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The new install version based on classical setup.py #1

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coissac merged 15 commits from pip-standard-orig-python into master 2019-03-29 15:25:03 +00:00
Conversation 2 Commits 15 Files Changed 40 +324 -1194
37 changed files with 324 additions and 1194 deletions
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3
python/obitools3/dms/column/column_idx.pxd
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@ -2,7 +2,8 @@
from obitools3.dms.capi.obitypes cimport index_t from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column from obitools3.dms.column.column cimport Column, \
Column_multi_elts
cdef class Column_idx(Column) : cdef class Column_idx(Column) :

5
python/obitools3/dms/taxo/taxo.pxd
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@ -1,4 +1,4 @@
#cython: language_level=3 # cython: language_level=3
from obitools3.dms.capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p from obitools3.dms.capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
@ -28,4 +28,5 @@ cdef class Taxonomy(OBIWrapper) :
cdef class Taxon : cdef class Taxon :
cdef ecotx_t* _pointer cdef ecotx_t* _pointer
cdef Taxonomy _tax cdef Taxonomy _tax

3
python/obitools3/dms/taxo/taxo.pyx
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@ -4,7 +4,6 @@ from obitools3.utils cimport str2bytes, bytes2str, tobytes, tostr
from obitools3.dms.capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p from obitools3.dms.capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
from obitools3.dms.dms cimport DMS from obitools3.dms.dms cimport DMS
from obitools3.dms.dms import DMS
from obitools3.dms.object cimport OBIWrapper from obitools3.dms.object cimport OBIWrapper
@ -321,7 +320,7 @@ cdef class Taxonomy(OBIWrapper) :
cdef class Taxon : # TODO dict subclass? cdef class Taxon : # TODO dict subclass?
def __init__(self, object taxon_capsule, Taxonomy tax) : def __init__(self, object taxon_capsule, Taxonomy tax) :
self._pointer = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL) self._pointer = <ecotx_t*>PyCapsule_GetPointer(taxon_capsule, NULL)
if self._pointer == NULL : if self._pointer == NULL :
raise Exception("Error reading a taxon (NULL pointer)") raise Exception("Error reading a taxon (NULL pointer)")
self._tax = tax self._tax = tax