Convert to pyproject style (#167)

* Remove testing changes

* Add robinhood to wheel build

* Add debug verbosity to build

* More debugging, decrease verbosity

* Update debug statement

* Include robinhood in source dist

Author: catanzaromj

.github/workflows/build_and_deploy.yml

@@ -18,10 +18,15 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Clone robinhood
+        run: |
+          git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
+
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.1
+        uses: pypa/cibuildwheel@v2.19.2
         env:
           CIBW_SKIP: "pp* cp36-* cp37-* *win_arm64 *_i686 *musllinux*"
+          CIBW_BUILD_VERBOSITY: 1
 
       - uses: actions/upload-artifact@v4
         with:
@@ -34,6 +39,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Clone robinhood
+        run: |
+          git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
+
       - name: Build sdist
         run: pipx run build --sdist
 

README.md

@@ -63,6 +63,15 @@ To be able to use `robin_hood` instead of STL, you only need to clone the reposi
 git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
 ```
 
+After cloning robinhood with the above command, install `ripser.py` with
+
+```
+pip install -v -e .
+```
+
+This will install a local, editable version of `ripser.py` with verbose output. In the verbose output,
+you will see confirmation that robinhood was found or not.
+
 <sup>1</sup> The Python package is already compiled with `robin_hood` by default.
 
 ## Usage

pyproject.toml

@@ -1,2 +1,58 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy", "cython"]
+requires = ["setuptools>=61.0", "wheel", "numpy", "Cython"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ripser"
+dynamic = ["version"]
+description = "A Lean Persistent Homology Library for Python"
+readme = "README.md"
+authors = [
+  { name = "Chris Tralie", email = "chris.tralie@gmail.com" },
+  { name = "Nathaniel Saul", email = "nat@riverasaul.com" },
+]
+maintainers = [
+  { name = "Chris Tralie", email = "chris.tralie@gmail.com" },
+  { name = "Nathaniel Saul", email = "nat@riverasaul.com" },
+  { name = "Michael Catanzaro", email = "catanzaromj@pm.me" },
+]
+
+dependencies = ["Cython", "numpy", "persim", "scipy", "scikit-learn"]
+
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Intended Audience :: Education",
+  "Intended Audience :: Financial and Insurance Industry",
+  "Intended Audience :: Healthcare Industry",
+  "Topic :: Scientific/Engineering :: Information Analysis",
+  "Topic :: Scientific/Engineering :: Mathematics",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python",
+]
+
+keywords = [
+  "topological data analysis",
+  "persistent homology",
+  "Rips filtration",
+  "algebraic topology",
+  "unsupervised learning",
+  "persistence diagrams",
+]
+
+[project.optional-dependencies]
+testing = ["pytest", "pytest-cov"]
+
+docs = ["sktda_docs_config"]
+
+examples = ["tadasets", "jupyter", "pillow"]
+
+[tool.setuptools.packages.find]
+where = ["ripser"]
+
+[project.urls]
+Homepage = "https://ripser.scikit-tda.org"
+Documentation = "https://ripser.scikit-tda.org"
+Repository = "https://github.com/scikit-tda/ripser.py"
+Issues = "https://github.com/scikit-tda/ripser.py/issues"
+Changelog = "https://github.com/scikit-tda/ripser.py/blob/master/RELEASE.txt"

ripser/_version.py

@@ -1 +1 @@
-__version__ = "0.6.8"
+__version__ = "0.6.9"

setup.py

@@ -1,9 +1,9 @@
-import sys
 import os
 import platform
+import re
+import sys
 
-from setuptools import setup
-from setuptools.extension import Extension
+from setuptools import Extension, setup
 
 # Ensure Cython is installed before we even attempt to install Ripser.py
 try:
@@ -14,21 +14,16 @@
     print("copy from www.cython.org or install it with `pip install Cython`")
     sys.exit(1)
 
-## Get version information from _version.py
-import re
 
-VERSIONFILE = "ripser/_version.py"
-verstrline = open(VERSIONFILE, "rt").read()
-VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
-mo = re.search(VSRE, verstrline, re.M)
-if mo:
-    verstr = mo.group(1)
-else:
-    raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
-
-# Use README.md as the package long description
-with open("README.md") as f:
-    long_description = f.read()
+def get_version():
+    VERSIONFILE = "ripser/_version.py"
+    verstrline = open(VERSIONFILE, "rt").read()
+    VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
+    mo = re.search(VSRE, verstrline, re.M)
+    if mo:
+        return mo.group(1)
+    else:
+        raise RuntimeError("Unable to find version string in %s." % (VERSIONFILE,))
 
 
 class CustomBuildExtCommand(build_ext):
@@ -67,6 +62,9 @@ def run(self):
 # Robinhood
 robinhood_path = os.path.join("ripser", "robinhood")
 if os.path.isdir(robinhood_path):
+    print(
+        "\nFound local copy of robinhood! Using robinhood for ripser.py compilation.\n"
+    )
     macros.extend([("USE_ROBINHOOD_HASHMAP", 1)])
 
     robinhood_include_path = os.path.join("src", "include")
@@ -78,6 +76,8 @@ def run(self):
         extra_compile_args.extend(
             ["-I" + os.path.join(robinhood_path, robinhood_include_path)]
         )
+else:
+    print("Did not find a local copy of robinhood. Proceeding anyways.")
 
 ext_modules = Extension(
     "pyRipser",
@@ -90,40 +90,7 @@ def run(self):
 
 
 setup(
-    name="ripser",
-    version=verstr,
-    description="A Lean Persistent Homology Library for Python",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    author="Chris Tralie, Nathaniel Saul",
-    author_email="chris.tralie@gmail.com, nat@riverasaul.com",
-    url="https://ripser.scikit-tda.org",
-    license="MIT",
-    packages=["ripser"],
     ext_modules=cythonize(ext_modules),
-    install_requires=["Cython", "numpy", "scipy", "scikit-learn", "persim"],
-    extras_require={
-        "testing": [  # `pip install -e ".[testing]"``
-            "pytest"
-        ],
-        "docs": [  # `pip install -e ".[docs]"`
-            "sktda_docs_config"
-        ],
-        "examples": ["persim", "tadasets", "jupyter", "pillow"],
-    },
     cmdclass={"build_ext": CustomBuildExtCommand},
-    python_requires=">=3.6",
-    classifiers=[
-        "Intended Audience :: Science/Research",
-        "Intended Audience :: Education",
-        "Intended Audience :: Financial and Insurance Industry",
-        "Intended Audience :: Healthcare Industry",
-        "Topic :: Scientific/Engineering :: Information Analysis",
-        "Topic :: Scientific/Engineering :: Mathematics",
-        "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-    ],
-    keywords="persistent homology, rips filtration, persistence diagrams, topology data analysis, algebraic topology, unsupervised learning",
+    version=get_version(),
 )

test/test_ripser.py

@@ -26,6 +26,7 @@ class TestLibrary:
     def test_import(self):
         import ripser
         from ripser import ripser, Rips
+
         assert 1
 
 
@@ -193,7 +194,7 @@ def test_greedyperm_circlebottleneck(self):
         h12 = res2["dgms"][1]
         assert res2["r_cover"] > 0
         assert np.max(np.abs(h11 - h12)) <= 2 * res2["r_cover"]
-    
+
     def test_cocycle_indices_greedyperm(self):
         """
         Make sure the original vertex indices are retained in the
@@ -206,26 +207,26 @@ def test_cocycle_indices_greedyperm(self):
         t = 2 * np.pi * np.random.rand(N)
         X = np.array([np.cos(t), np.sin(t)]).T
         res1 = ripser(X, n_perm=n_perm, do_cocycles=True, maxdim=1)
-        cocycles1 = res1['cocycles'][1]
-        idx_perm = res1['idx_perm']
+        cocycles1 = res1["cocycles"][1]
+        idx_perm = res1["idx_perm"]
         X = X[idx_perm, :]
         res2 = ripser(X, do_cocycles=True, maxdim=1)
-        cocycles2 = res2['cocycles'][1]
+        cocycles2 = res2["cocycles"][1]
         for cc1, cc2 in zip(cocycles1, cocycles2):
             assert cc1.shape[0] == cc2.shape[0]
             cc2[:, 0:-1] = idx_perm[cc2[:, 0:-1]]
             assert np.allclose(cc1, cc2)
-    
+
     def test_sparse_format(self):
         """
         Test to make sure different formats for sparse matrices
         yield the same answer.  Test courtesy of Umberto Lupo (@ulupo)
         """
-        data = np.array([6., 8., 2., 4., 5., 9., 10., 3., 1., 1.])
+        data = np.array([6.0, 8.0, 2.0, 4.0, 5.0, 9.0, 10.0, 3.0, 1.0, 1.0])
         row = np.array([0, 0, 0, 0, 1, 1, 1, 2, 2, 3])
         col = np.array([4, 1, 3, 2, 4, 3, 2, 3, 4, 4])
         dm = sparse.coo_matrix((data, (row, col)), shape=(5, 5))
-        dgms1 = ripser(dm, distance_matrix=True)['dgms']
-        dgms2 = ripser(dm.tocsr(), distance_matrix=True)['dgms']
+        dgms1 = ripser(dm, distance_matrix=True)["dgms"]
+        dgms2 = ripser(dm.tocsr(), distance_matrix=True)["dgms"]
         for dgm1k, dgm2k in zip(dgms1, dgms2):
-            assert(np.allclose(dgm1k, dgm2k))
+            assert np.allclose(dgm1k, dgm2k)