Dynamic versioning and updating python to match testing

.github/workflows/run-tests.yml

@@ -30,7 +30,7 @@ jobs:
   run_tests:
     strategy:
       matrix:
-        python_version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        python_version: ["3.11", "3.12", "3.13", "3.14"]
         os: [ubuntu-24.04, macos-14]
     runs-on: ${{ matrix.os }}
     env:

.gitignore

@@ -176,3 +176,4 @@ cython_debug/
 data/*
 testing.ipynb
 test_data/*
+src/zedprofiler/_version.py

docs/src/conf.py

@@ -12,6 +12,9 @@
 #
 import pathlib
 import sys
+import warnings
+
+warnings.filterwarnings("ignore", category=SyntaxWarning, module="mahotas")
 
 basedir = str(pathlib.Path(__file__).parent.parent.parent.resolve())
 

docs/src/notebooks/walkthrough.ipynb

@@ -47,7 +47,25 @@
      ]
     }
    ],
-   "source": "import warnings\nimport logging\nimport pathlib\n\nimport numpy as np\nimport pandas as pd\nimport tifffile\nfrom itables import show\n\nimport zedprofiler\nfrom zedprofiler.IO import loading_classes\n\nlogging.basicConfig(level=logging.WARNING)\nlogging.getLogger(\"matplotlib\").setLevel(logging.WARNING)\nwarnings.filterwarnings(\"ignore\", category=SyntaxWarning, module=\"mahotas\")"
+   "source": [
+    "import logging\n",
+    "import warnings\n",
+    "\n",
+    "# suppress third-party noise before any imports\n",
+    "logging.basicConfig(level=logging.WARNING)\n",
+    "logging.getLogger(\"matplotlib\").setLevel(logging.WARNING)\n",
+    "warnings.filterwarnings(\"ignore\", category=SyntaxWarning, module=\"mahotas\")\n",
+    "\n",
+    "import pathlib\n",
+    "\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import tifffile\n",
+    "from itables import show\n",
+    "\n",
+    "import zedprofiler\n",
+    "from zedprofiler.IO import loading_classes"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -456,7 +474,9 @@
     "\n",
     "Key parameters:\n",
     "- `thr`: minimum pixel intensity threshold below which pixels are excluded\n",
-    "- `fast_costes`: `\"Accurate\"` uses the full bisection algorithm for the Costes threshold; `\"Fast\"` uses a linear approximation"
+    "- `fast_costes`: `\"Accurate\"` uses the full bisection algorithm for the Costes threshold; `\"Fast\"` uses a linear approximation\n",
+    "\n",
+    "*For full feature definitions, see the [Colocalization](../features/colocalization.md) reference page.*"
    ]
   },
   {
@@ -494,7 +514,9 @@
     "- `radius`: radius of the structuring element used for background subtraction before the spectrum is computed\n",
     "- `subsample_size`: fraction of the image used during spectrum computation (speeds up processing on large volumes)\n",
     "- `image_sample_size`: fraction used for background estimation\n",
-    "- `mask_threshold`: threshold applied after interpolation to define the object mask"
+    "- `mask_threshold`: threshold applied after interpolation to define the object mask\n",
+    "\n",
+    "*For full feature definitions, see the [Granularity](../features/granularity.md) reference page.*"
    ]
   },
   {
@@ -533,7 +555,9 @@
     "- **Mean, median, standard deviation, max, min** of voxel intensities\n",
     "- **Integrated intensity**: sum of all voxel intensities (correlated with object volume)\n",
     "- **Mass displacement**: distance between the object's geometric centroid and its intensity-weighted centroid, indicating asymmetric signal distribution\n",
-    "- **Lower/upper quartile intensities**: robust measures of the intensity distribution"
+    "- **Lower/upper quartile intensities**: robust measures of the intensity distribution\n",
+    "\n",
+    "*For full feature definitions, see the [Intensity](../features/intensity.md) reference page.*"
    ]
   },
   {
@@ -565,7 +589,9 @@
     "\n",
     "Key parameters:\n",
     "- `distance_threshold`: maximum centroid-to-centroid distance (in voxels) for two objects to be considered neighbors\n",
-    "- `anisotropy_factor`: the ratio of z-spacing to xy-spacing (`anisotropy_spacing[0] / anisotropy_spacing[1]`); used to rescale z-distances to physical units before computing Euclidean distances, ensuring accurate neighbor relationships in anisotropic volumes"
+    "- `anisotropy_factor`: the ratio of z-spacing to xy-spacing (`anisotropy_spacing[0] / anisotropy_spacing[1]`); used to rescale z-distances to physical units before computing Euclidean distances, ensuring accurate neighbor relationships in anisotropic volumes\n",
+    "\n",
+    "*For full feature definitions, see the [Neighbors](../features/neighbors.md) reference page.*"
    ]
   },
   {
@@ -602,7 +628,9 @@
     "\n",
     "Key parameters:\n",
     "- `distance`: the pixel offset at which co-occurrence is measured; larger values capture coarser texture patterns\n",
-    "- `grayscale`: the number of intensity bins used to quantize the image before computing the GLCM; fewer bins are faster but lose intensity resolution"
+    "- `grayscale`: the number of intensity bins used to quantize the image before computing the GLCM; fewer bins are faster but lose intensity resolution\n",
+    "\n",
+    "*For full feature definitions, see the [Texture](../features/texture.md) reference page.*"
    ]
   },
   {
@@ -640,7 +668,9 @@
     "- **Extent**: ratio of object volume to bounding box volume (compactness)\n",
     "- **Euler number**: topological measure of holes/tunnels in the object\n",
     "- **Equivalent diameter**: diameter of a sphere with the same volume\n",
-    "- **Surface area**: estimated via marching cubes on the object boundary"
+    "- **Surface area**: estimated via marching cubes on the object boundary\n",
+    "\n",
+    "*For full feature definitions, see the [Volume, Size, and Shape](../features/areasizeshape.md) reference page.*"
    ]
   },
   {

pyproject.toml

@@ -4,18 +4,26 @@ requires = [ "setuptools>=82.0.1", "setuptools-scm>=10.0.5" ]
 
 [project]
 name = "zedprofiler"
-version = "0.0.1"
 description = "CPU-first handcrafted 3D featurization toolkit for high-throughput profiling"
 readme = "README.md"
+license = { file = "LICENSE" }
 authors = [
-  { name = "Your NameWay Lab" },
+  { name = "Mike Lippincott" },
+  { name = "Dave Bunten" },
+  { name = "Jenna Tomkinson" },
+  { name = "Vincent Rubinetti" },
+  { name = "Gregory Way" },
 ]
-requires-python = ">=3.13"
+requires-python = ">=3.11,<3.15"
 classifiers = [
+  "License :: OSI Approved :: BSD License",
   "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
 ]
+dynamic = [ "version" ]
 dependencies = [
   "beartype>=0.19",
   "bioio>=3.3",
@@ -29,10 +37,10 @@ dependencies = [
   "pyarrow>=23.0.1",
   "pydantic>=2.10",
   "scikit-image>=0.26",
-  "sphinx-conestack-theme>=1.1.1",
-  "sphinx-rtd-theme>=3.1",
   "tomli>=2.4.1",
 ]
+urls.Homepage = "https://zedprofiler.readthedocs.io"
+urls.Repository = "https://github.com/WayScience/ZedProfiler"
 scripts.ZedProfiler = "ZedProfiler.cli:trigger"
 
 [dependency-groups]
@@ -48,8 +56,8 @@ docs = [
   "myst-nb>=1.4",
   "plotly>=6.8",
   "pycytominer>=1.6",
-  "pydata-sphinx-theme>=0.17",
-  "sphinx>=9.1",
+  "sphinx>=7",
+  "sphinx-rtd-theme>=3.1",
 ]
 notebooks = [
   "black>=26.3.1",
@@ -60,7 +68,7 @@ notebooks = [
 ]
 
 [tool.setuptools_scm]
-version_file = "src/ZedProfiler/_version.py"
+version_file = "src/zedprofiler/_version.py"
 version_scheme = "no-guess-dev"
 local_scheme = "no-local-version"
 root = "."