Switch from Python setuptools to Pixi

.github/workflows/test.yml

@@ -12,25 +12,28 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.11']
     steps:
       - name: Checkout reposistory
         uses: actions/checkout@v3
         with:
           submodules: recursive
 
-      - name: Set up Python
-        uses: actions/setup-python@v3
+      - name: Install Python environment needed for the relpo command
+        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: '3.13'
 
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
+      - name: Install pixi
+        run: 'curl -fsSL https://pixi.sh/install.sh | sh'
 
-      - name: Install dependent packages
-        run: 'make deps'
+      - name: Add pixi to path
+        run: 'echo "${HOME}/.pixi/bin" >> $GITHUB_PATH'
+
+      # we have to install the environment without --lock, as otherwise the
+      # pyproject.toml sha1 changes due to different whitespace in the build
+      # environment
+      - name: Create the enviornment, which updates the lock file
+        run: 'make init'
 
       - name: Run tests
-        run: 'make test'
+        run: 'make testall'

LICENSE.md

@@ -0,0 +1,11 @@
+Copyright 2022 - 2025 The Regents of the University of Illinois
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

makefile

@@ -4,28 +4,56 @@
 
 ## Build
 #
-# directory with the unit tests
-PY_TEST_DIR ?=		tests
-# test file glob pattern
-PY_TEST_GLOB ?=		test_metrics.py
+TARG_DIR ?=		target
+DIST_DIR ?=		$(TARG_DIR)/dist
 
 
 ## Targets
 #
-# install dependencies
-.PHONY:			deps
-deps:
-			pip install -r requirements-nlp.txt
+$(DIST_DIR):
+		mkdir -p $(DIST_DIR)
 
-# run the unit test cases
-.PHONY:			test
+
+# install the pixi program
+.PHONY:		installpixi
+installpixi:
+		@echo "checking for pixi..."
+		@$(eval ex := $(shell which pixi > /dev/null 2>&1 ; echo $$?))
+		@if [ $(ex) -eq 1 ] ; then \
+			echo "pixi not found, install? (CNTL-C to stop)" ; \
+			read ; \
+			curl -fsSL https://pixi.sh/install.sh | sh ; \
+		fi
+		@echo "installed"
+
+# install pixi and the Python environments
+.PHONY:		init
+init:		installpixi
+		@echo "installing environment..."
+		@pixi install
+
+# run base module tests
+.PHONY:		test
 test:
-			@echo "Running tests in $(PY_TEST_DIR)/$(PY_TEST_GLOB)"
-			python -m unittest discover \
-				-s $(PY_TEST_DIR) -p '$(PY_TEST_GLOB)' -v
+		@echo "running unit tests..."
+		@pixi run test
+
+# run NLP specific tests
+.PHONY:		testnlp
+testnlp:
+		@echo "running NLP unit tests..."
+		@pixi run testnlp
+
+# run all tests
+.PHONY:		testall
+testall:	test testnlp
+
+# build the wheel
+.PHONY:		wheel
+wheel:		$(DIST_DIR)
+		@PX_DIST_DIR=$(DIST_DIR) pixi run build-wheel
 
-# clean derived objects
-.PHONY:			clean
+.PHONY:		clean
 clean:
-			@echo "removing __pycache__"
-			@find . -type d -name __pycache__ -prune -exec rm -r {} \;
+		@echo "removing target: $(TARG_DIR)"
+		@rm -fr $(TARG_DIR)

pyhealth/tasks/EEG_abnormal.py

@@ -1,9 +1,6 @@
 import os
 import pickle
-import pkg_resources
 import mne
-import pandas as pd
-import numpy as np
 
 
 def EEG_isAbnormal_fn(record):
@@ -155,7 +152,6 @@ def EEG_isAbnormal_fn(record):
         return samples
 
 
-
 if __name__ == "__main__":
     from pyhealth.datasets import TUABDataset
 
@@ -167,7 +163,3 @@ def EEG_isAbnormal_fn(record):
     EEG_abnormal_ds = dataset.set_task(EEG_isAbnormal_fn)
     print(EEG_abnormal_ds.samples[0])
     print(EEG_abnormal_ds.input_info)
-
-
-
-

pyhealth/tasks/EEG_events.py

@@ -1,10 +1,9 @@
 import os
 import pickle
-import pkg_resources
 import mne
-import pandas as pd
 import numpy as np
 
+
 def EEG_events_fn(record):
     """Processes a single patient for the EEG events task on TUEV.
 
@@ -191,7 +190,6 @@ def readEDF(fileName):
     return [signals, times, eventData, Rawdata]
 
 
-
 if __name__ == "__main__":
     from pyhealth.datasets import TUEVDataset
 
@@ -203,7 +201,3 @@ def readEDF(fileName):
     EEG_events_ds = dataset.set_task(EEG_events_fn)
     print(EEG_events_ds.samples[0])
     print(EEG_events_ds.input_info)
-
-
-
-

pyhealth/tasks/cardiology_detect.py

@@ -1,9 +1,6 @@
 import os
 import pickle
-import pkg_resources
 from scipy.io import loadmat
-import pandas as pd
-import numpy as np
 
 
 def cardiology_isAR_fn(record, epoch_sec=10, shift=5):

pyhealth/tasks/medical_coding.py

@@ -242,4 +242,4 @@ def main():
         if len(samples[0]['icd_codes']) > 0:
             print(f"  - Sample ICD codes: {samples[0]['icd_codes'][:5] if len(samples[0]['icd_codes']) > 5 else samples[0]['icd_codes']}")
 if __name__ == "__main__":
-    main()
+    main()

pyhealth/tasks/sleep_staging.py

@@ -1,6 +1,5 @@
 import os
 import pickle
-import pkg_resources
 import mne
 import pandas as pd
 import numpy as np
@@ -259,7 +258,8 @@ def sleep_staging_shhs_fn(record, epoch_seconds=30):
     # test whether the ogb and torch_scatter packages are ready
     dependencies = ["elementpath"]
     try:
-        pkg_resources.require(dependencies)
+        from importlib.metadata import version
+        version(dependencies)
         import xml.etree.ElementTree as ET
     except Exception as e:
         print(e)

pyhealth/tasks/temple_university_EEG_tasks.py

@@ -1,8 +1,6 @@
 import os
 import pickle
-import pkg_resources
 import mne
-import pandas as pd
 import numpy as np
 
 

pyproject.toml

@@ -0,0 +1,154 @@
+#@meta {desc: "PyHealth build configuration", date: "2025-07-16"}
+
+
+### Project
+#
+[project]
+name = "pyhealth"
+# must be kept in sync with git tags; is not updated by any automation tools
+version = "1.2.0"
+authors = [
+  {name = "John Wu", email = "johnwu3@illinois.edu"},
+  {name = "Chaoqi Yang"},
+  {name = "Zhenbang Wu"},
+  {name = "Patrick Jiang"},
+  {name = "Zhen Lin"},
+  {name = "Benjamin Danek"},
+  {name = "Junyi Gao"},
+  {name = "Paul Landes", email = "landes@mailc.net"},
+  {name = "Jimeng Sun"},
+]
+description = "A Python library for healthcare AI"
+readme = "README.rst"
+requires-python = ">=3.13,<3.14"
+dependencies = [
+  "torch~=2.7.1",
+  "torchvision",
+  "transformers~=4.53.2",
+  "rdkit==2025.3.3",
+  "scikit-learn!=1.7.0",
+  "networkx==3.5",
+  "mne~=1.10.0",
+  "urllib3~=2.5.0",
+  "numpy~=1.26.4",
+  "tqdm",
+  "polars~=1.31.0",
+  "pandas~=2.3.1",
+  "pandarallel~=1.6.5",
+  "pydantic~=2.11.7",
+]
+license = "BSD-3-Clause"
+license-files = ["LICENSE.md"]
+keywords = [
+  "heathcare AI",
+  "healthcare",
+  "electronic health records",
+  "EHRs",
+  "machine learning",
+  "data mining",
+  "neural networks",
+  "deep learning",
+]
+
+[project.urls]
+Homepage = "https://github.com/sunlabuiuc/PyHealth"
+Documentation = "https://pyhealth.readthedocs.io/en/latest/about.html"
+Repository = "https://github.com/sunlabuiuc/PyHealth.git"
+Issues = "https://github.com/sunlabuiuc/PyHealth/issues"
+Changelog = "https://github.com/sunlabuiuc/PyHealth/blob/master/CHANGELOG.md"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+
+### Hatchling
+#
+[tool.hatch.build.targets.wheel]
+packages = ["pyhealth"]
+
+
+### Pixi
+#
+# specifies properties for the whole workspace
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64", "linux-aarch64", "win-64"]
+preview = ["pixi-build"]
+
+# virtual environments (each under '.pixi/envs') for specific tasks
+[tool.pixi.environments]
+default = { features = ["pyverbase"], solve-group = "default" }
+test = { features = ["pyverbase", "test"] }
+base = { features = ["pyverbase", "base"] }
+nlp = { features = ["pyverbase", "nlp"] }
+build-pypi = { features = ["pyverbase", "build-pypi"], solve-group = "default" }
+build-env = { features = ["pyverbase", "build-env"], solve-group = "default" }
+
+# specify where to download the build backend that builds conda files
+[tool.pixi.package.build]
+backend = { name = "pixi-build-python", version = "0.1.*" }
+channels = [
+  "https://prefix.dev/pixi-build-backends",
+  "https://prefix.dev/conda-forge",
+]
+
+# set the Python requirement for its environment
+[tool.pixi.feature.pyverbase.dependencies]
+python = "~=3.13"
+
+# pixi directly supports depending on PyPI packages, the PyPA calls a
+# distributed package a 'distribution'
+[tool.pixi.feature.base.pypi-dependencies]
+pyhealth = { path = ".", editable = true }
+
+[tool.pixi.feature.test.pypi-dependencies]
+pyhealth = { path = ".", editable = true }
+
+[tool.pixi.feature.nlp.pypi-dependencies]
+pyhealth = { path = ".", editable = true }
+
+[tool.pixi.feature.nlp.dependencies]
+pip = "*"
+
+# dependencies for building the wheel
+[tool.pixi.feature.build-pypi.dependencies]
+hatchling = "==1.26.3"
+
+[tool.pixi.feature.build-env.dependencies]
+# pip for environment extract
+pip = "*"
+
+# dependencies needed during build/link time that are specific to the host
+# machine
+[tool.pixi.package.host-dependencies]
+hatchling = "==1.26.3"
+python = "~=3.13"
+
+
+## Tasks
+#
+# task to use hatchling to build the wheel
+[tool.pixi.feature.build-pypi.tasks]
+build-wheel = "python -m hatchling build -t wheel --dir $PX_DIST_DIR"
+
+# use Python built-in unittest library for tests
+[tool.pixi.feature.test.tasks.test]
+cmd = "python -m unittest discover -t tests -s tests/core -p 'test_*.py' -v"
+[tool.pixi.feature.nlp.tasks.testnlp]
+cmd = "python -m unittest discover -t tests -s tests/nlp -p 'test_*.py' -v"
+
+# default environment tasks
+[tool.pixi.tasks]
+# env sanity check
+defaultenv = "python -c 'import sys; print(sys.executable, sys.version)'"
+# build the conda distribution file
+build-conda = "pixi build --output-dir $PX_DIST_DIR"
+# export environment.yml
+export = "pixi workspace export conda-environment"
+
+# command-line program invocation
+[tool.pixi.tasks.invoke]
+args = [{ "arg" = "args", "default" = "" }]
+env = { CLASS = "zensols.relpo.cli", PYTHONPATH = "src" }
+cmd = "\npython -c \"from $CLASS import main;print('_'*80);main('{{args}}'.split())\""