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

Merged
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 +251 -595
23 changed files with 251 additions and 595 deletions
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Showing only changes of commit 1095a617a3 - Show all commits

4
python/obitools3/dms/column/typed_column/bool.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from ...capi.obitypes cimport index_t
from obitools3.dms.capi.obitypes cimport index_t
from ..column cimport Column, \
from obitools3.dms.column.column cimport Column, \
Column_multi_elts

16
python/obitools3/dms/column/typed_column/bool.pyx
View File

@ -2,14 +2,20 @@
from obitools3.dms.capi.obierrno cimport obi_errno
from ..column cimport register_column_class
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ...view.view cimport View
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
from obitools3.dms.capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
obi_get_bool_with_elt_idx_and_col_p_in_view, \
obi_set_bool_with_elt_name_and_col_p_in_view, \
obi_set_bool_with_elt_idx_and_col_p_in_view, \
@ -17,9 +23,9 @@ from ...capi.obiview cimport obi_get_bool_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_BOOL, \
from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
OBIBool_NA, \
OBITuple_NA, \
obibool_t

4
python/obitools3/dms/column/typed_column/char.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from ...capi.obitypes cimport index_t
from obitools3.dms.capi.obitypes cimport index_t
from ..column cimport Column, \
from obitools3.dms.column.column cimport Column, \
Column_multi_elts

17
python/obitools3/dms/column/typed_column/char.pyx
View File

@ -1,15 +1,20 @@
#cython: language_level=3
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.capi.obitypes cimport index_t
from ..column cimport register_column_class
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ...view.view cimport View
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
from obitools3.dms.capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
obi_get_char_with_elt_idx_and_col_p_in_view, \
obi_set_char_with_elt_name_and_col_p_in_view, \
obi_set_char_with_elt_idx_and_col_p_in_view, \
@ -17,9 +22,9 @@ from ...capi.obiview cimport obi_get_char_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_CHAR, \
from obitools3.dms.capi.obitypes cimport OBI_CHAR, \
OBIChar_NA, \
OBITuple_NA, \
obichar_t
@ -116,7 +121,7 @@ cdef class Column_multi_elts_char(Column_multi_elts):
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
global obi_errno
cdef bytes elt_name
cdef bytes elt_name
cdef obichar_t value_b
if value is None :
value_b = OBIChar_NA

4
python/obitools3/dms/column/typed_column/float.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from ...capi.obitypes cimport index_t
from obitools3.dms.capi.obitypes cimport index_t
from ..column cimport Column, \
from obitools3.dms.column.column cimport Column, \
Column_multi_elts

15
python/obitools3/dms/column/typed_column/float.pyx
View File

@ -1,15 +1,20 @@
#cython: language_level=3
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.capi.obitypes cimport index_t
from ..column cimport register_column_class
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ...view.view cimport View
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
from obitools3.dms.capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
obi_get_float_with_elt_idx_and_col_p_in_view, \
obi_set_float_with_elt_name_and_col_p_in_view, \
obi_set_float_with_elt_idx_and_col_p_in_view, \
@ -17,9 +22,9 @@ from ...capi.obiview cimport obi_get_float_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_FLOAT, \
from obitools3.dms.capi.obitypes cimport OBI_FLOAT, \
OBIFloat_NA, \
OBITuple_NA, \
obifloat_t

110
python/obitools3/dms/column/typed_column/int.cfiles
View File

@ -1,110 +0,0 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

4
python/obitools3/dms/column/typed_column/int.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from ...capi.obitypes cimport index_t
from obitools3.dms.capi.obitypes cimport index_t
from ..column cimport Column, \
from obitools3.dms.column.column cimport Column, \
Column_multi_elts

14
python/obitools3/dms/column/typed_column/int.pyx
View File

@ -1,15 +1,19 @@
#cython: language_level=3
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.capi.obitypes cimport index_t
from ..column cimport register_column_class
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ...view.view cimport View
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from ...capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
from obitools3.dms.capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
obi_get_int_with_elt_idx_and_col_p_in_view, \
obi_set_int_with_elt_name_and_col_p_in_view, \
obi_set_int_with_elt_idx_and_col_p_in_view, \
@ -17,9 +21,9 @@ from ...capi.obiview cimport obi_get_int_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_INT, \
from obitools3.dms.capi.obitypes cimport OBI_INT, \
OBIInt_NA, \
OBITuple_NA, \
obiint_t

110
python/obitools3/dms/column/typed_column/qual.cfiles
View File

@ -1,110 +0,0 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

110
python/obitools3/dms/column/typed_column/seq.cfiles
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@ -1,110 +0,0 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

110
python/obitools3/dms/column/typed_column/str.cfiles
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@ -1,110 +0,0 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
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