Fix/issue #471

environment.yml

@@ -3,7 +3,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python>=3.9,<3.11
+  - python>3.8,<3.11
+  - setuptools<80.9
   - cython==0.29.32
   - biopython==1.79
   - docutils==0.19

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools==65.4.1","wheel==0.37.1","Cython>=0.29.32","numpy==1.23.3","scipy==1.11.1"]
+requires = ["setuptools<80.9","wheel==0.37.1","Cython==0.29.32","numpy==1.23.3","scipy==1.11.1"]
 build-backend = "setuptools.build_meta"
 
-[pytest]
+[tool.pytest]
 markers = ["slow"]

requirements.txt

@@ -1,3 +1,4 @@
+setuptools<80.9
 cython==0.29.32
 biopython==1.79
 docutils==0.19

setup.cfg

@@ -1,3 +1,7 @@
+[options]
+setup_requires =
+    setuptools<80.9
+
 [aliases]
 test=pytest
 

setup.py

@@ -14,8 +14,9 @@
 import numpy as np
 
 ### See comment here https://github.com/cython/cython/issues/2498
-numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API",
-                                        "NPY_1_9_API_VERSION")])
+numpy_nodepr_api = dict(
+    define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_9_API_VERSION")]
+)
 
 here = path.abspath(path.dirname("__file__"))
 
@@ -32,33 +33,52 @@
 requirements = [line.rstrip() for line in open("requirements.txt", "rt")]
 
 
-extensions = [Extension("Mikado.utilities.overlap",
-                        sources=[path.join("Mikado", "utilities", "overlap.pyx")],
-                        **numpy_nodepr_api),
-              Extension("Mikado.utilities.f1",
-                        sources=[path.join("Mikado", "utilities", "f1.pyx")],
-                        **numpy_nodepr_api),
-              Extension("Mikado.scales.contrast",
-                        sources=[path.join("Mikado", "scales", "contrast.pyx")],
-                        **numpy_nodepr_api),
-              Extension("Mikado.utilities.intervaltree",
-                        sources=[path.join("Mikado", "utilities", "intervaltree.pyx")],
-                        **numpy_nodepr_api),
-              Extension("Mikado.serializers.blast_serializer.btop_parser",
-                        include_dirs=[np.get_include()],
-                        language="c++",
-                        sources=[path.join("Mikado", "serializers", "blast_serializer", "btop_parser.pyx")],
-                        **numpy_nodepr_api),
-              Extension("Mikado.serializers.blast_serializer.aln_string_parser",
-                        include_dirs=[np.get_include()],
-                        language="c++",
-                        sources=[path.join("Mikado", "serializers", "blast_serializer", "aln_string_parser.pyx")],
-                        **numpy_nodepr_api)
-              ]
+extensions = [
+    Extension(
+        "Mikado.utilities.overlap",
+        sources=[path.join("Mikado", "utilities", "overlap.pyx")],
+        **numpy_nodepr_api,
+    ),
+    Extension(
+        "Mikado.utilities.f1",
+        sources=[path.join("Mikado", "utilities", "f1.pyx")],
+        **numpy_nodepr_api,
+    ),
+    Extension(
+        "Mikado.scales.contrast",
+        sources=[path.join("Mikado", "scales", "contrast.pyx")],
+        **numpy_nodepr_api,
+    ),
+    Extension(
+        "Mikado.utilities.intervaltree",
+        sources=[path.join("Mikado", "utilities", "intervaltree.pyx")],
+        **numpy_nodepr_api,
+    ),
+    Extension(
+        "Mikado.serializers.blast_serializer.btop_parser",
+        include_dirs=[np.get_include()],
+        language="c++",
+        sources=[
+            path.join("Mikado", "serializers", "blast_serializer", "btop_parser.pyx")
+        ],
+        **numpy_nodepr_api,
+    ),
+    Extension(
+        "Mikado.serializers.blast_serializer.aln_string_parser",
+        include_dirs=[np.get_include()],
+        language="c++",
+        sources=[
+            path.join(
+                "Mikado", "serializers", "blast_serializer", "aln_string_parser.pyx"
+            )
+        ],
+        **numpy_nodepr_api,
+    ),
+]
 
 setup(
     name="Mikado",
-    python_requires=">3.6",
+    python_requires=">3.8,<3.11",
     version="2.3.4",
     description="A Python3 annotation program to select the best gene model in each locus",
     long_description=long_description,
@@ -67,44 +87,53 @@
     author_email="lucventurini@gmail.com",
     license="LGPL3",
     tests_require=["pytest"],
+    setup_requires=["setuptools<80.9"],
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)",
         "Operating System :: POSIX :: Linux",
         "Framework :: Pytest",
         "Intended Audience :: Science/Research",
-        'Programming Language :: Python :: 3.7',
-        "Programming Language :: Python :: 3.8",
-        'Programming Language :: Python :: 3.9'
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
-    ext_modules=cythonize(extensions, compiler_directives = {"language_level": "3"}),
+    ext_modules=cythonize(extensions, compiler_directives={"language_level": "3"}),
     zip_safe=False,
     keywords="rna-seq annotation genomics transcriptomics",
     packages=find_packages(),
     scripts=glob.glob("util/*.py"),
-    entry_points={"console_scripts": ["mikado = Mikado.__main__:main",
-                                      "daijin = Mikado.daijin.__main__:main",
-                                      ]},
+    entry_points={
+        "console_scripts": [
+            "mikado = Mikado.__main__:main",
+            "daijin = Mikado.daijin.__main__:main",
+        ]
+    },
     install_requires=requirements,
     extras_require={
         "postgresql": ["psycopg2"],
         "mysql": ["mysqlclient>=1.3.6"],
-        "bam": ["pysam>=0.8"]
+        "bam": ["pysam>=0.8"],
     },
     package_data={
-        "Mikado.configuration":
-            glob.glob("Mikado/configuration/*json") + glob.glob("Mikado/configuration/*yaml"),
-        "Mikado.configuration.scoring_files":
-            glob.glob("Mikado/configuration/scoring_files/*"),
-        "Mikado":
-            glob.glob(path.join("Mikado", "daijin", "*smk")) +
-            glob.glob(path.join("Mikado", "daijin", "*yaml")) + glob.glob("Mikado/daijin/*json"),
+        "Mikado.configuration": glob.glob("Mikado/configuration/*json")
+        + glob.glob("Mikado/configuration/*yaml"),
+        "Mikado.configuration.scoring_files": glob.glob(
+            "Mikado/configuration/scoring_files/*"
+        ),
+        "Mikado": glob.glob(path.join("Mikado", "daijin", "*smk"))
+        + glob.glob(path.join("Mikado", "daijin", "*yaml"))
+        + glob.glob("Mikado/daijin/*json"),
         "Mikado.utilities.overlap": [path.join("Mikado", "utilities", "overlap.pxd")],
-        "Mikado.utilities.intervaltree": [path.join("Mikado", "utilities", "intervaltree.pxd")],
-        "Mikado.serializers.blast_serializers": glob.glob(path.join("Mikado", "serializers", "blast_serializers",
-                                                                    "*pxd")),
-        "Mikado.tests.blast_data": glob.glob(path.join("Mikado", "tests", "blast_data", "*"))
-        },
-    include_package_data=True
+        "Mikado.utilities.intervaltree": [
+            path.join("Mikado", "utilities", "intervaltree.pxd")
+        ],
+        "Mikado.serializers.blast_serializers": glob.glob(
+            path.join("Mikado", "serializers", "blast_serializers", "*pxd")
+        ),
+        "Mikado.tests.blast_data": glob.glob(
+            path.join("Mikado", "tests", "blast_data", "*")
+        ),
+    },
+    include_package_data=True,
 )