=sandbox)
+            CondaInstall(sandbox=sandbox)
 
         stdout = capsys.readouterr().out.strip()
 

cotainr/tests/tracing/patches.py

@@ -6,6 +6,7 @@
 - see the LICENSE file for details.
 
 """
+
 import contextlib
 
 import pytest

cotainr/tests/tracing/stubs.py

@@ -7,7 +7,6 @@
 
 """
 
-
 import contextlib
 
 

cotainr/tests/tracing/test_coloured_output_formatter.py

@@ -6,6 +6,7 @@
 - see the LICENSE file for details.
 
 """
+
 import logging
 
 import pytest

cotainr/tests/tracing/test_console_spinner.py

@@ -6,6 +6,7 @@
 - see the LICENSE file for details.
 
 """
+
 import concurrent.futures
 import sys
 

cotainr/tests/tracing/test_log_dispatcher.py

@@ -94,7 +94,6 @@ def test_log_dispatcher_critical_logging(
 
         # Log test messages to log dispatcher loggers
         for logger in [log_dispatcher.logger_stdout, log_dispatcher.logger_stderr]:
-
             # Log messages
             for level, msg in log_level_msgs.items():
                 logger.log(level=level, msg=msg)
@@ -108,7 +107,8 @@ def test_log_dispatcher_critical_logging(
             assert isinstance(logger.handlers[0], logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         assert stdout.rstrip("\n").split("\n") == stdout_msgs
         assert stderr.rstrip("\n").split("\n") == stderr_msgs
 
@@ -139,7 +139,6 @@ def test_log_dispatcher_debug_logging(
 
         # Log test messages to log dispatcher loggers
         for logger in [log_dispatcher.logger_stdout, log_dispatcher.logger_stderr]:
-
             # Log messages
             for level, msg in log_level_msgs.items():
                 logger.log(level=level, msg=msg)
@@ -153,7 +152,8 @@ def test_log_dispatcher_debug_logging(
             assert isinstance(logger.handlers[0], logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         actual_stdout_msgs = stdout.rstrip("\n").split("\n")
         actual_stderr_msgs = stderr.rstrip("\n").split("\n")
         assert len(actual_stdout_msgs) == len(expected_stdout_msgs)
@@ -197,7 +197,6 @@ def test_log_dispatcher_info_logging(
 
         # Log test messages to log dispatcher loggers
         for logger in [log_dispatcher.logger_stdout, log_dispatcher.logger_stderr]:
-
             # Log messages
             for level, msg in log_level_msgs.items():
                 logger.log(level=level, msg=msg)
@@ -211,7 +210,8 @@ def test_log_dispatcher_info_logging(
             assert isinstance(logger.handlers[0], logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         assert stdout.rstrip("\n").split("\n") == stdout_msgs
         assert stderr.rstrip("\n").split("\n") == stderr_msgs
 
@@ -241,7 +241,6 @@ def test_log_dispatcher_warning_logging(
 
         # Log test messages to log dispatcher loggers
         for logger in [log_dispatcher.logger_stdout, log_dispatcher.logger_stderr]:
-
             # Log messages
             for level, msg in log_level_msgs.items():
                 logger.log(level=level, msg=msg)
@@ -255,7 +254,8 @@ def test_log_dispatcher_warning_logging(
             assert isinstance(logger.handlers[0], logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         assert stdout.rstrip("\n").split("\n") == stdout_msgs
         assert stderr.rstrip("\n").split("\n") == stderr_msgs
 
@@ -287,7 +287,6 @@ def test_log_to_file(
 
         # Log test messages to log dispatcher loggers
         for logger in [log_dispatcher.logger_stdout, log_dispatcher.logger_stderr]:
-
             # Log messages
             for level, msg in log_level_msgs.items():
                 logger.log(level=level, msg=msg)
@@ -334,7 +333,6 @@ def test_no_color_on_console(
 
         # Log test messages to log dispatcher loggers
         for logger in [log_dispatcher.logger_stdout, log_dispatcher.logger_stderr]:
-
             # Log messages
             for level, msg in log_level_msgs.items():
                 logger.log(level=level, msg=msg)
@@ -348,7 +346,8 @@ def test_no_color_on_console(
             assert isinstance(logger.handlers[0], logging.StreamHandler)
 
         # Check correct logging, incl. message format, coloring, log level, and output stream
-        stdout, stderr = capsys.readouterr()  # readouterr clears its content when returning
+        # readouterr clears its content when returning
+        stdout, stderr = capsys.readouterr()
         assert stdout.rstrip("\n").split("\n") == stdout_msgs
         assert stderr.rstrip("\n").split("\n") == stderr_msgs
 

cotainr/tests/tracing/test_message_spinner.py

@@ -6,6 +6,7 @@
 - see the LICENSE file for details.
 
 """
+
 import io
 import shutil
 import time

cotainr/tests/tracing/test_stream_write_proxy.py

@@ -6,6 +6,7 @@
 - see the LICENSE file for details.
 
 """
+
 import io
 
 import pytest
@@ -46,7 +47,7 @@ def test_failing_attribute_lookup_delegation(self):
             AttributeError,
             match=r"StringIO' object has no attribute 'some_nonsense_attribute_6021'$",
         ):
-            stream_write_proxy.some_nonsense_attribute_6021
+            _ = stream_write_proxy.some_nonsense_attribute_6021
 
     def test_successful_attribute_lookup_delegation(self):
         stream = io.StringIO("some text 6021")