Convert to pyproject.toml spec (#18)

* Convert setup.py spec to pyproject.toml spec

* Remove requirements.txt

* Update workflows to use optional installs

* Add pytestcov to optional testing deps

* Fix two dep typos and add build dep,

* Optional dep is called 'testing' not 'tests'

* Fix windows tests

* Add doc requirements

* Remove changelog from pyproject.toml

.github/workflows/tests.yml

@@ -5,7 +5,7 @@ on:
   push:
   pull_request:
   schedule:
-    - cron: '0 0 * * *'
+    - cron: "0 0 * * *"
 
 jobs:
   test-linux-macos:
@@ -25,18 +25,16 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .
+          pip install ".[testing]"
           : # pip install pytest nbmake
-          pip install pytest
-      - name: Run test 
+      - name: Run test
         run: |
           : # we were also testing the jupyter notebooks with the command below
           : # but some recent update broke this and we get "No such file or directory: 'latex'"
           : # so for now we don't test notebooks
           : # original command "pytest --nbmake ."
           pytest .
 
-
   test-windows:
     runs-on: windows-latest
     strategy:
@@ -54,10 +52,9 @@ jobs:
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip
-          pip install .
+          pip install ".[testing]"
           : # pip install pytest nbmake
-          pip install pytest
-      - name: Run test 
+      - name: Run test
         shell: bash -l {0}
         run: |
           : # we were also testing the jupyter notebooks with the command below
@@ -81,8 +78,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install pytest pytest-cov
+          pip install ".[testing]"
       - name: Tests
         run: |
           export NUMBA_DISABLE_JIT=1

.readthedocs.yml

@@ -14,7 +14,7 @@ sphinx:
 
 python:
   install:
-    - requirements: ./requirements.txt
+    - requirements: docs/requirements.txt
     - method: pip
       path: .
       extra_requirements:

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx
+sphinx_rtd_theme
+numpydoc
+ipython
+nbsphinx

pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["setuptools >= 61.0", "build", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "dreimac"
+dynamic = ["version"]
+description = "DREiMac: Dimensionality reduction with Eilenberg-MacLane coordinates"
+readme = "README.md"
+authors = [
+  { name = "Jose A. Perea", email = "[email protected]" },
+  { name = "Luis Scoccola", email = "[email protected]" },
+  { name = "Chris Tralie", email = "[email protected]" },
+]
+maintainers = [
+  { name = "Jose A. Perea", email = "[email protected]" },
+  { name = "Luis Scoccola", email = "[email protected]" },
+  { name = "Chris Tralie", email = "[email protected]" },
+]
+
+requires-python = ">=3.8, <3.12"
+
+dependencies = [
+  "matplotlib >= 3.6",
+  "numba >= 0.56",
+  "numpy >= 1.23",
+  "persim >=0.3",
+  "ripser >= 0.6",
+  "scipy >=1.10",
+]
+
+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",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "License :: OSI Approved :: Apache Software License",
+]
+
+keywords = ["dimensionality reduction", "topological data analysis"]
+
+[project.optional-dependencies]
+testing = ["pytest", "pytest-cov"]
+
+docs = ["sphinx", "sphinx_rtd_theme", "numpydoc", "ipykernel", "nbsphinx"]
+
+[project.urls]
+Homepage = "https://dreimac.scikit-tda.org"
+Documentation = "https://dreimac.scikit-tda.org"
+Repository = "https://github.com/scikit-tda/DREiMac"
+Issues = "https://github.com/scikit-tda/DREiMac/issues"

setup.py

@@ -1,55 +1,18 @@
 from setuptools import setup
-
-## Get version information from _version.py
 import re
 
-VERSIONFILE = "dreimac/_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()
-
 
-# get requirements
-def requirements():
-    with open("requirements.txt") as f:
-        return [line.strip() for line in f if line.strip()]
+def get_version():
+    VERSIONFILE = "dreimac/_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,))
 
 
 setup(
-    name="dreimac",
-    version=verstr,
-    description="DREiMac: Dimensionality reduction with Eilenberg-MacLane coordinates",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    author="Jose A. Perea, Luis Scoccola, Chris Tralie",
-    author_email="[email protected]",
-    license="Apache2",
-    packages=["dreimac"],
-    install_requires=requirements(),
-    extras_require={
-        "testing": ["pytest"],
-        "docs": ["sphinx", "sphinx_rtd_theme", "numpydoc", "ipykernel", "nbsphinx"],
-    },
-    python_requires=">=3.8,<3.12",
-    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",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-    ],
-    keywords="topological data analysis, dimensionality reduction",
+    version=get_version(),
 )