Merge pull request #261 from bedapub/260-homologs-folder-is-not-insta…

…lled

260 homologs folder is not installed

setup.py

@@ -1,38 +1,44 @@
 """ setup procedure """
 
-if __name__ == '__main__':
+if __name__ == "__main__":
 
     from setuptools import setup, find_packages
     import versioneer
 
-    reqs = open('requirements.txt', encoding='utf-8').readlines()
+    reqs = open("requirements.txt", encoding="utf-8").readlines()
     requires = [req.strip() for req in reqs]
 
     with open("README.md", "r") as fh:
-      long_description = fh.read()
+        long_description = fh.read()
 
-    setup(name='besca',
-          version=versioneer.get_version(),
-          cmdclass=versioneer.get_cmdclass(),
-          description='Collection of BEDA internal python functions for analysing single cell RNAseq data.',
-          long_description=long_description,
-          long_description_content_type="text/markdown",
-          classifiers=[
-            'Development Status :: 5 - Production/Stable',
-            'Intended Audience :: Developers',
-            'Topic :: Software Development :: Build Tools',
-            'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
-            'Programming Language :: Python :: 3',
-            'Programming Language :: Python :: 3.8'],
-          url='https://github.com/bedapub/besca',
-          license='GPLv3',
-          author='BEDA community',
-          author_email='[email protected]',
-          packages=find_packages(exclude=["devtools", "tests"]),
-          zip_safe=False,
-          package_data={'besca.datasets.data': ['*.h5ad'],
-                        'besca.st': ['*.css'],
-                        'besca.datasets.nomenclature': ['*.tsv'],
-                        'besca.datasets.mito_files': ['*.tsv'],
-                        'besca.datasets.genesets': ['*.gmt', '*.tsv']},
-          install_requires=requires)
+    setup(
+        name="besca",
+        version=versioneer.get_version(),
+        cmdclass=versioneer.get_cmdclass(),
+        description="Collection of BEDA internal python functions for analysing single cell RNAseq data.",
+        long_description=long_description,
+        long_description_content_type="text/markdown",
+        classifiers=[
+            "Development Status :: 5 - Production/Stable",
+            "Intended Audience :: Developers",
+            "Topic :: Software Development :: Build Tools",
+            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+            "Programming Language :: Python :: 3",
+            "Programming Language :: Python :: 3.8",
+        ],
+        url="https://github.com/bedapub/besca",
+        license="GPLv3",
+        author="BEDA community",
+        author_email="[email protected]",
+        packages=find_packages(exclude=["devtools", "tests"]),
+        zip_safe=False,
+        package_data={
+            "besca.datasets.data": ["*.h5ad"],
+            "besca.st": ["*.css"],
+            "besca.datasets.nomenclature": ["*.tsv"],
+            "besca.datasets.mito_files": ["*.tsv"],
+            "besca.datasets.genesets": ["*.gmt", "*.tsv"],
+            "besca.datasets.homologs": ["*.tsv"],
+        },
+        install_requires=requires,
+    )

workbooks/celltype_annotation_besca.ipynb

@@ -321,7 +321,7 @@
     "\n",
     "if species == \"mouse\":\n",
     "    # Genes converted to mouse homologs\n",
-    "    mousehuman_file = bescapath + \"/besca/datasets/homologs/MGItoHGNC.csv\"\n",
+    "    mousehuman_file = bescapath + \"/besca/datasets/homologs/MGItoHGNC.tsv\"\n",
     "    mousehuman = pd.read_csv(\n",
     "        mousehuman_file, sep=\"\\t\", header=\"infer\", encoding=\"unicode_escape\"\n",
     "    )\n",