Update from flake8 to ruff

Fixes timtroendle#36

LICENSE.md

@@ -1,4 +1,4 @@
-Copyright (c) 2017-2022 Tim Tröndle
+Copyright (c) 2017-2024 Tim Tröndle
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

README.md

@@ -74,7 +74,7 @@ The generated repository will have the following structure:
 ├── tests                   <- Automatic tests of the source code go in here.
 │   └── test_model.py       <- Demo file.
 ├── .editorconfig           <- Editor agnostic configuration settings.
-├── .flake8                 <- Linting settings for flake8.
+├── .ruff                   <- Linter and formatter settings for ruff.
 ├── .gitignore
 ├── environment.yaml        <- A file to create an environment to execute your project in.
 ├── LICENSE.md              <- MIT license description
@@ -87,7 +87,7 @@ The generated repository will have the following structure:
 ```
 ├── envs
 │   └── shell.yaml              <- An environment for shell rules.
-├── profiles                    <- Snakemake profiles.
+├── profiles
 │   └── cluster                 <- Cluster Snakemake profile folder.
 │       └── config.yaml         <- Cluster Snakemake profile.
 ├── rules

cluster/{{cookiecutter.project_short_name}}/.ruff.toml

@@ -0,0 +1 @@
+../../default/{{cookiecutter.project_short_name}}/.ruff.toml

default/{{cookiecutter.project_short_name}}/.ruff.toml

@@ -0,0 +1,36 @@
+line-length = 88
+preview = true # required to activate many pycodestyle errors and warnings as of 2024-05-01
+builtins = ["snakemake"]
+
+[format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = false
+line-ending = "auto"
+
+[lint]
+select = [
+    # pycodestyle errors
+    "E",
+    # pycodestyle warnings
+    "W",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+]
+ignore = [
+    # here and below, rules are redundant with formatter, see
+    # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
+    "E501",
+    "W191",
+    "E111",
+    "E114",
+    "E117",
+]

default/{{cookiecutter.project_short_name}}/Snakefile

@@ -6,7 +6,7 @@ configfile: "config/default.yaml"
 include: "./rules/sync.smk"
 localrules: all, report, clean
 {%- endif %}
-min_version("7.8")
+min_version("8.10")
 
 {% if cookiecutter._add_cluster_infrastructure == True -%}
 onstart:

default/{{cookiecutter.project_short_name}}/environment.yaml

@@ -4,5 +4,4 @@ channels:
     - bioconda
 dependencies:
     - python=3.11
-    - flake8=3.8.3
     - snakemake-minimal=8.10.7