Minor changes for pip release

python/obitools3/commands/import.pyx

@@ -73,7 +73,7 @@ def addOptions(parser):
                      action="store_true", dest="import:preread",
                      default=False,
                      help="Do a first readthrough of the dataset if it contains huge dictionaries (more than 100 keys) for "
-                          "a much faster import.")
+                          "a much faster import. This option is not recommended and will slow down the import in any other case.")
 
 
 def run(config):

python/obitools3/dms/capi/obidmscolumn.pxd

@@ -63,6 +63,8 @@ cdef extern from "obidmscolumn.h" nogil:
     
     char* obi_get_elements_names(OBIDMS_column_p column)
     
+    char* obi_column_formatted_infos(OBIDMS_column_p column)
+
     index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
     
     int obi_column_write_comments(OBIDMS_column_p column, const char* comments)

python/obitools3/dms/column/column.pyx

@@ -14,6 +14,7 @@ from ..capi.obidms cimport obi_import_column
 from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
                                  obi_close_column, \
                                  obi_get_elements_names, \
+                                 obi_column_formatted_infos, \
                                  obi_column_write_comments
                                      
 from ..capi.obiutils cimport obi_format_date
@@ -38,7 +39,7 @@ from obitools3.utils cimport tobytes, \
  
 from obitools3.dms.column import typed_column
  
-from libc.stdlib  cimport free
+from libc.stdlib cimport free
  
 import importlib
 import inspect
@@ -288,9 +289,15 @@ cdef class Column(OBIWrapper) :
     @OBIWrapper.checkIsActive
     def __repr__(self) :
         cdef bytes s
+        #cdef char* s_b
+        #cdef str s_str
+        #s_b = obi_column_formatted_infos(self.pointer())
+        #s_str = bytes2str(s_b)
+        #free(s_b)
         s = self._alias + b", data type: " + self.data_type
+        #return s_str
         return bytes2str(s)
-
+    
          
     def close(self):  # TODO discuss, can't be called bc then bug when closing view that tries to close it in C
     

python/obitools3/parsers/embl.pyx

@@ -177,7 +177,7 @@ def emblIterator_dir(dir_path,
     for filename in files:
         if read==only:
             return
-        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files, len(files)))
+        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files+1, len(files)))
         f = uopen(filename)
         if only is not None:
             only_f = only-read

python/obitools3/parsers/genbank.pyx

@@ -176,7 +176,7 @@ def genbankIterator_dir(dir_path,
     for filename in files:
         if read==only:
             return
-        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files, len(files)))
+        print("Parsing file %s (%d/%d)" % (tostr(filename), read_files+1, len(files)))
         f = uopen(filename)
         if only is not None:
             only_f = only-read

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0b19'
+serial= '0b20'
 
 version ="%d.%d.%s" % (major,minor,serial)

setup.py

@@ -89,9 +89,10 @@ PACKAGE     = "OBITools3"
 VERSION     = version
 AUTHOR      = 'Celine Mercier'
 EMAIL       = 'celine.mercier@metabarcoding.org'
-URL         = "http://metabarcoding.org/obitools3"
+URL         = "https://metabarcoding.org/obitools3"
+PLATFORMS   = "posix"
 LICENSE     = "CeCILL-V2"
-DESCRIPTION = "Tools and library for DNA metabarcoding",
+DESCRIPTION = "A package for the management of analyses and data in DNA metabarcoding."
 PYTHONMIN   = '3.5'
 
 SRC       = 'python'
@@ -148,12 +149,18 @@ classifiers=['Development Status :: 4 - Beta',
              'Topic :: Utilities',
              ]
 
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
 setup(name=PACKAGE,
       description=DESCRIPTION,
+      long_description=long_description,
+      long_description_content_type="text/markdown",
       classifiers=classifiers,
       version=VERSION,
       author=AUTHOR,
       author_email=EMAIL,
+      platforms=PLATFORMS,
       license=LICENSE,
       url=URL,
       ext_modules=xx,