Merge pull request #239 from GoekeLab/clare_dev

Installation & Docs Updates

Author: ClareRobin

.gitattributes

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

.readthedocs.yaml

@@ -17,5 +17,5 @@ Installation from our GitHub repository
 
     git clone https://github.com/GoekeLab/xpore.git
     cd xpore
-    python setup.py install
+    pip install .
 

docs/source/installation.rst

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "xpore"
+authors = [{name = "Ploy N. Pratanwanich", email = "naruemon.p@chula.ac.th"}]
+maintainers = [
+	{name = "Ploy N. Pratanwanich", email = "naruemon.p@chula.ac.th"},
+]
+requires-python = ">=3.8"
+description = "xpore is a python package for Nanopore data analysis of differential RNA modifications."
+dependencies = [
+	"numpy>=1.18.0",
+	"pandas>=0.25.3",
+	"scipy>=1.4.1",
+	"PyYAML",
+	"h5py>=2.10.0",
+	"pyensembl>=1.8.5",
+	"ujson>=4.0.1"
+]
+readme = "README.md"
+license = {text = "MIT"}
+classifiers = [
+	# Trove classifiers
+	# (https://pypi.python.org/pypi?%3Aaction=list_classifiers)
+	"Development Status :: 1 - Planning",
+	"License :: OSI Approved :: MIT License",
+	"Programming Language :: Python",
+	"Programming Language :: Python :: 3.8",
+	"Topic :: Software Development :: Libraries",
+	"Topic :: Scientific/Engineering :: Bio-Informatics",
+	"Intended Audience :: Science/Research",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = ["pytest"]
+docs = ["sphinx", "sphinx_rtd_theme"]
+
+[project.urls]
+homepage = "https://github.com/GoekeLab/xpore"
+
+[project.scripts]
+xpore = "xpore.scripts.xpore:main"
+
+[tool.setuptools]
+include-package-data = true # set explicitly in case it changes in the future
+
+[tool.setuptools.packages.find]
+include = ["xpore*"]
+
+[tool.setuptools.dynamic]
+version = {attr = "xpore.__version__"}