Move to hatchling build system (#55)

* Bumps minimum Python version to 3.8 and minimum Pandas version to 2.0.0.
* Incorporates linting via ruff, black, and isort.
* Expands python-package GitHub workflow to test more OSes and Python version.
* Fixes failing tests and adds new tests.

.github/workflows/python-package.yml

@@ -1,35 +1,96 @@
-# This workflow will install Python dependencies, run tests
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
+  # based on https://github.com/pypa/hatch/blob/master/.github/workflows/test.yml
 name: tests
 
-on: [ push ]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  STABLE_PYTHON_VERSION: '3.11'
+  PYTHONUNBUFFERED: "1"
+  FORCE_COLOR: "1"
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+    name: Python ${{ matrix.python-version }} on ${{ startsWith(matrix.os, 'macos-') && 'macOS' || startsWith(matrix.os, 'windows-') && 'Windows' || 'Linux' }}
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7.15, 3.10.8]
+        python-version: ["3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[dev] --no-cache-dir
+
+      - name: Ensure latest pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install Hatch
+        run: pip install hatch
+
+      - name: Install vflow
+        run: python -m pip install -e .
+
+      - name: Check styles
+        run: hatch run style:check
+
       - name: Test with pytest
-        run: |
-          pytest --cov=./ --cov-report=xml
-      - name: Lint with pylint
-        run: |
-          pylint vflow *.py --rcfile=.pylintrc
-      - name: "Upload coverage to Codecov"
-        uses: codecov/codecov-action@v2
+        run: hatch run full
+
+      - name: Disambiguate coverage filename
+        run: mv .coverage ".coverage.${{ matrix.os }}.${{ matrix.python-version }}"
+
+      - name: Upload coverage data
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-data
+          path: .coverage.*
+
+  coverage:
+    name: Report coverage
+    runs-on: ubuntu-latest
+    needs:
+      - build
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ env.STABLE_PYTHON_VERSION }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.STABLE_PYTHON_VERSION }}
+
+      - name: Install Hatch
+        run: pip install hatch
+
+      - name: Download coverage data
+        uses: actions/download-artifact@v3
+        with:
+          name: coverage-data
+
+      - name: Combine coverage data
+        run: hatch run coverage:combine
+
+      - name: Export coverage reports
+        run: hatch run coverage:report-xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.gitignore

@@ -1,3 +1,5 @@
+# -*- mode: gitignore; -*-
+
 **mlruns
 **.ipynb_checkpoints
 **cache*
@@ -48,3 +50,54 @@ notebooks/data/*
 .hypothesis
 **coverage*
 codecov
+
+# -- Emacs
+# https://github.com/github/gitignore/blob/main/Global/Emacs.gitignore
+
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+# network security
+/network-security.data

Makefile

@@ -0,0 +1,22 @@
+VERSION ?= $(shell git rev-parse --short HEAD)
+CONDA_ENV_NAME ?= vflow
+HATCH_ENV_NAME ?= test
+
+.PHONY: build_conda_env build_ipykernel test_% run_tests fix_styles
+
+build_conda_env:
+	conda create -n $(CONDA_ENV_NAME) -y python==3.10 pip
+	conda run -n $(CONDA_ENV_NAME) --no-capture-output pip install -r requirements.txt
+	conda run -n $(CONDA_ENV_NAME) --no-capture-output pip install . ipykernel
+
+build_ipykernel:
+	conda run -n $(CONDA_ENV_NAME) python -m ipykernel install --user --name $(CONDA_ENV_NAME) --display-name "Python [conda:$(CONDA_ENV_NAME)]"
+
+test_%:
+	hatch -v run dev $(PYTEST_ARGS) tests/test_$*.py
+
+run_tests:
+	hatch -v run cov
+
+fix_styles:
+	hatch -v run style:fmt

README.md

@@ -98,7 +98,17 @@ See the [docs](https://yu-group.github.io/veridical-flow/) for reference on the
 
 ## Installation
 
-Install with `pip install vflow` (see [here](https://github.com/Yu-Group/veridical-flow/blob/master/docs/troubleshooting.md) for help). For dev version (unstable), clone the repo and run `python setup.py develop` from the repo directory.
+### Stable version
+
+```bash
+pip install vflow
+```
+
+### Development version (unstable)
+
+```bash
+pip install vflow@git+https://github.com/Yu-Group/veridical-flow
+```
 
 # References
 

hatch.toml

@@ -0,0 +1,62 @@
+# based on https://github.com/pypa/hatch/blob/master/hatch.toml
+
+[envs.default]
+dependencies = [
+  "coverage[toml]",
+  "pytest-cov",
+  "pytest-randomly",
+  "pytest-rerunfailures",
+  "pytest-xdist",
+]
+
+[envs.default.scripts]
+# --cov must not come before an argument in order to use the sources defined by config
+_cov = "pytest --cov --cov-report=term-missing --cov-config=pyproject.toml"
+dev = "pytest -p no:randomly --no-cov {args:tests}"
+cov = "_cov -p no:randomly {args:tests}"
+full = "_cov -n auto --reruns 5 --reruns-delay 3 -r aR {args:tests}"
+
+[envs.dev]
+template = "default"
+dependencies = [
+  "jupyterlab",
+  "torch>=1.0.0",
+  "torchvision",
+  "tqdm",
+  "scikit-learn>=0.23.0",
+]
+
+[envs.dev.env-vars]
+PIP_INDEX_URL = "https://download.pytorch.org/whl/cpu"
+PIP_EXTRA_INDEX_URL = "https://pypi.org/simple/"
+
+[envs.style]
+detached = true
+dependencies = [
+  "ruff",
+  "black",
+  "isort",
+]
+
+[envs.style.scripts]
+check = [
+  "ruff vflow tests",
+  "black --check --diff vflow tests",
+  "isort --check --diff --profile black vflow tests",
+]
+fmt = [
+  "isort --profile black ./vflow ./tests",
+  "black ./vflow ./tests",
+  "check",
+]
+
+[envs.coverage]
+detached = true
+dependencies = [
+  "coverage[toml]",
+  "lxml",
+]
+
+[envs.coverage.scripts]
+combine = "coverage combine {args}"
+report-xml = "coverage xml -i"

pyproject.toml

@@ -1,3 +1,55 @@
 [build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling", "hatch-requirements-txt"]
+build-backend = "hatchling.build"
+
+[project]
+name = "vflow"
+version = "0.1.2"
+authors = [
+  { name="Chandan Singh", email="[email protected]" },
+  { name="James Duncan", email="[email protected]" },
+  { name="Abhineet Agarwal", email="[email protected]" },
+  { name="Rush Kapoor", email="[email protected] " },
+]
+maintainers = [
+  { name="James Duncan", email="[email protected]" },
+]
+description = "A framework for doing stability analysis with PCS."
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+  "Intended Audience :: Science/Research",
+  "Development Status :: 3 - Alpha",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Artificial Intelligence",
+  "Operating System :: OS Independent",
+]
+license = {text = "MIT"}
+dynamic = ["dependencies"]
+
+[project.urls]
+Homepage = "https://vflow.csinva.io/"
+Issues = "https://github.com/Yu-Group/veridical-flow/issues"
+
+[project.optional-dependencies]
+gpu = ["torch"]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.metadata.hooks.requirements_txt]
+files = ["requirements.txt"]
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "/.github",
+  "/notebooks",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["vflow"]
+
+[tool.coverage.run]
+branch = true
+source_pkgs = ["vflow", "tests"]

requirements.txt

@@ -0,0 +1,9 @@
+numpy
+scipy
+matplotlib
+networkx
+pandas>=2.0.0
+joblib
+pytest
+ray
+mlflow