From 45cff80d56dae3a0e9066a87f9ebb4a81673034b Mon Sep 17 00:00:00 2001
From: Tobias Krause <tobiaspk1@gmail.com>
Date: Tue, 9 Apr 2024 12:06:25 -0400
Subject: [PATCH] Refactor to use poetry

---
 .gitignore     |  2 ++
 pyproject.toml | 62 ++++++++++++++++++++------------------------------
 2 files changed, 27 insertions(+), 37 deletions(-)

diff --git a/.gitignore b/.gitignore
index 830008c..4de198f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -82,3 +82,5 @@ venv.bak/
 # mkdocs documentation
 /site
 
+# Others
+.pypi_token
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 89d6400..1b7e319 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,48 +1,36 @@
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-[project]
+[tool.poetry]
 name = "scSpectra"
 version = "0.2.0"
 description = "Supervised discovery of interpretable gene programs from single-cell data"
 authors = [
-    { name = "Russel Z. Kunes", email = "KunesR@mskcc.org" },
-    { name = "Thomas Walle", email = "t.walle@dkfz-heidelberg.de" },
+    "Russel Z. Kunes <KunesR@mskcc.org>",
+    "Thomas Walle <t.walle@dkfz-heidelberg.de>"
 ]
 maintainers = [
-    { name = "Russel Z. Kunes", email = "KundesR@mskcc.org" },
-    { name = "Tobias Krause", email = "krauset@mskcc.org" }
-]
-dependencies = [
-    "numpy>=1.20.3",
-    "scipy>=1.7.3",
-    "scanpy>=1.8.2",
-    "torch>=1.10.1",
-    "opt-einsum>=3.3.0",
-    "pandas>=1.3.5",
-    "tqdm>=4.62.3",
-    "pyvis>=0.1.9",
+    "Russel Z. Kunes <KundesR@mskcc.org>",
+    "Tobias Krause <krauset@mskcc.org>"
 ]
-requires-python = ">=3.8"
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
+license = "MIT"
+packages = [
+    {include = "Spectra", from="src"},
+    {include = "Spectra/load", from="src"},
 ]
 
-[tool.setuptools.packages.find]
-where = ["src"]
+[tool.poetry.dependencies]
+python = "^3.8"
+numpy = "^1.20.3"
+scipy = "^1.7.3"
+scanpy = "^1.8.2"
+torch = "^1.10.1"
+opt-einsum = "^3.3.0"
+pandas = "^1.3.5"
+tqdm = "^4.62.3"
+pyvis = "^0.1.9"
 
-[tools.setuptools]
-include-package-data = true
-packages = ["Spectra", "Spectra.load"]
-
-[tool.setuptools.package-data]
-default_gene_sets = ["Spectra/data/default_gene_sets.json"]
-sample_data = ["Spectra/data/sample_data.json"]
-
-[project.urls]
-"Publication" = "https://www.nature.com/articles/s41587-023-01940-3"
-"bioRxiv" = "https://www.biorxiv.org/content/10.1101/2022.12.20.521311v1"
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
 
+[tool.poetry.urls]
+Publication = "https://www.nature.com/articles/s41587-023-01940-3"
+bioRxiv = "https://www.biorxiv.org/content/10.1101/2022.12.20.521311v1"