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Merge branch 'pip-standard' of git@git.metabarcoding.org:obitools/obitools3.git into pip-standard

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This commit is contained in:
Eric Coissac
2019-03-26 15:54:49 +01:00
parent 1095a617a3 5a05258fcb
commit cd88c37a7e
6 changed files with 47 additions and 35 deletions
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4
python/obitools3/dms/column/typed_column/qual.pxd
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@ -1,9 +1,9 @@
# #cython: language_level=3
from ...capi.obitypes cimport index_t
from obitools3.dms.capi.obitypes cimport index_t
from ..column_idx cimport Column_idx, \
from obitools3.dms.column_idx cimport Column_idx, \
Column_multi_elts_idx

17
python/obitools3/dms/column/typed_column/qual.pyx
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@ -1,17 +1,22 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno
from ..column cimport register_column_class
from obitools3.dms.column cimport register_column_class
from ...view.view cimport View
from obitools3.dms.view.view cimport View
from ..column cimport Column
from obitools3.dms.column cimport Column
from obitools3.utils cimport tobytes, bytes2str, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
from obitools3.dms.capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
obi_get_qual_char_with_elt_idx_and_col_p_in_view, \
obi_set_qual_char_with_elt_name_and_col_p_in_view, \
obi_set_qual_char_with_elt_idx_and_col_p_in_view, \
@ -21,9 +26,9 @@ from ...capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view,
obi_set_qual_int_with_elt_idx_and_col_p_in_view, \
Obiview_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obitypes cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
from obitools3.dms.capi.obitypes cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
from libc.stdlib cimport malloc, free
from libc.stdint cimport uint8_t

4
python/obitools3/dms/column/typed_column/seq.pxd
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@ -1,9 +1,9 @@
# #cython: language_level=3
from ...capi.obitypes cimport index_t
from obitools3.dms.capi.obitypes cimport index_t
from ..column_idx cimport Column_idx, \
from obitools3.dms.column_idx cimport Column_idx, \
Column_multi_elts_idx

17
python/obitools3/dms/column/typed_column/seq.pyx
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@ -1,17 +1,20 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno
from ..column cimport register_column_class
from obitools3.dms.column.column cimport Column, register_column_class
from ...view.view cimport View
from ..column cimport Column
from obitools3.dms.view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
from obitools3.dms.capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
obi_get_seq_with_elt_idx_and_col_p_in_view, \
obi_set_seq_with_elt_name_and_col_p_in_view, \
obi_set_seq_with_elt_idx_and_col_p_in_view, \
@ -21,9 +24,9 @@ from ...capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
obi_set_array_with_col_p_in_view, \
Obiview_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obitypes cimport OBI_SEQ, \
from obitools3.dms.capi.obitypes cimport OBI_SEQ, \
OBISeq_NA, \
OBITuple_NA

4
python/obitools3/dms/column/typed_column/str.pxd
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@ -1,9 +1,9 @@
# #cython: language_level=3
from ...capi.obitypes cimport index_t
from obitools3.dms.capi.obitypes cimport index_t
from ..column_idx cimport Column_idx, \
from obitools3.dms.column_idx cimport Column_idx, \
Column_multi_elts_idx

36
python/obitools3/dms/column/typed_column/str.pyx
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@ -1,30 +1,34 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno
from ..column cimport register_column_class
from obitools3.dms.column.column cimport Column, register_column_class
from ...view.view cimport View
from ..column cimport Column
from obitools3.dms.view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view, \
obi_get_array_with_col_p_in_view, \
obi_set_array_with_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view, \
obi_get_array_with_col_p_in_view, \
obi_set_array_with_col_p_in_view, \
Obiview_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obitypes cimport OBI_STR, \
OBIStr_NA, \
OBITuple_NA, \
const_char_p
from obitools3.dms.capi.obitypes cimport OBI_STR, \
OBIStr_NA, \
OBITuple_NA, \
const_char_p
from libc.stdint cimport int32_t
from libc.stdlib cimport calloc, free