Merge pull request #420 from lnccbrown/419-drop-black-in-favor-of-ruf…

…f-formatter

.github/workflows/build_and_publish.yml

@@ -41,13 +41,13 @@ jobs:
           pip install -e .
 
       - name: Run mypy
-        run: mypy src
+        run: mypy src/hssm
 
-      - name: Check styling
-        run: black . --check
+      - name: Check formatting
+        run: ruff format --check .
 
       - name: Linting
-        run: ruff check .
+        run: ruff check src/hssm
 
       - name: Run tests
         run: pytest -n auto -s

.github/workflows/run_tests.yml

@@ -39,13 +39,13 @@ jobs:
           pip install -e .
 
       - name: Run mypy
-        run: mypy src
+        run: mypy src/hssm
 
-      - name: Check styling
-        run: black . --check
+      - name: Check formatting
+        run: ruff format --check .
 
       - name: Linting
-        run: ruff check .
+        run: ruff check src/hssm
 
       - name: Run tests
         run: pytest -n auto -s

.pre-commit-config.yaml

@@ -5,31 +5,13 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.4.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
-  - repo: https://github.com/psf/black
-    rev: 23.10.1
-    hooks:
-      - id: black-jupyter
-        args:
-          - --line-length=88
-          - --include='\.pyi?$'
-
-          # these folders wont be formatted by black
-          - --exclude="""\.git |
-            \.__pycache__|
-            \.hg|
-            \.mypy_cache|
-            \.tox|
-            \.venv|
-            _build|
-            buck-out|
-            build|
-            dist"""
+      - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1 # Use the sha / tag you want to point at
+    rev: v1.10.0 # Use the sha / tag you want to point at
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]

pyproject.toml

@@ -16,58 +16,42 @@ keywords = ["HSSM", "sequential sampling models", "bayesian", "bayes", "mcmc"]
 
 [tool.poetry.dependencies]
 python = ">=3.10,<3.12"
-pymc = ">=5.12"
+pymc = "^5.14.0"
 arviz = "^0.18.0"
-onnx = "^1.12.0"
+onnx = "^1.16.0"
 jax = "^0.4.25"
 jaxlib = "^0.4.25"
-ssm-simulators = "^0.7.0"
-huggingface-hub = "^0.15.1"
+ssm-simulators = "^0.7.2"
+huggingface-hub = "^0.23.0"
 bambi = "^0.13.0"
 numpyro = "^0.14.0"
-hddm-wfpt = "^0.1.1"
+hddm-wfpt = "^0.1.4"
 seaborn = "^0.13.2"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.3.1"
-black = { extras = ["jupyter"], version = "^23.10.1" }
-mypy = "^1.6.1"
+pytest = "^8.2.0"
+mypy = "^1.10.0"
 pre-commit = "^2.20.0"
 jupyterlab = "^4.0.2"
 ipykernel = "^6.16.0"
 ipywidgets = "^8.0.3"
-ruff = "^0.1.3"
-mkdocs = "^1.4.3"
-mkdocs-material = "^9.1.17"
-mkdocstrings-python = "^1.1.2"
-mkdocs-jupyter = "^0.24.1"
+ruff = "^0.4.3"
 graphviz = "^0.20.1"
-pytest-xdist = "^3.5.0"
+pytest-xdist = "^3.6.1"
 onnxruntime = "^1.17.1"
-
-[tool.black]
-line-length = 88
-include = '\.pyi?$'
-exclude = '''
-/(
-    \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-)/
-'''
-
-[tool.isort]
-profile = "black"
+mkdocs = "^1.6.0"
+mkdocs-material = "^9.5.21"
+mkdocstrings-python = "^1.10.0"
+mkdocs-jupyter = "^0.24.7"
 
 [tool.ruff]
 line-length = 88
 target-version = "py310"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 unfixable = ["E711"]
 
 select = [
@@ -166,9 +150,9 @@ ignore = [
     "TID252",
 ]
 
-exclude = [".github", "docs", "notebook", "tests"]
+exclude = [".github", "docs", "notebook", "tests/*"]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
 [tool.mypy]

src/hssm/distribution_utils/onnx/onnx2pt.py

@@ -17,9 +17,7 @@ def onnx_add(a, b, axis=None, broadcast=True):
     return [pt.add(a, b)]
 
 
-def pytensor_gemm(
-    a, b, c=0.0, alpha=1.0, beta=1.0, transA=0, transB=0
-):  # pylint: disable=C0103
+def pytensor_gemm(a, b, c=0.0, alpha=1.0, beta=1.0, transA=0, transB=0):  # pylint: disable=C0103
     """Perform the GEMM op.
 
     Numpy-backed implementatio, of ONNX General Matrix Multiply (GeMM) op.

src/hssm/distribution_utils/onnx/onnx2xla.py

@@ -102,9 +102,7 @@ def onnx_add(a, b, axis=None, broadcast=True):
 
 
 # Added by HSSM Developers
-def onnx_gemm(
-    a, b, c=0.0, alpha=1.0, beta=1.0, transA=0, transB=0
-):  # pylint: disable=C0103
+def onnx_gemm(a, b, c=0.0, alpha=1.0, beta=1.0, transA=0, transB=0):  # pylint: disable=C0103
     """Numpy-backed implementatio of Onnx Gemm op."""
     a = jnp.transpose(a) if transA else a
     b = jnp.transpose(b) if transB else b