kssdtree 2.0.8__tar.gz → 2.1.0__tar.gz

{kssdtree-2.0.8/kssdtree.egg-info → kssdtree-2.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: kssdtree
-Version: 2.0.8
+Version: 2.1.0
 Summary: Kssdtree is a versatile Python package for phylogenetic analysis. It also provides one-stop tree construction and visualization. It can handle DNA sequences of both fasta or fastq format, whether gzipped or not. 
 Home-page: https://github.com/yhlink/kssdtree
 Download-URL: https://pypi.org/project/kssdtree
@@ -10,3 +10,9 @@ Requires-Dist: pyqt5
 Requires-Dist: ete3
 Requires-Dist: requests
 Requires-Dist: pandas
+Dynamic: author
+Dynamic: author-email
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: summary

{kssdtree-2.0.8 → kssdtree-2.1.0}/iseq2comem.c

@@ -196,7 +196,7 @@ const char gzpipe_cmd[] = "gzip -dc";
 const char gzpipe_cmd[] = "zcat -fc";
 #endif
 llong *fasta2co(char *seqfname, llong *co, char *pipecmd) {
-    printf("The fasta2co seqfname is: %s\n", seqfname);
+    // printf("The fasta2co seqfname is: %s\n", seqfname);
     llong tuple = 0LLU, crvstuple = 0LLU,
             unituple, drtuple, pfilter;
     memset(co, 0LLU, hashsize * sizeof(llong));
@@ -207,12 +207,12 @@ llong *fasta2co(char *seqfname, llong *co, char *pipecmd) {
         sprintf(fas_fname, "%s %s", pipecmd, seqfname);
     else
         sprintf(fas_fname, "%s %s", gzpipe_cmd, seqfname);
-    printf("The fasta2co fas_fname is: %s\n", fas_fname);
+    // printf("The fasta2co fas_fname is: %s\n", fas_fname);
     if (is_gz_file(seqfname)){
-        printf(".gz format\n");
+        // printf(".gz format\n");
         if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n");
     }else{
-        printf("not .gz format\n");
+        // printf("not .gz format\n");
         #ifdef _WIN32
         if ((infp = fopen(seqfname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n");
         #else
@@ -291,7 +291,7 @@ llong *fasta2co(char *seqfname, llong *co, char *pipecmd) {
 #define CT_MAX 0xfLLU
 
 llong *fastq2co(char *seqfname, llong *co, char *pipecmd, int Q, int M) {
-    printf("The fastq2co seqfname is: %s\n", seqfname);
+    // printf("The fastq2co seqfname is: %s\n", seqfname);
     if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX);
     llong tuple = 0LLU, crvstuple = 0LLU, unituple, drtuple, pfilter;
     memset(co, 0LLU, hashsize * sizeof(llong));
@@ -301,12 +301,12 @@ llong *fastq2co(char *seqfname, llong *co, char *pipecmd, int Q, int M) {
         sprintf(fq_fname, "%s %s", pipecmd, seqfname);
     else
         sprintf(fq_fname, "%s %s", gzpipe_cmd, seqfname);
-    printf("The fastq2co fq_fname is: %s\n", fq_fname);
+    // printf("The fastq2co fq_fname is: %s\n", fq_fname);
     if (is_gz_file(seqfname)){
-        printf(".gz format\n");
+        // printf(".gz format\n");
         if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n");
     }else{
-        printf("not .gz format\n");
+        // printf("not .gz format\n");
         #ifdef _WIN32
         if ((infp = fopen(seqfname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n");
         #else
@@ -388,7 +388,7 @@ llong *fastq2co(char *seqfname, llong *co, char *pipecmd, int Q, int M) {
 #define OCCRC_MAX 0xffffLLU
 
 llong *fastq2koc(char *seqfname, llong *co, char *pipecmd, int Q) {
-    printf("The fastq2koc seqfname is: %s\n", seqfname);
+    // printf("The fastq2koc seqfname is: %s\n", seqfname);
     llong tuple = 0LLU, crvstuple = 0LLU, unituple, drtuple, pfilter;
     memset(co, 0LLU, hashsize * sizeof(llong));
     FILE *infp;
@@ -397,12 +397,12 @@ llong *fastq2koc(char *seqfname, llong *co, char *pipecmd, int Q) {
         sprintf(fq_fname, "%s %s", pipecmd, seqfname);
     else
         sprintf(fq_fname, "%s %s", gzpipe_cmd, seqfname);
-    printf("The fastq2koc fq_fname is: %s\n", fq_fname);
+    // printf("The fastq2koc fq_fname is: %s\n", fq_fname);
     if (is_gz_file(seqfname)){
-        printf(".gz format\n");
+        // printf(".gz format\n");
         if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n");
     }else{
-        printf("not .gz format\n");
+        // printf("not .gz format\n");
         #ifdef _WIN32
         if ((infp = fopen(seqfname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n");
         #else

{kssdtree-2.0.8 → kssdtree-2.1.0/kssdtree.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: kssdtree
-Version: 2.0.8
+Version: 2.1.0
 Summary: Kssdtree is a versatile Python package for phylogenetic analysis. It also provides one-stop tree construction and visualization. It can handle DNA sequences of both fasta or fastq format, whether gzipped or not. 
 Home-page: https://github.com/yhlink/kssdtree
 Download-URL: https://pypi.org/project/kssdtree
@@ -10,3 +10,9 @@ Requires-Dist: pyqt5
 Requires-Dist: ete3
 Requires-Dist: requests
 Requires-Dist: pandas
+Dynamic: author
+Dynamic: author-email
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: summary

{kssdtree-2.0.8 → kssdtree-2.1.0}/kssdtree.py

@@ -7,6 +7,8 @@ import platform
 import shutil
 import time
 import requests
+import pkgutil
+import argparse
 
 
 def shuffle(k=None, s=None, l=None, o=None):
@@ -347,6 +349,8 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, databa
                     shutil.rmtree(temp_dir2)
                 if os.path.exists(temp_phy):
                     os.remove(temp_phy)
+            else:
+                pass
         else:
             print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
             return False
@@ -355,7 +359,7 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, databa
             if not toolutils.is_positive_integer(N):
                 print("N must > 0 !!!")
                 return False
-            if shuf_file != 'L3K9.shuf':
+            if 'L3K9.shuf' not in shuf_file:
                 print("shuf_file must be set to 'L3K9.shuf'")
                 return False
             timeStamp = int(time.mktime(time.localtime(time.time())))
@@ -531,3 +535,5 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, databa
     else:
         print('Pipeline error, please see https://kssdtree.readthedocs.io/en/latest!!!')
         return False
+
+

{kssdtree-2.0.8 → kssdtree-2.1.0}/setup.py

@@ -1,33 +1,54 @@
 import sys
 from setuptools import setup, Extension, find_packages
 from os import environ
+from setuptools.command.install import install
 import os
 
+from setuptools.command.build_ext import build_ext
+import sys, os, subprocess
+
+class CustomBuildExt(build_ext):
+    def run(self):
+        super().run()
+        self.fix_rpath()
+
+    def fix_rpath(self):
+        if sys.platform != "darwin":
+            return
+
+        conda_lib = os.path.join(sys.prefix, "lib")
+
+        for ext in self.extensions:
+            so_path = self.get_ext_fullpath(ext.name)
+            if not os.path.exists(so_path):
+                continue
+
+            subprocess.run(
+                ["install_name_tool", "-delete_rpath", conda_lib, so_path],
+                stdout=subprocess.DEVNULL,
+                stderr=subprocess.DEVNULL,
+            )
+            subprocess.run(
+                ["install_name_tool", "-delete_rpath", "@loader_path", so_path],
+                stdout=subprocess.DEVNULL,
+                stderr=subprocess.DEVNULL,
+            )
+            subprocess.run(
+                ["install_name_tool", "-delete_rpath", "@loader_path", so_path],
+                stdout=subprocess.DEVNULL,
+                stderr=subprocess.DEVNULL,
+            )
+
+
 extra_compile_args = []
 extra_link_args = []
 if 'darwin' in sys.platform:
-    target_dirs = ["gcc-9", "gcc-10", "gcc-11", "gcc-12", "gcc-13", "gcc-14", "gcc-15"]
-    path = "/opt/homebrew/bin/"
-    directories = [dir for dir in os.listdir(path) if dir in target_dirs]
-    if len(directories) > 0:
-        gcc_version = directories[0]
-        if 'gcc-9' == gcc_version:
-            gcc_path = "/opt/homebrew/bin/gcc-9"
-        elif 'gcc-10' == gcc_version:
-            gcc_path = "/opt/homebrew/bin/gcc-10"
-        elif 'gcc-11' == gcc_version:
-            gcc_path = "/opt/homebrew/bin/gcc-11"
-        elif 'gcc-12' == gcc_version:
-            gcc_path = "/opt/homebrew/bin/gcc-12"
-        elif 'gcc-13' == gcc_version:
-            gcc_path = "/opt/homebrew/bin/gcc-13"
-        elif 'gcc-14' == gcc_version:
-            gcc_path = "/opt/homebrew/bin/gcc-14"
-        else:
-            gcc_path = ""
-        extra_compile_args = ['-fopenmp']
-        extra_link_args = ['-fopenmp']
-        os.environ["CC"] = gcc_path
+    extra_compile_args = ['-fopenmp']
+    extra_link_args = ['-fopenmp']
+    # clang
+    # os.environ["CC"] = '/usr/bin/gcc'
+    os.environ["CC"] = '/opt/homebrew/bin/gcc-12'
+
 else:
     if environ.get('CC') and 'clang' in environ['CC']:
         # clang
@@ -37,6 +58,7 @@ else:
         # GNU
         extra_compile_args = ['-fopenmp']
         extra_link_args = ['-fopenmp']
+
 MOD1 = 'kssd'
 MOD2 = 'nj'
 MOD3 = 'dnj'
@@ -59,6 +81,7 @@ sources2 = ['align.c',
             'buildtree.c',
             'sequence.c',
             'pynj.c']
+
 sources3 = ['bytescale.c',
             'dnj.c',
             'str.c',
@@ -87,7 +110,7 @@ require_pakages = [
 
 setup(
     name='kssdtree',
-    version='2.0.8',
+    version='2.1.0',
     author='Hang Yang',
     author_email='yhlink1207@gmail.com',
     description="Kssdtree is a versatile Python package for phylogenetic analysis. It also provides one-stop tree construction and visualization. It can handle DNA sequences of both fasta or fastq format, whether gzipped or not. ",
@@ -107,6 +130,8 @@ setup(
     install_requires=require_pakages,
     dependency_links=['https://pypi.python.org/simple/'],
     zip_safe=False,
-    include_package_data=True
+    include_package_data=True,
+    cmdclass={
+        "build_ext": CustomBuildExt,
+    }
 )
-