use ruff only for linting and formatting (to match airflow repo) (#655)

* update requirements

* remove black and isort

* remove commented out stuff

Author: jklugherz

.github/workflows/unit-tests.yml

@@ -30,10 +30,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r requirements.txt
           pip install -r requirements-dev.txt
-      - name: Check Import Sort
-        run: isort . --check --diff
-      - name: Check Black
-        run: black . --check --diff
       - name: Check Ruff
         run: ruff . --output-format github
       - name: Unit Tests

pyproject.toml

@@ -14,40 +14,6 @@ include = ["v03_pipeline*"]
 exclude = ["v03_pipeline.bin", "v03_pipeline*test*"]
 namespaces = false
 
-[tool.black]
-line-length = 88
-skip-string-normalization = true
-extend-exclude = '''
-(
-    download_and_create_reference_datasets/v02
-    | gcloud_dataproc
-    | hail_scripts/computed_fields
-    | hail_scripts/elasticsearch
-    | hail_scripts/update_models
-    | hail_scripts/utils
-    | kubernetes
-    | luigi_pipeline/lib
-    | luigi_pipeline/seqr.*\.py$
-    | luigi_pipeline/tests/data
-)
-'''
-
-[tool.isort]
-include_trailing_comma = 'True'
-known_external_package = ['hail_scripts']
-line_length = 88
-profile = 'black'
-sections = ['FUTURE', 'STDLIB', 'THIRDPARTY', 'EXTERNAL_PACKAGE', 'FIRSTPARTY', 'LOCALFOLDER']
-skip_glob = [
-    'download_and_create_reference_datasets/v02/*',
-    'gcloud_dataproc/*',
-    'hail_scripts/computed_fields/*',
-    'hail_scripts/elasticsearch/*',
-    'hail_scripts/update_models/*',
-    'hail_scripts/utils/*',
-    'kubernetes/*'
-]
-
 [tool.mypy]
 packages = 'v03_pipeline'
 python_version = "3.10"
@@ -71,7 +37,6 @@ ignore = [
     "G004",  # logging-f-string, these are fine for now
 
     # Rule Groupings
-    "I",     # isort is enabled so this is unnecessary (for now, maybe we want to disable isort)
     "D",     # pydocstyle is for docs... we have none
     "FBT",   # flake-boolean-trap... disallows boolean args to functions... fixing this code will require refactors.
     "ANN",   # flake8-annotations is for typed code

requirements-dev.in

@@ -1,9 +1,7 @@
 -c requirements.txt
-black>=23.7.0
 coverage>=7.2.2
-isort>=5.12.0
 mypy>=1.2.0
 nose-py3>=1.6.3 # bug in regular nose here: https://github.com/nose-devs/nose/issues/1099#issuecomment-577647469
 pip-tools>=6.12.3
 responses>=0.23.1
-ruff>=0.0.259
+ruff>=0.1.8

requirements-dev.txt

@@ -10,11 +10,9 @@ alabaster==0.7.13
     # via sphinx
 babel==2.13.1
     # via sphinx
-black==23.11.0
-    # via -r requirements-dev.in
 build==1.0.3
     # via pip-tools
-certifi==2023.7.22
+certifi==2023.11.17
     # via
     #   -c requirements.txt
     #   requests
@@ -25,7 +23,6 @@ charset-normalizer==3.3.2
 click==8.1.7
     # via
     #   -c requirements.txt
-    #   black
     #   pip-tools
 coverage==7.3.2
     # via
@@ -35,14 +32,12 @@ docutils==0.20.1
     # via
     #   -c requirements.txt
     #   sphinx
-idna==3.4
+idna==3.6
     # via
     #   -c requirements.txt
     #   requests
 imagesize==1.4.1
     # via sphinx
-isort==5.12.0
-    # via -r requirements-dev.in
 jinja2==3.1.2
     # via
     #   -c requirements.txt
@@ -54,9 +49,7 @@ markupsafe==2.1.3
 mypy==1.7.0
     # via -r requirements-dev.in
 mypy-extensions==1.0.0
-    # via
-    #   black
-    #   mypy
+    # via mypy
 nose-py3==1.6.3
     # via -r requirements-dev.in
 numpy==1.26.2
@@ -66,16 +59,11 @@ numpy==1.26.2
 packaging==23.2
     # via
     #   -c requirements.txt
-    #   black
     #   build
     #   sphinx
-pathspec==0.11.2
-    # via black
 pip-tools==7.3.0
     # via -r requirements-dev.in
-platformdirs==4.0.0
-    # via black
-pygments==2.16.1
+pygments==2.17.2
     # via
     #   -c requirements.txt
     #   sphinx
@@ -92,7 +80,7 @@ requests==2.31.0
     #   sphinx
 responses==0.24.1
     # via -r requirements-dev.in
-ruff==0.1.5
+ruff==0.1.10
     # via -r requirements-dev.in
 six==1.16.0
     # via
@@ -122,15 +110,13 @@ sphinxcontrib-serializinghtml==1.1.9
     # via sphinx
 tomli==2.0.1
     # via
-    #   black
     #   build
     #   mypy
     #   pip-tools
     #   pyproject-hooks
 typing-extensions==4.8.0
     # via
     #   -c requirements.txt
-    #   black
     #   mypy
 urllib3==2.0.7
     # via