Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git

distutils.ext/obidistutils/core.py

@@ -40,6 +40,7 @@ def findPackage(root,base=None):
     
 def findCython(root,base=None,pyrexs=None):
     setupdir = os.path.dirname(sys.argv[0])
+    csourcedir = os.path.join(setupdir,"src")
     pyrexs=[]
 
     if base is None:
@@ -53,6 +54,7 @@ def findCython(root,base=None,pyrexs=None):
                                     [pyrex]
                                     )
                           )
+            pyrexs[-1].include_dirs.append(csourcedir)
             try:
                 cfiles = os.path.splitext(pyrex)[0]+".cfiles"
                 cfilesdir = os.path.dirname(cfiles)

python/obitools3/obidms/_obiseq.pyx

@@ -18,10 +18,10 @@ cdef class OBI_Seq(dict) :
 
     # sequence id property getter and setter
     @property
-    def id(self):
+    def id(self):  # @ReservedAssignment
         return self._id
     @id.setter
-    def id(self, str new_id):
+    def id(self, str new_id):  # @ReservedAssignment @DuplicatedSignature
         self._id = new_id
         self[bytes2str(ID_COLUMN)] = new_id
 
@@ -30,7 +30,7 @@ cdef class OBI_Seq(dict) :
     def seq(self):
         return self._seq
     @seq.setter
-    def seq(self, object new_seq):
+    def seq(self, object new_seq):  # @DuplicatedSignature
         self._seq = new_seq
         self["SEQ"] = new_seq   # TODO discuss
 
@@ -39,7 +39,7 @@ cdef class OBI_Seq(dict) :
     def definition(self):
         return self._definition
     @definition.setter
-    def definition(self, object new_definition):
+    def definition(self, object new_definition):  # @DuplicatedSignature
         self._definition = new_definition
         self[bytes2str(DEFINITION_COLUMN)] = new_definition
 
@@ -51,7 +51,7 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
     def seq(self):
         return self._seq
     @seq.setter
-    def seq(self, object new_seq):
+    def seq(self, object new_seq):  # @DuplicatedSignature
         self._seq = new_seq
         self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
 
@@ -60,7 +60,7 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
     def quality(self):
         return self._quality
     @quality.setter
-    def quality(self, object new_quality):
+    def quality(self, object new_quality):  # @DuplicatedSignature
         self._quality = new_quality
         self[bytes2str(QUALITY_COLUMN)] = new_quality
 
@@ -74,10 +74,10 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
 
     # sequence id property getter and setter
     @property
-    def id(self):
+    def id(self):               # @ReservedAssignment @DuplicatedSignature
         return self[bytes2str(ID_COLUMN)]
     @id.setter
-    def id(self, str new_id):
+    def id(self, str new_id):   # @ReservedAssignment @DuplicatedSignature
         self[bytes2str(ID_COLUMN)] = new_id
 
     # sequence definition property getter and setter
@@ -85,7 +85,7 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
     def definition(self):
         return self[bytes2str(DEFINITION_COLUMN)]
     @definition.setter
-    def definition(self, str new_def):
+    def definition(self, str new_def): # @DuplicatedSignature
         self[bytes2str(DEFINITION_COLUMN)] = new_def
 
     # nuc_seq property getter and setter
@@ -93,7 +93,7 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
     def nuc_seq(self):
         return self[bytes2str(NUC_SEQUENCE_COLUMN)]
     @nuc_seq.setter
-    def nuc_seq(self, object new_seq):
+    def nuc_seq(self, object new_seq): # @DuplicatedSignature
         self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
 
     # quality property getter and setter
@@ -101,7 +101,7 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
     def quality(self):
         return self[bytes2str(QUALITY_COLUMN)]
     @quality.setter
-    def quality(self, object new_qual):
+    def quality(self, object new_qual): # @DuplicatedSignature
         if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists
             self[bytes2str(QUALITY_COLUMN)] = new_qual
         else :  # Quality is in str form