Added pyproject.toml.

pyproject.toml

@@ -0,0 +1,68 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "chewBBACA"
+version = "3.3.2"
+requires-python = ">=3.7"
+dependencies = [
+    "numpy~=1.24.3",
+    "scipy~=1.10.1",
+    "biopython>=1.79",
+    "plotly>=5.8.0",
+    "SPARQLWrapper>=2.0.0",
+    "pandas>=1.5.1,<2.1",
+    "requests>=2.27.1",
+    "pyrodigal>=3.0.0"
+]
+authors = [
+    {name = "Rafael Mamede"},
+    {name = "Pedro Cerqueira"},
+    {name = "Mickael Silva"},
+    {name = "João Carriço"},
+    {name = "Mário Ramirez"}
+]
+maintainers = [
+  {name = "UMMI", email = "[email protected]"}
+]
+description = "A complete suite for gene-by-gene schema creation and strain identification."
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = [
+    "bioinformatics",
+    "genomics",
+    "mlst",
+    "bacteria",
+    "cgmlst",
+    "wgmlst",
+    "outbreak detection",
+    "allele calling",
+    "bacterial typing",
+    "bacterial genome analysis"
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Natural Language :: English",
+    "Operating System :: Unix",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.scripts]
+"chewBBACA.py" = "CHEWBBACA.chewBBACA:main"
+"chewie" = "CHEWBBACA.chewBBACA:main"
+
+[project.urls]
+Repository = "https://github.com/B-UMMI/chewBBACA"
+Documentation = "https://chewbbaca.readthedocs.io/en/latest/index.html"
+Changelog = "https://github.com/B-UMMI/chewBBACA/blob/master/CHANGELOG.md"

setup.py

@@ -1,45 +1,46 @@
 from setuptools import setup, find_namespace_packages
 
-import CHEWBBACA
+#import CHEWBBACA
 
-VERSION = CHEWBBACA.__version__
+#VERSION = CHEWBBACA.__version__
 
 packages = find_namespace_packages(
   exclude=[
-    "CHEWBBACA.tests*"
+    "CHEWBBACA.tests*",
+    "CHEWBBACA.docs*"
   ]
 )
 
-install_requires = (
-  'numpy~=1.24.3',
-  'scipy~=1.10.1',
-  'biopython>=1.79',
-  'plotly>=5.8.0',
-  'SPARQLWrapper>=2.0.0',
-  'pandas>=1.5.1,<2.1',
-  'requests>=2.27.1',
-  'pyrodigal>=3.0.0'
-)
+# install_requires = (
+#   'numpy~=1.24.3',
+#   'scipy~=1.10.1',
+#   'biopython>=1.79',
+#   'plotly>=5.8.0',
+#   'SPARQLWrapper>=2.0.0',
+#   'pandas>=1.5.1,<2.1',
+#   'requests>=2.27.1',
+#   'pyrodigal>=3.0.0'
+# )
 
 setup(
-  name = 'chewBBACA',
+  # name = 'chewBBACA',
   packages=packages,
-  version = VERSION,
-  description = 'A complete suite for gene-by-gene schema creation and strain identification.',
-  author = 'Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez',
-  author_email = '[email protected]',
-  url = 'https://github.com/B-UMMI/chewBBACA', 
-  keywords = ['cgMLST', 'bacterial typing', 'nomenclature server'],
-  install_requires = install_requires,
-  python_requires = '>=3.7',
+  # version = VERSION,
+  # description = 'A complete suite for gene-by-gene schema creation and strain identification.',
+  # author = 'Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez',
+  # author_email = '[email protected]',
+  # url = 'https://github.com/B-UMMI/chewBBACA', 
+  # keywords = ['cgMLST', 'bacterial typing', 'nomenclature server'],
+  # install_requires = install_requires,
+  # python_requires = '>=3.7',
   include_package_data = True,
-  entry_points={'console_scripts': ["chewBBACA.py = CHEWBBACA.chewBBACA:main",
-                                    "chewie = CHEWBBACA.chewBBACA:main"]
-                },
-  project_urls={
-    'Documentation': 'https://chewbbaca.readthedocs.io/en/latest/index.html',
-    'Source': 'https://github.com/B-UMMI/chewBBACA',
-  },
-  maintainer_email='[email protected]',
-  maintainer='UMMI'
+  # entry_points={'console_scripts': ["chewBBACA.py = CHEWBBACA.chewBBACA:main",
+  #                                   "chewie = CHEWBBACA.chewBBACA:main"]
+  #               },
+  # project_urls={
+  #   'Documentation': 'https://chewbbaca.readthedocs.io/en/latest/index.html',
+  #   'Source': 'https://github.com/B-UMMI/chewBBACA',
+  # },
+  # maintainer_email='[email protected]',
+  # maintainer='UMMI'
 )