Merge pull request #60 from AllenInstitute/pixi_example

Pixi example

.gitignore

@@ -101,6 +101,10 @@ venv.bak/
 # mkdocs documentation
 /site
 
+#Pixi
+pixi.lock
+.pixi/
+
 # mypy
 .mypy_cache/
 

acpreprocessing/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.dev397+gf424fe1.d20241113'
+__version_tuple__ = version_tuple = (0, 1, 'dev397', 'gf424fe1.d20241113')

pyproject.toml

@@ -0,0 +1,80 @@
+[project]
+name = "acpreprocessing"
+description='Axonal connectomics processing'
+requires-python = ">3.8,<3.12"
+version = "0.0.1"
+dynamic = ["dependencies"] 
+
+[tool.setuptools.dynamic]
+dependencies = { file = ["requirements.txt"] }
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-mock",
+    "pytest-cov",
+    "codecov",
+]
+
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+py-modules = [
+    "acpreprocessing",
+]
+
+[tool.setuptools_scm]
+version_file = "acpreprocessing/_version.py"
+
+# some downgrades from pixi's expectations
+[tool.pixi.system-requirements]
+linux = "5.0.0"
+libc = "2.27"
+
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["linux-64"]
+
+[tool.pixi.pypi-dependencies]
+acpreprocessing = { path = ".", editable = true }
+
+# conda-enabled features
+[tool.pixi.feature.pixi-base.dependencies]
+numpy = "1.26.0"
+imageio = "*"
+matplotlib = "*"
+
+# version-specific python features
+[tool.pixi.feature.py310.dependencies]
+python = "3.10.*"
+[tool.pixi.feature.py311.dependencies]
+python = "3.11.*"
+
+
+[tool.pixi.feature.conda-lab.dependencies]
+jupyterlab = "*"
+
+[tool.pixi.feature.scalene.dependencies]
+scalene = "*"
+
+[tool.pixi.environments]
+py310 = ["py310"]
+py310-test = ["py310", "test"]
+py311 = ["py311"]
+py311-test = ["py311", "test"]
+py310-conda = ["py310", "pixi-base"]
+py310-conda-test = ["py310", "pixi-base", "test"]
+py311-conda = ["py311", "pixi-base"]
+py311-conda-test = ["py311", "pixi-base", "test"]
+py311-conda-lab = ["py311", "pixi-base", "conda-lab"]
+py311-conda-scalene = ["py311", "pixi-base", "scalene"]
+py311-conda-scalene-lab = ["py311", "pixi-base", "scalene", "conda-lab"]
+
+
+[tool.coverage.run]
+omit = ["test/*",]
+
+[tool.pixi.feature.test.tasks]
+test = "pytest  --cov --cov-report=xml --junitxml=test-reports/test.xml"

requirements.txt

@@ -1,11 +1,13 @@
 pillow
 tifffile==2020.7.4
 scikit-image
-numpy
-imageio<2.21
+numpy==1.26.0
+imageio
+# "imageio<2.21",
 matplotlib
 argschema
 natsort
 requests
 cloud-volume>=8.5.5
-zarr
+zarr
+h5py