migrate to hatch

CHANGELOG.md

@@ -1,3 +1,8 @@
+# 0.0.10 - 2024-07-04
+
+- Migrate to hatch to ease development and include multiple authors.
+- Add @johnarevalo to the author list.
+
 # 0.0.9 - 2022-11-23
 
 - Stop excluding `README.md` from the build, because setup.py depends on this

CONTRIBUTING.md

@@ -0,0 +1,65 @@
+We use [hatch] to develop harmonypy.
+
+Copy the harmonypy code to your computer:
+
+```
+git clone https://github.com/slowkow/harmonpy
+```
+
+Then change to the newly created directory:
+
+```
+cd harmonypy
+```
+
+Install hatch:
+
+```
+pipx install hatch
+```
+
+Create a new environment just for harmonypy:
+
+```
+hatch env create
+```
+
+Once we have hatch and an environment, then we can enter a new shell:
+
+```
+hatch shell
+```
+
+In this environment, we can run tests:
+
+```
+hatch test
+```
+
+And we can also build the files needed for PyPI:
+
+```
+hatch build
+```
+
+We should double-check that the contents of the `.tar.gz` file do not include any files we do not want to publish:
+
+```
+tar tvf dist/harmonypy-0.0.10.tar.gz
+-rw-r--r--  0 0      0          97 Feb  1  2020 harmonypy-0.0.10/harmonypy/__init__.py
+-rw-r--r--  0 0      0       12783 Feb  1  2020 harmonypy-0.0.10/harmonypy/harmony.py
+-rw-r--r--  0 0      0        4559 Feb  1  2020 harmonypy-0.0.10/harmonypy/lisi.py
+-rw-r--r--  0 0      0        1824 Feb  1  2020 harmonypy-0.0.10/.gitignore
+-rw-r--r--  0 0      0       35149 Feb  1  2020 harmonypy-0.0.10/LICENSE
+-rw-r--r--  0 0      0        3126 Feb  1  2020 harmonypy-0.0.10/README.md
+-rw-r--r--  0 0      0        1026 Feb  1  2020 harmonypy-0.0.10/pyproject.toml
+```
+
+When we're ready, we can publish to PyPI:
+
+```
+hatch publish
+```
+
+[hatch]: https://hatch.pypa.io
+

MANIFEST.in

@@ -1,6 +1,4 @@
 include README.md
 prune data*
 prune tests*
-exclude publish_to_pypi.md
 exclude MANIFEST.in
-exclude Makefile

harmonypy/__init__.py

@@ -1,3 +1,4 @@
 from .harmony import Harmony, run_harmony
 from .lisi import compute_lisi
-from .version import __version__
+
+__version__ = '0.0.10'

pyproject.toml

@@ -0,0 +1,46 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "harmonypy"
+dynamic = ["version"]
+description = "A data integration algorithm."
+readme = "README.md"
+license = ""
+requires-python = ">=3.6"
+authors = [
+    { name = "Kamil Slowikowski", email = "kslowikowski@gmail.com" },
+    { name = "John Arevalo" }
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "numpy",
+    "pandas",
+    "scikit-learn",
+    "scipy",
+]
+
+[project.urls]
+Homepage = "https://github.com/slowkow/harmonypy"
+
+[tool.hatch.version]
+path = "harmonypy/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/harmonypy",
+]
+
+[tool.hatch.envs.test]
+dependencies = [
+  "pytest"
+]