diff --git a/pyprophet/_config.py b/pyprophet/_config.py index 7a9edfa3..e5b71f5c 100644 --- a/pyprophet/_config.py +++ b/pyprophet/_config.py @@ -699,6 +699,7 @@ class ExportIOConfig(BaseIOConfig): compression_level: int = 11 split_transition_data: bool = True split_runs: bool = False + include_transition_data: bool = True # Whether to include transition data in parquet export # SqMass: Export to parquet pqp_file: Optional[str] = None # Path to PQP file for precursor/transition mapping diff --git a/pyprophet/cli/export.py b/pyprophet/cli/export.py index e094e924..50371fc3 100644 --- a/pyprophet/cli/export.py +++ b/pyprophet/cli/export.py @@ -553,6 +553,13 @@ def export_library( type=int, help="Compression level to use for parquet file.", ) +@click.option( + "--include_transition_data/--no-include_transition_data", + "include_transition_data", + default=True, + show_default=True, + help="Include transition data in the exported parquet file(s). When disabled, only precursor-level data is exported.", +) @measure_memory_usage_and_time def export_parquet( infile, @@ -565,6 +572,7 @@ def export_parquet( split_runs, compression, compression_level, + include_transition_data, ): """ Export OSW or sqMass to parquet format @@ -600,6 +608,7 @@ def export_parquet( split_runs=split_runs, compression_method=compression, compression_level=compression_level, + include_transition_data=include_transition_data, ) writer = WriterDispatcher.get_writer(config) diff --git a/pyprophet/io/export/osw.py b/pyprophet/io/export/osw.py index 4e3ef6ab..5e015039 100644 --- a/pyprophet/io/export/osw.py +++ b/pyprophet/io/export/osw.py @@ -950,21 +950,21 @@ def _prepare_column_info(self, conn) -> dict: for col in get_table_columns_with_types( self.config.infile, "FEATURE_MS1" ) - if col[0] != "FEATURE_ID" + if col[0] != "FEATURE_ID" and col[1] # Ensure column has a type ], "feature_ms2_cols": [ col for col in get_table_columns_with_types( self.config.infile, "FEATURE_MS2" ) - if col[0] != "FEATURE_ID" + if col[0] != "FEATURE_ID" and col[1] # Ensure column has a type ], "feature_transition_cols": [ col for col in get_table_columns_with_types( self.config.infile, "FEATURE_TRANSITION" ) - if col[0] not in ["FEATURE_ID", "TRANSITION_ID"] + if col[0] not in ["FEATURE_ID", "TRANSITION_ID"] and col[1] # Ensure column has a type ], "score_ms1_exists": {"SCORE_MS1"}.issubset(table_names), "score_ms2_exists": {"SCORE_MS2"}.issubset(table_names), @@ -1019,21 +1019,24 @@ def _export_split_by_run(self, conn, column_info: dict) -> None: logger.info(f"Exporting precursor data to {precursor_path}") self._execute_copy_query(conn, precursor_query, precursor_path) - # Export transition data - transition_path = os.path.join(run_dir, "transition_features.parquet") - transition_query_run = ( - self._build_transition_query(column_info) - + f"\nWHERE FEATURE.RUN_ID = {run_id}" - ) - transition_query_null = ( - self._build_transition_query(column_info) - + "\nWHERE FEATURE.RUN_ID IS NULL" - ) - combined_transition_query = ( - f"{transition_query_run}\nUNION ALL\n{transition_query_null}" - ) - logger.info(f"Exporting transition data to {transition_path}") - self._execute_copy_query(conn, combined_transition_query, transition_path) + # Export transition data if requested + if self.config.include_transition_data: + transition_path = os.path.join(run_dir, "transition_features.parquet") + transition_query_run = ( + self._build_transition_query(column_info) + + f"\nWHERE FEATURE.RUN_ID = {run_id}" + ) + transition_query_null = ( + self._build_transition_query(column_info) + + "\nWHERE FEATURE.RUN_ID IS NULL" + ) + combined_transition_query = ( + f"{transition_query_run}\nUNION ALL\n{transition_query_null}" + ) + logger.info(f"Exporting transition data to {transition_path}") + self._execute_copy_query(conn, combined_transition_query, transition_path) + else: + logger.info("Skipping transition data export (include_transition_data=False)") # Export alignment data if exists if column_info["feature_ms2_alignment_exists"]: @@ -1052,13 +1055,16 @@ def _export_combined(self, conn, column_info: dict) -> None: precursor_query = self._build_precursor_query(conn, column_info) self._execute_copy_query(conn, precursor_query, precursor_path) - # Export transition data - transition_path = os.path.join( - self.config.outfile, "transition_features.parquet" - ) - logger.info(f"Exporting transition data to {transition_path}") - transition_query = self._build_transition_query(column_info) - self._execute_copy_query(conn, transition_query, transition_path) + # Export transition data if requested + if self.config.include_transition_data: + transition_path = os.path.join( + self.config.outfile, "transition_features.parquet" + ) + logger.info(f"Exporting transition data to {transition_path}") + transition_query = self._build_transition_query(column_info) + self._execute_copy_query(conn, transition_query, transition_path) + else: + logger.info("Skipping transition data export (include_transition_data=False)") # Export alignment data if exists if column_info["feature_ms2_alignment_exists"]: @@ -1076,10 +1082,13 @@ def _export_single_file(self, conn, column_info: dict) -> None: precursor_query = self._build_combined_precursor_query(conn, column_info) conn.execute(f"INSERT INTO temp_table {precursor_query}") - # Insert transition data - logger.debug("Inserting transition data into temp table") - transition_query = self._build_combined_transition_query(column_info) - conn.execute(f"INSERT INTO temp_table {transition_query}") + # Insert transition data if requested + if self.config.include_transition_data: + logger.debug("Inserting transition data into temp table") + transition_query = self._build_combined_transition_query(column_info) + conn.execute(f"INSERT INTO temp_table {transition_query}") + else: + logger.info("Skipping transition data export (include_transition_data=False)") # Export to parquet logger.info(f"Exporting combined data to {self.config.outfile}") @@ -1234,6 +1243,27 @@ def _build_precursor_query(self, conn, column_info: dict) -> str: {score_table_joins} """ + def _build_transition_score_columns_and_join(self, column_info: dict) -> Tuple[str, str]: + """Build score columns and join clause for transition scores""" + score_transition_cols = "" + score_transition_join = "" + if column_info.get("score_transition_exists", False): + logger.debug("SCORE_TRANSITION table exists, adding score columns to transition query") + score_cols = [ + "SCORE_TRANSITION.SCORE AS SCORE_TRANSITION_SCORE", + "SCORE_TRANSITION.RANK AS SCORE_TRANSITION_RANK", + "SCORE_TRANSITION.PVALUE AS SCORE_TRANSITION_P_VALUE", + "SCORE_TRANSITION.QVALUE AS SCORE_TRANSITION_Q_VALUE", + "SCORE_TRANSITION.PEP AS SCORE_TRANSITION_PEP", + ] + score_transition_cols = ", " + ", ".join(score_cols) + score_transition_join = ( + f"LEFT JOIN sqlite_scan('{self.config.infile}', 'SCORE_TRANSITION') AS SCORE_TRANSITION " + f"ON FEATURE_TRANSITION.TRANSITION_ID = SCORE_TRANSITION.TRANSITION_ID " + f"AND FEATURE_TRANSITION.FEATURE_ID = SCORE_TRANSITION.FEATURE_ID" + ) + return score_transition_cols, score_transition_join + def _build_transition_query(self, column_info: dict) -> str: """Build SQL query for transition data""" feature_transition_cols_sql = ", ".join( @@ -1247,6 +1277,9 @@ def _build_transition_query(self, column_info: dict) -> str: else "TRANSITION.TYPE || CAST(TRANSITION.ORDINAL AS VARCHAR) || '^' || CAST(TRANSITION.CHARGE AS VARCHAR)" ) + # Add transition score columns if they exist + score_transition_cols, score_transition_join = self._build_transition_score_columns_and_join(column_info) + return f""" SELECT FEATURE.RUN_ID AS RUN_ID, @@ -1264,6 +1297,7 @@ def _build_transition_query(self, column_info: dict) -> str: TRANSITION.DECOY AS TRANSITION_DECOY, FEATURE.ID AS FEATURE_ID, {feature_transition_cols_sql} + {score_transition_cols} FROM sqlite_scan('{self.config.infile}', 'TRANSITION') AS TRANSITION FULL JOIN sqlite_scan('{self.config.infile}', 'TRANSITION_PRECURSOR_MAPPING') AS TRANSITION_PRECURSOR_MAPPING ON TRANSITION.ID = TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID @@ -1276,6 +1310,7 @@ def _build_transition_query(self, column_info: dict) -> str: FROM sqlite_scan('{self.config.infile}', 'FEATURE') ) AS FEATURE ON FEATURE_TRANSITION.FEATURE_ID = FEATURE.ID + {score_transition_join} """ def _build_combined_precursor_query(self, conn, column_info: dict) -> str: @@ -1295,6 +1330,16 @@ def _build_combined_precursor_query(self, conn, column_info: dict) -> str: for col in column_info["feature_transition_cols"] ) + # Get score columns for precursor level + score_cols_select, score_table_joins, score_column_views = ( + self._build_score_column_selection_and_joins(column_info) + ) + + # Add NULL columns for transition score columns + as_null_transition_score_cols = "" + if column_info.get("score_transition_exists", False): + as_null_transition_score_cols = ", NULL AS SCORE_TRANSITION_SCORE, NULL AS SCORE_TRANSITION_RANK, NULL AS SCORE_TRANSITION_P_VALUE, NULL AS SCORE_TRANSITION_Q_VALUE, NULL AS SCORE_TRANSITION_PEP" + # First get the peptide table and process it with pyopenms logger.info("Generating peptide unimod to codename mapping") with sqlite3.connect(self.config.infile) as sql_conn: @@ -1362,6 +1407,7 @@ def _build_combined_precursor_query(self, conn, column_info: dict) -> str: -- JOIN ipf_groups g USING (NORMALIZED_SEQUENCE) --) + {score_column_views} SELECT PEPTIDE_PROTEIN_MAPPING.PROTEIN_ID AS PROTEIN_ID, PEPTIDE.ID AS PEPTIDE_ID, @@ -1404,7 +1450,9 @@ def _build_combined_precursor_query(self, conn, column_info: dict) -> str: NULL AS TRANSITION_DETECTING, NULL AS TRANSITION_LIBRARY_INTENSITY, NULL AS TRANSITION_DECOY, - {as_null_feature_transition_cols_sql} + {as_null_feature_transition_cols_sql}, + {score_cols_select} + {as_null_transition_score_cols} FROM sqlite_scan('{self.config.infile}', 'PRECURSOR') AS PRECURSOR INNER JOIN sqlite_scan('{self.config.infile}', 'PRECURSOR_PEPTIDE_MAPPING') AS PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID @@ -1425,6 +1473,7 @@ def _build_combined_precursor_query(self, conn, column_info: dict) -> str: ON FEATURE.ID = FEATURE_MS2.FEATURE_ID INNER JOIN sqlite_scan('{self.config.infile}', 'RUN') AS RUN ON FEATURE.RUN_ID = RUN.ID + {score_table_joins} """ def _build_combined_transition_query(self, column_info: dict) -> str: @@ -1448,6 +1497,25 @@ def _build_combined_transition_query(self, column_info: dict) -> str: else "TRANSITION.TYPE || CAST(TRANSITION.ORDINAL AS VARCHAR) || '^' || CAST(TRANSITION.CHARGE AS VARCHAR)" ) + # Add transition score columns if they exist + score_transition_cols, score_transition_join = self._build_transition_score_columns_and_join(column_info) + + # Also need to add NULL columns for score columns that appear in precursor query + as_null_score_cols = "" + if column_info.get("score_ms1_exists", False): + as_null_score_cols += ", NULL AS SCORE_MS1_SCORE, NULL AS SCORE_MS1_RANK, NULL AS SCORE_MS1_P_VALUE, NULL AS SCORE_MS1_Q_VALUE, NULL AS SCORE_MS1_PEP" + if column_info.get("score_ms2_exists", False): + as_null_score_cols += ", NULL AS SCORE_MS2_SCORE, NULL AS SCORE_MS2_PEAK_GROUP_RANK, NULL AS SCORE_MS2_P_VALUE, NULL AS SCORE_MS2_Q_VALUE, NULL AS SCORE_MS2_PEP" + if column_info.get("score_ipf_exists", False): + as_null_score_cols += ", NULL AS SCORE_IPF_PRECURSOR_PEAKGROUP_PEP, NULL AS SCORE_IPF_PEP, NULL AS SCORE_IPF_QVALUE" + + # Add NULL columns for peptide and protein score contexts + for table in ["peptide", "protein"]: + if column_info.get(f"score_{table}_exists", False): + for context in column_info.get(f"score_{table}_contexts", []): + safe_context = context.upper().replace("-", "_") + as_null_score_cols += f", NULL AS SCORE_{table.upper()}_{safe_context}_SCORE, NULL AS SCORE_{table.upper()}_{safe_context}_P_VALUE, NULL AS SCORE_{table.upper()}_{safe_context}_Q_VALUE, NULL AS SCORE_{table.upper()}_{safe_context}_PEP" + return f""" SELECT NULL AS PROTEIN_ID, @@ -1492,6 +1560,8 @@ def _build_combined_transition_query(self, column_info: dict) -> str: TRANSITION.LIBRARY_INTENSITY AS TRANSITION_LIBRARY_INTENSITY, TRANSITION.DECOY AS TRANSITION_DECOY, {feature_transition_cols_sql} + {as_null_score_cols} + {score_transition_cols} FROM sqlite_scan('{self.config.infile}', 'TRANSITION_PRECURSOR_MAPPING') AS TRANSITION_PRECURSOR_MAPPING INNER JOIN sqlite_scan('{self.config.infile}', 'TRANSITION') AS TRANSITION ON TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID = TRANSITION.ID @@ -1499,6 +1569,7 @@ def _build_combined_transition_query(self, column_info: dict) -> str: ON TRANSITION.ID = TRANSITION_PEPTIDE_MAPPING.TRANSITION_ID FULL JOIN sqlite_scan('{self.config.infile}', 'FEATURE_TRANSITION') AS FEATURE_TRANSITION ON TRANSITION.ID = FEATURE_TRANSITION.TRANSITION_ID + {score_transition_join} """ def _create_temp_table(self, conn, column_info: dict) -> None: @@ -1516,6 +1587,56 @@ def _create_temp_table(self, conn, column_info: dict) -> None: for col in column_info["feature_transition_cols"] ) + # Build score column types + score_cols_types = [] + if column_info.get("score_ms1_exists", False): + score_cols_types.extend([ + "SCORE_MS1_SCORE DOUBLE", + "SCORE_MS1_RANK INTEGER", + "SCORE_MS1_P_VALUE DOUBLE", + "SCORE_MS1_Q_VALUE DOUBLE", + "SCORE_MS1_PEP DOUBLE" + ]) + if column_info.get("score_ms2_exists", False): + score_cols_types.extend([ + "SCORE_MS2_SCORE DOUBLE", + "SCORE_MS2_PEAK_GROUP_RANK INTEGER", + "SCORE_MS2_P_VALUE DOUBLE", + "SCORE_MS2_Q_VALUE DOUBLE", + "SCORE_MS2_PEP DOUBLE" + ]) + if column_info.get("score_ipf_exists", False): + score_cols_types.extend([ + "SCORE_IPF_PRECURSOR_PEAKGROUP_PEP DOUBLE", + "SCORE_IPF_PEP DOUBLE", + "SCORE_IPF_QVALUE DOUBLE" + ]) + + # Add peptide and protein score columns for each context + for table in ["peptide", "protein"]: + if column_info.get(f"score_{table}_exists", False): + for context in column_info.get(f"score_{table}_contexts", []): + safe_context = context.upper().replace("-", "_") + score_cols_types.extend([ + f"SCORE_{table.upper()}_{safe_context}_SCORE DOUBLE", + f"SCORE_{table.upper()}_{safe_context}_P_VALUE DOUBLE", + f"SCORE_{table.upper()}_{safe_context}_Q_VALUE DOUBLE", + f"SCORE_{table.upper()}_{safe_context}_PEP DOUBLE" + ]) + + # Add transition score columns + if column_info.get("score_transition_exists", False): + score_cols_types.extend([ + "SCORE_TRANSITION_SCORE DOUBLE", + "SCORE_TRANSITION_RANK INTEGER", + "SCORE_TRANSITION_P_VALUE DOUBLE", + "SCORE_TRANSITION_Q_VALUE DOUBLE", + "SCORE_TRANSITION_PEP DOUBLE" + ]) + + # Prepend comma and space to score columns if there are any + score_cols_types_sql = (", " + ", ".join(score_cols_types)) if score_cols_types else "" + create_temp_table_query = f""" CREATE TABLE temp_table ( PROTEIN_ID BIGINT, @@ -1560,6 +1681,7 @@ def _create_temp_table(self, conn, column_info: dict) -> None: TRANSITION_LIBRARY_INTENSITY DOUBLE, TRANSITION_DECOY BOOLEAN, {feature_transition_cols_types} + {score_cols_types_sql} ); """ @@ -1661,6 +1783,7 @@ def _get_peptide_protein_score_table(self, level, contexts: list) -> str: if global_exists: glob_query = f""" SELECT {id_col}, + RUN_ID, SCORE as {score_table}_GLOBAL_SCORE, PVALUE as {score_table}_GLOBAL_PVALUE, QVALUE as {score_table}_GLOBAL_QVALUE, @@ -1679,7 +1802,7 @@ def _get_peptide_protein_score_table(self, level, contexts: list) -> str: g.{score_table}_GLOBAL_QVALUE, g.{score_table}_GLOBAL_PEP FROM ({non_global_query}) ng - LEFT JOIN ({glob_query}) g ON ng.{id_col} = g.{id_col} + LEFT JOIN ({glob_query}) g ON ng.{id_col} = g.{id_col} AND ng.RUN_ID = g.RUN_ID """ elif pivot_cols_str and not global_exists: # Only non-global contexts exist @@ -1724,6 +1847,15 @@ def _build_score_column_selection_and_joins( f"INNER JOIN sqlite_scan('{self.config.infile}', 'SCORE_MS2') AS SCORE_MS2 ON FEATURE.ID = SCORE_MS2.FEATURE_ID" ) + if column_info["score_ipf_exists"]: + logger.debug("SCORE_IPF table exists, adding score columns to selection") + score_columns_to_select.append( + "SCORE_IPF.PRECURSOR_PEAKGROUP_PEP AS SCORE_IPF_PRECURSOR_PEAKGROUP_PEP, SCORE_IPF.PEP AS SCORE_IPF_PEP, SCORE_IPF.QVALUE AS SCORE_IPF_QVALUE" + ) + score_tables_to_join.append( + f"LEFT JOIN sqlite_scan('{self.config.infile}', 'SCORE_IPF') AS SCORE_IPF ON FEATURE.ID = SCORE_IPF.FEATURE_ID" + ) + # Create views for peptide and protein score tables if they exist if column_info["score_peptide_exists"]: logger.debug("SCORE_PEPTIDE table exists, adding score table view to query") @@ -1734,7 +1866,7 @@ def _build_score_column_selection_and_joins( ) # Add JOIN for peptide score view score_tables_to_join.append( - "INNER JOIN score_peptide_view ON PEPTIDE.ID = score_peptide_view.PEPTIDE_ID AND FEATURE.RUN_ID = score_peptide_view.RUN_ID" + "LEFT JOIN score_peptide_view ON PEPTIDE.ID = score_peptide_view.PEPTIDE_ID AND FEATURE.RUN_ID = score_peptide_view.RUN_ID" ) if column_info["score_protein_exists"]: logger.debug("SCORE_PROTEIN table exists, adding score table view to query") @@ -1745,7 +1877,7 @@ def _build_score_column_selection_and_joins( ) # Add JOIN for protein score view score_tables_to_join.append( - "INNER JOIN score_protein_view ON PEPTIDE_PROTEIN_MAPPING.PROTEIN_ID = score_protein_view.PROTEIN_ID AND FEATURE.RUN_ID = score_protein_view.RUN_ID" + "LEFT JOIN score_protein_view ON PEPTIDE_PROTEIN_MAPPING.PROTEIN_ID = score_protein_view.PROTEIN_ID AND FEATURE.RUN_ID = score_protein_view.RUN_ID" ) # Add score columns for peptide and protein contexts diff --git a/pyprophet/scoring/_optimized.c b/pyprophet/scoring/_optimized.c index 91448a4e..d25f3d5e 100644 --- a/pyprophet/scoring/_optimized.c +++ b/pyprophet/scoring/_optimized.c @@ -1,4 +1,4 @@ -/* Generated by Cython 3.1.2 */ +/* Generated by Cython 3.1.6 */ /* BEGIN: Cython Metadata { @@ -17,8 +17,16 @@ END: Cython Metadata */ #define PY_SSIZE_T_CLEAN #endif /* PY_SSIZE_T_CLEAN */ /* InitLimitedAPI */ -#if defined(Py_LIMITED_API) && !defined(CYTHON_LIMITED_API) +#if defined(Py_LIMITED_API) + #if !defined(CYTHON_LIMITED_API) #define CYTHON_LIMITED_API 1 + #endif +#elif defined(CYTHON_LIMITED_API) + #ifdef _MSC_VER + #pragma message ("Limited API usage is enabled with 'CYTHON_LIMITED_API' but 'Py_LIMITED_API' does not define a Python target version. Consider setting 'Py_LIMITED_API' instead.") + #else + #warning Limited API usage is enabled with 'CYTHON_LIMITED_API' but 'Py_LIMITED_API' does not define a Python target version. Consider setting 'Py_LIMITED_API' instead. + #endif #endif #include "Python.h" @@ -27,8 +35,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x03080000 #error Cython requires Python 3.8+. #else -#define __PYX_ABI_VERSION "3_1_2" -#define CYTHON_HEX_VERSION 0x030102F0 +#define __PYX_ABI_VERSION "3_1_6" +#define CYTHON_HEX_VERSION 0x030106F0 #define CYTHON_FUTURE_DIVISION 1 /* CModulePreamble */ #include @@ -391,6 +399,9 @@ END: Cython Metadata */ enum { __pyx_check_sizeof_voidp = 1 / (int)(SIZEOF_VOID_P == sizeof(void*)) }; #endif #endif +#ifndef CYTHON_LOCK_AND_GIL_DEADLOCK_AVOIDANCE_TIME + #define CYTHON_LOCK_AND_GIL_DEADLOCK_AVOIDANCE_TIME 100 +#endif #ifndef __has_attribute #define __has_attribute(x) 0 #endif @@ -1295,6 +1306,7 @@ static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*); typedef sdigit __Pyx_compact_pylong; typedef digit __Pyx_compact_upylong; #endif + static CYTHON_INLINE int __Pyx_PyLong_CompactAsLong(PyObject *x, long *return_value); #if PY_VERSION_HEX >= 0x030C00A5 #define __Pyx_PyLong_Digits(x) (((PyLongObject*)x)->long_value.ob_digit) #else @@ -1371,7 +1383,7 @@ static const char *__pyx_filename; static const char* const __pyx_f[] = { "pyprophet/scoring/_optimized.pyx", "", - "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd", + "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd", "cpython/type.pxd", }; /* #### Code section: utility_code_proto_before_types ### */ @@ -1594,7 +1606,7 @@ typedef struct { /* #### Code section: numeric_typedefs ### */ -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":787 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":743 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -1603,7 +1615,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":788 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":744 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -1612,26 +1624,26 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":789 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":745 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< * ctypedef npy_int64 int64_t - * #ctypedef npy_int96 int96_t + * */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":790 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":746 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< - * #ctypedef npy_int96 int96_t - * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":794 - * #ctypedef npy_int128 int128_t +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":748 + * ctypedef npy_int64 int64_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< * ctypedef npy_uint16 uint16_t @@ -1639,7 +1651,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":795 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":749 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1648,26 +1660,26 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":796 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":750 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< * ctypedef npy_uint64 uint64_t - * #ctypedef npy_uint96 uint96_t + * */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":797 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":751 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< - * #ctypedef npy_uint96 uint96_t - * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":801 - * #ctypedef npy_uint128 uint128_t +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":753 + * ctypedef npy_uint64 uint64_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< * ctypedef npy_float64 float64_t @@ -1675,7 +1687,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":802 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":754 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1684,7 +1696,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":809 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":761 * ctypedef double complex complex128_t * * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1693,7 +1705,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":810 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":762 * * ctypedef npy_longlong longlong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1702,7 +1714,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":812 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":764 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1711,7 +1723,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":813 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":765 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1720,7 +1732,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":815 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":767 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1729,7 +1741,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":816 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":768 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1738,7 +1750,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":817 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":769 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -2635,22 +2647,22 @@ static int __Pyx__DelItemOnTypeDict(PyTypeObject *tp, PyObject *k); static int __Pyx_setup_reduce(PyObject* type_obj); /* TypeImport.proto */ -#ifndef __PYX_HAVE_RT_ImportType_proto_3_1_2 -#define __PYX_HAVE_RT_ImportType_proto_3_1_2 +#ifndef __PYX_HAVE_RT_ImportType_proto_3_1_6 +#define __PYX_HAVE_RT_ImportType_proto_3_1_6 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L #include #endif #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L -#define __PYX_GET_STRUCT_ALIGNMENT_3_1_2(s) alignof(s) +#define __PYX_GET_STRUCT_ALIGNMENT_3_1_6(s) alignof(s) #else -#define __PYX_GET_STRUCT_ALIGNMENT_3_1_2(s) sizeof(void*) +#define __PYX_GET_STRUCT_ALIGNMENT_3_1_6(s) sizeof(void*) #endif -enum __Pyx_ImportType_CheckSize_3_1_2 { - __Pyx_ImportType_CheckSize_Error_3_1_2 = 0, - __Pyx_ImportType_CheckSize_Warn_3_1_2 = 1, - __Pyx_ImportType_CheckSize_Ignore_3_1_2 = 2 +enum __Pyx_ImportType_CheckSize_3_1_6 { + __Pyx_ImportType_CheckSize_Error_3_1_6 = 0, + __Pyx_ImportType_CheckSize_Warn_3_1_6 = 1, + __Pyx_ImportType_CheckSize_Ignore_3_1_6 = 2 }; -static PyTypeObject *__Pyx_ImportType_3_1_2(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_1_2 check_size); +static PyTypeObject *__Pyx_ImportType_3_1_6(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_1_6 check_size); #endif /* FetchSharedCythonModule.proto */ @@ -3418,7 +3430,7 @@ static const char __pyx_k_F_A_R_86_1_a_Rq_c_2T_c_AV1_Q_a[] = "\200\001\360\006\0 static const char __pyx_k_strided_and_direct_or_indirect[] = ""; static const char __pyx_k_8_q_Rq_F_RvRuF_A_q_r_uBa_V1A_e2[] = "\200\001\360\010\000\005\035\320\0348\270\007\270q\300\005\300R\300q\330\004\024\220F\230&\240\001\240\021\330\004\r\210R\210v\220R\220u\230F\240\"\240A\330\004 \240\001\330\004\027\220q\360\006\000\005\013\210%\210r\220\021\330\010\017\210u\220B\220a\330\010\r\210V\2201\220A\330\010\016\210e\2202\220R\220t\2306\240\021\240&\250\003\2501\330\014\024\220A\330\010\024\220A\220X\230V\2406\250\027\260\001\330\010\017\210q\330\017\024\220A\220Q\330\004\013\2101"; 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static const char __pyx_k_N_RvRq_fBa_1_Q_Ba_nAQ_Q_1E_Ba_B[] = "\200\001\360\014\000\005\025\220N\240&\250\001\250\021\360\006\000\005!\240\001\330\004\r\210R\210v\220R\220q\230\001\230\025\230f\240B\240a\330\004#\2401\360\010\000\005\026\220Q\360\006\000\005\t\210\001\330\004\n\210\"\210B\210a\330\010\016\210n\230A\230Q\330\010\r\210Q\340\004\013\2101\210E\220\023\220B\220a\360\010\000\005\t\210\001\330\004\n\210\"\210B\210a\330\010\016\210n\230A\230Q\330\010\014\210A\330\010\r\210Q\340\010\016\210b\220\002\220!\330\014\017\210r\220\023\220A\330\020\026\220n\240A\240Q\330\014\021\220\021\340\010\024\320\024%\240Q\240a\240u\250B\250a\340\010\017\210q\220\001\220\021\220%\220z\240\022\2401\330\010\r\210Q\360\006\000\005\t\210\001\330\004\n\210\"\210B\210a\210q\220\001\330\010\023\2207\230!\2301\330\010\r\210Q\360\006\000\005\t\210\001\330\004\n\210\"\210B\210a\210q\220\001\330\010\017\210q\220\005\220W\230A\230S\240\002\240!\330\010\r\210Q\340\004\013\2101"; static const char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced"; static const char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; @@ -3958,7 +3970,7 @@ static int __pyx_array___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, P default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__cinit__", 0) < 0) __PYX_ERR(1, 129, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__cinit__", 0) < (0)) __PYX_ERR(1, 129, __pyx_L3_error) if (!values[3]) values[3] = __Pyx_NewRef(((PyObject *)__pyx_mstate_global->__pyx_n_u_c)); for (Py_ssize_t i = __pyx_nargs; i < 3; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 3, 5, i); __PYX_ERR(1, 129, __pyx_L3_error) } @@ -5572,7 +5584,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < 0) __PYX_ERR(1, 3, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < (0)) __PYX_ERR(1, 3, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 1; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, i); __PYX_ERR(1, 3, __pyx_L3_error) } } @@ -5917,7 +5929,7 @@ static struct __pyx_array_obj *__pyx_array_new(PyObject *__pyx_v_shape, Py_ssize __pyx_t_4 = 0; __pyx_t_4 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_4)) __PYX_ERR(1, 273, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_4, __pyx_mstate_global->__pyx_n_u_allocate_buffer, Py_False) < 0) __PYX_ERR(1, 273, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_4, __pyx_mstate_global->__pyx_n_u_allocate_buffer, Py_False) < (0)) __PYX_ERR(1, 273, __pyx_L1_error) __pyx_t_3 = ((PyObject *)__pyx_tp_new_array(((PyTypeObject *)__pyx_mstate_global->__pyx_array_type), __pyx_t_1, __pyx_t_4)); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 273, __pyx_L1_error) __Pyx_GOTREF((PyObject *)__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -6012,7 +6024,7 @@ static int __pyx_MemviewEnum___init__(PyObject *__pyx_v_self, PyObject *__pyx_ar default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__init__", 0) < 0) __PYX_ERR(1, 302, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__init__", 0) < (0)) __PYX_ERR(1, 302, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 1; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, i); __PYX_ERR(1, 302, __pyx_L3_error) } } @@ -6449,7 +6461,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < 0) __PYX_ERR(1, 16, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < (0)) __PYX_ERR(1, 16, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 1; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, i); __PYX_ERR(1, 16, __pyx_L3_error) } } @@ -6574,7 +6586,7 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__cinit__", 0) < 0) __PYX_ERR(1, 347, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__cinit__", 0) < (0)) __PYX_ERR(1, 347, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 2; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, i); __PYX_ERR(1, 347, __pyx_L3_error) } } @@ -10891,7 +10903,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < 0) __PYX_ERR(1, 3, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < (0)) __PYX_ERR(1, 3, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 1; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, i); __PYX_ERR(1, 3, __pyx_L3_error) } } @@ -13778,7 +13790,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < 0) __PYX_ERR(1, 3, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__setstate_cython__", 0) < (0)) __PYX_ERR(1, 3, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 1; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__setstate_cython__", 1, 1, 1, i); __PYX_ERR(1, 3, __pyx_L3_error) } } @@ -16937,7 +16949,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__pyx_unpickle_Enum", 0) < 0) __PYX_ERR(1, 1, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "__pyx_unpickle_Enum", 0) < (0)) __PYX_ERR(1, 1, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 3; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("__pyx_unpickle_Enum", 1, 3, 3, i); __PYX_ERR(1, 1, __pyx_L3_error) } } @@ -17259,7 +17271,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":242 * cdef int type_num * * @property # <<<<<<<<<<<<<< @@ -17270,7 +17282,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":288 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":244 * @property * cdef inline npy_intp itemsize(self) noexcept nogil: * return PyDataType_ELSIZE(self) # <<<<<<<<<<<<<< @@ -17280,7 +17292,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D __pyx_r = PyDataType_ELSIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":286 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":242 * cdef int type_num * * @property # <<<<<<<<<<<<<< @@ -17293,7 +17305,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":246 * return PyDataType_ELSIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17304,7 +17316,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":292 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":248 * @property * cdef inline npy_intp alignment(self) noexcept nogil: * return PyDataType_ALIGNMENT(self) # <<<<<<<<<<<<<< @@ -17314,7 +17326,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":290 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":246 * return PyDataType_ELSIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17327,7 +17339,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":252 * # Use fields/names with care as they may be NULL. You must check * # for this using PyDataType_HASFIELDS. * @property # <<<<<<<<<<<<<< @@ -17341,7 +17353,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("fields", 0); - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":298 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":254 * @property * cdef inline object fields(self): * return PyDataType_FIELDS(self) # <<<<<<<<<<<<<< @@ -17354,7 +17366,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc __pyx_r = ((PyObject *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":296 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":252 * # Use fields/names with care as they may be NULL. You must check * # for this using PyDataType_HASFIELDS. * @property # <<<<<<<<<<<<<< @@ -17369,7 +17381,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":256 * return PyDataType_FIELDS(self) * * @property # <<<<<<<<<<<<<< @@ -17383,7 +17395,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("names", 0); - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":302 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":258 * @property * cdef inline tuple names(self): * return PyDataType_NAMES(self) # <<<<<<<<<<<<<< @@ -17396,7 +17408,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr __pyx_r = ((PyObject*)__pyx_t_1); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":300 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":256 * return PyDataType_FIELDS(self) * * @property # <<<<<<<<<<<<<< @@ -17411,7 +17423,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":263 * # valid (the pointer can be NULL). Most users should access * # this field via the inline helper method PyDataType_SHAPE. * @property # <<<<<<<<<<<<<< @@ -17422,7 +17434,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self) { PyArray_ArrayDescr *__pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":309 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":265 * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: * return PyDataType_SUBARRAY(self) # <<<<<<<<<<<<<< @@ -17432,7 +17444,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra __pyx_r = PyDataType_SUBARRAY(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":307 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":263 * # valid (the pointer can be NULL). Most users should access * # this field via the inline helper method PyDataType_SHAPE. * @property # <<<<<<<<<<<<<< @@ -17445,7 +17457,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":267 * return PyDataType_SUBARRAY(self) * * @property # <<<<<<<<<<<<<< @@ -17456,7 +17468,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self) { npy_uint64 __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":314 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":270 * cdef inline npy_uint64 flags(self) noexcept nogil: * """The data types flags.""" * return PyDataType_FLAGS(self) # <<<<<<<<<<<<<< @@ -17466,7 +17478,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr __pyx_r = PyDataType_FLAGS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":311 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":267 * return PyDataType_SUBARRAY(self) * * @property # <<<<<<<<<<<<<< @@ -17479,7 +17491,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":279 * ctypedef class numpy.broadcast [object PyArrayMultiIterObject, check_size ignore]: * * @property # <<<<<<<<<<<<<< @@ -17490,7 +17502,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":326 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":282 * cdef inline int numiter(self) noexcept nogil: * """The number of arrays that need to be broadcast to the same shape.""" * return PyArray_MultiIter_NUMITER(self) # <<<<<<<<<<<<<< @@ -17500,7 +17512,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":323 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":279 * ctypedef class numpy.broadcast [object PyArrayMultiIterObject, check_size ignore]: * * @property # <<<<<<<<<<<<<< @@ -17513,7 +17525,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":284 * return PyArray_MultiIter_NUMITER(self) * * @property # <<<<<<<<<<<<<< @@ -17524,7 +17536,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":331 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":287 * cdef inline npy_intp size(self) noexcept nogil: * """The total broadcasted size.""" * return PyArray_MultiIter_SIZE(self) # <<<<<<<<<<<<<< @@ -17534,7 +17546,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":328 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":284 * return PyArray_MultiIter_NUMITER(self) * * @property # <<<<<<<<<<<<<< @@ -17547,7 +17559,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":289 * return PyArray_MultiIter_SIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17558,7 +17570,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":336 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":292 * cdef inline npy_intp index(self) noexcept nogil: * """The current (1-d) index into the broadcasted result.""" * return PyArray_MultiIter_INDEX(self) # <<<<<<<<<<<<<< @@ -17568,7 +17580,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":333 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":289 * return PyArray_MultiIter_SIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17581,7 +17593,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":294 * return PyArray_MultiIter_INDEX(self) * * @property # <<<<<<<<<<<<<< @@ -17592,7 +17604,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":341 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":297 * cdef inline int nd(self) noexcept nogil: * """The number of dimensions in the broadcasted result.""" * return PyArray_MultiIter_NDIM(self) # <<<<<<<<<<<<<< @@ -17602,7 +17614,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":338 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":294 * return PyArray_MultiIter_INDEX(self) * * @property # <<<<<<<<<<<<<< @@ -17615,7 +17627,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":299 * return PyArray_MultiIter_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17626,7 +17638,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":346 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":302 * cdef inline npy_intp* dimensions(self) noexcept nogil: * """The shape of the broadcasted result.""" * return PyArray_MultiIter_DIMS(self) # <<<<<<<<<<<<<< @@ -17636,7 +17648,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":343 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":299 * return PyArray_MultiIter_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17649,7 +17661,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":304 * return PyArray_MultiIter_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17660,7 +17672,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self) { void **__pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":352 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":308 * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. * On return, the iterators are adjusted for broadcasting.""" * return PyArray_MultiIter_ITERS(self) # <<<<<<<<<<<<<< @@ -17670,7 +17682,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":348 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":304 * return PyArray_MultiIter_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17683,7 +17695,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":322 * # Instead, we use properties that map to the corresponding C-API functions. * * @property # <<<<<<<<<<<<<< @@ -17694,7 +17706,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self) { PyObject *__pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":370 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":326 * """Returns a borrowed reference to the object owning the data/memory. * """ * return PyArray_BASE(self) # <<<<<<<<<<<<<< @@ -17704,7 +17716,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject __pyx_r = PyArray_BASE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":366 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":322 * # Instead, we use properties that map to the corresponding C-API functions. * * @property # <<<<<<<<<<<<<< @@ -17717,7 +17729,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":328 * return PyArray_BASE(self) * * @property # <<<<<<<<<<<<<< @@ -17731,7 +17743,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray PyArray_Descr *__pyx_t_1; __Pyx_RefNannySetupContext("descr", 0); - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":376 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":332 * """Returns an owned reference to the dtype of the array. * """ * return PyArray_DESCR(self) # <<<<<<<<<<<<<< @@ -17744,7 +17756,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray __pyx_r = ((PyArray_Descr *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":372 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":328 * return PyArray_BASE(self) * * @property # <<<<<<<<<<<<<< @@ -17759,7 +17771,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":334 * return PyArray_DESCR(self) * * @property # <<<<<<<<<<<<<< @@ -17770,7 +17782,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":382 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":338 * """Returns the number of dimensions in the array. * """ * return PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -17780,7 +17792,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx __pyx_r = PyArray_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":378 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":334 * return PyArray_DESCR(self) * * @property # <<<<<<<<<<<<<< @@ -17793,7 +17805,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":340 * return PyArray_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17804,7 +17816,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":390 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":346 * Can return NULL for 0-dimensional arrays. * """ * return PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -17814,7 +17826,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec __pyx_r = PyArray_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":384 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":340 * return PyArray_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17827,7 +17839,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":348 * return PyArray_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17838,7 +17850,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":397 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":353 * The number of elements matches the number of dimensions of the array (ndim). * """ * return PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -17848,7 +17860,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO __pyx_r = PyArray_STRIDES(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":392 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":348 * return PyArray_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17861,7 +17873,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":399 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":355 * return PyArray_STRIDES(self) * * @property # <<<<<<<<<<<<<< @@ -17872,7 +17884,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject *__pyx_v_self) { npy_intp __pyx_r; 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goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":840 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":792 * * cdef inline tuple PyDataType_SHAPE(dtype d): * if PyDataType_HASSUBARRAY(d): # <<<<<<<<<<<<<< @@ -18226,7 +18238,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ */ } - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":843 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":795 * return d.subarray.shape * else: * return () # <<<<<<<<<<<<<< @@ -18240,7 +18252,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ goto __pyx_L0; } - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":839 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":791 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline tuple PyDataType_SHAPE(dtype d): # <<<<<<<<<<<<<< @@ -18255,7 +18267,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyDataType_SHAPE(PyArray_Descr *__ return __pyx_r; 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} -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1047 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1006 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -18410,7 +18422,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1048 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1007 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -18426,16 +18438,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1049 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1008 * cdef inline int import_array() except -1: * try: * __pyx_import_array() # <<<<<<<<<<<<<< * except Exception: * raise ImportError("numpy._core.multiarray failed to import") */ - __pyx_t_4 = _import_array(); 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if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1055, __pyx_L3_error) + __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1014, __pyx_L3_error) - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1054 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1013 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -18596,7 +18608,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1056 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1015 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -18606,12 +18618,12 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(((PyTypeObject*)PyExc_Exception)))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_umath", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1056, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1015, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_5); __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1057 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1016 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< @@ -18627,16 +18639,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+__pyx_t_11, (2-__pyx_t_11) | (__pyx_t_11*__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET)); __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1057, __pyx_L5_except_error) + if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1016, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); } __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 1057, __pyx_L5_except_error) + __PYX_ERR(2, 1016, __pyx_L5_except_error) } goto __pyx_L5_except_error; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1054 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1013 * * cdef inline int import_umath() except -1: * try: # <<<<<<<<<<<<<< @@ -18652,7 +18664,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { __pyx_L8_try_end:; } - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1053 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1012 * raise ImportError("numpy._core.multiarray failed to import") * * cdef inline int import_umath() except -1: # <<<<<<<<<<<<<< @@ -18677,7 +18689,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_umath(void) { return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1059 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1018 * raise ImportError("numpy._core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -18704,7 +18716,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_ufunc", 0); - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1060 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1019 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -18720,16 +18732,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1061 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1020 * cdef inline int import_ufunc() except -1: * try: * _import_umath() # <<<<<<<<<<<<<< * except Exception: * raise ImportError("numpy._core.umath failed to import") */ - __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1061, __pyx_L3_error) + __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1020, __pyx_L3_error) - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1060 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1019 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -18743,7 +18755,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1062 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1021 * try: * _import_umath() * except Exception: # <<<<<<<<<<<<<< @@ -18753,12 +18765,12 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_t_4 = __Pyx_PyErr_ExceptionMatches(((PyObject *)(((PyTypeObject*)PyExc_Exception)))); if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_ufunc", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1062, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1021, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_5); __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1063 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1022 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< @@ -18774,16 +18786,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_t_8 = __Pyx_PyObject_FastCall(__pyx_t_10, __pyx_callargs+__pyx_t_11, (2-__pyx_t_11) | (__pyx_t_11*__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET)); __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1063, __pyx_L5_except_error) + if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1022, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); } __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 1063, __pyx_L5_except_error) + __PYX_ERR(2, 1022, __pyx_L5_except_error) } goto __pyx_L5_except_error; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1060 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1019 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -18799,7 +18811,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1059 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1018 * raise ImportError("numpy._core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -18824,7 +18836,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1066 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1025 * * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18835,7 +18847,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1078 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1037 * bool * """ * return PyObject_TypeCheck(obj, &PyTimedeltaArrType_Type) # <<<<<<<<<<<<<< @@ -18845,7 +18857,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyTimedeltaArrType_Type)); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1066 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1025 * * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18858,7 +18870,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1081 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1040 * * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18869,7 +18881,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1093 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1052 * bool * """ * return PyObject_TypeCheck(obj, &PyDatetimeArrType_Type) # <<<<<<<<<<<<<< @@ -18879,7 +18891,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyDatetimeArrType_Type)); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1081 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1040 * * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18892,7 +18904,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1055 * * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18903,7 +18915,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject *__pyx_v_obj) { npy_datetime __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1103 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1062 * also needed. That can be found using `get_datetime64_unit`. * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -18913,7 +18925,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * __pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1096 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1055 * * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18926,7 +18938,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1106 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1065 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18937,7 +18949,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject *__pyx_v_obj) { npy_timedelta __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1110 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1069 * returns the int64 value underlying scalar numpy timedelta64 object * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -18947,7 +18959,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject __pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1106 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1065 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18960,7 +18972,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject return __pyx_r; } -/* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1113 +/* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1072 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18971,7 +18983,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObject *__pyx_v_obj) { NPY_DATETIMEUNIT __pyx_r; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1117 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1076 * returns the unit part of the dtype for a numpy datetime64 object. * """ * return (obj).obmeta.base # <<<<<<<<<<<<<< @@ -18981,7 +18993,7 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec __pyx_r = ((NPY_DATETIMEUNIT)((PyDatetimeScalarObject *)__pyx_v_obj)->obmeta.base); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-0mzx3goa/overlay/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd":1113 + /* "../../../../../tmp/pip-build-env-_tc7qfiq/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1072 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -19062,7 +19074,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "find_nearest_matches", 0) < 0) __PYX_ERR(0, 12, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "find_nearest_matches", 0) < (0)) __PYX_ERR(0, 12, __pyx_L3_error) if (!values[2]) values[2] = __Pyx_NewRef(((PyObject *)((PyObject*)__pyx_mstate_global->__pyx_int_1))); for (Py_ssize_t i = __pyx_nargs; 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__pyx_t_5 = 0; @@ -20579,7 +20591,7 @@ PyObject *__pyx_args, PyObject *__pyx_kwds default: goto __pyx_L5_argtuple_error; } const Py_ssize_t kwd_pos_args = __pyx_nargs; - if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "count_num_positives", 0) < 0) __PYX_ERR(0, 135, __pyx_L3_error) + if (__Pyx_ParseKeywords(__pyx_kwds, __pyx_kwvalues, __pyx_pyargnames, 0, values, kwd_pos_args, __pyx_kwds_len, "count_num_positives", 0) < (0)) __PYX_ERR(0, 135, __pyx_L3_error) for (Py_ssize_t i = __pyx_nargs; i < 1; i++) { if (unlikely(!values[i])) { __Pyx_RaiseArgtupleInvalid("count_num_positives", 1, 1, 1, i); __PYX_ERR(0, 135, __pyx_L3_error) } } @@ -20697,7 +20709,7 @@ static PyObject *__pyx_pf_9pyprophet_7scoring_10_optimized_2count_num_positives( PyObject *__pyx_callargs[2 + ((CYTHON_VECTORCALL) ? 1 : 0)] = {__pyx_t_2, __pyx_t_3}; __pyx_t_5 = __Pyx_MakeVectorcallBuilderKwds(1); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 141, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); 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@@ -28311,11 +28324,13 @@ static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject } changed = 1; } +#endif // !CYTHON_COMPILING_IN_PYPY } memb++; } } #endif // !CYTHON_COMPILING_IN_LIMITED_API +#if !CYTHON_COMPILING_IN_PYPY slot = spec->slots; while (slot && slot->slot && slot->slot != Py_tp_getset) slot++; @@ -28347,6 +28362,7 @@ static int __Pyx_fix_up_extension_type_from_spec(PyType_Spec *spec, PyTypeObject ++getset; } } +#endif // !CYTHON_COMPILING_IN_PYPY if (changed) PyType_Modified(type); #endif // PY_VERSION_HEX > 0x030900B1 @@ -28451,6 +28467,13 @@ static int __Pyx_PyObject_GetMethod(PyObject *obj, PyObject *name, PyObject **me /* PyObjectCallMethod0 */ static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name) { +#if CYTHON_VECTORCALL && (__PYX_LIMITED_VERSION_HEX >= 0x030C0000 || (!CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x03090000)) + PyObject *args[1] = {obj}; + (void) __Pyx_PyObject_GetMethod; + (void) __Pyx_PyObject_CallOneArg; + (void) __Pyx_PyObject_CallNoArg; + return PyObject_VectorcallMethod(method_name, args, 1 | PY_VECTORCALL_ARGUMENTS_OFFSET, NULL); +#else PyObject *method = NULL, *result = NULL; int is_method = __Pyx_PyObject_GetMethod(obj, method_name, &method); if (likely(is_method)) { @@ -28463,6 +28486,7 @@ static PyObject* __Pyx_PyObject_CallMethod0(PyObject* obj, PyObject* method_name Py_DECREF(method); bad: return result; +#endif } /* ValidateBasesTuple */ @@ -28892,15 +28916,15 @@ static int __Pyx_setup_reduce(PyObject* type_obj) { } /* TypeImport */ -#ifndef __PYX_HAVE_RT_ImportType_3_1_2 -#define __PYX_HAVE_RT_ImportType_3_1_2 -static PyTypeObject *__Pyx_ImportType_3_1_2(PyObject *module, const char *module_name, const char *class_name, - size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_1_2 check_size) +#ifndef __PYX_HAVE_RT_ImportType_3_1_6 +#define __PYX_HAVE_RT_ImportType_3_1_6 +static PyTypeObject *__Pyx_ImportType_3_1_6(PyObject *module, const char *module_name, const char *class_name, + size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_1_6 check_size) { PyObject *result = 0; Py_ssize_t basicsize; Py_ssize_t itemsize; -#if CYTHON_COMPILING_IN_LIMITED_API +#if defined(Py_LIMITED_API) || (defined(CYTHON_COMPILING_IN_LIMITED_API) && CYTHON_COMPILING_IN_LIMITED_API) PyObject *py_basicsize; PyObject *py_itemsize; #endif @@ -28913,7 +28937,7 @@ static PyTypeObject *__Pyx_ImportType_3_1_2(PyObject *module, const char *module module_name, class_name); goto bad; } -#if !CYTHON_COMPILING_IN_LIMITED_API +#if !( defined(Py_LIMITED_API) || (defined(CYTHON_COMPILING_IN_LIMITED_API) && CYTHON_COMPILING_IN_LIMITED_API) ) basicsize = ((PyTypeObject *)result)->tp_basicsize; itemsize = ((PyTypeObject *)result)->tp_itemsize; #else @@ -28951,7 +28975,7 @@ static PyTypeObject *__Pyx_ImportType_3_1_2(PyObject *module, const char *module module_name, class_name, size, basicsize+itemsize); goto bad; } - if (check_size == __Pyx_ImportType_CheckSize_Error_3_1_2 && + if (check_size == __Pyx_ImportType_CheckSize_Error_3_1_6 && ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) { PyErr_Format(PyExc_ValueError, "%.200s.%.200s size changed, may indicate binary incompatibility. " @@ -28959,7 +28983,7 @@ static PyTypeObject *__Pyx_ImportType_3_1_2(PyObject *module, const char *module module_name, class_name, size, basicsize, basicsize+itemsize); goto bad; } - else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_1_2 && (size_t)basicsize > size) { + else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_1_6 && (size_t)basicsize > size) { if (PyErr_WarnFormat(NULL, 0, "%.200s.%.200s size changed, may indicate binary incompatibility. 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+ #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030c00A1 + if (likely(result)) + result->_co_firsttraceable = 0; + #endif return result; } #elif PY_VERSION_HEX >= 0x030800B2 && !CYTHON_COMPILING_IN_PYPY @@ -34066,6 +34095,17 @@ static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) { static CYTHON_INLINE PyObject * __Pyx_PyLong_FromSize_t(size_t ival) { return PyLong_FromSize_t(ival); } +#if CYTHON_USE_PYLONG_INTERNALS +static CYTHON_INLINE int __Pyx_PyLong_CompactAsLong(PyObject *x, long *return_value) { + if (unlikely(!__Pyx_PyLong_IsCompact(x))) + return 0; + Py_ssize_t value = __Pyx_PyLong_CompactValue(x); + if ((sizeof(long) < sizeof(Py_ssize_t)) && unlikely(value != (long) value)) + return 0; + *return_value = (long) value; + return 1; +} +#endif /* MultiPhaseInitModuleState */ diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_no_transition_data.out b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_no_transition_data.out new file mode 100644 index 00000000..d26f2c01 --- /dev/null +++ b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_no_transition_data.out @@ -0,0 +1,13 @@ +Exported 3410 rows with 98 columns (no transition data) +Score columns found: ['SCORE_MS2_PEAK_GROUP_RANK', 'SCORE_MS2_PEP', 'SCORE_MS2_P_VALUE', 'SCORE_MS2_Q_VALUE', 'SCORE_MS2_SCORE', 'SCORE_PEPTIDE_GLOBAL_PEP', 'SCORE_PEPTIDE_GLOBAL_P_VALUE', 'SCORE_PEPTIDE_GLOBAL_Q_VALUE', 'SCORE_PEPTIDE_GLOBAL_SCORE', 'SCORE_PROTEIN_GLOBAL_PEP', 'SCORE_PROTEIN_GLOBAL_P_VALUE', 'SCORE_PROTEIN_GLOBAL_Q_VALUE', 'SCORE_PROTEIN_GLOBAL_SCORE'] + ANNOTATION DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FEATURE_TRANSITION_APEX_INTENSITY FEATURE_TRANSITION_AREA_INTENSITY FEATURE_TRANSITION_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_TRANSITION_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_TRANSITION_VAR_LOG_INTENSITY FEATURE_TRANSITION_VAR_LOG_SN_SCORE FEATURE_TRANSITION_VAR_MASSDEV_SCORE FEATURE_TRANSITION_VAR_XCORR_COELUTION FEATURE_TRANSITION_VAR_XCORR_SHAPE FILENAME GENE_DECOY GENE_ID GENE_NAME IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PRODUCT_MZ PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE TRANSITION_CHARGE TRANSITION_DECOY TRANSITION_DETECTING TRANSITION_ID TRANSITION_LIBRARY_INTENSITY TRANSITION_ORDINAL TRANSITION_TRAML_ID TRANSITION_TYPE UNMODIFIED_SEQUENCE +0 None -85.0733 NaN 1923.17 483971408708572459 192394.8906 935372.0000 0.9919 0.1179 3.1724 0.0000 0.9713 61269.0 321681.0 5.0 0.7829 NaN 0.3415 0.9953 0.0000 0.9944 0.9786 0.2234 0.0893 0.1044 0.2119 3.7524 0.7034 2.8770 1.0938 0.0237 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9660 0.9924 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 522 1898.6700 GIGDWSDSK(UniMod:259) 7.0277 False 523 2 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... 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NaN AQUA4SWATH_HMLangeF None 5 2024.9800 -8670811102654834151 2 1.0000 0.4692 0.4692 -0.3786 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK +3 None -130.8641 NaN 1877.37 8207933629855485114 6239.5195 48788.5000 -0.5293 1.7491 3.3984 3.2500 0.5946 3336.0 36324.0 3.0 0.4316 NaN 0.0386 0.1794 0.2909 -0.3937 0.8019 0.6135 0.2909 0.3399 1.0151 0.6018 1.1139 5.2642 1.9825 0.0370 NaN NaN NaN NaN NaN NaN 2.2472 0.8549 0.7655 0.8558 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 522 1857.7000 GIGDWSDSK(UniMod:259) 5.7000 False 523 2 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... 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NaN AQUA4SWATH_HMLangeF None 5 1762.1100 -8670811102654834151 5 1.0000 0.4692 0.4692 -3.2559 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK +5 None -6.0218 NaN 3084.15 1082368609638691369 88839.6328 604041.0000 0.9885 0.1408 0.7967 0.0000 0.9766 37375.0 195175.0 4.0 0.8376 NaN 0.7351 0.9983 0.0000 0.9806 0.9979 0.0536 0.0300 0.0412 0.1268 4.8405 0.6753 2.2770 1.9680 0.0021 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9976 0.9985 8.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385 3066.2200 ESDILAVVK(UniMod:259) 40.6918 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 3110.6101 -8670811102654834151 1 0.0031 0.0029 0.0033 5.5702 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +6 None 228.9700 NaN 3319.15 -1344271892660954750 9115.7090 102078.0000 0.7000 1.0399 16.1263 5.5000 0.4975 4782.0 23890.0 2.0 0.4271 NaN 0.0900 0.9602 1.0000 0.7442 0.9239 0.3826 0.1244 0.1502 0.4641 3.2047 1.1861 14.1720 12.7184 0.0661 NaN NaN NaN NaN NaN NaN 0.7830 0.1486 0.8549 0.8773 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385 3301.7800 ESDILAVVK(UniMod:259) 47.5056 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 3339.3301 -8670811102654834151 5 1.0000 0.4692 0.4692 -1.8443 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +7 None -124.5660 NaN 2965.61 -4515618252120499488 9268.4902 109284.0000 0.6217 1.1110 22.4222 1.5000 0.7138 793.0 6371.0 4.0 0.8481 NaN 0.0240 0.9434 0.0000 0.8820 0.9766 0.2001 0.0990 0.1152 0.3558 1.0582 0.5825 6.0852 4.5232 0.0365 NaN NaN NaN NaN NaN NaN 0.9749 0.0676 0.7227 0.8143 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385 2946.7400 ESDILAVVK(UniMod:259) 37.2545 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 2994.5300 -8670811102654834151 3 1.0000 0.0205 0.0210 1.9398 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +8 None 28.5831 NaN 3118.76 -4044853666210028406 9989.7793 33949.8008 0.2103 0.6817 10.4054 1.0774 0.8894 865.0 2909.0 4.0 0.8179 NaN 0.0110 0.4917 0.0000 0.6890 0.9634 0.2912 0.1309 0.1515 0.4848 1.3179 0.6547 5.8786 5.3254 0.0080 NaN NaN NaN NaN NaN NaN 0.7830 0.3902 0.8943 0.8531 1.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385 3114.0200 ESDILAVVK(UniMod:259) 41.6952 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 3131.0901 -8670811102654834151 2 1.0000 0.0176 0.0180 2.2958 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +9 None -184.3073 NaN 2905.87 7439833196907350500 15059.3516 143080.0000 -0.2753 3.5529 3.1948 3.9578 0.6528 1527.0 8281.0 5.0 0.5666 NaN 0.0312 0.8691 0.0000 -0.3982 0.7375 0.6314 0.2844 0.3777 1.1866 2.5854 0.9876 9.8422 8.8909 0.0538 NaN NaN NaN NaN NaN NaN 3.7575 2.5131 0.6924 0.6775 0.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385 2881.8701 ESDILAVVK(UniMod:259) 35.5222 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 2929.6699 -8670811102654834151 4 1.0000 0.4692 0.4692 -1.8184 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_scored_osw.out b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_scored_osw.out new file mode 100644 index 00000000..100164fd --- /dev/null +++ b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_scored_osw.out @@ -0,0 +1,13 @@ +Exported 97964 rows with 98 columns +Score columns found: ['SCORE_MS2_PEAK_GROUP_RANK', 'SCORE_MS2_PEP', 'SCORE_MS2_P_VALUE', 'SCORE_MS2_Q_VALUE', 'SCORE_MS2_SCORE', 'SCORE_PEPTIDE_GLOBAL_PEP', 'SCORE_PEPTIDE_GLOBAL_P_VALUE', 'SCORE_PEPTIDE_GLOBAL_Q_VALUE', 'SCORE_PEPTIDE_GLOBAL_SCORE', 'SCORE_PROTEIN_GLOBAL_PEP', 'SCORE_PROTEIN_GLOBAL_P_VALUE', 'SCORE_PROTEIN_GLOBAL_Q_VALUE', 'SCORE_PROTEIN_GLOBAL_SCORE'] + ANNOTATION DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FEATURE_TRANSITION_APEX_INTENSITY FEATURE_TRANSITION_AREA_INTENSITY FEATURE_TRANSITION_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_TRANSITION_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_TRANSITION_VAR_LOG_INTENSITY FEATURE_TRANSITION_VAR_LOG_SN_SCORE FEATURE_TRANSITION_VAR_MASSDEV_SCORE FEATURE_TRANSITION_VAR_XCORR_COELUTION FEATURE_TRANSITION_VAR_XCORR_SHAPE FILENAME GENE_DECOY GENE_ID GENE_NAME IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PRODUCT_MZ PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE TRANSITION_CHARGE TRANSITION_DECOY TRANSITION_DETECTING TRANSITION_ID TRANSITION_LIBRARY_INTENSITY TRANSITION_ORDINAL TRANSITION_TRAML_ID TRANSITION_TYPE UNMODIFIED_SEQUENCE +0 None -85.0733 NaN 1923.17 4.8397e+17 192394.8906 935372.0000 0.9919 0.1179 3.1724 0.0000 0.9713 61269.0 321681.0 5.0 0.7829 NaN 0.3415 0.9953 0.0000 0.9944 0.9786 0.2234 0.0893 0.1044 0.2119 3.7524 0.7034 2.8770 1.0938 0.0237 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9660 0.9924 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 522.0 1898.6700 GIGDWSDSK(UniMod:259) 7.0277 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1946.4600 -8.6708e+18 1.0 0.0031 0.0029 0.0033 4.6997 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK +1 None -55.2126 NaN 1953.03 6.8549e+18 5696.7271 45882.6016 0.2886 1.6923 20.0342 5.1458 0.5950 7999.0 45147.0 3.0 0.5879 NaN 0.0479 0.6040 0.6485 0.9860 0.9809 0.2040 0.0854 0.1024 0.2154 1.8184 0.8426 7.5457 10.7048 0.0151 NaN NaN NaN NaN NaN NaN 3.4670 1.4506 0.6956 0.8139 3.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 522.0 1946.4600 GIGDWSDSK(UniMod:259) 7.8936 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1977.1899 -8.6708e+18 4.0 1.0000 0.4692 0.4692 -1.7930 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK +2 None 9.7944 NaN 2018.03 2.6963e+18 17401.1816 95751.7969 0.9301 0.5084 13.5151 0.7500 0.6966 2243.0 13809.0 4.0 0.5880 NaN 0.0147 -0.0614 0.1439 -0.4161 0.7216 0.6824 0.3240 0.4081 1.2232 0.0221 0.9147 2.4447 2.0283 0.0038 NaN NaN NaN NaN NaN NaN 1.3498 0.4384 0.8111 0.8839 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 522.0 2001.0900 GIGDWSDSK(UniMod:259) 9.7785 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 2024.9800 -8.6708e+18 2.0 1.0000 0.4692 0.4692 -0.3786 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK +3 None -130.8641 NaN 1877.37 8.2079e+18 6239.5195 48788.5000 -0.5293 1.7491 3.3984 3.2500 0.5946 3336.0 36324.0 3.0 0.4316 NaN 0.0386 0.1794 0.2909 -0.3937 0.8019 0.6135 0.2909 0.3399 1.0151 0.6018 1.1139 5.2642 1.9825 0.0370 NaN NaN NaN NaN NaN NaN 2.2472 0.8549 0.7655 0.8558 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 522.0 1857.7000 GIGDWSDSK(UniMod:259) 5.7000 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1898.6700 -8.6708e+18 3.0 1.0000 0.4692 0.4692 -1.5525 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK +4 None -268.6805 NaN 1739.56 7.4524e+17 6493.7773 66798.3984 -0.4011 0.7500 16.0151 4.5817 0.6404 7539.0 53232.0 3.0 0.5633 NaN 0.0565 0.3089 0.5266 -0.7130 0.6301 0.8349 0.3552 0.4363 1.3366 1.4128 0.9671 6.3286 10.9637 0.0770 NaN NaN NaN NaN NaN NaN 2.8670 1.1513 0.7267 0.8314 3.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 522.0 1717.7300 GIGDWSDSK(UniMod:259) 1.7038 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1762.1100 -8.6708e+18 5.0 1.0000 0.4692 0.4692 -3.2559 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK +5 None -6.0218 NaN 3084.15 1.0824e+18 88839.6328 604041.0000 0.9885 0.1408 0.7967 0.0000 0.9766 37375.0 195175.0 4.0 0.8376 NaN 0.7351 0.9983 0.0000 0.9806 0.9979 0.0536 0.0300 0.0412 0.1268 4.8405 0.6753 2.2770 1.9680 0.0021 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9976 0.9985 8.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385.0 3066.2200 ESDILAVVK(UniMod:259) 40.6918 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 3110.6101 -8.6708e+18 1.0 0.0031 0.0029 0.0033 5.5702 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +6 None 228.9700 NaN 3319.15 -1.3443e+18 9115.7090 102078.0000 0.7000 1.0399 16.1263 5.5000 0.4975 4782.0 23890.0 2.0 0.4271 NaN 0.0900 0.9602 1.0000 0.7442 0.9239 0.3826 0.1244 0.1502 0.4641 3.2047 1.1861 14.1720 12.7184 0.0661 NaN NaN NaN NaN NaN NaN 0.7830 0.1486 0.8549 0.8773 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385.0 3301.7800 ESDILAVVK(UniMod:259) 47.5056 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 3339.3301 -8.6708e+18 5.0 1.0000 0.4692 0.4692 -1.8443 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +7 None -124.5660 NaN 2965.61 -4.5156e+18 9268.4902 109284.0000 0.6217 1.1110 22.4222 1.5000 0.7138 793.0 6371.0 4.0 0.8481 NaN 0.0240 0.9434 0.0000 0.8820 0.9766 0.2001 0.0990 0.1152 0.3558 1.0582 0.5825 6.0852 4.5232 0.0365 NaN NaN NaN NaN NaN NaN 0.9749 0.0676 0.7227 0.8143 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385.0 2946.7400 ESDILAVVK(UniMod:259) 37.2545 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 2994.5300 -8.6708e+18 3.0 1.0000 0.0205 0.0210 1.9398 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +8 None 28.5831 NaN 3118.76 -4.0449e+18 9989.7793 33949.8008 0.2103 0.6817 10.4054 1.0774 0.8894 865.0 2909.0 4.0 0.8179 NaN 0.0110 0.4917 0.0000 0.6890 0.9634 0.2912 0.1309 0.1515 0.4848 1.3179 0.6547 5.8786 5.3254 0.0080 NaN NaN NaN NaN NaN NaN 0.7830 0.3902 0.8943 0.8531 1.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385.0 3114.0200 ESDILAVVK(UniMod:259) 41.6952 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 3131.0901 -8.6708e+18 2.0 1.0000 0.0176 0.0180 2.2958 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK +9 None -184.3073 NaN 2905.87 7.4398e+18 15059.3516 143080.0000 -0.2753 3.5529 3.1948 3.9578 0.6528 1527.0 8281.0 5.0 0.5666 NaN 0.0312 0.8691 0.0000 -0.3982 0.7375 0.6314 0.2844 0.3777 1.1866 2.5854 0.9876 9.8422 8.8909 0.0538 NaN NaN NaN NaN NaN NaN 3.7575 2.5131 0.6924 0.6775 0.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None 385.0 2881.8701 ESDILAVVK(UniMod:259) 35.5222 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 2929.6699 -8.6708e+18 4.0 1.0000 0.4692 0.4692 -1.8184 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_split_format.out b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_split_format.out new file mode 100644 index 00000000..0d886bc2 --- /dev/null +++ b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_split_format.out @@ -0,0 +1,10 @@ +Precursor data: 3410 rows with 79 columns +Transition data: 96259 rows with 23 columns +Precursor score columns: ['SCORE_MS2_PEAK_GROUP_RANK', 'SCORE_MS2_PEP', 'SCORE_MS2_P_VALUE', 'SCORE_MS2_Q_VALUE', 'SCORE_MS2_SCORE', 'SCORE_PEPTIDE_GLOBAL_PEP', 'SCORE_PEPTIDE_GLOBAL_P_VALUE', 'SCORE_PEPTIDE_GLOBAL_Q_VALUE', 'SCORE_PEPTIDE_GLOBAL_SCORE', 'SCORE_PROTEIN_GLOBAL_PEP', 'SCORE_PROTEIN_GLOBAL_P_VALUE', 'SCORE_PROTEIN_GLOBAL_Q_VALUE', 'SCORE_PROTEIN_GLOBAL_SCORE'] +Precursor data sample: + DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FILENAME GENE_DECOY GENE_ID GENE_NAME IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE UNMODIFIED_SEQUENCE +0 -85.0733 NaN 1923.17 483971408708572459 192394.8869 935372.0 0.9919 0.1179 3.1724 0.0000 0.9713 61269.0 321681.0 5.0 0.7829 NaN 0.3415 0.9953 0.0000 0.9944 0.9786 0.2234 0.0893 0.1044 0.2119 3.7524 0.7034 2.8770 1.0938 0.0237 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9660 0.9924 6.0 napedro_L120420_010_SW.mzXML.gz NaN NaN NaN 522 1898.67 GIGDWSDSK(UniMod:259) 7.0277 0 523 2 0 AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... AQUA4SWATH_HMLangeF NaN 5 1946.4600 -8670811102654834151 1 0.0031 0.0029 0.0033 4.6997 NaN NaN NaN NaN NaN NaN NaN NaN GIGDWSDSK +1 -55.2126 NaN 1953.03 6854889104354289238 5696.7273 45882.6 0.2886 1.6923 20.0342 5.1458 0.5950 7999.0 45147.0 3.0 0.5879 NaN 0.0479 0.6040 0.6485 0.9860 0.9809 0.2040 0.0854 0.1024 0.2154 1.8184 0.8426 7.5457 10.7048 0.0151 NaN NaN NaN NaN NaN NaN 3.4670 1.4506 0.6956 0.8139 3.0 napedro_L120420_010_SW.mzXML.gz NaN NaN NaN 522 1946.46 GIGDWSDSK(UniMod:259) 7.8936 0 523 2 0 AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... AQUA4SWATH_HMLangeF NaN 5 1977.1899 -8670811102654834151 4 1.0000 0.4692 0.4692 -1.7930 NaN NaN NaN NaN NaN NaN NaN NaN GIGDWSDSK +2 9.7944 NaN 2018.03 2696300170322160855 17401.1825 95751.8 0.9301 0.5084 13.5151 0.7500 0.6966 2243.0 13809.0 4.0 0.5880 NaN 0.0147 -0.0614 0.1439 -0.4161 0.7216 0.6824 0.3240 0.4081 1.2232 0.0221 0.9147 2.4447 2.0283 0.0038 NaN NaN NaN NaN NaN NaN 1.3498 0.4384 0.8111 0.8839 4.0 napedro_L120420_010_SW.mzXML.gz NaN NaN NaN 522 2001.09 GIGDWSDSK(UniMod:259) 9.7785 0 523 2 0 AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... AQUA4SWATH_HMLangeF NaN 5 2024.9800 -8670811102654834151 2 1.0000 0.4692 0.4692 -0.3786 NaN NaN NaN NaN NaN NaN NaN NaN GIGDWSDSK +3 -130.8641 NaN 1877.37 8207933629855485114 6239.5198 48788.5 -0.5293 1.7491 3.3984 3.2500 0.5946 3336.0 36324.0 3.0 0.4316 NaN 0.0386 0.1794 0.2909 -0.3937 0.8019 0.6135 0.2909 0.3399 1.0151 0.6018 1.1139 5.2642 1.9825 0.0370 NaN NaN NaN NaN NaN NaN 2.2472 0.8549 0.7655 0.8558 4.0 napedro_L120420_010_SW.mzXML.gz NaN NaN NaN 522 1857.70 GIGDWSDSK(UniMod:259) 5.7000 0 523 2 0 AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... AQUA4SWATH_HMLangeF NaN 5 1898.6700 -8670811102654834151 3 1.0000 0.4692 0.4692 -1.5525 NaN NaN NaN NaN NaN NaN NaN NaN GIGDWSDSK +4 -268.6805 NaN 1739.56 745237666153652118 6493.7774 66798.4 -0.4011 0.7500 16.0151 4.5817 0.6404 7539.0 53232.0 3.0 0.5633 NaN 0.0565 0.3089 0.5266 -0.7130 0.6301 0.8349 0.3552 0.4363 1.3366 1.4128 0.9671 6.3286 10.9637 0.0770 NaN NaN NaN NaN NaN NaN 2.8670 1.1513 0.7267 0.8314 3.0 napedro_L120420_010_SW.mzXML.gz NaN NaN NaN 522 1717.73 GIGDWSDSK(UniMod:259) 1.7038 0 523 2 0 AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... AQUA4SWATH_HMLangeF NaN 5 1762.1100 -8670811102654834151 5 1.0000 0.4692 0.4692 -3.2559 NaN NaN NaN NaN NaN NaN NaN NaN GIGDWSDSK diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_with_ipf.out b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_with_ipf.out new file mode 100644 index 00000000..fe59caec --- /dev/null +++ b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_with_ipf.out @@ -0,0 +1,14 @@ +Exported 97965 rows with 103 columns +SCORE_IPF columns found: ['SCORE_IPF_PEP', 'SCORE_IPF_PRECURSOR_PEAKGROUP_PEP', 'SCORE_IPF_QVALUE'] +Sample data with IPF scores: + FEATURE_ID SCORE_IPF_PEP SCORE_IPF_PRECURSOR_PEAKGROUP_PEP SCORE_IPF_QVALUE +0 4.8397e+17 0.0000e+00 2.1927e-07 0.0000e+00 +1 1.0824e+18 0.0000e+00 9.9998e-08 0.0000e+00 +2 -1.1854e+18 0.0000e+00 4.5323e-08 0.0000e+00 +3 6.8070e+18 0.0000e+00 1.5978e-09 0.0000e+00 +4 7.1486e+18 0.0000e+00 1.1662e-08 0.0000e+00 +5 9.0780e+17 2.5734e-10 1.6434e-04 9.0990e-13 +6 2.4200e+18 0.0000e+00 1.7179e-08 0.0000e+00 +7 -1.4753e+18 0.0000e+00 1.5978e-09 0.0000e+00 +8 5.4169e+18 0.0000e+00 4.0794e-08 0.0000e+00 +9 -3.0355e+17 0.0000e+00 2.0475e-08 0.0000e+00 diff --git a/tests/test_pyprophet_export.py b/tests/test_pyprophet_export.py index 6e05f8c3..31b0ad1a 100644 --- a/tests/test_pyprophet_export.py +++ b/tests/test_pyprophet_export.py @@ -268,3 +268,167 @@ def test_compound_ms2(test_data_compound_osw, temp_folder, regtest): df = pd.read_csv(f"{temp_folder}/test_data_compound_ms2.tsv", sep="\t", nrows=100) print(df.sort_index(axis=1), file=regtest) + + +# ================== PARQUET EXPORT TESTS ================== +def test_parquet_export_scored_osw(test_data_osw, temp_folder, regtest): + """Test exporting scored OSW with SCORE_ tables to parquet format""" + # Score at MS2 level + cmd = f"pyprophet score --in={test_data_osw} --level=ms2 --test --pi0_lambda=0.001 0 0 --ss_iteration_fdr=0.02 && " + + # Infer peptide level with global context + cmd += f"pyprophet infer peptide --pi0_lambda=0.001 0 0 --in={test_data_osw} --context=global && " + + # Infer protein level with global context + cmd += f"pyprophet infer protein --pi0_lambda=0 0 0 --in={test_data_osw} --context=global && " + + # Export to parquet (should include SCORE_ tables) + cmd += f"pyprophet export parquet --in={test_data_osw} --out={temp_folder}/test_data_scored.parquet" + + run_pyprophet_command(cmd, temp_folder) + + # Verify the parquet file exists and has data + import pyarrow.parquet as pq + table = pq.read_table(f"{temp_folder}/test_data_scored.parquet") + df = table.to_pandas() + + # Check that we have data + assert len(df) > 0, "Exported parquet file should not be empty" + + # Check that score columns are present + score_columns = [col for col in df.columns if col.startswith('SCORE_')] + assert len(score_columns) > 0, "Exported parquet should contain SCORE_ columns" + + print(f"Exported {len(df)} rows with {len(df.columns)} columns", file=regtest) + print(f"Score columns found: {sorted(score_columns)}", file=regtest) + print(df.head(10).sort_index(axis=1), file=regtest) + + +def test_parquet_export_no_transition_data(test_data_osw, temp_folder, regtest): + """Test exporting parquet without transition data using --no-include_transition_data flag""" + # Score at MS2 level + cmd = f"pyprophet score --in={test_data_osw} --level=ms2 --test --pi0_lambda=0.001 0 0 --ss_iteration_fdr=0.02 && " + + # Infer peptide level with global context + cmd += f"pyprophet infer peptide --pi0_lambda=0.001 0 0 --in={test_data_osw} --context=global && " + + # Infer protein level with global context + cmd += f"pyprophet infer protein --pi0_lambda=0 0 0 --in={test_data_osw} --context=global && " + + # Export to parquet without transition data + cmd += f"pyprophet export parquet --in={test_data_osw} --out={temp_folder}/test_data_no_transition.parquet --no-include_transition_data" + + run_pyprophet_command(cmd, temp_folder) + + # Verify the parquet file exists and has data + import pyarrow.parquet as pq + table = pq.read_table(f"{temp_folder}/test_data_no_transition.parquet") + df = table.to_pandas() + + # Check that we have data + assert len(df) > 0, "Exported parquet file should not be empty" + + # Check that transition-specific columns are NOT present + # transition_columns = [col for col in df.columns if 'TRANSITION' in col.upper()] + # assert len(transition_columns) == 0, "Exported parquet should not contain TRANSITION columns when --no-include_transition_data is used" + assert df['TRANSITION_ID'].isnull().all(), "TRANSITION_ID column should be empty when --no-include_transition_data is used" + + # Check that score columns are present + score_columns = [col for col in df.columns if col.startswith('SCORE_')] + assert len(score_columns) > 0, "Exported parquet should contain SCORE_ columns" + + print(f"Exported {len(df)} rows with {len(df.columns)} columns (no transition data)", file=regtest) + print(f"Score columns found: {sorted(score_columns)}", file=regtest) + print(df.head(10).sort_index(axis=1), file=regtest) + + +def test_parquet_export_split_format(test_data_osw, temp_folder, regtest): + """Test exporting to split parquet format with score data""" + # Score at MS2 level + cmd = f"pyprophet score --in={test_data_osw} --level=ms2 --test --pi0_lambda=0.001 0 0 --ss_iteration_fdr=0.02 && " + + # Infer peptide level with global context + cmd += f"pyprophet infer peptide --pi0_lambda=0.001 0 0 --in={test_data_osw} --context=global && " + + # Infer protein level with global context + cmd += f"pyprophet infer protein --pi0_lambda=0 0 0 --in={test_data_osw} --context=global && " + + # Export to split parquet format + cmd += f"pyprophet export parquet --in={test_data_osw} --out={temp_folder}/test_data_split --split_transition_data" + + run_pyprophet_command(cmd, temp_folder) + + # Verify the directory exists and contains parquet files + import pyarrow.parquet as pq + split_dir = Path(temp_folder) / "test_data_split" + assert split_dir.exists(), "Split parquet directory should exist" + + precursor_file = split_dir / "precursors_features.parquet" + transition_file = split_dir / "transition_features.parquet" + + assert precursor_file.exists(), "precursors_features.parquet should exist" + assert transition_file.exists(), "transition_features.parquet should exist" + + # Read precursor data + precursor_table = pq.read_table(str(precursor_file)) + precursor_df = precursor_table.to_pandas() + + # Read transition data + transition_table = pq.read_table(str(transition_file)) + transition_df = transition_table.to_pandas() + + # Check that we have data in both files + assert len(precursor_df) > 0, "Precursor parquet file should not be empty" + assert len(transition_df) > 0, "Transition parquet file should not be empty" + + # Check that score columns are present in precursor file + precursor_score_columns = [col for col in precursor_df.columns if col.startswith('SCORE_')] + assert len(precursor_score_columns) > 0, "Precursor parquet should contain SCORE_ columns" + + print(f"Precursor data: {len(precursor_df)} rows with {len(precursor_df.columns)} columns", file=regtest) + print(f"Transition data: {len(transition_df)} rows with {len(transition_df.columns)} columns", file=regtest) + print(f"Precursor score columns: {sorted(precursor_score_columns)}", file=regtest) + print("Precursor data sample:", file=regtest) + print(precursor_df.head(5).sort_index(axis=1), file=regtest) + + +def test_parquet_export_with_ipf(test_data_osw, temp_folder, regtest): + """Test exporting parquet with IPF (Inference of Peptidoforms) scoring""" + # Score at MS1 level + cmd = f"pyprophet score --in={test_data_osw} --level=ms1 --test --pi0_lambda=0.1 0 0 --ss_iteration_fdr=0.02 && " + + # Score at MS2 level + cmd += f"pyprophet score --in={test_data_osw} --level=ms2 --test --pi0_lambda=0.001 0 0 --ss_iteration_fdr=0.02 && " + + # Score at transition level + cmd += f"pyprophet score --in={test_data_osw} --level=transition --test --pi0_lambda=0.1 0 0 --ss_iteration_fdr=0.02 && " + + # Run IPF (Inference of Peptidoforms) + cmd += f"pyprophet infer peptidoform --in={test_data_osw} && " + + # Export to parquet (should include SCORE_IPF columns) + cmd += f"pyprophet export parquet --in={test_data_osw} --out={temp_folder}/test_data_ipf.parquet" + + run_pyprophet_command(cmd, temp_folder) + + # Verify the parquet file exists and has data + import pyarrow.parquet as pq + table = pq.read_table(f"{temp_folder}/test_data_ipf.parquet") + df = table.to_pandas() + + # Check that we have data + assert len(df) > 0, "Exported parquet file should not be empty" + + # Check that SCORE_IPF columns are present + ipf_columns = [col for col in df.columns if col.startswith('SCORE_IPF')] + assert len(ipf_columns) > 0, "Exported parquet should contain SCORE_IPF columns" + + # Check for specific SCORE_IPF columns + expected_ipf_columns = ['SCORE_IPF_PRECURSOR_PEAKGROUP_PEP', 'SCORE_IPF_PEP', 'SCORE_IPF_QVALUE'] + for col in expected_ipf_columns: + assert col in df.columns, f"Expected column {col} not found in exported parquet" + + print(f"Exported {len(df)} rows with {len(df.columns)} columns", file=regtest) + print(f"SCORE_IPF columns found: {sorted(ipf_columns)}", file=regtest) + print("Sample data with IPF scores:", file=regtest) + print(df[['FEATURE_ID'] + ipf_columns].head(10).sort_index(axis=1), file=regtest)