Convert relative import an delete cfiles

This commit is contained in:
2019-03-26 16:14:03 +01:00
parent cd88c37a7e
commit 0b4ea49539
14 changed files with 14 additions and 565 deletions

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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

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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

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@ -2,7 +2,7 @@
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column
cdef class Column_idx(Column) :

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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

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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

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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

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@ -3,7 +3,7 @@
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx

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@ -2,16 +2,15 @@
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.column cimport register_column_class
from obitools3.dms.view.view cimport View
from obitools3.dms.column cimport Column
from obitools3.dms.column.column cimport Column, \
register_column_class
from obitools3.utils cimport tobytes, bytes2str, \
obi_errno_to_exception

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@ -3,7 +3,7 @@
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx

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@ -2,7 +2,7 @@
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno

View File

@ -3,7 +3,7 @@
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx

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@ -2,7 +2,7 @@
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column_idx cimport Column_idx, \
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx

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@ -1,8 +1,8 @@
#cython: language_level=3
from .object cimport OBIWrapper
from obitools3.dms.object cimport OBIWrapper
from .capi.obidms cimport OBIDMS_p
from obitools3.dms.capi.obidms cimport OBIDMS_p
cdef class DMS(OBIWrapper):