Merge pull request #39 from uncbiag/package

Add package configuration

.github/workflows/github-hosted-action.yml

@@ -9,14 +9,16 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.8
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt pytest
-    - name: Test with unittest
+        pip install -e .
+        pip install pytest
+    - name: Test with pytest
       run: |
-        python -m unittest -k CPU
+        pytest

README.md

@@ -1,6 +1,25 @@
+# OAI Analysis 2
+
 [<img src="https://github.com/uncbiag/OAI_analysis_2/actions/workflows/github-hosted-action.yml/badge.svg">](https://github.com/uncbiag/OAI_analysis_2/actions)
+[![PyPI - Version](https://img.shields.io/pypi/v/oai-analysis.svg)](https://pypi.org/project/oai-analysis)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/oai-analysis.svg)](https://pypi.org/project/oai-analysis)
 
-# OAI Analysis 2
+**Table of Contents**
+
+- [Installation](#installation)
+- [Introduction](#introduction)
+- [Development](#development)
+- [Citation](#citation)
+- [Acknowledgements](#acknowledgements)
+- [License](#license)
+
+## Installation
+
+```console
+pip install oai-analysis
+```
+
+## Introduction
 
 This repository contains open-source analysis approaches for the [Osteoarthritis Initiative (OAI)](https://nda.nih.gov/oai/) magnetic resonance image (MRI) data.
 The analysis code is largely written in Python with the help of [ITK](http://itk.org) and [VTK](http://vtk.org) for data I/O and mesh processing
@@ -32,17 +51,18 @@ We are currently working on the following features which should be available in
 2. **Workflow management**: Whereas *OAI Analysis* used custom code to avoid recomputing results, we are switching to [Dagster](https://dagster.io/) to manage data dependencies in *OAI Analysis 2*.
 3. **Distribution of analysis results**: As we are planning on not only distributing code, but also analysis results (such as segmentations, meshes, thickness maps) we are planning on supporting data access via the [Interplanetary File System (IPFS)](https://ipfs.io/).
 
-### Installation of dependencies and testing
+## Development
+
+Contributions are appreciated and welcome.
 
 ```
-git clone https://github.com/uncbiag/oai_analysis_2
-cd oai_analysis_2
-pip install -r requirements.txt
-python -m unittest -v discover
+git clone https://github.com/uncbiag/OAI_analysis_2
+cd OAI_analysis_2
+pip install -e .
+pip install pytest
+pytest
 ```
 
-Currently, this should declare that the segmentation test passed, and the registration test failed.
-
 To view the demo notebooks:
 ```
 cd notebooks
@@ -51,7 +71,7 @@ jupyter notebook
 
 upload test data to https://data.kitware.com/#collection/6205586c4acac99f42957ac3/folder/620559344acac99f42957d63
 
-### Related manuscripts
+## Citation
 
 While we used the following stationary velocity field registration approach available in [easyReg](https://github.com/uncbiag/easyreg) for *OAI Analysis*
 [[paper]](https://biag.cs.unc.edu/publication/dblp-confcvpr-shen-hxn-19/)
@@ -101,7 +121,11 @@ Results obtained by the *OAI Analysis* pipeline can be found in this manuscript
 }
 ```
 
-### Acknowledgements
+## Acknowledgements
 
 This work was developed with support in part from the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) 
 under award numbers [1R44AR074375](https://reporter.nih.gov/search/Naf5qSR3eUStFkMfGm6KpQ/project-details/9777582) and [1R01AR072013](https://reporter.nih.gov/search/eE7eB34dVUGoY1nLF3kZNA/project-details/9368542).
+
+## License
+
+`oai-analysis` is distributed under the terms of the [Apache-2.0](https://spdx.org/licenses/Apache-2.0.html) license.

notebooks/DaskComputation.ipynb

@@ -54,10 +54,10 @@
         "import sys\n",
         "sys.path.append(\"./OAI_analysis_2/\")\n",
         "\n",
-        "import oai_analysis_2\n",
-        "from oai_analysis_2 import mesh_processing as mp\n",
-        "from oai_analysis_2 import utils\n",
-        "from oai_analysis_2.analysis_object import AnalysisObject\n",
+        "import oai_analysis\n",
+        "from oai_analysis import mesh_processing as mp\n",
+        "from oai_analysis import utils\n",
+        "from oai_analysis.analysis_object import AnalysisObject\n",
         "from dask import delayed, compute, visualize\n",
         "from dask.distributed import Client, progress, LocalCluster"
       ]

notebooks/DaskComputationCoiled.ipynb

@@ -33,8 +33,8 @@
     "import random\n",
     "import itk\n",
     "import vtk\n",
-    "import oai_analysis_2\n",
-    "from oai_analysis_2 import dask_processing as dp"
+    "import oai_analysis\n",
+    "from oai_analysis import dask_processing as dp"
    ]
   },
   {

notebooks/FullDemo.ipynb

@@ -49,9 +49,9 @@
     "# Remove this once the pip package is available\n",
     "import sys\n",
     "sys.path.append(\"./OAI_analysis_2/\")\n",
-    "import oai_analysis_2\n",
-    "import oai_analysis_2.mesh_processing as mp\n",
-    "from oai_analysis_2.analysis_object import AnalysisObject\n",
+    "import oai_analysis\n",
+    "import oai_analysis.mesh_processing as mp\n",
+    "from oai_analysis.analysis_object import AnalysisObject\n",
     "\n",
     "# To enable running the itkwidgets window on colab\n",
     "from google.colab import output\n",

notebooks/SegmentationDemo.ipynb

@@ -59,7 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from oai_analysis_2.analysis_object import AnalysisObject\n",
+    "from oai_analysis.analysis_object import AnalysisObject\n",
     "obj = AnalysisObject()\n",
     "FC, TC = obj.segment(test_volume)"
    ]

oai_analysis/__about__.py

@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2023-present OAI Analysis Development Team
+#
+# SPDX-License-Identifier: Apache-2.0
+__version__ = "2.0.0"

oai_analysis_2/__init__.py → oai_analysis/__init__.py

@@ -1,5 +1,5 @@
 __version__ = '0.1'
 
 #from .analysis_object import AnalysisObject
-#from oai_analysis_2 import mesh_processing
+#from oai_analysis import mesh_processing
 

oai_analysis_2/analysis_object.py → oai_analysis/analysis_object.py

@@ -1,8 +1,8 @@
 import itk
 import torch
-from oai_analysis_2 import utils
-import oai_analysis_2.segmentation.segmenter
-import oai_analysis_2.registration
+from oai_analysis import utils
+import oai_analysis.segmentation.segmenter
+import oai_analysis.registration
 
 import os
 
@@ -25,17 +25,17 @@ def __init__(self):
             output_prob=True,
             output_itk=True,
         )
-        self.segmenter = oai_analysis_2.segmentation.segmenter.Segmenter3DInPatchClassWise(
+        self.segmenter = oai_analysis.segmentation.segmenter.Segmenter3DInPatchClassWise(
             mode="pred", config=segmenter_config
         )
 
         ## Initialize registerer
-        #self.registerer = oai_analysis_2.registration.AVSM_Registration(
+        #self.registerer = oai_analysis.registration.AVSM_Registration(
         #    ckpoint_path=os.path.join(utils.get_data_dir(), "pre_trained_registration_model"),
         #    config_path =os.path.join(utils.get_data_dir(), "avsm_settings")
         #
 
-        self.registerer = oai_analysis_2.registration.ICON_Registration()
+        self.registerer = oai_analysis.registration.ICON_Registration()
 
         ## Load Atlas
         self.atlas_image = itk.imread(os.path.join(utils.get_data_dir(), "atlas_60_LEFT_baseline_NMI/atlas_image.nii.gz"))

oai_analysis_2/dask_processing.py → oai_analysis/dask_processing.py

@@ -115,7 +115,7 @@ def deform_probmap_delayed(phi_AB, image_A, image_B, prob, image_type="FC"):
 def get_thickness(warped_image, mesh_type):
     import itk
     import numpy as np
-    from oai_analysis_2 import mesh_processing as mp
+    from oai_analysis import mesh_processing as mp
 
     distance_inner, _ = mp.get_thickness_mesh(warped_image, mesh_type=mesh_type)
     distance_inner_itk = mp.get_itk_mesh(distance_inner)
@@ -126,12 +126,12 @@ def get_thickness(warped_image, mesh_type):
 def segment_method(image_A):
     import itk
     from itk import IntensityWindowingImageFilter as IntensityWindowingImageFilter
-    import oai_analysis_2
+    import oai_analysis
     import torch
     import os
     from os.path import exists
-    from oai_analysis_2 import utils
-    from oai_analysis_2.segmentation import segmenter
+    from oai_analysis import utils
+    from oai_analysis.segmentation import segmenter
     import numpy as np
     import urllib.request
     import gc
@@ -167,7 +167,7 @@ def segment_method(image_A):
         output_itk=True,
     )
 
-    segmenter = oai_analysis_2.segmentation.segmenter.Segmenter3DInPatchClassWise(
+    segmenter = oai_analysis.segmentation.segmenter.Segmenter3DInPatchClassWise(
         mode="pred", config=segmenter_config
     )
 

pyproject.toml

@@ -0,0 +1,167 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "oai-analysis"
+dynamic = ["version"]
+description = 'Image analysis for the Osteoarthritis Initiative (OAI) knee magnetic resonance image (MRI) dataset.'
+readme = "README.md"
+requires-python = ">=3.8"
+license = "MIT"
+keywords = []
+authors = [
+  { name = "Marc Niethammer", email = "[email protected]" },
+  { name = "Hastings Greer", email = "[email protected]" },
+  { name = "Matt McCormick", email = "[email protected]" },
+  { name = "Pranjal Sahu", email = "[email protected]" },
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python :: Implementation :: PyPy",
+]
+dependencies = [
+  "torch",
+  "itk==5.3",
+  "trimesh",
+  "vtk",
+  "icon_registration==0.3.4",
+  "girder_client",
+  "scikit-image",
+]
+
+[project.urls]
+Documentation = "https://github.com/uncbiag/OAI_analysis_2#readme"
+Issues = "https://github.com/uncbiag/OAI_analysis_2/issues"
+Source = "https://github.com/uncbiag/OAI_analysis_2"
+
+[tool.hatch.version]
+path = "oai_analysis/__about__.py"
+
+[tool.hatch.envs.default]
+dependencies = [
+  "coverage[toml]>=6.5",
+  "pytest",
+]
+[tool.hatch.envs.default.scripts]
+test = "pytest {args:tests}"
+test-cov = "coverage run -m pytest {args:tests}"
+cov-report = [
+  "- coverage combine",
+  "coverage report",
+]
+cov = [
+  "test-cov",
+  "cov-report",
+]
+
+[[tool.hatch.envs.all.matrix]]
+python = ["3.7", "3.8", "3.9", "3.10", "3.11"]
+
+[tool.hatch.envs.lint]
+detached = true
+dependencies = [
+  "black>=23.1.0",
+  "mypy>=1.0.0",
+  "ruff>=0.0.243",
+]
+[tool.hatch.envs.lint.scripts]
+typing = "mypy --install-types --non-interactive {args:oai_analysis tests}"
+style = [
+  "ruff {args:.}",
+  "black --check --diff {args:.}",
+]
+fmt = [
+  "black {args:.}",
+  "ruff --fix {args:.}",
+  "style",
+]
+all = [
+  "style",
+  "typing",
+]
+
+[tool.black]
+target-version = ["py37"]
+line-length = 120
+skip-string-normalization = true
+
+[tool.ruff]
+target-version = "py37"
+line-length = 120
+select = [
+  "A",
+  "ARG",
+  "B",
+  "C",
+  "DTZ",
+  "E",
+  "EM",
+  "F",
+  "FBT",
+  "I",
+  "ICN",
+  "ISC",
+  "N",
+  "PLC",
+  "PLE",
+  "PLR",
+  "PLW",
+  "Q",
+  "RUF",
+  "S",
+  "T",
+  "TID",
+  "UP",
+  "W",
+  "YTT",
+]
+ignore = [
+  # Allow non-abstract empty methods in abstract base classes
+  "B027",
+  # Allow boolean positional values in function calls, like `dict.get(... True)`
+  "FBT003",
+  # Ignore checks for possible passwords
+  "S105", "S106", "S107",
+  # Ignore complexity
+  "C901", "PLR0911", "PLR0912", "PLR0913", "PLR0915",
+]
+unfixable = [
+  # Don't touch unused imports
+  "F401",
+]
+
+[tool.ruff.isort]
+known-first-party = ["oai_analysis"]
+
+[tool.ruff.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.per-file-ignores]
+# Tests can use magic values, assertions, and relative imports
+"tests/**/*" = ["PLR2004", "S101", "TID252"]
+
+[tool.coverage.run]
+source_pkgs = ["oai_analysis", "tests"]
+branch = true
+parallel = true
+omit = [
+  "oai_analysis/__about__.py",
+]
+
+[tool.coverage.paths]
+oai_analysis = ["oai_analysis", "*/oai-analysis/oai_analysis"]
+tests = ["tests", "*/oai-analysis/tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+  "no cov",
+  "if __name__ == .__main__.:",
+  "if TYPE_CHECKING:",
+]