Feature/update from template

.github/workflows/pre-commit.yaml

@@ -0,0 +1,10 @@
+name: pre-commit
+
+on: [pull_request]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: pre-commit/[email protected]

.github/workflows/publish.yml

@@ -15,4 +15,4 @@ jobs:
       with:
         pypi-token: ${{ secrets.PYPI_API_TOKEN }}
         gh-token: ${{ secrets.GITHUB_TOKEN }}
-        parse-changelog: true
+        parse-changelog: true

.pre-commit-config.yaml

@@ -0,0 +1,60 @@
+# To use:
+#
+#     pre-commit run -a
+#
+# Or:
+#
+#     pre-commit install  # (runs every time you commit in git)
+#
+# To update this file:
+#
+#     pre-commit autoupdate
+#
+# See https://github.com/pre-commit/pre-commit
+
+repos:
+  # Standard hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: name-tests-test
+      - id: detect-private-key
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-xml
+      - id: check-yaml
+        args: ['--unsafe']  # Fixes errors parsing custom jinja templates
+      # - id: check-json
+      # - id: pretty-format-json
+      #   args: ['--autofix']  
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      # - id: trailing-whitespace
+      - id: fix-byte-order-marker
+
+  # Formatter for python
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi ]
+  # Checks for spelling mistakes
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0 #TODO latest version  2.3.0 finds a lot of spelling mistakes but fails on "assertIn"
+    hooks:
+      - id: codespell
+        args: ['--write-changes']
+        exclude: \.(svg|pyc|lock|json)$

.vscode/extensions.json

@@ -1,17 +1,17 @@
 {
-    "recommendations": [
-        "ms-python.python",
-        "ms-python.vscode-pylance",
-        "ms-python.pylint",
-        "ms-python.black-formatter",
-        "njpwerner.autodocstring",
-        "charliermarsh.ruff",
-        "mhutchie.git-graph",
-        "eamodio.gitlens",
-        "tamasfe.even-better-toml",
-        "Codium.codium",
-        "ms-azuretools.vscode-docker",
-        "ryanluker.vscode-coverage-gutters",
-        "jjjermiah.pixi-vscode"       
-    ]
-}
+  "recommendations": [
+    "ms-python.python",
+    "ms-python.vscode-pylance",
+    "ms-python.pylint",
+    "ms-python.black-formatter",
+    "njpwerner.autodocstring",
+    "charliermarsh.ruff",
+    "mhutchie.git-graph",
+    "eamodio.gitlens",
+    "tamasfe.even-better-toml",
+    "Codium.codium",
+    "ms-azuretools.vscode-docker",
+    "ryanluker.vscode-coverage-gutters",
+    "jjjermiah.pixi-vscode"
+  ]
+}

.vscode/settings.json

@@ -21,4 +21,4 @@
 	"python.analysis.autoImportCompletions": false,
 	"python.analysis.typeCheckingMode": "off",
 	"python.defaultInterpreterPath": "/workspaces/bencher/.pixi/envs/default/bin/python" //vscode gets it wrong more than right and mostly gets in the way
-}
+}

bencher.deps.yaml

@@ -7,3 +7,4 @@ apt_tools:
 pip_language-toolchain:
   - uv #use uv instead of pip
   - pip #update to the latest pip
+  - pre-commit

bencher/example/benchmark_data.py

@@ -1,6 +1,6 @@
 """This file contains an example of how to define benchmarking parameters sweeps. Categorical values are defined as enums and passed to EnumSweep classes, other types of sweeps are defined by their respective classes.
 
-You can define a subclass which contains an input configuration which can be passed to a function in a type safe way. You can combine the subclass with a higher level class which contains more configuation parameters.  This is to help manage the complexity of large configuration/parameter spaces. 
+You can define a subclass which contains an input configuration which can be passed to a function in a type safe way. You can combine the subclass with a higher level class which contains more configuation parameters.  This is to help manage the complexity of large configuration/parameter spaces.
 """
 
 import math

bencher/example/example_dataframe.py

@@ -6,7 +6,6 @@
 
 
 class ExampleMergeDataset(bch.ParametrizedSweep):
-
     value = bch.FloatSweep(default=0, bounds=[0, 10])
     repeats_x = bch.IntSweep(default=2, bounds=[2, 4])
     # repeats_y = bch.IntSweep(default=2, bounds=[2, 4])

bencher/example/example_image1.py

@@ -72,7 +72,6 @@ def example_image_vid_sequential1(
 
 
 if __name__ == "__main__":
-
     ex_run_cfg = bch.BenchRunCfg()
     ex_run_cfg.use_sample_cache = True
     ex_run_cfg.overwrite_sample_cache = True

bencher/results/bench_result_base.py

@@ -87,7 +87,7 @@ def to_dataset(
 
         ds_out = self.ds if result_var is None else self.ds[result_var.name]
 
-        match (reduce):
+        match reduce:
             case ReduceType.REDUCE:
                 ds_reduce_mean = ds_out.mean(dim="repeat", keep_attrs=True)
                 ds_reduce_std = ds_out.std(dim="repeat", keep_attrs=True)

docs/requirements.txt

@@ -1,4 +1,4 @@
 holobench
 sphinxcontrib-napoleon
 sphinx-rtd-theme
-sphinx-autoapi
+sphinx-autoapi