migrate linting from flake8, isort, autoflake to ruff (same as atomat…

…e2, jobflow now)

.pre-commit-config.yaml

@@ -1,46 +1,27 @@
 default_language_version:
-  python: python3.9
-#exclude: '^src/{{ package_name }}/some/directory/'
+  python: python3
+exclude: ^(.github/|tests/test_data/abinit/)
 repos:
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.4.5
+  hooks:
+  - id: ruff
+    args: [--fix]
+  - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/myint/autoflake
-  rev: v2.2.1
-  hooks:
-  - id: autoflake
-- repo: https://github.com/psf/black
-  rev: 24.1.1
-  hooks:
-  - id: black
 - repo: https://github.com/asottile/blacken-docs
   rev: 1.16.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
     exclude: README.md
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-  - id: isort
-- repo: https://github.com/pycqa/flake8
-  rev: 6.1.0
-  hooks:
-  - id: flake8
-    entry: pflake8
-    files: ^src/
-    additional_dependencies:
-    - pyproject-flake8
-    - flake8-bugbear
-    - flake8-typing-imports
-    - flake8-docstrings
-    - flake8-rst-docstrings
-    - flake8-rst
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:
@@ -49,23 +30,18 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.8.0
+  rev: v1.10.0
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
-    - types-pkg_resources==0.1.2
     - types-paramiko
     - pydantic~=2.0
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.6
   hooks:
   - id: codespell
     stages: [commit, commit-msg]
-    args: [--ignore-words-list, 'titel,statics,ba,nd,te,nin', --skip, '*.svg']
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
-  hooks:
-    - id: pyupgrade
-      args: [--py39-plus]
+    args: [--ignore-words-list, 'titel,statics,ba,nd,te']
+    types_or: [python, rst, markdown]

doc/source/conf.py

@@ -14,10 +14,10 @@
 import os
 import sys
 
-# sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(
     0, os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), ".."))
 )
+import jobflow_remote
 
 # -- Project information -----------------------------------------------------
 
@@ -26,8 +26,6 @@
 author = "Guido Petretto, Matthew Evans, David Waroquiers"
 
 
-import jobflow_remote
-
 # The short X.Y version
 version = jobflow_remote.__version__
 # The full version, including alpha/beta/rc tags

pyproject.toml

@@ -1,7 +1,3 @@
-[build-system]
-requires = ["setuptools >= 42", "versioningit  ~=  1.0", "wheel"]
-build-backend = "setuptools.build_meta"
-
 [project]
 name = "jobflow-remote"
 description = "Jobflow Remote is a Python package to run jobflow workflows on remote resources"
@@ -11,50 +7,44 @@ license = { text = "modified BSD" }
 authors = [{ name = "Guido Petretto", email = "[email protected]" }]
 dynamic = ["version"]
 classifiers = [
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
     "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Information Technology",
     "Intended Audience :: Science/Research",
     "Intended Audience :: System Administrators",
-    "Intended Audience :: Information Technology",
     "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.9",
     "Topic :: Other/Nonlisted Topic",
     "Topic :: Scientific/Engineering",
 ]
 requires-python = ">=3.9"
-dependencies =[
+dependencies = [
+    "fabric ~= 3.2",
+    "flufl.lock ~= 8.0",
     "jobflow >= 0.1.14",
+    "psutil ~= 5.9",
     "pydantic ~= 2.4",
-    "fabric ~= 3.2",
-    "tomlkit ~= 0.12",
     "qtoolkit ~= 0.1, >= 0.1.4",
-    "typer ~= 0.9",
     "rich ~= 13.7",
-    "psutil ~= 5.9",
-    "supervisor ~= 4.2",
     "ruamel.yaml ~= 0.17",
     "schedule ~= 1.2",
-    "flufl.lock ~= 8.0"
+    "supervisor ~= 4.2",
+    "tomlkit ~= 0.12",
+    "typer ~= 0.9",
 ]
 
 [project.optional-dependencies]
-dev = [
-    "pre-commit>=3.0.0",
-]
-tests = [
-    "pytest ~= 8.0",
-    "pytest-cov ~= 4.0",
-    "docker ~= 7.0",
-]
+dev = ["pre-commit>=3.0.0"]
+tests = ["docker ~= 7.0", "pytest ~= 8.0", "pytest-cov ~= 4.0"]
 docs = [
-    "sphinx",
-    "sphinx_design",
+    "autodoc_pydantic>=2.0.0",
     "pydata-sphinx-theme",
+    "sphinx",
     "sphinx-copybutton",
-    "autodoc_pydantic>=2.0.0",
-    "sphinxcontrib-mermaid"
+    "sphinx_design",
+    "sphinxcontrib-mermaid",
 ]
 
 [project.scripts]
@@ -69,22 +59,14 @@ changelog = "https://matgenix.github.io/jobflow-remote/changelog"
 [tool.setuptools.package-data]
 jobflow_remote = ["py.typed"]
 
+[build-system]
+requires = ["setuptools >= 42", "versioningit  ~=  1.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
 [tool.versioningit.vcs]
 method = "git"
 default-tag = "0.0.1"
 
-[tool.isort]
-profile = "black"
-
-[tool.flake8]
-max-line-length = 88
-max-doc-length = 88
-select = "C, E, F, W, B"
-extend-ignore = "E203, W503, E501, F401, RST21"
-min-python-version = "3.9.0"
-docstring-convention = "numpy"
-rst-roles = "class, func, ref, obj"
-
 [tool.mypy]
 ignore_missing_imports = true
 strict_optional = false
@@ -104,9 +86,9 @@ warn_required_dynamic_aliases = true
 [tool.pytest.ini_options]
 filterwarnings = [
     "ignore:.*POTCAR.*:UserWarning",
-    "ignore:.*magmom.*:UserWarning",
-    "ignore:.*is not gzipped.*:UserWarning",
     "ignore:.*input structure.*:UserWarning",
+    "ignore:.*is not gzipped.*:UserWarning",
+    "ignore:.*magmom.*:UserWarning",
     "ignore::DeprecationWarning",
 ]
 
@@ -122,14 +104,7 @@ source = ["src/"]
 skip_covered = true
 show_missing = true
 exclude_lines = [
+    '^\s*@overload( |$)',
     '^\s*assert False(,|$)',
     'if typing.TYPE_CHECKING:',
-    '^\s*@overload( |$)',
 ]
-
-[tool.autoflake]
-in-place = true
-remove-all-unused-imports = true
-remove-unused-variables = true
-ignore-init-module-imports = true
-expand-star-imports = true

src/jobflow_remote/cli/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 # Import the submodules with a local app to register them to the main app
 import jobflow_remote.cli.admin
 import jobflow_remote.cli.execution

src/jobflow_remote/cli/runner.py

@@ -181,7 +181,7 @@ def stop(
                 "Wait until the daemon has stopped. NOTE: this may take a while if a large file is being transferred!"
             ),
         ),
-    ] = False
+    ] = False,
 ):
     """
     Send a stop signal to the Runner processes.

src/jobflow_remote/remote/host/remote.py

@@ -79,7 +79,6 @@ def _create_connection(self):
             # if the authentication is ssh-key + OTP paramiko already
             # handles it. Don't use the alternative strategy.
             if not self._connection.connect_kwargs.get("key_filename"):
-
                 if not config:
                     config = Config()
                     config.authentication.strategy_class = InteractiveAuthStrategy

src/jobflow_remote/testing/__init__.py

@@ -88,8 +88,6 @@ def self_replace(n: int):
     """
     Create a replace Job with the same job n times.
     """
-    from jobflow import Flow
-
     if n > 0:
         return Response(replace=self_replace(n - 1))
 

src/jobflow_remote/testing/cli.py

@@ -35,8 +35,8 @@ def run_check_cli(
     )
 
     # note that stderr is not captured separately
-    assert error == (
-        result.exit_code != 0
+    assert (
+        error == (result.exit_code != 0)
     ), f"cli should have {'not ' if not error else ''}failed. exit code: {result.exit_code}. stdout: {result.stdout}"
 
     if required_out:

tests/db/cli/test_flow.py

@@ -1,5 +1,4 @@
 def test_flows_list(job_controller, four_jobs):
-
     from jobflow_remote.testing.cli import run_check_cli
 
     columns = ["DB id", "Name", "State", "Flow id", "Num Jobs", "Last updated"]
@@ -19,7 +18,6 @@ def test_flows_list(job_controller, four_jobs):
 
 
 def test_delete(job_controller, four_jobs):
-
     from jobflow_remote.testing.cli import run_check_cli
 
     run_check_cli(
@@ -40,7 +38,6 @@ def test_delete(job_controller, four_jobs):
 
 
 def test_flow_info(job_controller, four_jobs):
-
     from jobflow_remote.testing.cli import run_check_cli
 
     columns = ["DB id", "Name", "State", "Job id", "(Index)", "Worker"]