diff --git a/python/obitools3/dms/column/typed_column/bool.pxd b/python/obitools3/dms/column/typed_column/bool.pxd index 41209c0..22cf51b 100755 --- a/python/obitools3/dms/column/typed_column/bool.pxd +++ b/python/obitools3/dms/column/typed_column/bool.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/bool.pyx b/python/obitools3/dms/column/typed_column/bool.pyx index 54377fd..ae113b8 100755 --- a/python/obitools3/dms/column/typed_column/bool.pyx +++ b/python/obitools3/dms/column/typed_column/bool.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/char.pxd b/python/obitools3/dms/column/typed_column/char.pxd index c67db85..7614c4f 100755 --- a/python/obitools3/dms/column/typed_column/char.pxd +++ b/python/obitools3/dms/column/typed_column/char.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/char.pyx b/python/obitools3/dms/column/typed_column/char.pyx index 1ba7e89..d4e8c39 100755 --- a/python/obitools3/dms/column/typed_column/char.pyx +++ b/python/obitools3/dms/column/typed_column/char.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/float.pxd b/python/obitools3/dms/column/typed_column/float.pxd index 07e9f7b..edd898e 100755 --- a/python/obitools3/dms/column/typed_column/float.pxd +++ b/python/obitools3/dms/column/typed_column/float.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/float.pyx b/python/obitools3/dms/column/typed_column/float.pyx index 3a0702b..f00e123 100755 --- a/python/obitools3/dms/column/typed_column/float.pyx +++ b/python/obitools3/dms/column/typed_column/float.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/int.cfiles b/python/obitools3/dms/column/typed_column/int.cfiles deleted file mode 100644 index 72668a9..0000000 --- a/python/obitools3/dms/column/typed_column/int.cfiles +++ /dev/null @@ -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 - - - - - - - diff --git a/python/obitools3/dms/column/typed_column/int.pxd b/python/obitools3/dms/column/typed_column/int.pxd index 0cac022..51be9f3 100755 --- a/python/obitools3/dms/column/typed_column/int.pxd +++ b/python/obitools3/dms/column/typed_column/int.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/int.pyx b/python/obitools3/dms/column/typed_column/int.pyx index 5d9150e..2359d0a 100755 --- a/python/obitools3/dms/column/typed_column/int.pyx +++ b/python/obitools3/dms/column/typed_column/int.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/qual.cfiles b/python/obitools3/dms/column/typed_column/qual.cfiles deleted file mode 100644 index 72668a9..0000000 --- a/python/obitools3/dms/column/typed_column/qual.cfiles +++ /dev/null @@ -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 - - - - - - - diff --git a/python/obitools3/dms/column/typed_column/seq.cfiles b/python/obitools3/dms/column/typed_column/seq.cfiles deleted file mode 100644 index 72668a9..0000000 --- a/python/obitools3/dms/column/typed_column/seq.cfiles +++ /dev/null @@ -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 - - - - - - - diff --git a/python/obitools3/dms/column/typed_column/str.cfiles b/python/obitools3/dms/column/typed_column/str.cfiles deleted file mode 100644 index 72668a9..0000000 --- a/python/obitools3/dms/column/typed_column/str.cfiles +++ /dev/null @@ -1,110 +0,0 @@ -../../../../../src/obi_lcs.h -../../../../../src/obi_lcs.c -../../../../../src/obierrno.h -../../../../../src/obierrno.c 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