add license

LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2022~2023 yodeng <[email protected]>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

recipe/meta.yaml

@@ -21,4 +21,4 @@ requirements:
 
 about:
     home: https://github.com/yodeng/fsplit
-    license: BSD
+    license: MIT

setup.py

@@ -1,34 +1,127 @@
 import os
+import sys
+import sysconfig
 
 from setuptools import setup
-from src.version import __version__
-
-
-def getdes():
-    des = ""
-    with open(os.path.join(os.getcwd(), "README.md")) as fi:
-        des = fi.read()
-    return des
-
-
-setup(
-    name="fsplit",
-    version=__version__,
-    packages=["fsplit"],
-    package_data={"fsplit": ["gsplit", ]},
-    package_dir={"fsplit": "src"},
-    author="Deng Yong",
-    author_email="[email protected]",
-    url="",
-    license="BSD",
-    install_requires=[],
-    python_requires='>=2.7.10, <=3.11',
-    long_description=getdes(),
-    long_description_content_type='text/markdown',
-    entry_points={
-        'console_scripts': [
-            'fsplit = fsplit.main:main',
-            'gsplit = fsplit.main:gsplit',
+from functools import partial
+from setuptools.extension import Extension
+
+
+class Packages(object):
+
+    def __init__(self, pkg_name=""):
+        self.name = pkg_name
+        self.base_dir = os.path.dirname(__file__)
+        basejoin = partial(self._join, self.base_dir)
+        self.source_dir = basejoin("src")
+        self.version_file = basejoin("src/_version.py")
+        self.des_file = basejoin("README.md")
+        self.req_file = basejoin("requirements.txt")
+
+    def _join(self, *args):
+        return os.path.join(*args)
+
+    @property
+    def listdir(self):
+        df, nc = [], []
+        if os.path.isdir(self.name):
+            nc = os.listdir(self.name)
+        for a, b, c in os.walk(self.source_dir):
+            if os.path.basename(a).startswith("__"):
+                continue
+            for i in c:
+                if i.startswith("__") or not i.endswith(".py") or i in nc:
+                    continue
+                p = os.path.join(a[len(self.source_dir)+1:], i)
+                df.append(p)
+        return df
+
+    @property
+    def description(self):
+        des = ""
+        if os.path.isfile(self.des_file):
+            with open(self.des_file) as fi:
+                des = fi.read()
+        return des
+
+    @property
+    def version(self):
+        v = {}
+        if not os.path.isfile(self.version_file):
+            for f in os.listdir(self.source_dir):
+                if f.endswith("version.py"):
+                    self.version_file = os.path.join(self.source_dir, f)
+                    break
+        with open(self.version_file) as fi:
+            c = fi.read()
+        exec(compile(c, self.version_file, "exec"), v)
+        return v["__version__"]
+
+    @property
+    def requirements(self):
+        requires = []
+        if os.path.isfile(self.req_file):
+            with open(self.req_file) as fi:
+                for line in fi:
+                    line = line.strip()
+                    requires.append(line)
+        return requires
+
+    @property
+    def _extensions(self):
+        exts = []
+        for f in self.listdir:
+            e = Extension(self.name + "." + os.path.splitext(f)[0].replace("/", "."),
+                          [os.path.join(self.source_dir, f), ], extra_compile_args=["-O3", ],)
+            e.cython_directives = {
+                'language_level': sysconfig._PY_VERSION_SHORT_NO_DOT[0]}
+            exts.append(e)
+        return exts
+
+    @property
+    def _package_dir(self):
+        pd = {}
+        for a, b, v in os.walk(self.source_dir):
+            p = a.replace(self.source_dir, self.name).replace("/", ".")
+            pd[p] = a.replace(self.source_dir, "src")
+        return pd
+
+    def install(self, ext=False):
+        kwargs = {}
+        kwargs.update(
+            name=self.name,
+            version=self.version,
+            license="MIT",
+            packages=list(self._package_dir.keys()),
+            package_dir=self._package_dir,
+            package_data={self.name: ["gsplit", ]},
+            install_requires=self.requirements,
+            python_requires='>=2.7.10, <=3.11',
+            long_description=self.description,
+            long_description_content_type='text/markdown',
+            entry_points={'console_scripts': self._entrys},
+            author="yodeng",
+            author_email="[email protected]",
+            url="https://github.com/yodeng/fsplit",
+        )
+        if ext:
+            kwargs.pop("package_dir")
+            kwargs["ext_modules"] = self._extensions
+        setup(**kwargs)
+
+    @property
+    def _entrys(self):
+        eps = [
+            '{0} = {0}.main:main'.format(self.name),
+            '{0} = {1}.main:{0}'.format("gsplit", self.name),
         ]
-    }
-)
+        return eps
+
+
+def main():
+    pkgs = Packages("fsplit")
+    pkgs.install()
+
+
+if __name__ == "__main__":
+    main()

src/bcl.py

@@ -70,15 +70,16 @@ def make_bcl_cmd(self):
                "--barcode-mismatches", self.mis,
                "-p", self.nproc,
                "--sample-sheet", self.samplesheet]
-        return " ".join(cmd)
+        return cmd
 
     def call(self, cmd, run=True):
         if self.print_cmd:
             self.logs.info(cmd)
         if not run:
             return
         with open(os.devnull, "w") as fo:
-            subprocess.check_call(cmd, shell=True, stdout=fo, stderr=fo)
+            subprocess.check_call(cmd, shell=isinstance(
+                cmd, str) and True or False, stdout=fo, stderr=fo)
 
     def stats(self, j):
         with open(j) as fi: