package healed

pymutspec/__init__.py

@@ -1,4 +1,4 @@
 from pymutspec import annotation, draw, io, constants, utils
 
 # Define the pymutspec version
-__version__ = "0.0.11"
+__version__ = "0.0.12"

pyproject.toml

@@ -1,17 +1,39 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
 [project]
 name = "PyMutSpec"
-version = "0.0.11"
+version = "0.0.12"
+description = "Mutational spectra analysis package"
 authors = [
   { name="kpotoh", email="axepon@mail.ru" },
 ]
-description = "Mutational spectra analysis package"
 license = { file = "LICENSE" }
-readme = "README.md"
+readme = {file = "README.md", content-type = "text/markdown"}
 requires-python = ">=3.8"
 classifiers = [
+    "Operating System :: OS Independent",
+    "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
     "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy~=1.22.2",
+    "pandas~=1.4.0",
+    "seaborn==0.12.2",
+    "biopython==1.79",
+    "ete3==3.1.2",
+    "tqdm~=4.62.3",
+    "PyYAML~=6.0",
+    "pytest~=7.1.2",
+    "click~=8.1.3",
 ]
 
 [project.urls]

scripts/legacy/setup.py

@@ -0,0 +1,63 @@
+import os
+import re
+from setuptools import setup, find_packages
+
+path_to_pyproject = 'pyproject.toml'
+
+
+def read_specs(path: str):
+    specs = dict()
+    with open(path, 'r') as fin:
+        for line in fin:
+            if line.startswith('name'):
+                specs['name'] = re.match('name = "(.+)"', line).group(1)
+            elif line.startswith('version'):
+                specs['version'] = re.match('version = "(.+)"', line).group(1)
+            elif line.startswith('description'):
+                specs['description'] = re.match('description = "(.+)"', line).group(1)
+            elif line.startswith('requires-python'):
+                specs['python_requires'] = re.match('requires-python = "(.+)"', line).group(1)
+                break
+    return specs
+
+
+def read_requirements(path: str):
+    with open(path, encoding="utf-8") as file:
+        requirements = []
+        extra_index_urls = []
+        for line in file:
+            line = line.strip()
+            if line:
+                if line.startswith('-f'):
+                    extra_index_urls.append(line.split()[1])
+                elif line.startswith('#'):
+                    continue
+                else:
+                    requirements.append(line)
+        return requirements, extra_index_urls
+
+
+requirements, _ = read_requirements("requirements.txt")
+
+scripts = []
+if os.path.exists("scripts"):
+    for file in os.listdir("scripts"):
+        if file.endswith(".py") and not file.startswith("_"):
+            fp = os.path.join("scripts", file)
+            with open(fp) as fin:
+                if "python" in fin.readline():
+                    scripts.append(fp)
+
+specs = read_specs(path_to_pyproject)
+
+setup(
+    author="kpotoh",
+    author_email="axepon@mail.ru",
+    url="https://github.com/mitoclub/PyMutSpec",
+    license="MIT",
+    install_requires=requirements,
+    scripts=scripts,
+    packages=find_packages(),
+    package_data={'pymutspec': ['utils/configs/log_settings.yaml']},
+    **specs
+)

setup.py

@@ -1,59 +1,15 @@
 import os
-import re
 from setuptools import setup, find_packages
 
-path_to_pyproject = 'pyproject.toml'
-
-
-def read_specs(path: str):
-    specs = dict()
-    with open(path, 'r') as fin:
-        for line in fin:
-            if line.startswith('name'):
-                specs['name'] = re.match('name = "(.+)"', line).group(1)
-            elif line.startswith('version'):
-                specs['version'] = re.match('version = "(.+)"', line).group(1)
-            elif line.startswith('description'):
-                specs['description'] = re.match('description = "(.+)"', line).group(1)
-            elif line.startswith('requires-python'):
-                specs['python_requires'] = re.match('requires-python = "(.+)"', line).group(1)
-                break
-    return specs
-
-
-extra_index_urls = []
-packages = []
 scripts = []
-
-with open("requirements.txt", encoding="utf-8") as file:
-    for line in map(str.strip, file):
-        if line:
-            if line.startswith("-f"):
-                extra_index_urls.append(line.split()[1])
-            elif line.startswith("#"):
-                continue
-            else:
-                packages.append(line)
-
 if os.path.exists("scripts"):
     for file in os.listdir("scripts"):
         if file.endswith(".py") and not file.startswith("_"):
             fp = os.path.join("scripts", file)
-            with open(fp) as fin:
-                if "python" in fin.readline():
-                    scripts.append(fp)
-
-specs = read_specs(path_to_pyproject)
+            scripts.append(fp)
 
 setup(
-    author="kpotoh",
-    author_email="axepon@mail.ru",
-    url="https://github.com/mitoclub/PyMutSpec",
-    license="MIT",
-    install_requires=packages,
-    dependency_links=extra_index_urls,
-    scripts=scripts,
     packages=find_packages(),
+    scripts=scripts,
     package_data={'pymutspec': ['utils/configs/log_settings.yaml']},
-    **specs
 )