Remove flake8 and replace it by ruff (#716)

* Accommodate for `score_metric` for search and `termset_pairwise_similarity`

* pip needed

* pip needed

* added 3.12 support

* formatted

* fixed poetry's pip problem

* flake8 removed

* manage upto 3.11

* just lint 3.12

* adressed/ignored a few rules

* timeout=30

* formatted

* addressed a few more rules

* fixed error

* formatted

* cleanup

.github/workflows/main.yaml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10' ]
+        python-version: [ '3.9', '3.10', '3.12' ]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -25,15 +25,15 @@ jobs:
       - name: Install dependencies
         run: |
           pip install tox
-      - name: Check code quality with flake8
-        run: tox -e flake8
+      - name: Check code quality with ruff
+        run: tox -e lint
 
   test:
     strategy:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, windows-latest ]
-        python-version: [ "3.9", "3.10" ]
+        python-version: [ "3.9", "3.10", "3.11" ]
         exclude:
           - os: windows-latest
             python-version: "3.9"

pyproject.toml

@@ -60,6 +60,7 @@ tox = "*"
 
 [tool.poetry.group.dev.dependencies]
 seaborn = "^0.12.2"
+pip = "^24.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
@@ -91,3 +92,38 @@ reverse_relative = true
 skip = '.git,*.pdf,*.svg,poetry.lock,*.obo,*.ttl,*.ofn,*.gaf,*.tsv,*.json,input'
 ignore-regex = '(^\s*"image/\S+": ".*|[a-z]*\.\.\.)'
 ignore-words-list = 'ptd,ot,nd,ser,oger,gard,te,fo,fof,bu,ue,ois,processus,infarction,infarctions'
+
+[tool.ruff]
+lint.extend-ignore = [
+    "D211",  # `no-blank-line-before-class`
+    "D212",  # `multi-line-summary-first-line`
+    "E731",  # Do not assign a `lambda` expression, use a `def`
+    "B005",  # Using `.strip()` with multi-character strings is misleading the reader
+    "S101",  # Use of `assert` detected
+    "S607",  # Starting a process with a partial executable path
+    "S608",  # Possible SQL injection vector through string-based query construction
+    "S603",  # `subprocess` call: check for execution of untrusted input
+    ]
+lint.exclude = ["src/oaklib/datamodels/*"]
+line-length = 120
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+lint.fixable = ["ALL"]
+
+# Select or ignore from https://beta.ruff.rs/docs/rules/
+lint.select = [
+    "B",  # bugbear
+    # "D",  # pydocstyle
+    "E",  # pycodestyle errors
+    "F",  # Pyflakes
+    "I",  # isort 
+    "S",  # flake8-bandit
+    "W",  # Warning
+]
+
+lint.unfixable = []
+target-version = "py310"
+
+[tool.ruff.lint.mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 10