From 86af0f4e0a61e4acc5848166ff6778a1872d7e40 Mon Sep 17 00:00:00 2001
From: David Bickel <david.bickel@santero.be>
Date: Tue, 26 Nov 2024 10:09:01 +0100
Subject: [PATCH] Enable installation with setuptools

---
 Makefile         | 11 ++++++++++-
 environment.yml  | 13 ++++++-------
 pyproject.toml   | 36 ++++++++++++++++++++++++++++++++++++
 requirements.txt |  1 +
 4 files changed, 53 insertions(+), 8 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/Makefile b/Makefile
index 861edd5..eb38c0a 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,16 @@
+PACKAGE_NAME = entry_cli
+
+.PHONY: init install uninstall test
+
 init:
 	conda env create -f environment.yml
 
+install:
+	pip install --upgrade pip setuptools
+	pip install -e .
+
 test:
 	nosetests tests
 
-.PHONY: init test
+uninstall:
+	pip uninstall -y $(PACKAGE_NAME)
diff --git a/environment.yml b/environment.yml
index 9fcd9d9..82ec9dc 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,11 +1,10 @@
 name: entry-cli-env
 channels:
-  - rdkit
-  - conda-forge
   - defaults
 dependencies:
-- python
-- numpy
-- nose
-- openbabel=3.1.1
-- rdkit=2019.03.4.0
+  - python=3.7
+  - numpy
+  - nose
+  - conda-forge::openbabel=3.1.1
+  - rdkit::rdkit=2019.03.4.0
+  - setuptools
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..9e6b2ad
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,36 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "entry-cli"
+description = "Command line app for predicting bacterial accumulation."
+dynamic = ["version"]
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+authors = [
+    {name = "Bryon Drown"},
+    {name = "swansonk14", email = "swansonk.14@gmail.com"},
+    {name = "Andrew Wilkinson"}
+]
+requires-python = ">= 3"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+]
+keywords = []
+
+[project.urls]
+Repository = "https://github.com/HergenrotherLab/entry-cli"
+
+[project.scripts]
+entry-cli = "entry_cli.calc_props:main"
+
+[tool.setuptools]
+packages = ["entry_cli"]
+
+[tool.setuptools.dynamic]
+version = {attr = "entry_cli.__version__"}
diff --git a/requirements.txt b/requirements.txt
index b74fb3e..b8e86d8 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,3 +4,4 @@ nose
 numpy
 openbabel=3.1.1
 rdkit=2019.03.4.0
+setuptools