Merge pull request #365 from dyson-ai/feature/update_from_template

Feature/update from template

.gitattributes

@@ -41,3 +41,6 @@
 *.pkl filter=lfs diff=lfs merge=lfs -text
 # numpy file format
 *.npy filter=lfs diff=lfs merge=lfs -text
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.github/dependabot.yml

@@ -26,3 +26,7 @@ updates:
         #try to group all third party library updates into a single pr
         patterns:
           - "*"
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly

.github/workflows/ci.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: CI
 
 on:
@@ -13,38 +10,26 @@ permissions:
   contents: read
 
 jobs:
-
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: psf/black@stable
-  ruff:
-    runs-on: ubuntu-latest
-    needs: [black]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: chartboost/ruff-action@v1
-  build:
+  ci:
     runs-on: ubuntu-latest
-    needs: [ruff]
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flit
-        flit install --extras test
-    - run: |
-        pylint $(git ls-files '*.py')
-    - name: Test with pytest
-      run: |
-        coverage run -m pytest
-    - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Checkout
+        uses: actions/checkout@v4
+      - uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.22.0
+          cache: true
+      - name: Format and lint
+        run: |
+          pixi run fmt
+          pixi run lint 
+      - name: Assert no changes
+        run: |
+            git diff --exit-code     
+      - name: Test
+        run: |
+          pixi run coverage      
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -167,7 +167,12 @@ cython_debug/
 hashed_vars_comparison_tmp
 .vscode/active_file.cfg
 test/test_bench_server.html
+.vscode/active_file.cfg
 
 #COLCON
 install/**
 log/**
+# pixi environments
+.pixi
+*.egg-info
+

.vscode/tasks.json

@@ -120,10 +120,10 @@
 			"command": "scripts/update_from_template_ours.sh"
 		},
 		{
-			"label": "rename template project name and commit",
+			"label": "rename template project",
 			"detail": "Replaces all instances of the template project name with a new name. ",
 			"type": "shell",
-			"command": "scripts/rename_project.sh ${input:new_project_name}; git commit -a -m 'rename project'"
+			"command": "scripts/rename_project.sh ${input:new_project_name}"
 		},
 		{
 			"label": "first time setup of project",

CHANGELOG.md

@@ -2,4 +2,4 @@ Changelog
 
 ## [0.3.10]
 
-Before changelogs
+Before changelogs

README.md

@@ -47,4 +47,4 @@ Bencher is designed to work with stochastic pure functions with no side effects.
 
 ### Example Output
 
-https://dyson-ai.github.io/bencher/
+https://dyson-ai.github.io/bencher/

bencher/results/panel_result.py

@@ -25,7 +25,7 @@ def to_panes(
         target_dimension: int = 0,
         container=None,
         level: int = None,
-        **kwargs
+        **kwargs,
     ) -> Optional[pn.pane.panel]:
         if hv_dataset is None:
             hv_dataset = self.to_hv_dataset(ReduceType.SQUEEZE, level=level)

deps.yaml

@@ -9,3 +9,6 @@ apt_tools:
 pip_tools:
   - flit
   - pip #updates to latest pip
+
+pip:
+  - pip

pyproject.toml

@@ -7,8 +7,7 @@ description = "A package for benchmarking the performance of arbitrary functions
 readme = "README.md"
 
 #incompatible with setuptools
-# requires-python = ">= 3.10"
-
+requires-python = "==3.10"
 
 dependencies = [
   "holoviews>=1.15,<=1.18.3",
@@ -30,14 +29,23 @@ dependencies = [
   "moviepy>=1.0.3,<=1.0.3",
 ]
 
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["linux-64"]
+
+[tool.pixi.dependencies]
+
+[tool.pixi.pypi-dependencies]
+holobench = { path = ".", editable = true }
+
 [project.optional-dependencies]
 test = [
   "black>=23,<=24.4.2",
   "pylint>=2.16,<=3.1.0",
   "pytest-cov>=4.1,<=5.0.0",
   "pytest>=7.4,<=8.2.0",
-  "hypothesis>=6.82,<=6.101.0",
-  "ruff>=0.0.280,<=0.4.4",
+  "hypothesis>=6.82,<=6.100.5",
+  "ruff>=0.0.280,<=0.4.3",
   "coverage>=7.2.7,<=7.5.1",
 ]
 
@@ -46,18 +54,26 @@ Repository = "https://github.com/dyson-ai/bencher"
 Home = "https://github.com/dyson-ai/bencher"
 Documentation = "https://bencher.readthedocs.io/en/latest/"
 
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
 
-[tool.flit.module]
-name = "bencher"
-
+# Environments
+[tool.pixi.environments]
+default = { solve-group = "default" }
+test = { features = ["test"], solve-group = "default" }
 
-[build-system]
-requires = ["flit_core >=3.2,<4"]
-build-backend = "flit_core.buildapi"
+[tool.pixi.tasks]
+pr = "pixi install; git commit -a -m'update pixi.lock';git push"
 
+[tool.pixi.feature.test.tasks]
+fmt = "black ."
+lint = "ruff check . --fix ; pylint $(git ls-files '*.py')"
+test = "pytest"
+coverage = "coverage run -m pytest; coverage xml -o coverage.xml"
 
-[tool.setuptools_scm]
-# lol just to keep colcon happy
+[tool.setuptools.packages.find]
+include = ["python_template"]
 
 [tool.pylint]
 extension-pkg-whitelist = ["numpy", "scipy"]
@@ -70,20 +86,18 @@ enable = "no-else-return,consider-using-in"
 [tool.black]
 line-length = 100
 
-
 [tool.ruff]
 # Never enforce `E501` (line length violations).
 #"F841" will auto remove unused variables which is annoying during development, pylint catches this anyway
-lint.ignore = ["E501", "E902", "F841"]
-
+ignore = ["E501", "E902", "F841"]
 
 # Same as Black.
 line-length = 100
 
 target-version = "py310"
 
 # Allow unused variables when underscore-prefixed.
-lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
 # Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
 [tool.ruff.lint.per-file-ignores]

scripts/launch_vscode.sh

@@ -18,7 +18,7 @@ docker stop "$CONTAINER_NAME" || true
 
 CONTAINER_HEX=$(printf $CONTAINER_NAME | xxd -p | tr '\n' ' ' | sed 's/\\s//g' | tr -d ' ');
 
-rocker --nvidia --x11 --user --pull --git --image-name "$CONTAINER_NAME" --name "$CONTAINER_NAME" --volume "${PWD}":/workspaces/"${CONTAINER_NAME}":Z --oyr-run-arg " --detach" --deps-dependencies ubuntu:22.04 
+rocker --nvidia --x11 --user --pull --git --image-name "$CONTAINER_NAME" --name "$CONTAINER_NAME" --volume "${PWD}":/workspaces/"${CONTAINER_NAME}":Z --deps --oyr-run-arg " --detach" ubuntu:22.04 
 
 # docker pull ghcr.io/red5d/docker-autocompose:latest
 # docker run --rm -v /var/run/docker.sock:/var/run/docker.sock ghcr.io/red5d/docker-autocompose $CONTAINER_NAME > .devcontainer/docker-compose.yaml