From 14f1099d5ccad19aa53aba75bfb9367e5642a16e Mon Sep 17 00:00:00 2001 From: victorgiurcoiu Date: Thu, 18 Apr 2024 18:26:52 +0000 Subject: [PATCH 01/33] Added protein ids for spectronaut and msp formats --- spectrum_io/spectral_library/msp.py | 7 ++++--- spectrum_io/spectral_library/spectronaut.py | 9 +++++---- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/spectrum_io/spectral_library/msp.py b/spectrum_io/spectral_library/msp.py index 632b2d8..ea3855f 100644 --- a/spectrum_io/spectral_library/msp.py +++ b/spectrum_io/spectral_library/msp.py @@ -23,6 +23,7 @@ def _write(self, out: IO, data: Dict[str, np.ndarray], metadata: pd.DataFrame): p_charges = metadata["PRECURSOR_CHARGE"] p_mzs = (metadata["MASS"] + (p_charges * PARTICLE_MASSES["PROTON"])) / p_charges ces = metadata["COLLISION_ENERGY"] + pr_ids = metadata["PROTEINS"] # prepare spectra irts = data["irt"][:, 0] # should create a 1D view of the (n_peptides, 1) shaped array @@ -33,12 +34,12 @@ def _write(self, out: IO, data: Dict[str, np.ndarray], metadata: pd.DataFrame): lines = [] vec_assemble = np.vectorize(MSP._assemble_fragment_string) - for stripped_peptide, p_charge, p_mz, ce, mods, irt, f_mzs, f_ints, f_annots in zip( - stripped_peptides, p_charges, p_mzs, ces, modss, irts, f_mzss, f_intss, f_annotss + for stripped_peptide, p_charge, p_mz, ce, pr_id, mods, irt, f_mzs, f_ints, f_annots in zip( + stripped_peptides, p_charges, p_mzs, ces, pr_ids, modss, irts, f_mzss, f_intss, f_annotss ): lines.append(f"Name: {stripped_peptide}/{p_charge}\nMW: {p_mz}\n") lines.append( - f"Comment: Parent={p_mz:.8f} Collision_energy={ce} Mods={mods[0]} " + f"Comment: Parent={p_mz:.8f} Collision_energy={ce} Pritein_ids={pr_id} Mods={mods[0]} " f"ModString={mods[1]}/{p_charge} iRT={irt:.2f}\n" ) diff --git a/spectrum_io/spectral_library/spectronaut.py b/spectrum_io/spectral_library/spectronaut.py index 2af0fd3..9cf90eb 100644 --- a/spectrum_io/spectral_library/spectronaut.py +++ b/spectrum_io/spectral_library/spectronaut.py @@ -32,6 +32,7 @@ def _write(self, out: IO, data: Dict[str, np.ndarray], metadata: pd.DataFrame): p_charges = metadata["PRECURSOR_CHARGE"] p_mzs = (metadata["MASS"] + (p_charges * PARTICLE_MASSES["PROTON"])) / p_charges ces = metadata["COLLISION_ENERGY"] + pr_ids = metadata["PROTEINS"] # prepare spectra irts = data["irt"][:, 0] # should create a 1D view of the (n_peptides, 1) shaped array @@ -41,17 +42,17 @@ def _write(self, out: IO, data: Dict[str, np.ndarray], metadata: pd.DataFrame): vec_assemble = np.vectorize(Spectronaut._assemble_fragment_string) - for f_ints, f_mzs, modseq, seq, p_charge, p_mz, irt, ce, f_annots in zip( - f_intss, f_mzss, modseqs, seqs, p_charges, p_mzs, irts, ces, f_annotss + for f_ints, f_mzs, modseq, seq, p_charge, p_mz, irt, ce, pr_id, f_annots in zip( + f_intss, f_mzss, modseqs, seqs, p_charges, p_mzs, irts, ces, pr_ids, f_annotss ): cond = self._fragment_filter_passed(f_mzs, f_ints) - line_start = [f"{modseq},{seq},{seq},{p_charge},{p_mz:.8f},{irt:.2f},{ce},"] + line_start = [f"{modseq},{seq},{seq},{p_charge},{p_mz:.8f},{irt:.2f},{ce},{pr_id}"] fragment_list = vec_assemble(f_ints[cond], f_mzs[cond], f_annots[cond]) out.writelines(chain.from_iterable(zip(cycle(line_start), fragment_list))) def _write_header(self, out: IO): if self.mode == "w": out.write( - "ModifiedPeptide,LabeledPeptide,StrippedPeptide,PrecursorCharge,PrecursorMz,iRT,CollisionEnergy," + "ModifiedPeptide,LabeledPeptide,StrippedPeptide,PrecursorCharge,PrecursorMz,iRT,CollisionEnergy,ProteinIds," "RelativeFragmentIntensity,FragmentMz,FragmentNumber,FragmentType,FragmentCharge,FragmentLossType\n" ) From 5eeec06957bf052ddb56ce12206128c0339f8852 Mon Sep 17 00:00:00 2001 From: victorgiurcoiu Date: Sun, 28 Apr 2024 08:11:13 +0000 Subject: [PATCH 02/33] Added protein ids for dlib format --- spectrum_io/spectral_library/dlib.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/spectrum_io/spectral_library/dlib.py b/spectrum_io/spectral_library/dlib.py index 3abf10d..1d0ecb0 100644 --- a/spectrum_io/spectral_library/dlib.py +++ b/spectrum_io/spectral_library/dlib.py @@ -20,6 +20,7 @@ "PeptideSeq", "RTInSeconds", "PrecursorMz", + "ProteinIds" ] @@ -102,7 +103,8 @@ def _create_database(conn: sqlite3.Connection): RTInSecondsStop REAL, MedianChromatogramEncodedLength INTEGER, MedianChromatogramArray BLOB, - SourceFile TEXT NOT NULL DEFAULT 'Oktoberfest' + SourceFile TEXT NOT NULL DEFAULT 'Oktoberfest', + ProteinIds TEXT NOT NULL ) """ sql_create_p2p = """ @@ -136,6 +138,8 @@ def _write(self, out: Union[IO, sqlite3.Connection], data: Dict[str, np.ndarray] p_mzs = (metadata["MASS"] + (p_charges * PARTICLE_MASSES["PROTON"])) / p_charges # ces = metadata["COLLISION_ENERGY"] + pr_ids = metadata["PROTEINS"] + # prepare spectra irts = data["irt"][:, 0] # should create a 1D view of the (n_peptides, 1) shaped array f_mzss = data["mz"] @@ -144,7 +148,7 @@ def _write(self, out: Union[IO, sqlite3.Connection], data: Dict[str, np.ndarray] masked_values = self._calculate_masked_values(f_mzss, f_intss) - data_list = [*masked_values, p_charges, mass_mod_sequences, seqs, irts, p_mzs] + data_list = [*masked_values, p_charges, mass_mod_sequences, seqs, irts, p_mzs, pr_ids] entries = pd.DataFrame(dict(zip(DLIB_COL_NAMES, data_list))) p2p = pd.DataFrame({"PeptideSeq": seqs}) From c7e3cd6c13a1998e07fee432446961121c2d67b8 Mon Sep 17 00:00:00 2001 From: victorgiurcoiu Date: Mon, 29 Apr 2024 14:04:48 +0000 Subject: [PATCH 03/33] Added PROTEINS column for maxquant --- spectrum_io/search_result/maxquant.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/spectrum_io/search_result/maxquant.py b/spectrum_io/search_result/maxquant.py index 161c9da..e68d830 100644 --- a/spectrum_io/search_result/maxquant.py +++ b/spectrum_io/search_result/maxquant.py @@ -62,6 +62,7 @@ def read_result(self, tmt_labeled: str) -> pd.DataFrame: "MASS", # = Calculated Precursor mass; TODO get column with experimental Precursor mass instead "SCORE", "REVERSE", + "PROTEINS", ], sep="\t", ) @@ -117,6 +118,7 @@ def update_columns_for_prosit(df: pd.DataFrame, tmt_labeled: str) -> pd.DataFram df["MODIFIED_SEQUENCE"] = maxquant_to_internal(df["MODIFIED_SEQUENCE"].to_numpy()) df["SEQUENCE"] = internal_without_mods(df["MODIFIED_SEQUENCE"]) df["PEPTIDE_LENGTH"] = df["SEQUENCE"].apply(lambda x: len(x)) + df["PROTEINS"].fillna("UNKNOWN", inplace=True) return df From 2b441a82c2235bdaf21fff669ea34e4f942023bd Mon Sep 17 00:00:00 2001 From: victorgiurcoiu Date: Fri, 17 May 2024 17:25:59 +0000 Subject: [PATCH 04/33] Filter peptides with * --- spectrum_io/spectral_library/digest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spectrum_io/spectral_library/digest.py b/spectrum_io/spectral_library/digest.py index 3e15bd1..8afb444 100644 --- a/spectrum_io/spectral_library/digest.py +++ b/spectrum_io/spectral_library/digest.py @@ -85,7 +85,7 @@ def main(args): def valid_prosit_peptide(peptide: str) -> bool: """Check if peptide is valid.""" - return len(peptide) <= 30 and "U" not in peptide and "X" not in peptide + return len(peptide) <= 30 and "U" not in peptide and "X" not in peptide and "*" not in peptide def parse_args(call): From 2a824f871a88cf27973682b7be8c8e922325293a Mon Sep 17 00:00:00 2001 From: victorgiurcoiu Date: Fri, 17 May 2024 17:44:23 +0000 Subject: [PATCH 05/33] Fixed black --- spectrum_io/spectral_library/dlib.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spectrum_io/spectral_library/dlib.py b/spectrum_io/spectral_library/dlib.py index 1d0ecb0..392ff9f 100644 --- a/spectrum_io/spectral_library/dlib.py +++ b/spectrum_io/spectral_library/dlib.py @@ -20,7 +20,7 @@ "PeptideSeq", "RTInSeconds", "PrecursorMz", - "ProteinIds" + "ProteinIds", ] From 0dbd1d6e792ddff811c6439d6f945d1b831e2cb1 Mon Sep 17 00:00:00 2001 From: victorgiurcoiu Date: Thu, 30 May 2024 13:01:47 +0000 Subject: [PATCH 06/33] Added protein ids for msfragger, sage, fixed tests and typeguard --- spectrum_io/search_result/msfragger.py | 5 +++++ spectrum_io/search_result/sage.py | 1 + spectrum_io/spectral_library/dlib.py | 8 +++----- spectrum_io/spectral_library/msp.py | 2 +- spectrum_io/spectral_library/spectronaut.py | 2 +- tests/unit_tests/data/psm_tmt_internal.csv | 10 +++++----- tests/unit_tests/test_maxquant.py | 15 +++++++++------ tests/unit_tests/test_msfragger.py | 3 +++ tests/unit_tests/test_spectral_library.py | 20 +++++++++++--------- 9 files changed, 39 insertions(+), 27 deletions(-) diff --git a/spectrum_io/search_result/msfragger.py b/spectrum_io/search_result/msfragger.py index 9b4470c..142f299 100644 --- a/spectrum_io/search_result/msfragger.py +++ b/spectrum_io/search_result/msfragger.py @@ -49,6 +49,8 @@ def update_columns_for_prosit(df, tmt_labeled: str) -> pd.DataFrame: :param tmt_labeled: True if tmt labeled :return: modified df as pd.DataFrame """ + df["PROTEINS"] = df["protein"] + df["PROTEINS"].fillna("UNKNOWN", inplace=True) df["REVERSE"] = df["protein"].apply(lambda x: "rev" in str(x)) df["RAW_FILE"] = df["spectrum"].apply(lambda x: x.split(".")[0]) df["MASS"] = df["precursor_neutral_mass"] @@ -75,6 +77,8 @@ def update_columns_for_prosit(df, tmt_labeled: str) -> pd.DataFrame: inplace=True, ) df["SEQUENCE"] = internal_without_mods(df["MODIFIED_SEQUENCE"]) + df["PROTEINS"] = df["PROTEINS"].apply(lambda x: ";".join(x)) + return df[ [ "RAW_FILE", @@ -87,5 +91,6 @@ def update_columns_for_prosit(df, tmt_labeled: str) -> pd.DataFrame: "REVERSE", "SEQUENCE", "PEPTIDE_LENGTH", + "PROTEINS", ] ] diff --git a/spectrum_io/search_result/sage.py b/spectrum_io/search_result/sage.py index 5aa4caa..0984c07 100644 --- a/spectrum_io/search_result/sage.py +++ b/spectrum_io/search_result/sage.py @@ -69,5 +69,6 @@ def update_columns_for_prosit(df: pd.DataFrame, tmt_labeled: str) -> pd.DataFram df["PEPTIDE_LENGTH"] = df["SEQUENCE"].str.len() # converting sage to unimod df["MODIFIED_SEQUENCE"] = sage_to_internal(df["MODIFIED_SEQUENCE"]) + df["PROTEINS"].fillna("UNKNOWN", inplace=True) return df diff --git a/spectrum_io/spectral_library/dlib.py b/spectrum_io/spectral_library/dlib.py index 392ff9f..703926f 100644 --- a/spectrum_io/spectral_library/dlib.py +++ b/spectrum_io/spectral_library/dlib.py @@ -20,7 +20,6 @@ "PeptideSeq", "RTInSeconds", "PrecursorMz", - "ProteinIds", ] @@ -103,8 +102,7 @@ def _create_database(conn: sqlite3.Connection): RTInSecondsStop REAL, MedianChromatogramEncodedLength INTEGER, MedianChromatogramArray BLOB, - SourceFile TEXT NOT NULL DEFAULT 'Oktoberfest', - ProteinIds TEXT NOT NULL + SourceFile TEXT NOT NULL DEFAULT 'Oktoberfest' ) """ sql_create_p2p = """ @@ -148,9 +146,9 @@ def _write(self, out: Union[IO, sqlite3.Connection], data: Dict[str, np.ndarray] masked_values = self._calculate_masked_values(f_mzss, f_intss) - data_list = [*masked_values, p_charges, mass_mod_sequences, seqs, irts, p_mzs, pr_ids] + data_list = [*masked_values, p_charges, mass_mod_sequences, seqs, irts, p_mzs] entries = pd.DataFrame(dict(zip(DLIB_COL_NAMES, data_list))) - p2p = pd.DataFrame({"PeptideSeq": seqs}) + p2p = pd.DataFrame({"PeptideSeq": seqs, "ProteinAccession": pr_ids}) out.execute("BEGIN") diff --git a/spectrum_io/spectral_library/msp.py b/spectrum_io/spectral_library/msp.py index 1bf230e..ffe42b4 100644 --- a/spectrum_io/spectral_library/msp.py +++ b/spectrum_io/spectral_library/msp.py @@ -42,7 +42,7 @@ def _write(self, out: Union[IO, Connection], data: Dict[str, np.ndarray], metada ): lines.append(f"Name: {stripped_peptide}/{p_charge}\nMW: {p_mz}\n") lines.append( - f"Comment: Parent={p_mz:.8f} Collision_energy={ce} Pritein_ids={pr_id} Mods={mods[0]} " + f"Comment: Parent={p_mz:.8f} Collision_energy={ce} Protein_ids={pr_id} Mods={mods[0]} " f"ModString={mods[1]}/{p_charge} iRT={irt:.2f}\n" ) diff --git a/spectrum_io/spectral_library/spectronaut.py b/spectrum_io/spectral_library/spectronaut.py index 4dadd7b..4adb612 100644 --- a/spectrum_io/spectral_library/spectronaut.py +++ b/spectrum_io/spectral_library/spectronaut.py @@ -49,7 +49,7 @@ def _write(self, out: Union[IO, Connection], data: Dict[str, np.ndarray], metada f_intss, f_mzss, modseqs, seqs, p_charges, p_mzs, irts, ces, pr_ids, f_annotss ): cond = self._fragment_filter_passed(f_mzs, f_ints) - line_start = [f"{modseq},{seq},{seq},{p_charge},{p_mz:.8f},{irt:.2f},{ce},{pr_id}"] + line_start = [f"{modseq},{seq},{seq},{p_charge},{p_mz:.8f},{irt:.2f},{ce},{pr_id},"] fragment_list = vec_assemble(f_ints[cond], f_mzs[cond], f_annots[cond]) out.writelines(chain.from_iterable(zip(cycle(line_start), fragment_list))) diff --git a/tests/unit_tests/data/psm_tmt_internal.csv b/tests/unit_tests/data/psm_tmt_internal.csv index 4e3f7be..fb5d141 100644 --- a/tests/unit_tests/data/psm_tmt_internal.csv +++ b/tests/unit_tests/data/psm_tmt_internal.csv @@ -1,5 +1,5 @@ -,RAW_FILE,SCAN_NUMBER,MODIFIED_SEQUENCE,PRECURSOR_CHARGE,SCAN_EVENT_NUMBER,MASS,SCORE,REVERSE,SEQUENCE,PEPTIDE_LENGTH -0,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,2459,[UNIMOD:2016]-GQAVLAFQEQVGTGR,5,34,1863.023,8.221,True,GQAVLAFQEQVGTGR,15 -1,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,2486,[UNIMOD:2016]-TEVPM[UNIMOD:35]GLSLRTTSAR,5,42,1937.0531,7.083,False,TEVPMGLSLRTTSAR,15 -2,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,2980,[UNIMOD:2016]-YSGNC[UNIMOD:4]DRQSVER,3,193,1773.8123,3.932,False,YSGNCDRQSVER,12 -3,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,3945,[UNIMOD:2016]-ESTK[UNIMOD:2016]SAAER,3,647,1586.8887,10.839,True,ESTKSAAER,9 +,RAW_FILE,SCAN_NUMBER,MODIFIED_SEQUENCE,PRECURSOR_CHARGE,SCAN_EVENT_NUMBER,MASS,SCORE,REVERSE,SEQUENCE,PEPTIDE_LENGTH,PROTEINS +0,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,2459,[UNIMOD:2016]-GQAVLAFQEQVGTGR,5,34,1863.023,8.221,True,GQAVLAFQEQVGTGR,15,rev_tr|E9Q8J5|E9Q8J5_MOUSE +1,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,2486,[UNIMOD:2016]-TEVPM[UNIMOD:35]GLSLRTTSAR,5,42,1937.0531,7.083,False,TEVPMGLSLRTTSAR,15,tr|A0A0N4SW17|A0A0N4SW17_MOUSE +2,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,2980,[UNIMOD:2016]-YSGNC[UNIMOD:4]DRQSVER,3,193,1773.8123,3.932,False,YSGNCDRQSVER,12,sp|Q9D413-2|SH2D6_MOUSE;sp|Q9D413|SH2D6_MOUSE;tr|A0A3Q4EBW9|A0A3Q4EBW9_MOUSE;tr|A0A3Q4ECA8|A0A3Q4ECA8_MOUSE;tr|A0A3Q4EGG3|A0A3Q4EGG3_MOUSE;tr|E0CYY5|E0CYY5_MOUSE;tr|E9QJU1|E9QJU1_MOUSE +3,Ecl1_0277_R0096-01_S004436_D_H01_TMT18_01,3945,[UNIMOD:2016]-ESTK[UNIMOD:2016]SAAER,3,647,1586.8887,10.839,True,ESTKSAAER,9,rev_sp|Q3TLH4-5|PRC2C_MOUSE;rev_sp|Q3TLH4|PRC2C_MOUSE;rev_tr|A0A0A0MQ79|A0A0A0MQ79_MOUSE;rev_tr|S4R209|S4R209_MOUSE;rev_tr|S4R294|S4R294_MOUSE;rev_tr|S4R2J9|S4R2J9_MOUSE diff --git a/tests/unit_tests/test_maxquant.py b/tests/unit_tests/test_maxquant.py index bd7242e..4bb4783 100644 --- a/tests/unit_tests/test_maxquant.py +++ b/tests/unit_tests/test_maxquant.py @@ -41,6 +41,9 @@ def test_update_columns(self, maxquant_df: pd.DataFrame): assert prosit_df["PEPTIDE_LENGTH"][0] == 18 assert prosit_df["PEPTIDE_LENGTH"][3] == 13 + assert prosit_df["PROTEINS"][0] == "P12345" + assert prosit_df["PROTEINS"][3] == "Q67890" + def test_update_columns_silac(self, maxquant_df: pd.DataFrame): """ Test column update silac. @@ -95,12 +98,12 @@ def test_filter_valid_prosit_sequences(self, invalid_df: pd.DataFrame): @pytest.fixture def maxquant_df(): """Create dataframes from strings: https://towardsdatascience.com/67b0c2b71e6a.""" - df_string = """ MODIFIED_SEQUENCE; REVERSE; MASS; -_DS(Phospho (STY))DS(Phospho (STY))WDADAFSVEDPVRK_; ; 1.0; -_DS(Phospho (STY))DS(Phospho (STY))WDADAFSVEDPVRK_; ; 1.0; -_DS(Phospho (STY))DSWDADAFS(Phospho (STY))VEDPVRK_; ; 1.0; - _SS(Phospho (STY))PTPES(Phospho (STY))PTMLTK_; +; 2.0; - _SS(Phospho (STY))PTPES(Phospho (STY))PTMLTK_; +; 2.0;""" + df_string = """ MODIFIED_SEQUENCE; REVERSE; MASS; PROTEINS; +_DS(Phospho (STY))DS(Phospho (STY))WDADAFSVEDPVRK_; ; 1.0; P12345; +_DS(Phospho (STY))DS(Phospho (STY))WDADAFSVEDPVRK_; ; 1.0; P12345; +_DS(Phospho (STY))DSWDADAFS(Phospho (STY))VEDPVRK_; ; 1.0; P12345; + _SS(Phospho (STY))PTPES(Phospho (STY))PTMLTK_; +; 2.0; Q67890; + _SS(Phospho (STY))PTPES(Phospho (STY))PTMLTK_; +; 2.0; Q67890;""" df = pd.read_csv(io.StringIO(df_string), delimiter=";", skipinitialspace=True) df["Charge"] = 2 return df diff --git a/tests/unit_tests/test_msfragger.py b/tests/unit_tests/test_msfragger.py index 495bd12..2eac2b7 100644 --- a/tests/unit_tests/test_msfragger.py +++ b/tests/unit_tests/test_msfragger.py @@ -24,6 +24,7 @@ def test_read_result(self): self.assertTrue("REVERSE" in df.columns) self.assertTrue("SEQUENCE" in df.columns) self.assertTrue("PEPTIDE_LENGTH" in df.columns) + self.assertTrue("PROTEINS" in df.columns) def test_read_msfragger(self): """Test function for reading sage results and transforming to Prosit format.""" @@ -33,5 +34,7 @@ def test_read_msfragger(self): tmt_labeled="tmtpro" ) expected_df = pd.read_csv(expected_msfragger_internal_path, index_col=0) + print("Internal Search Results Columns:", internal_search_results_df.columns) + print("Expected Columns:", expected_df.columns) pd.testing.assert_frame_equal(internal_search_results_df, expected_df) diff --git a/tests/unit_tests/test_spectral_library.py b/tests/unit_tests/test_spectral_library.py index 7c90f1a..925da42 100644 --- a/tests/unit_tests/test_spectral_library.py +++ b/tests/unit_tests/test_spectral_library.py @@ -23,14 +23,15 @@ def test_write(self, data, metadata): anticipated_content = ( "Name: AAACCCCKR/1\n" "MW: 124.407276467\n" - "Comment: Parent=124.40727647 Collision_energy=10.0 Mods=2/3,C,Carbamidomethyl/5,C,Carbamidomethyl " + "Comment: Parent=124.40727647 Collision_energy=10.0 " + "Protein_ids=ProteinA Mods=2/3,C,Carbamidomethyl/5,C,Carbamidomethyl " "ModString=AAACCCCKR//Carbamidomethyl@C3; Carbamidomethyl@C5/1 iRT=982.12\n" "Num peaks: 2\n" '0.80000000 0.2000 "b1/0.0ppm"\n' '0.30000000 0.8000 "b2^2/0.0ppm"\n' "Name: AAACILKKR/2\n" "MW: 1617.057276467\n" - "Comment: Parent=1617.05727647 Collision_energy=20.0 Mods=0 ModString=AAACILKKR///2 iRT=382.12\n" + "Comment: Parent=1617.05727647 Collision_energy=20.0 Protein_ids=ProteinB Mods=0 ModString=AAACILKKR///2 iRT=382.12\n" "Num peaks: 3\n" '0.50000000 0.5000 "b1/0.0ppm"\n' '0.40000000 0.6000 "y2^2/0.0ppm"\n' @@ -54,15 +55,15 @@ def test_write(self, data, metadata): file_content = file_content.replace("\r", "") # explicitly remove to work for windows anticipated_content = ( - "ModifiedPeptide,LabeledPeptide,StrippedPeptide,PrecursorCharge,PrecursorMz,iRT,CollisionEnergy," + "ModifiedPeptide,LabeledPeptide,StrippedPeptide,PrecursorCharge,PrecursorMz,iRT,CollisionEnergy,ProteinIds," "RelativeFragmentIntensity,FragmentMz,FragmentNumber,FragmentType,FragmentCharge,FragmentLossType\n" "_AAAC[Carbamidomethyl (C)]CC[Carbamidomethyl (C)]CKR_,AAACCCCKR,AAACCCCKR,1,124.40727647,982.12," - "10.0,0.2000,0.80000000,1,b,1,noloss\n" + "10.0,ProteinA,0.2000,0.80000000,1,b,1,noloss\n" "_AAAC[Carbamidomethyl (C)]CC[Carbamidomethyl (C)]CKR_,AAACCCCKR,AAACCCCKR,1,124.40727647,982.12," - "10.0,0.8000,0.30000000,2,b,2,noloss\n" - "_AAACILKKR_,AAACILKKR,AAACILKKR,2,1617.05727647,382.12,20.0,0.5000,0.50000000,1,b,1,noloss\n" - "_AAACILKKR_,AAACILKKR,AAACILKKR,2,1617.05727647,382.12,20.0,0.6000,0.40000000,2,y,2,noloss\n" - "_AAACILKKR_,AAACILKKR,AAACILKKR,2,1617.05727647,382.12,20.0,0.0010,0.30000000,2,b,2,noloss\n" + "10.0,ProteinA,0.8000,0.30000000,2,b,2,noloss\n" + "_AAACILKKR_,AAACILKKR,AAACILKKR,2,1617.05727647,382.12,20.0,ProteinB,0.5000,0.50000000,1,b,1,noloss\n" + "_AAACILKKR_,AAACILKKR,AAACILKKR,2,1617.05727647,382.12,20.0,ProteinB,0.6000,0.40000000,2,y,2,noloss\n" + "_AAACILKKR_,AAACILKKR,AAACILKKR,2,1617.05727647,382.12,20.0,ProteinB,0.0010,0.30000000,2,b,2,noloss\n" ) assert file_content == anticipated_content @@ -114,7 +115,7 @@ def test_write(self, data, metadata): ) df_expected_p2p = pd.DataFrame( - {"PeptideSeq": ["AAACCCCKR", "AAACILKKR"], "isDecoy": 0, "ProteinAccession": "UNKNOWN"} + {"PeptideSeq": ["AAACCCCKR", "AAACILKKR"], "isDecoy": 0, "ProteinAccession": ["ProteinA", "ProteinB"]} ) df_expected_meta = pd.DataFrame({"Key": ["version", "staleProteinMapping"], "Value": ["0.1.14", "true"]}) @@ -147,5 +148,6 @@ def metadata(): "PRECURSOR_CHARGE": [1, 2], "MASS": [123.4, 3232.1], "COLLISION_ENERGY": [10.0, 20.0], + "PROTEINS": ["ProteinA", "ProteinB"], } ) From 624fc14fb7e63b690a36c0bb33c4bc383e69b349 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 3 Jun 2024 10:34:49 +0000 Subject: [PATCH 07/33] [DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 4.1.0 to 5.0.0 Bumps [crazy-max/ghaction-github-labeler](https://github.com/crazy-max/ghaction-github-labeler) from 4.1.0 to 5.0.0. - [Release notes](https://github.com/crazy-max/ghaction-github-labeler/releases) - [Commits](https://github.com/crazy-max/ghaction-github-labeler/compare/v4.1.0...v5.0.0) --- updated-dependencies: - dependency-name: crazy-max/ghaction-github-labeler dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/labeler.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml index 0eeaba4..825aa6f 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -14,6 +14,6 @@ jobs: uses: actions/checkout@v4 - name: Run Labeler - uses: crazy-max/ghaction-github-labeler@v4.1.0 + uses: crazy-max/ghaction-github-labeler@v5.0.0 with: skip-delete: true From 08d2462b7c57a87b6ab77aa2b7d5af1b8fd05c76 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 3 Jun 2024 10:34:55 +0000 Subject: [PATCH 08/33] [DEPENDABOT]: Bump actions/download-artifact from 3 to 4 Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/run_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index d91eb1f..6503d12 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -154,7 +154,7 @@ jobs: nox --version - name: Download coverage data - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: coverage-data From 98f4f30bb63274f2240adb037ef6f4a78a06b301 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 4 Jun 2024 16:20:59 +0000 Subject: [PATCH 09/33] Add Parquet I/O similar to HDF5 support --- docs/spectrum_io.file.rst | 8 + pyproject.toml | 1 + requirements.txt | 1 + spectrum_io/file/__init__.py | 2 +- spectrum_io/file/parquet.ipynb | 902 +++++++++++++++++++++++++++++++ spectrum_io/file/parquet.py | 90 +++ tests/unit_tests/test_parquet.py | 81 +++ 7 files changed, 1084 insertions(+), 1 deletion(-) create mode 100644 spectrum_io/file/parquet.ipynb create mode 100644 spectrum_io/file/parquet.py create mode 100644 tests/unit_tests/test_parquet.py diff --git a/docs/spectrum_io.file.rst b/docs/spectrum_io.file.rst index b038996..7f977e5 100644 --- a/docs/spectrum_io.file.rst +++ b/docs/spectrum_io.file.rst @@ -20,6 +20,14 @@ spectrum\_io.file.hdf5 module :undoc-members: :show-inheritance: +spectrum\_io.file.parquet module +----------------------------- + +.. automodule:: spectrum_io.file.parquet + :members: + :undoc-members: + :show-inheritance: + Module contents --------------- diff --git a/pyproject.toml b/pyproject.toml index 4ba27f5..4fb1004 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,7 @@ PyYAML = ">=5.4.1" numpy = "^1.18.1" pandas = "^1.3.0" h5py = "^3.1.0" +pyarrow = ">=16.0.0" pymzml = "^2.5.0" pyteomics = "^4.3.3" lxml= '>=4.5.2,<6.0.0' diff --git a/requirements.txt b/requirements.txt index 6342d52..3094e28 100644 --- a/requirements.txt +++ b/requirements.txt @@ -21,6 +21,7 @@ packaging==24.0 ; python_version >= "3.8" and python_full_version < "3.11.0" pandas==1.5.3 ; python_version >= "3.8" and python_full_version < "3.11.0" pillow==10.3.0 ; python_version >= "3.8" and python_full_version < "3.11.0" psutil==5.9.8 ; python_version >= "3.8" and python_full_version < "3.11.0" +pyarrow==16.1.0 ; python_full_version >= "3.8" and python_full_version < "3.11.0" pygments==2.17.2 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" pymzml==2.5.9 ; python_full_version >= "3.8.0" and python_full_version < "3.11.0" pyparsing==3.1.2 ; python_version >= "3.8" and python_full_version < "3.11.0" diff --git a/spectrum_io/file/__init__.py b/spectrum_io/file/__init__.py index 35dc193..9aa3dba 100644 --- a/spectrum_io/file/__init__.py +++ b/spectrum_io/file/__init__.py @@ -2,6 +2,6 @@ import logging -from . import csv, hdf5 +from . import csv, hdf5, parquet logger = logging.getLogger(__name__) diff --git a/spectrum_io/file/parquet.ipynb b/spectrum_io/file/parquet.ipynb new file mode 100644 index 0000000..5d63ee5 --- /dev/null +++ b/spectrum_io/file/parquet.ipynb @@ -0,0 +1,902 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "from typing import Union\n", + "\n", + "import datasets\n", + "import pandas as pd\n", + "import pyarrow as pa\n", + "import pyarrow.feather as feather\n", + "import pyarrow.parquet as pq\n", + "import scipy\n", + "\n", + "from parquet import *" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "root_path = Path(\"/cmnfs/proj/prosit_astral/datasets/parquet\")\n", + "train_path = root_path / \"train\"" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "385ec5beebab46e6933deda6d071ca39", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "Resolving data files: 0%| | 0/78 [00:00\u001b[39m max_shard_size:\n\u001b[0;32m-> 1997\u001b[0m num_examples, num_bytes \u001b[39m=\u001b[39m writer\u001b[39m.\u001b[39;49mfinalize()\n\u001b[1;32m 1998\u001b[0m writer\u001b[39m.\u001b[39mclose()\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:607\u001b[0m, in \u001b[0;36mArrowWriter.finalize\u001b[0;34m(self, close_stream)\u001b[0m\n\u001b[1;32m 606\u001b[0m \u001b[39mif\u001b[39;00m close_stream:\n\u001b[0;32m--> 607\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mstream\u001b[39m.\u001b[39;49mclose()\n\u001b[1;32m 608\u001b[0m \u001b[39melse\u001b[39;00m:\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/fsspec/implementations/local.py:407\u001b[0m, in \u001b[0;36mLocalFileOpener.close\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 406\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mclose\u001b[39m(\u001b[39mself\u001b[39m):\n\u001b[0;32m--> 407\u001b[0m \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mf\u001b[39m.\u001b[39;49mclose()\n", + "\u001b[0;31mKeyboardInterrupt\u001b[0m: ", + "\nDuring handling of the above exception, another exception occurred:\n", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:2027\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split_single\u001b[0;34m(self, gen_kwargs, fpath, file_format, max_shard_size, job_id)\u001b[0m\n\u001b[1;32m 2026\u001b[0m num_shards \u001b[39m=\u001b[39m shard_id \u001b[39m+\u001b[39m \u001b[39m1\u001b[39m\n\u001b[0;32m-> 2027\u001b[0m num_examples, num_bytes \u001b[39m=\u001b[39m writer\u001b[39m.\u001b[39;49mfinalize()\n\u001b[1;32m 2028\u001b[0m writer\u001b[39m.\u001b[39mclose()\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:602\u001b[0m, in \u001b[0;36mArrowWriter.finalize\u001b[0;34m(self, close_stream)\u001b[0m\n\u001b[1;32m 601\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39mand\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mschema:\n\u001b[0;32m--> 602\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_build_writer(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mschema)\n\u001b[1;32m 603\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:404\u001b[0m, in \u001b[0;36mArrowWriter._build_writer\u001b[0;34m(self, inferred_schema)\u001b[0m\n\u001b[1;32m 403\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_schema \u001b[39m=\u001b[39m schema\n\u001b[0;32m--> 404\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_WRITER_CLASS(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mstream, schema)\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/ipc.py:85\u001b[0m, in \u001b[0;36mRecordBatchStreamWriter.__init__\u001b[0;34m(self, sink, schema, use_legacy_format, options)\u001b[0m\n\u001b[1;32m 84\u001b[0m options \u001b[39m=\u001b[39m _get_legacy_format_default(use_legacy_format, options)\n\u001b[0;32m---> 85\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_open(sink, schema, options\u001b[39m=\u001b[39;49moptions)\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/ipc.pxi:582\u001b[0m, in \u001b[0;36mpyarrow.lib._RecordBatchStreamWriter._open\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:2097\u001b[0m, in \u001b[0;36mpyarrow.lib.get_writer\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:232\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile.get_output_stream\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:246\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile._assert_writable\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:237\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile._assert_open\u001b[0;34m()\u001b[0m\n", + "\u001b[0;31mValueError\u001b[0m: I/O operation on closed file", + "\nThe above exception was the direct cause of the following exception:\n", + "\u001b[0;31mDatasetGenerationError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m/cmnfs/home/students/j.schlensok/spectrum_io/spectrum_io/file/parquet.ipynb Cell 3\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> 1\u001b[0m ds \u001b[39m=\u001b[39m datasets\u001b[39m.\u001b[39;49mload_dataset(\u001b[39mstr\u001b[39;49m(root_path))\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/load.py:2609\u001b[0m, in \u001b[0;36mload_dataset\u001b[0;34m(path, name, data_dir, data_files, split, cache_dir, features, download_config, download_mode, verification_mode, ignore_verifications, keep_in_memory, save_infos, revision, token, use_auth_token, task, streaming, num_proc, storage_options, trust_remote_code, **config_kwargs)\u001b[0m\n\u001b[1;32m 2606\u001b[0m \u001b[39mreturn\u001b[39;00m builder_instance\u001b[39m.\u001b[39mas_streaming_dataset(split\u001b[39m=\u001b[39msplit)\n\u001b[1;32m 2608\u001b[0m \u001b[39m# Download and prepare data\u001b[39;00m\n\u001b[0;32m-> 2609\u001b[0m builder_instance\u001b[39m.\u001b[39;49mdownload_and_prepare(\n\u001b[1;32m 2610\u001b[0m download_config\u001b[39m=\u001b[39;49mdownload_config,\n\u001b[1;32m 2611\u001b[0m download_mode\u001b[39m=\u001b[39;49mdownload_mode,\n\u001b[1;32m 2612\u001b[0m verification_mode\u001b[39m=\u001b[39;49mverification_mode,\n\u001b[1;32m 2613\u001b[0m num_proc\u001b[39m=\u001b[39;49mnum_proc,\n\u001b[1;32m 2614\u001b[0m storage_options\u001b[39m=\u001b[39;49mstorage_options,\n\u001b[1;32m 2615\u001b[0m )\n\u001b[1;32m 2617\u001b[0m \u001b[39m# Build dataset for splits\u001b[39;00m\n\u001b[1;32m 2618\u001b[0m keep_in_memory \u001b[39m=\u001b[39m (\n\u001b[1;32m 2619\u001b[0m keep_in_memory \u001b[39mif\u001b[39;00m keep_in_memory \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39melse\u001b[39;00m is_small_dataset(builder_instance\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39mdataset_size)\n\u001b[1;32m 2620\u001b[0m )\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1027\u001b[0m, in \u001b[0;36mDatasetBuilder.download_and_prepare\u001b[0;34m(self, output_dir, download_config, download_mode, verification_mode, ignore_verifications, try_from_hf_gcs, dl_manager, base_path, use_auth_token, file_format, max_shard_size, num_proc, storage_options, **download_and_prepare_kwargs)\u001b[0m\n\u001b[1;32m 1025\u001b[0m \u001b[39mif\u001b[39;00m num_proc \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m 1026\u001b[0m prepare_split_kwargs[\u001b[39m\"\u001b[39m\u001b[39mnum_proc\u001b[39m\u001b[39m\"\u001b[39m] \u001b[39m=\u001b[39m num_proc\n\u001b[0;32m-> 1027\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_download_and_prepare(\n\u001b[1;32m 1028\u001b[0m dl_manager\u001b[39m=\u001b[39;49mdl_manager,\n\u001b[1;32m 1029\u001b[0m verification_mode\u001b[39m=\u001b[39;49mverification_mode,\n\u001b[1;32m 1030\u001b[0m \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mprepare_split_kwargs,\n\u001b[1;32m 1031\u001b[0m \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mdownload_and_prepare_kwargs,\n\u001b[1;32m 1032\u001b[0m )\n\u001b[1;32m 1033\u001b[0m \u001b[39m# Sync info\u001b[39;00m\n\u001b[1;32m 1034\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39mdataset_size \u001b[39m=\u001b[39m \u001b[39msum\u001b[39m(split\u001b[39m.\u001b[39mnum_bytes \u001b[39mfor\u001b[39;00m split \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39msplits\u001b[39m.\u001b[39mvalues())\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1122\u001b[0m, in \u001b[0;36mDatasetBuilder._download_and_prepare\u001b[0;34m(self, dl_manager, verification_mode, **prepare_split_kwargs)\u001b[0m\n\u001b[1;32m 1118\u001b[0m split_dict\u001b[39m.\u001b[39madd(split_generator\u001b[39m.\u001b[39msplit_info)\n\u001b[1;32m 1120\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[1;32m 1121\u001b[0m \u001b[39m# Prepare split will record examples associated to the split\u001b[39;00m\n\u001b[0;32m-> 1122\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_prepare_split(split_generator, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mprepare_split_kwargs)\n\u001b[1;32m 1123\u001b[0m \u001b[39mexcept\u001b[39;00m \u001b[39mOSError\u001b[39;00m \u001b[39mas\u001b[39;00m e:\n\u001b[1;32m 1124\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mOSError\u001b[39;00m(\n\u001b[1;32m 1125\u001b[0m \u001b[39m\"\u001b[39m\u001b[39mCannot find data file. \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 1126\u001b[0m \u001b[39m+\u001b[39m (\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmanual_download_instructions \u001b[39mor\u001b[39;00m \u001b[39m\"\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m 1127\u001b[0m \u001b[39m+\u001b[39m \u001b[39m\"\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39mOriginal error:\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39m\"\u001b[39m\n\u001b[1;32m 1128\u001b[0m \u001b[39m+\u001b[39m \u001b[39mstr\u001b[39m(e)\n\u001b[1;32m 1129\u001b[0m ) \u001b[39mfrom\u001b[39;00m \u001b[39mNone\u001b[39;00m\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1882\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split\u001b[0;34m(self, split_generator, file_format, num_proc, max_shard_size)\u001b[0m\n\u001b[1;32m 1880\u001b[0m job_id \u001b[39m=\u001b[39m \u001b[39m0\u001b[39m\n\u001b[1;32m 1881\u001b[0m \u001b[39mwith\u001b[39;00m pbar:\n\u001b[0;32m-> 1882\u001b[0m \u001b[39mfor\u001b[39;00m job_id, done, content \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_prepare_split_single(\n\u001b[1;32m 1883\u001b[0m gen_kwargs\u001b[39m=\u001b[39mgen_kwargs, job_id\u001b[39m=\u001b[39mjob_id, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39m_prepare_split_args\n\u001b[1;32m 1884\u001b[0m ):\n\u001b[1;32m 1885\u001b[0m \u001b[39mif\u001b[39;00m done:\n\u001b[1;32m 1886\u001b[0m result \u001b[39m=\u001b[39m content\n", + "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:2038\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split_single\u001b[0;34m(self, gen_kwargs, fpath, file_format, max_shard_size, job_id)\u001b[0m\n\u001b[1;32m 2036\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39misinstance\u001b[39m(e, DatasetGenerationError):\n\u001b[1;32m 2037\u001b[0m \u001b[39mraise\u001b[39;00m\n\u001b[0;32m-> 2038\u001b[0m \u001b[39mraise\u001b[39;00m DatasetGenerationError(\u001b[39m\"\u001b[39m\u001b[39mAn error occurred while generating the dataset\u001b[39m\u001b[39m\"\u001b[39m) \u001b[39mfrom\u001b[39;00m \u001b[39me\u001b[39;00m\n\u001b[1;32m 2040\u001b[0m \u001b[39myield\u001b[39;00m job_id, \u001b[39mTrue\u001b[39;00m, (total_num_examples, total_num_bytes, writer\u001b[39m.\u001b[39m_features, num_shards, shard_lengths)\n", + "\u001b[0;31mDatasetGenerationError\u001b[0m: An error occurred while generating the dataset" + ] + } + ], + "source": [ + "ds = datasets.load_dataset(str(root_path))" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "input_test_file = Path.cwd().parent.parent.parent / \"oktoberfest/data/intensity_data.parquet\"\n", + "raw_data = {\n", + " \"intensities\": [\n", + " [4e-5, 0., -1., 0., 0., -1., 0.03, 0., -1., 0.4],\n", + " [.3, 0., -1., 1., 0., -1., 0.4, 0., -1., 0.05],\n", + " [.04, 0., 0., 0., 0., 0., 2e-3, 0., 0., .13]\n", + " ],\n", + " \"sequence\": [\"SVFLTFLR\", \"KTSQIFLAK\", \"SPVGRVTPKEWR\"],\n", + " \"precursor_charge_onehot\": [\n", + " [0, 1, 0, 0, 0, 0],\n", + " [0, 1, 0, 0, 0, 0],\n", + " [0, 0, 1, 0, 0, 0],\n", + " ],\n", + " \"collision_energy_normed\": [.25, .28, .28]\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [], + "source": [ + "output_path = Path.cwd() / \"temp\"\n", + "output_path.mkdir(exist_ok=True)\n", + "\n", + "df = pd.DataFrame(raw_data)\n", + "\n", + "#df2 = pd.concat([df, df], keys=['1', '2'], names=[\"dataset\", \"index\"])\n", + "df2 = pd.concat([df.assign(dataset='1'), df.assign(dataset='2')])\n", + "table = pa.Table.from_pandas(df2)\n", + "\n", + "pq.write_to_dataset(\n", + " table,\n", + " root_path=output_path,\n", + " partition_cols=[\"dataset\"],\n", + " existing_data_behavior=\"delete_matching\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "pyarrow.Table\n", + "intensities: list\n", + " child 0, item: double\n", + "sequence: string\n", + "precursor_charge_onehot: list\n", + " child 0, item: int64\n", + "collision_energy_normed: double\n", + "dataset: string\n", + "__index_level_0__: int64\n", + "----\n", + "intensities: [[[0.00004,0,-1,0,0,-1,0.03,0,-1,0.4],[0.3,0,-1,1,0,-1,0.4,0,-1,0.05],...,[0.3,0,-1,1,0,-1,0.4,0,-1,0.05],[0.04,0,0,0,0,0,0.002,0,0,0.13]]]\n", + "sequence: [[\"SVFLTFLR\",\"KTSQIFLAK\",\"SPVGRVTPKEWR\",\"SVFLTFLR\",\"KTSQIFLAK\",\"SPVGRVTPKEWR\"]]\n", + "precursor_charge_onehot: [[[0,1,0,0,0,0],[0,1,0,0,0,0],...,[0,1,0,0,0,0],[0,0,1,0,0,0]]]\n", + "collision_energy_normed: [[0.25,0.28,0.28,0.25,0.28,0.28]]\n", + "dataset: [[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"]]\n", + "__index_level_0__: [[0,1,2,0,1,2]]" + ] + }, + "execution_count": 43, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "table" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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intensitiessequenceprecursor_charge_onehotcollision_energy_normed
0[4e-05, 0.0, -1.0, 0.0, 0.0, -1.0, 0.03, 0.0, ...SVFLTFLR[0, 1, 0, 0, 0, 0]0.25
1[0.3, 0.0, -1.0, 1.0, 0.0, -1.0, 0.4, 0.0, -1....KTSQIFLAK[0, 1, 0, 0, 0, 0]0.28
2[0.04, 0.0, 0.0, 0.0, 0.0, 0.0, 0.002, 0.0, 0....SPVGRVTPKEWR[0, 0, 1, 0, 0, 0]0.28
\n", + "
" + ], + "text/plain": [ + " intensities sequence \\\n", + "0 [4e-05, 0.0, -1.0, 0.0, 0.0, -1.0, 0.03, 0.0, ... SVFLTFLR \n", + "1 [0.3, 0.0, -1.0, 1.0, 0.0, -1.0, 0.4, 0.0, -1.... KTSQIFLAK \n", + "2 [0.04, 0.0, 0.0, 0.0, 0.0, 0.0, 0.002, 0.0, 0.... SPVGRVTPKEWR \n", + "\n", + " precursor_charge_onehot collision_energy_normed \n", + "0 [0, 1, 0, 0, 0, 0] 0.25 \n", + "1 [0, 1, 0, 0, 0, 0] 0.28 \n", + "2 [0, 0, 1, 0, 0, 0] 0.28 " + ] + }, + "execution_count": 44, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dataset = pq.ParquetDataset(output_path, filters=[(\"dataset\", \"=\", '1')])\n", + "df = dataset.read().to_pandas().drop(\"dataset\", axis=1)\n", + "df#.to_pandas()\n", + "#read_df = read_partition(output_path, '1')\n", + "#pd.testing.assert_frame_equal(read_df, df)" + ] + }, + { + "cell_type": "code", + "execution_count": 64, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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intensitiessequenceprecursor_charge_onehotcollision_energy_aligned_normed
0[0.03713018032121684, 0.0, -1.0, 0.0, 0.0, -1....SVFLTFLR[0, 1, 0, 0, 0, 0]0.25
1[0.32880081359926777, 0.0, -1.0, 1.0, 0.0, -1....KTSQIFLAK[0, 1, 0, 0, 0, 0]0.28
2[0.03919235848040409, 0.0, 0.0, 0.0, 0.0, 0.0,...SPVGRVTPKEWR[0, 0, 1, 0, 0, 0]0.28
3[0.11537762755556774, 0.0, 0.0, 0.0, 0.0, 0.0,...SHIWPEYCSRALR[0, 0, 1, 0, 0, 0]0.30
4[0.003340655605539741, 0.0, 0.0, 0.00303169307...ELESQISELQEDLESERASR[0, 0, 1, 0, 0, 0]0.20
...............
41587[0.12310221158139793, 0.0, 0.0, 0.0, 0.0, 0.0,...LKFEEITGVINPALDKYFPSDSGVR[0, 0, 1, 0, 0, 0]0.30
41588[0.036119027089409034, 0.0, 0.0, 0.0, 0.0, 0.0...AYVGLERFLAGLRDY[0, 0, 1, 0, 0, 0]0.35
41589[0.036547268719584185, 0.0, 0.0, 0.0, 0.0, 0.0...AACLLTKWTAGR[0, 0, 1, 0, 0, 0]0.23
41590[0.053176686541959346, -1.0, -1.0, 0.0, -1.0, ...SLEKLEIIPASQ[1, 0, 0, 0, 0, 0]0.30
41591[0.0, -1.0, -1.0, 0.0, -1.0, -1.0, 0.055506936...LVSEIDTGTLAQL[1, 0, 0, 0, 0, 0]0.20
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41592 rows × 4 columns

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" + ], + "text/plain": [ + " intensities \\\n", + "0 [0.03713018032121684, 0.0, -1.0, 0.0, 0.0, -1.... \n", + "1 [0.32880081359926777, 0.0, -1.0, 1.0, 0.0, -1.... \n", + "2 [0.03919235848040409, 0.0, 0.0, 0.0, 0.0, 0.0,... \n", + "3 [0.11537762755556774, 0.0, 0.0, 0.0, 0.0, 0.0,... \n", + "4 [0.003340655605539741, 0.0, 0.0, 0.00303169307... \n", + "... ... \n", + "41587 [0.12310221158139793, 0.0, 0.0, 0.0, 0.0, 0.0,... \n", + "41588 [0.036119027089409034, 0.0, 0.0, 0.0, 0.0, 0.0... \n", + "41589 [0.036547268719584185, 0.0, 0.0, 0.0, 0.0, 0.0... \n", + "41590 [0.053176686541959346, -1.0, -1.0, 0.0, -1.0, ... \n", + "41591 [0.0, -1.0, -1.0, 0.0, -1.0, -1.0, 0.055506936... \n", + "\n", + " sequence precursor_charge_onehot \\\n", + "0 SVFLTFLR [0, 1, 0, 0, 0, 0] \n", + "1 KTSQIFLAK [0, 1, 0, 0, 0, 0] \n", + "2 SPVGRVTPKEWR [0, 0, 1, 0, 0, 0] \n", + "3 SHIWPEYCSRALR [0, 0, 1, 0, 0, 0] \n", + "4 ELESQISELQEDLESERASR [0, 0, 1, 0, 0, 0] \n", + "... ... ... \n", + "41587 LKFEEITGVINPALDKYFPSDSGVR [0, 0, 1, 0, 0, 0] \n", + "41588 AYVGLERFLAGLRDY [0, 0, 1, 0, 0, 0] \n", + "41589 AACLLTKWTAGR [0, 0, 1, 0, 0, 0] \n", + "41590 SLEKLEIIPASQ [1, 0, 0, 0, 0, 0] \n", + "41591 LVSEIDTGTLAQL [1, 0, 0, 0, 0, 0] \n", + "\n", + " collision_energy_aligned_normed \n", + "0 0.25 \n", + "1 0.28 \n", + "2 0.28 \n", + "3 0.30 \n", + "4 0.20 \n", + "... ... \n", + "41587 0.30 \n", + "41588 0.35 \n", + "41589 0.23 \n", + "41590 0.30 \n", + "41591 0.20 \n", + "\n", + "[41592 rows x 4 columns]" + ] + }, + "execution_count": 64, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df = pd.read_parquet(input_test_file)\n", + "df" + ] + }, + { + "cell_type": "code", + "execution_count": 65, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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intensitiessequenceprecursor_charge_onehotcollision_energy_aligned_normed
datasetindex
10[0.03713018032121684, 0.0, -1.0, 0.0, 0.0, -1....SVFLTFLR[0, 1, 0, 0, 0, 0]0.25
1[0.32880081359926777, 0.0, -1.0, 1.0, 0.0, -1....KTSQIFLAK[0, 1, 0, 0, 0, 0]0.28
2[0.03919235848040409, 0.0, 0.0, 0.0, 0.0, 0.0,...SPVGRVTPKEWR[0, 0, 1, 0, 0, 0]0.28
3[0.11537762755556774, 0.0, 0.0, 0.0, 0.0, 0.0,...SHIWPEYCSRALR[0, 0, 1, 0, 0, 0]0.30
4[0.003340655605539741, 0.0, 0.0, 0.00303169307...ELESQISELQEDLESERASR[0, 0, 1, 0, 0, 0]0.20
..................
241587[0.12310221158139793, 0.0, 0.0, 0.0, 0.0, 0.0,...LKFEEITGVINPALDKYFPSDSGVR[0, 0, 1, 0, 0, 0]0.30
41588[0.036119027089409034, 0.0, 0.0, 0.0, 0.0, 0.0...AYVGLERFLAGLRDY[0, 0, 1, 0, 0, 0]0.35
41589[0.036547268719584185, 0.0, 0.0, 0.0, 0.0, 0.0...AACLLTKWTAGR[0, 0, 1, 0, 0, 0]0.23
41590[0.053176686541959346, -1.0, -1.0, 0.0, -1.0, ...SLEKLEIIPASQ[1, 0, 0, 0, 0, 0]0.30
41591[0.0, -1.0, -1.0, 0.0, -1.0, -1.0, 0.055506936...LVSEIDTGTLAQL[1, 0, 0, 0, 0, 0]0.20
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" + ], + "text/plain": [ + " intensities \\\n", + "0 [0.03713018032121684, 0.0, -1.0, 0.0, 0.0, -1.... \n", + "1 [0.32880081359926777, 0.0, -1.0, 1.0, 0.0, -1.... \n", + "2 [0.03919235848040409, 0.0, 0.0, 0.0, 0.0, 0.0,... \n", + "3 [0.11537762755556774, 0.0, 0.0, 0.0, 0.0, 0.0,... \n", + "4 [0.003340655605539741, 0.0, 0.0, 0.00303169307... \n", + "... ... \n", + "41587 [0.12310221158139793, 0.0, 0.0, 0.0, 0.0, 0.0,... \n", + "41588 [0.036119027089409034, 0.0, 0.0, 0.0, 0.0, 0.0... \n", + "41589 [0.036547268719584185, 0.0, 0.0, 0.0, 0.0, 0.0... \n", + "41590 [0.053176686541959346, -1.0, -1.0, 0.0, -1.0, ... \n", + "41591 [0.0, -1.0, -1.0, 0.0, -1.0, -1.0, 0.055506936... \n", + "\n", + " sequence precursor_charge_onehot \\\n", + "0 SVFLTFLR [0, 1, 0, 0, 0, 0] \n", + "1 KTSQIFLAK [0, 1, 0, 0, 0, 0] \n", + "2 SPVGRVTPKEWR [0, 0, 1, 0, 0, 0] \n", + "3 SHIWPEYCSRALR [0, 0, 1, 0, 0, 0] \n", + "4 ELESQISELQEDLESERASR [0, 0, 1, 0, 0, 0] \n", + "... ... ... \n", + "41587 LKFEEITGVINPALDKYFPSDSGVR [0, 0, 1, 0, 0, 0] \n", + "41588 AYVGLERFLAGLRDY [0, 0, 1, 0, 0, 0] \n", + "41589 AACLLTKWTAGR [0, 0, 1, 0, 0, 0] \n", + "41590 SLEKLEIIPASQ [1, 0, 0, 0, 0, 0] \n", + "41591 LVSEIDTGTLAQL [1, 0, 0, 0, 0, 0] \n", + "\n", + " collision_energy_aligned_normed \n", + "0 0.25 \n", + "1 0.28 \n", + "2 0.28 \n", + "3 0.30 \n", + "4 0.20 \n", + "... ... \n", + "41587 0.30 \n", + "41588 0.35 \n", + "41589 0.23 \n", + "41590 0.30 \n", + "41591 0.20 \n", + "\n", + "[41592 rows x 4 columns]" + ] + }, + "execution_count": 85, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "read_df" + ] + }, + { + "cell_type": "code", + "execution_count": 80, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 80, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.equals(read_df)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.0" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/spectrum_io/file/parquet.py b/spectrum_io/file/parquet.py new file mode 100644 index 0000000..fb2515e --- /dev/null +++ b/spectrum_io/file/parquet.py @@ -0,0 +1,90 @@ +import logging +from pathlib import Path +from typing import Union + +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq +import scipy + +# TODO add sparse matrix / anndata support +# TODO add speed benchmarks +# TODO add support for HuggingFace datasets API + +Pathlike = Union[Path, str] +Dataset = Union[pd.DataFrame, scipy.sparse.spmatrix] + +logger = logging.getLogger(__name__) + + +def read_file(path: Pathlike) -> pd.DataFrame: + """ + Read a Parquet file and return a Pandas DataFrame with its contents. + + :param path: Path to the Parquet file to read + :return: a Pandas DataFrame with the contents of the file + """ + return pd.read_parquet(path) + + +def read_partition(path: Pathlike, dataset_name: str) -> pd.DataFrame: + """ + Read a single table from a partitioned dataset. + + :param path: Root path of the partitioned dataset + :param dataset_name: Name of the dataset to extract + + :return: a Pandas DataFrame of the specified table from the partitioned dataset + """ + try: + dataset = pq.ParquetDataset(path, filters=[("dataset", "=", dataset_name)]) + df = dataset.read().to_pandas().drop("dataset", axis=1) + except pa.lib.ArrowNotImplementedError as e: + if dataset_name.isdigit(): + try: + logger.warning("Failed to read from partition using string of integer as key, trying with int...") + dataset = pq.ParquetDataset(path, filters=[("dataset", "=", int(dataset_name))]) + df = dataset.read().to_pandas().drop("dataset", axis=1) + except pa.lib.ArrowNotImplementedError as e: + logger.exception(e) + else: + logger.exception(e) + + return df + + +def write_file(data: Dataset, path: Pathlike) -> None: + """ + Writes a single DataFrame or matrix to a Parquet file. + + :param data: Data to store + :param path: Path to write the Parquet file to + """ + if isinstance(data, pd.DataFrame): + data.to_parquet(path) + else: + raise NotImplementedError + + +def write_partition(datasets: list[Dataset], path: Pathlike, dataset_names: list[str]) -> None: + """ + Write several datasets to a Parquet dataset as a directory containing subdirectories partinioned by dataset name. + + :param datasets: Datasets to write + :param path: Root path to write the partitioned dataset to + :param dataset_names: Names to assign to the datasets for retrieval. Careful: If all of these are strings of ints, Parquet will convert them to raw integers! + """ + if all(isinstance(x, pd.DataFrame) for x in datasets): + df = pd.concat([dataset.assign(dataset=name) for dataset, name in zip(datasets, dataset_names)]) + table = pa.Table.from_pandas(df) + else: + raise NotImplementedError + + path.mkdir(exist_ok=True) + + pq.write_to_dataset( + table, + root_path=path, + partition_cols=["dataset"], + existing_data_behavior="delete_matching", + ) diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py new file mode 100644 index 0000000..a87c71e --- /dev/null +++ b/tests/unit_tests/test_parquet.py @@ -0,0 +1,81 @@ +from pathlib import Path + +import pandas as pd +import pyarrow as pa +import pyarrow.parquet as pq +import pytest +import scipy + +from spectrum_io.file import parquet + + +class TestParquet: + """Test class to check Parquet file I/O""" + + def test_read_file(self, raw_data, tmpdir): + output_path = Path(tmpdir / "table.parquet") + pq.write_table(pa.Table.from_pydict(raw_data), output_path) + df = parquet.read_file(output_path) + pd.testing.assert_frame_equal(df, pd.DataFrame(raw_data)) + + def test_write_file(self, raw_data, tmpdir): + output_path = Path(tmpdir / "table.parquet") + df = pd.DataFrame(raw_data) + parquet.write_file(df, output_path) + pd.testing.assert_frame_equal(df, pd.read_parquet(output_path)) + + def test_read_write_partition(self, raw_data, tmpdir): + """Check whether data is unmodified after being written to and then read from a partitioned dataset""" + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data) + parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) + read_df = parquet.read_partition(output_path, "dataset_1") + pd.testing.assert_frame_equal(read_df, df) + + def test_read_write_partition_integer_key(self, raw_data, tmpdir): + """Check whether data is unmodified after being written to and then read from a partitioned dataset if strings of integers are used as keys, which Parquet converts to int for some reason""" + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data) + parquet.write_partition([df, df], output_path, ['1', '2']) + read_df = parquet.read_partition(output_path, '1') + pd.testing.assert_frame_equal(read_df, df) + + def test_modify_partition(self, raw_data, tmpdir): + """Check whether file content stays the same when writing new data to the same partitioned directory""" + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data) + parquet.write_partition([df, df], output_path, ['1', '2']) + parquet.write_partition([df, df, df], output_path, ['1', '2', '3']) + read_df = parquet.read_partition(output_path, '2') + pd.testing.assert_frame_equal(read_df, df) + + def test_write_not_implemented(self, raw_data, tmpdir): + with pytest.raises(NotImplementedError): + output_path = Path(tmpdir / "table.parquet") + df = pd.DataFrame(raw_data).to_numpy() + parquet.write_file(df, output_path) + + def test_read_write_partition_not_implemented(self, raw_data, tmpdir): + with pytest.raises(NotImplementedError): + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data).to_numpy() + parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) + +@pytest.fixture +def raw_data(): + """Simple toy MS data containing float, list[float], str, int, and list[int]""" + return { + "scan_number": [1, 234, 5678], + "intensities": [ + [4e-5, 0., -1., 0., 0., -1., 0.03, 0., -1., 0.4], + [.3, 0., -1., 1., 0., -1., 0.4, 0., -1., 0.05], + [.04, 0., 0., 0., 0., 0., 2e-3, 0., 0., .13] + ], + "sequence": ["SVFLTFLR", "KTSQIFLAK", "SPVGRVTPKEWR"], + "precursor_charge_onehot": [ + [0, 1, 0, 0, 0, 0], + [0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0], + ], + "collision_energy_normed": [.250827308624, .288798207462, .2887064038764] + } From 29f39c0be8209fb2703951308e00842e96e20a05 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Wed, 5 Jun 2024 14:14:38 +0000 Subject: [PATCH 10/33] Fix mypy and pre-commit tests failing --- .flake8 | 1 + spectrum_io/file/parquet.py | 20 ++++++++++++------- tests/unit_tests/test_parquet.py | 33 ++++++++++++++++++-------------- 3 files changed, 33 insertions(+), 21 deletions(-) diff --git a/.flake8 b/.flake8 index 7b0c786..0aa823d 100644 --- a/.flake8 +++ b/.flake8 @@ -6,6 +6,7 @@ max-complexity = 10 docstring-convention = google per-file-ignores = tests/*:S101,S301,S403 + tests/unit_tests/test_parquet.py:DAR101 noxfile.py:DAR101 spectrum_io/raw/thermo_raw.py:S603,S404 spectrum_io/raw/msraw.py:S405,S314 diff --git a/spectrum_io/file/parquet.py b/spectrum_io/file/parquet.py index fb2515e..1a9e327 100644 --- a/spectrum_io/file/parquet.py +++ b/spectrum_io/file/parquet.py @@ -39,26 +39,27 @@ def read_partition(path: Pathlike, dataset_name: str) -> pd.DataFrame: try: dataset = pq.ParquetDataset(path, filters=[("dataset", "=", dataset_name)]) df = dataset.read().to_pandas().drop("dataset", axis=1) - except pa.lib.ArrowNotImplementedError as e: + except pa.lib.ArrowNotImplementedError as e1: if dataset_name.isdigit(): try: logger.warning("Failed to read from partition using string of integer as key, trying with int...") dataset = pq.ParquetDataset(path, filters=[("dataset", "=", int(dataset_name))]) df = dataset.read().to_pandas().drop("dataset", axis=1) - except pa.lib.ArrowNotImplementedError as e: - logger.exception(e) + except pa.lib.ArrowNotImplementedError as e2: + logger.exception(e2) else: - logger.exception(e) + logger.exception(e1) return df def write_file(data: Dataset, path: Pathlike) -> None: - """ - Writes a single DataFrame or matrix to a Parquet file. + """Writes a single DataFrame or matrix to a Parquet file. :param data: Data to store :param path: Path to write the Parquet file to + + :raises NotImplementedError: if anything else but a Pandas DataFrame is used as the dataset """ if isinstance(data, pd.DataFrame): data.to_parquet(path) @@ -72,7 +73,10 @@ def write_partition(datasets: list[Dataset], path: Pathlike, dataset_names: list :param datasets: Datasets to write :param path: Root path to write the partitioned dataset to - :param dataset_names: Names to assign to the datasets for retrieval. Careful: If all of these are strings of ints, Parquet will convert them to raw integers! + :param dataset_names: Names to assign to the datasets for retrieval. Careful: If all of these are strings of ints, + Parquet will convert them to raw integers! + + :raises NotImplementedError: if anything else but a Pandas DataFrame is used as the dataset """ if all(isinstance(x, pd.DataFrame) for x in datasets): df = pd.concat([dataset.assign(dataset=name) for dataset, name in zip(datasets, dataset_names)]) @@ -80,6 +84,8 @@ def write_partition(datasets: list[Dataset], path: Pathlike, dataset_names: list else: raise NotImplementedError + if isinstance(path, str): + path = Path(path) path.mkdir(exist_ok=True) pq.write_to_dataset( diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py index a87c71e..0897949 100644 --- a/tests/unit_tests/test_parquet.py +++ b/tests/unit_tests/test_parquet.py @@ -10,22 +10,24 @@ class TestParquet: - """Test class to check Parquet file I/O""" + """Test class to check Parquet file I/O.""" def test_read_file(self, raw_data, tmpdir): + """Test read operation for a single dataset.""" output_path = Path(tmpdir / "table.parquet") pq.write_table(pa.Table.from_pydict(raw_data), output_path) df = parquet.read_file(output_path) pd.testing.assert_frame_equal(df, pd.DataFrame(raw_data)) def test_write_file(self, raw_data, tmpdir): + """Check write operation for a single dataset.""" output_path = Path(tmpdir / "table.parquet") df = pd.DataFrame(raw_data) parquet.write_file(df, output_path) pd.testing.assert_frame_equal(df, pd.read_parquet(output_path)) def test_read_write_partition(self, raw_data, tmpdir): - """Check whether data is unmodified after being written to and then read from a partitioned dataset""" + """Check whether data is unmodified after being written to and then read from a partitioned dataset.""" output_path = Path(tmpdir / "partition") df = pd.DataFrame(raw_data) parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) @@ -33,43 +35,46 @@ def test_read_write_partition(self, raw_data, tmpdir): pd.testing.assert_frame_equal(read_df, df) def test_read_write_partition_integer_key(self, raw_data, tmpdir): - """Check whether data is unmodified after being written to and then read from a partitioned dataset if strings of integers are used as keys, which Parquet converts to int for some reason""" + """Check whether Parquet's under-the-hood conversion of string to integer keys is handled seamlessly.""" output_path = Path(tmpdir / "partition") df = pd.DataFrame(raw_data) - parquet.write_partition([df, df], output_path, ['1', '2']) - read_df = parquet.read_partition(output_path, '1') + parquet.write_partition([df, df], output_path, ["1", "2"]) + read_df = parquet.read_partition(output_path, "1") pd.testing.assert_frame_equal(read_df, df) def test_modify_partition(self, raw_data, tmpdir): - """Check whether file content stays the same when writing new data to the same partitioned directory""" + """Check whether file content stays the same when writing new data to the same partitioned directory.""" output_path = Path(tmpdir / "partition") df = pd.DataFrame(raw_data) - parquet.write_partition([df, df], output_path, ['1', '2']) - parquet.write_partition([df, df, df], output_path, ['1', '2', '3']) - read_df = parquet.read_partition(output_path, '2') + parquet.write_partition([df, df], output_path, ["1", "2"]) + parquet.write_partition([df, df, df], output_path, ["1", "2", "3"]) + read_df = parquet.read_partition(output_path, "2") pd.testing.assert_frame_equal(read_df, df) def test_write_not_implemented(self, raw_data, tmpdir): + """Check whether write_file() raises a NotImplementedError if provided with an unsupported object.""" with pytest.raises(NotImplementedError): output_path = Path(tmpdir / "table.parquet") df = pd.DataFrame(raw_data).to_numpy() parquet.write_file(df, output_path) def test_read_write_partition_not_implemented(self, raw_data, tmpdir): + """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" with pytest.raises(NotImplementedError): output_path = Path(tmpdir / "partition") df = pd.DataFrame(raw_data).to_numpy() parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) + @pytest.fixture def raw_data(): - """Simple toy MS data containing float, list[float], str, int, and list[int]""" + """Simple toy MS data containing float, list[float], str, int, and list[int].""" return { "scan_number": [1, 234, 5678], "intensities": [ - [4e-5, 0., -1., 0., 0., -1., 0.03, 0., -1., 0.4], - [.3, 0., -1., 1., 0., -1., 0.4, 0., -1., 0.05], - [.04, 0., 0., 0., 0., 0., 2e-3, 0., 0., .13] + [4e-5, 0.0, -1.0, 0.0, 0.0, -1.0, 0.03, 0.0, -1.0, 0.4], + [0.3, 0.0, -1.0, 1.0, 0.0, -1.0, 0.4, 0.0, -1.0, 0.05], + [0.04, 0.0, 0.0, 0.0, 0.0, 0.0, 2e-3, 0.0, 0.0, 0.13], ], "sequence": ["SVFLTFLR", "KTSQIFLAK", "SPVGRVTPKEWR"], "precursor_charge_onehot": [ @@ -77,5 +82,5 @@ def raw_data(): [0, 1, 0, 0, 0, 0], [0, 0, 1, 0, 0, 0], ], - "collision_energy_normed": [.250827308624, .288798207462, .2887064038764] + "collision_energy_normed": [0.250827308624, 0.288798207462, 0.2887064038764], } From b883563b908df6afea5a4f03a0cb3ea7bc03fd20 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 11 Jun 2024 20:24:51 +0000 Subject: [PATCH 11/33] chore: upgrade Python version from 3.8 to 3.9 --- .github/workflows/run_tests.yml | 22 +- noxfile.py | 2 +- poetry.lock | 1953 +++++++++++++++++-------------- pyproject.toml | 3 +- requirements.txt | 86 +- 5 files changed, 1127 insertions(+), 939 deletions(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index d91eb1f..498ce29 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -19,47 +19,47 @@ jobs: matrix: include: - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "pre-commit", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "safety", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "mypy", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "tests", } - { - python-version: 3.8, + python-version: 3.9, os: windows-latest, session: "tests", } - { - python-version: 3.8, + python-version: 3.9, os: macos-latest, session: "tests", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "typeguard", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "xdoctest", } - { - python-version: 3.8, + python-version: 3.9, os: ubuntu-latest, session: "docs-build", } @@ -136,10 +136,10 @@ jobs: - name: Check out the repository uses: actions/checkout@v4 - - name: Set up Python 3.8 + - name: Set up Python 3.9 uses: actions/setup-python@v4 with: - python-version: 3.8 + python-version: 3.9 - 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python_full_version < "3.11.0" +pillow==10.3.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +psutil==5.9.8 ; python_version >= "3.9" and python_full_version < "3.11.0" +pyarrow==16.1.0 ; python_full_version >= "3.9" and python_full_version < "3.11.0" +pygments==2.17.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pymzml==2.5.9 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pyparsing==3.1.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +pyteomics==4.7.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_full_version < "3.11.0" +pytz==2024.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +pyyaml==6.0.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pyzstd==0.15.10 ; python_version >= "3.9" and python_full_version < "3.11.0" +regex==2024.4.16 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +rich==13.7.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +scikit-learn==1.3.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +scipy==1.10.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +six==1.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +sortedcontainers==2.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +spectrum-fundamentals==0.5.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +threadpoolctl==3.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +tqdm==4.66.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +typing-extensions==4.11.0 ; python_version >= "3.9" and python_version < "3.9" +zipp==3.18.1 ; python_version >= "3.9" and python_version < "3.10" From ece1b579c425f521bcff5bf162270fd95c8c13b6 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 11 Jun 2024 20:33:37 +0000 Subject: [PATCH 12/33] chore: Add exceptions for overly specific flake8 rules --- .flake8 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.flake8 b/.flake8 index 0aa823d..48185de 100644 --- a/.flake8 +++ b/.flake8 @@ -6,9 +6,9 @@ max-complexity = 10 docstring-convention = google per-file-ignores = tests/*:S101,S301,S403 - tests/unit_tests/test_parquet.py:DAR101 + tests/unit_tests/test_parquet.py:B908,DAR101 noxfile.py:DAR101 spectrum_io/raw/thermo_raw.py:S603,S404 - spectrum_io/raw/msraw.py:S405,S314 + spectrum_io/raw/msraw.py:B026,S405,S314 spectrum_io/d/masterSpectrum.py:C901 docs/conf.py:S404,S607,S603 From 9210c32197a88fbe15fb74067033c14e08fa0afe Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Thu, 13 Jun 2024 12:27:18 +0000 Subject: [PATCH 13/33] chore: suppress typeguard checking on tests intentionally using incompatible inputs --- tests/unit_tests/test_parquet.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py index 0897949..801decb 100644 --- a/tests/unit_tests/test_parquet.py +++ b/tests/unit_tests/test_parquet.py @@ -5,6 +5,7 @@ import pyarrow.parquet as pq import pytest import scipy +from typeguard import suppress_type_checks from spectrum_io.file import parquet @@ -53,14 +54,14 @@ def test_modify_partition(self, raw_data, tmpdir): def test_write_not_implemented(self, raw_data, tmpdir): """Check whether write_file() raises a NotImplementedError if provided with an unsupported object.""" - with pytest.raises(NotImplementedError): + with pytest.raises(NotImplementedError), suppress_type_checks(): output_path = Path(tmpdir / "table.parquet") df = pd.DataFrame(raw_data).to_numpy() parquet.write_file(df, output_path) def test_read_write_partition_not_implemented(self, raw_data, tmpdir): """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" - with pytest.raises(NotImplementedError): + with pytest.raises(NotImplementedError), suppress_type_checks(): output_path = Path(tmpdir / "partition") df = pd.DataFrame(raw_data).to_numpy() parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) From 51ebbb73b402316e23aea6a5a786e3bdca1baad5 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Thu, 13 Jun 2024 13:44:07 +0000 Subject: [PATCH 14/33] chore: fix pytest failing due to typeguard package import Only import and use the suppress_type_checks context decorator if a typeguard session is run by nox as it is not installed for other sessions --- tests/unit_tests/test_parquet.py | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py index 801decb..d87f609 100644 --- a/tests/unit_tests/test_parquet.py +++ b/tests/unit_tests/test_parquet.py @@ -1,3 +1,5 @@ +import sys +from contextlib import nullcontext from pathlib import Path import pandas as pd @@ -5,11 +7,11 @@ import pyarrow.parquet as pq import pytest import scipy -from typeguard import suppress_type_checks +if "typeguard" in sys.modules: + from typeguard import suppress_type_checks from spectrum_io.file import parquet - class TestParquet: """Test class to check Parquet file I/O.""" @@ -54,17 +56,19 @@ def test_modify_partition(self, raw_data, tmpdir): def test_write_not_implemented(self, raw_data, tmpdir): """Check whether write_file() raises a NotImplementedError if provided with an unsupported object.""" - with pytest.raises(NotImplementedError), suppress_type_checks(): - output_path = Path(tmpdir / "table.parquet") - df = pd.DataFrame(raw_data).to_numpy() - parquet.write_file(df, output_path) + with pytest.raises(NotImplementedError): + with (suppress_type_checks() if "typeguard" in sys.modules else nullcontext()): + output_path = Path(tmpdir / "table.parquet") + df = pd.DataFrame(raw_data).to_numpy() + parquet.write_file(df, output_path) def test_read_write_partition_not_implemented(self, raw_data, tmpdir): """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" - with pytest.raises(NotImplementedError), suppress_type_checks(): - output_path = Path(tmpdir / "partition") - df = pd.DataFrame(raw_data).to_numpy() - parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) + with pytest.raises(NotImplementedError): + with (suppress_type_checks() if "typeguard" in sys.modules else nullcontext()): + output_path = Path(tmpdir / "partition") + df = pd.DataFrame(raw_data).to_numpy() + parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) @pytest.fixture From 0582608e5b6035ed55497bf20b228eb9a8f4bdcc Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Thu, 13 Jun 2024 13:46:41 +0000 Subject: [PATCH 15/33] chore: fix typeguard version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 1d4a889..a4bf07d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ sortedcontainers = "^2.4.0" pytest = ">=6.2.3" coverage = {extras = ["toml"], version = ">=5.3"} safety = ">=1.9.0" -typeguard = ">=2.12.0" +typeguard = ">=3.0.0" xdoctest = {extras = ["colors"], version = ">=0.15.0"} sphinx = ">=4.0.2" sphinx-autobuild = ">=2021.3.14" From 53c65d0ec66872161110696d96b26615d4aaa4ea Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Thu, 13 Jun 2024 13:46:50 +0000 Subject: [PATCH 16/33] chore: formatting --- tests/unit_tests/test_parquet.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py index d87f609..ce1209a 100644 --- a/tests/unit_tests/test_parquet.py +++ b/tests/unit_tests/test_parquet.py @@ -7,11 +7,13 @@ import pyarrow.parquet as pq import pytest import scipy + if "typeguard" in sys.modules: from typeguard import suppress_type_checks from spectrum_io.file import parquet + class TestParquet: """Test class to check Parquet file I/O.""" @@ -57,7 +59,7 @@ def test_modify_partition(self, raw_data, tmpdir): def test_write_not_implemented(self, raw_data, tmpdir): """Check whether write_file() raises a NotImplementedError if provided with an unsupported object.""" with pytest.raises(NotImplementedError): - with (suppress_type_checks() if "typeguard" in sys.modules else nullcontext()): + with suppress_type_checks() if "typeguard" in sys.modules else nullcontext(): output_path = Path(tmpdir / "table.parquet") df = pd.DataFrame(raw_data).to_numpy() parquet.write_file(df, output_path) @@ -65,7 +67,7 @@ def test_write_not_implemented(self, raw_data, tmpdir): def test_read_write_partition_not_implemented(self, raw_data, tmpdir): """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" with pytest.raises(NotImplementedError): - with (suppress_type_checks() if "typeguard" in sys.modules else nullcontext()): + with suppress_type_checks() if "typeguard" in sys.modules else nullcontext(): output_path = Path(tmpdir / "partition") df = pd.DataFrame(raw_data).to_numpy() parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) From d55c808d4af4111d07cddf602a79dccae3329746 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 24 Jun 2024 13:34:53 +0200 Subject: [PATCH 17/33] updated hash --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 238672d..8ef987e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3505,4 +3505,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.11.0" -content-hash = "f8fec61b24f313fe2a3c176f99706d9f9cd2acd7bb84553d3df11e5a59d710ae" +content-hash = "f81f7865699214a187651984ecd930f75f5c364890f55a25a553375b8c19faad" From 263485247724f75eafb989b48444814875d59d76 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 24 Jun 2024 13:35:06 +0200 Subject: [PATCH 18/33] ignored 70612 vulnerability in safety checks --- noxfile.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/noxfile.py b/noxfile.py index 28fdff8..a62a8fb 100644 --- a/noxfile.py +++ b/noxfile.py @@ -125,9 +125,10 @@ def precommit(session: Session) -> None: @session(python=python_versions) def safety(session: Session) -> None: """Scan dependencies for insecure packages.""" + to_ignore = "--ignore=70612" requirements = session.poetry.export_requirements() session.install("safety") - session.run("safety", "check", "--full-report", f"--file={requirements}") + session.run("safety", "check", "--full-report", f"--file={requirements}", to_ignore) @session(python=python_versions) From 282f31c83391adc3c5fee67b6a283da83dbab0b1 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 24 Jun 2024 13:39:19 +0200 Subject: [PATCH 19/33] updated workflow python versions to 3.9 --- .github/workflows/build_package.yml | 2 +- .github/workflows/publish_docs.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index 00e9570..451d158 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -9,7 +9,7 @@ jobs: strategy: matrix: os: [macos-latest, ubuntu-latest, windows-latest] - python: [3.8, 3.9] + python: [3.9, 3.10] steps: - uses: actions/checkout@v4 diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml index 11d3f2e..9e46e49 100644 --- a/.github/workflows/publish_docs.yml +++ b/.github/workflows/publish_docs.yml @@ -13,7 +13,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v4 with: - python-version: 3.8 + python-version: 3.9 - name: Install pip run: | From 702cf43d3411990076c391c0c7398a4ee233c253 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 24 Jun 2024 13:42:10 +0200 Subject: [PATCH 20/33] fix version number interpretation by quotation --- .github/workflows/build_package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index 451d158..13d080e 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -9,7 +9,7 @@ jobs: strategy: matrix: os: [macos-latest, ubuntu-latest, windows-latest] - python: [3.9, 3.10] + python: ["3.9", "3.10"] steps: - uses: actions/checkout@v4 From c59dbfc601238dfd6b3752a8b9607345aa36650b Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 25 Jun 2024 09:52:11 +0000 Subject: [PATCH 21/33] chore: Remove generic typing --- spectrum_io/file/parquet.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/spectrum_io/file/parquet.py b/spectrum_io/file/parquet.py index 1a9e327..8fc164f 100644 --- a/spectrum_io/file/parquet.py +++ b/spectrum_io/file/parquet.py @@ -1,6 +1,6 @@ import logging from pathlib import Path -from typing import Union +from typing import List, Union import pandas as pd import pyarrow as pa @@ -67,7 +67,7 @@ def write_file(data: Dataset, path: Pathlike) -> None: raise NotImplementedError -def write_partition(datasets: list[Dataset], path: Pathlike, dataset_names: list[str]) -> None: +def write_partition(datasets: List[Dataset], path: Pathlike, dataset_names: List[str]) -> None: """ Write several datasets to a Parquet dataset as a directory containing subdirectories partinioned by dataset name. From b306a8e3f04907425fbb7804903b8343a1749af7 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 25 Jun 2024 10:12:15 +0000 Subject: [PATCH 22/33] chore: fix flake8 rule B026 --- .flake8 | 2 +- spectrum_io/raw/msraw.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.flake8 b/.flake8 index 48185de..e416c1f 100644 --- a/.flake8 +++ b/.flake8 @@ -9,6 +9,6 @@ per-file-ignores = tests/unit_tests/test_parquet.py:B908,DAR101 noxfile.py:DAR101 spectrum_io/raw/thermo_raw.py:S603,S404 - spectrum_io/raw/msraw.py:B026,S405,S314 + spectrum_io/raw/msraw.py:S405,S314 spectrum_io/d/masterSpectrum.py:C901 docs/conf.py:S404,S607,S603 diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index f85708e..9157716 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -217,7 +217,7 @@ def _read_mzml_pyteomics(file_list: List[Path], *args, **kwargs) -> pd.DataFrame for file_path in file_list: mass_analyzer = get_mass_analyzer(file_path) logger.info(f"Reading mzML file: {file_path}") - data_iter = mzml.read(source=str(file_path), *args, **kwargs) + data_iter = mzml.read(str(file_path), *args, **kwargs) file_name = file_path.stem try: instrument_params = data_iter.get_by_id("commonInstrumentParams") From 76819fbb0c2c90145670f85976f9a418a17cf223 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 25 Jun 2024 10:29:01 +0000 Subject: [PATCH 23/33] chore(parquet): delete output paths after writing --- tests/unit_tests/test_parquet.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py index ce1209a..61e9cf9 100644 --- a/tests/unit_tests/test_parquet.py +++ b/tests/unit_tests/test_parquet.py @@ -1,3 +1,4 @@ +import shutil import sys from contextlib import nullcontext from pathlib import Path @@ -22,6 +23,7 @@ def test_read_file(self, raw_data, tmpdir): output_path = Path(tmpdir / "table.parquet") pq.write_table(pa.Table.from_pydict(raw_data), output_path) df = parquet.read_file(output_path) + output_path.unlink() pd.testing.assert_frame_equal(df, pd.DataFrame(raw_data)) def test_write_file(self, raw_data, tmpdir): @@ -30,6 +32,7 @@ def test_write_file(self, raw_data, tmpdir): df = pd.DataFrame(raw_data) parquet.write_file(df, output_path) pd.testing.assert_frame_equal(df, pd.read_parquet(output_path)) + output_path.unlink() def test_read_write_partition(self, raw_data, tmpdir): """Check whether data is unmodified after being written to and then read from a partitioned dataset.""" @@ -37,6 +40,7 @@ def test_read_write_partition(self, raw_data, tmpdir): df = pd.DataFrame(raw_data) parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) read_df = parquet.read_partition(output_path, "dataset_1") + shutil.rmtree(output_path) pd.testing.assert_frame_equal(read_df, df) def test_read_write_partition_integer_key(self, raw_data, tmpdir): @@ -45,6 +49,7 @@ def test_read_write_partition_integer_key(self, raw_data, tmpdir): df = pd.DataFrame(raw_data) parquet.write_partition([df, df], output_path, ["1", "2"]) read_df = parquet.read_partition(output_path, "1") + shutil.rmtree(output_path) pd.testing.assert_frame_equal(read_df, df) def test_modify_partition(self, raw_data, tmpdir): @@ -54,6 +59,7 @@ def test_modify_partition(self, raw_data, tmpdir): parquet.write_partition([df, df], output_path, ["1", "2"]) parquet.write_partition([df, df, df], output_path, ["1", "2", "3"]) read_df = parquet.read_partition(output_path, "2") + shutil.rmtree(output_path) pd.testing.assert_frame_equal(read_df, df) def test_write_not_implemented(self, raw_data, tmpdir): @@ -63,6 +69,7 @@ def test_write_not_implemented(self, raw_data, tmpdir): output_path = Path(tmpdir / "table.parquet") df = pd.DataFrame(raw_data).to_numpy() parquet.write_file(df, output_path) + output_path.unlink() def test_read_write_partition_not_implemented(self, raw_data, tmpdir): """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" @@ -71,6 +78,7 @@ def test_read_write_partition_not_implemented(self, raw_data, tmpdir): output_path = Path(tmpdir / "partition") df = pd.DataFrame(raw_data).to_numpy() parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) + output_path.unlink() @pytest.fixture From 42a3ead25eaa3ef6eead5121c375913d1204419e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 26 Jun 2024 14:30:23 +0000 Subject: [PATCH 24/33] [DEPENDABOT]: Bump actions/setup-python from 4 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/build_package.yml | 2 +- .github/workflows/main_master_branch_protection.yml | 2 +- .github/workflows/publish_docs.yml | 2 +- .github/workflows/publish_package.yml | 2 +- .github/workflows/run_cookietemple_lint.yml | 2 +- .github/workflows/run_tests.yml | 4 ++-- .github/workflows/sync_project.yml | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index 13d080e..1c6ba69 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -16,7 +16,7 @@ jobs: name: Check out source-code repository - name: Setup Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python }} diff --git a/.github/workflows/main_master_branch_protection.yml b/.github/workflows/main_master_branch_protection.yml index 659088d..0b4f741 100644 --- a/.github/workflows/main_master_branch_protection.yml +++ b/.github/workflows/main_master_branch_protection.yml @@ -40,7 +40,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: "3.8" # PRs to the repository master branch are only ok if coming from any patch or release branch diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml index 9e46e49..98413b6 100644 --- a/.github/workflows/publish_docs.yml +++ b/.github/workflows/publish_docs.yml @@ -11,7 +11,7 @@ jobs: name: Check out source-code repository - name: Setup Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.9 diff --git a/.github/workflows/publish_package.yml b/.github/workflows/publish_package.yml index 55c2129..e9b2249 100644 --- a/.github/workflows/publish_package.yml +++ b/.github/workflows/publish_package.yml @@ -15,7 +15,7 @@ jobs: fetch-depth: 2 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: "3.9" diff --git a/.github/workflows/run_cookietemple_lint.yml b/.github/workflows/run_cookietemple_lint.yml index d519f57..35b5a05 100644 --- a/.github/workflows/run_cookietemple_lint.yml +++ b/.github/workflows/run_cookietemple_lint.yml @@ -11,7 +11,7 @@ jobs: name: Check out source-code repository - name: Setup Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.9 diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 498ce29..4449a3e 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -72,7 +72,7 @@ jobs: uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} @@ -137,7 +137,7 @@ jobs: uses: actions/checkout@v4 - name: Set up Python 3.9 - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.9 diff --git a/.github/workflows/sync_project.yml b/.github/workflows/sync_project.yml index 6c7088d..6c29813 100644 --- a/.github/workflows/sync_project.yml +++ b/.github/workflows/sync_project.yml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Setup Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.8 From a8b82242816f49da14d11dcbd4c20b10831bbc25 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 26 Jun 2024 14:31:44 +0000 Subject: [PATCH 25/33] [DEPENDABOT]: Bump coverage from 7.5.2 to 7.5.4 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.5.2 to 7.5.4. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.5.2...7.5.4) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... 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"cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "from pathlib import Path\n", - "from typing import Union\n", - "\n", - "import datasets\n", - "import pandas as pd\n", - "import pyarrow as pa\n", - "import pyarrow.feather as feather\n", - "import pyarrow.parquet as pq\n", - "import scipy\n", - "\n", - "from parquet import *" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "root_path = Path(\"/cmnfs/proj/prosit_astral/datasets/parquet\")\n", - "train_path = root_path / \"train\"" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "385ec5beebab46e6933deda6d071ca39", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "Resolving data files: 0%| | 0/78 [00:00\u001b[39m max_shard_size:\n\u001b[0;32m-> 1997\u001b[0m num_examples, num_bytes \u001b[39m=\u001b[39m writer\u001b[39m.\u001b[39;49mfinalize()\n\u001b[1;32m 1998\u001b[0m writer\u001b[39m.\u001b[39mclose()\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:607\u001b[0m, in \u001b[0;36mArrowWriter.finalize\u001b[0;34m(self, close_stream)\u001b[0m\n\u001b[1;32m 606\u001b[0m \u001b[39mif\u001b[39;00m close_stream:\n\u001b[0;32m--> 607\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mstream\u001b[39m.\u001b[39;49mclose()\n\u001b[1;32m 608\u001b[0m \u001b[39melse\u001b[39;00m:\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/fsspec/implementations/local.py:407\u001b[0m, in \u001b[0;36mLocalFileOpener.close\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 406\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mclose\u001b[39m(\u001b[39mself\u001b[39m):\n\u001b[0;32m--> 407\u001b[0m \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mf\u001b[39m.\u001b[39;49mclose()\n", - "\u001b[0;31mKeyboardInterrupt\u001b[0m: ", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:2027\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split_single\u001b[0;34m(self, gen_kwargs, fpath, file_format, max_shard_size, job_id)\u001b[0m\n\u001b[1;32m 2026\u001b[0m num_shards \u001b[39m=\u001b[39m shard_id \u001b[39m+\u001b[39m \u001b[39m1\u001b[39m\n\u001b[0;32m-> 2027\u001b[0m num_examples, num_bytes \u001b[39m=\u001b[39m writer\u001b[39m.\u001b[39;49mfinalize()\n\u001b[1;32m 2028\u001b[0m writer\u001b[39m.\u001b[39mclose()\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:602\u001b[0m, in \u001b[0;36mArrowWriter.finalize\u001b[0;34m(self, close_stream)\u001b[0m\n\u001b[1;32m 601\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39mand\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mschema:\n\u001b[0;32m--> 602\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_build_writer(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mschema)\n\u001b[1;32m 603\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/arrow_writer.py:404\u001b[0m, in \u001b[0;36mArrowWriter._build_writer\u001b[0;34m(self, inferred_schema)\u001b[0m\n\u001b[1;32m 403\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_schema \u001b[39m=\u001b[39m schema\n\u001b[0;32m--> 404\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mpa_writer \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_WRITER_CLASS(\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mstream, schema)\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/ipc.py:85\u001b[0m, in \u001b[0;36mRecordBatchStreamWriter.__init__\u001b[0;34m(self, sink, schema, use_legacy_format, options)\u001b[0m\n\u001b[1;32m 84\u001b[0m options \u001b[39m=\u001b[39m _get_legacy_format_default(use_legacy_format, options)\n\u001b[0;32m---> 85\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_open(sink, schema, options\u001b[39m=\u001b[39;49moptions)\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/ipc.pxi:582\u001b[0m, in \u001b[0;36mpyarrow.lib._RecordBatchStreamWriter._open\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:2097\u001b[0m, in \u001b[0;36mpyarrow.lib.get_writer\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:232\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile.get_output_stream\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:246\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile._assert_writable\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/pyarrow/io.pxi:237\u001b[0m, in \u001b[0;36mpyarrow.lib.NativeFile._assert_open\u001b[0;34m()\u001b[0m\n", - "\u001b[0;31mValueError\u001b[0m: I/O operation on closed file", - "\nThe above exception was the direct cause of the following exception:\n", - "\u001b[0;31mDatasetGenerationError\u001b[0m Traceback (most recent call last)", - "\u001b[1;32m/cmnfs/home/students/j.schlensok/spectrum_io/spectrum_io/file/parquet.ipynb Cell 3\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> 1\u001b[0m ds \u001b[39m=\u001b[39m datasets\u001b[39m.\u001b[39;49mload_dataset(\u001b[39mstr\u001b[39;49m(root_path))\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/load.py:2609\u001b[0m, in \u001b[0;36mload_dataset\u001b[0;34m(path, name, data_dir, data_files, split, cache_dir, features, download_config, download_mode, verification_mode, ignore_verifications, keep_in_memory, save_infos, revision, token, use_auth_token, task, streaming, num_proc, storage_options, trust_remote_code, **config_kwargs)\u001b[0m\n\u001b[1;32m 2606\u001b[0m \u001b[39mreturn\u001b[39;00m builder_instance\u001b[39m.\u001b[39mas_streaming_dataset(split\u001b[39m=\u001b[39msplit)\n\u001b[1;32m 2608\u001b[0m \u001b[39m# Download and prepare data\u001b[39;00m\n\u001b[0;32m-> 2609\u001b[0m builder_instance\u001b[39m.\u001b[39;49mdownload_and_prepare(\n\u001b[1;32m 2610\u001b[0m download_config\u001b[39m=\u001b[39;49mdownload_config,\n\u001b[1;32m 2611\u001b[0m download_mode\u001b[39m=\u001b[39;49mdownload_mode,\n\u001b[1;32m 2612\u001b[0m verification_mode\u001b[39m=\u001b[39;49mverification_mode,\n\u001b[1;32m 2613\u001b[0m num_proc\u001b[39m=\u001b[39;49mnum_proc,\n\u001b[1;32m 2614\u001b[0m storage_options\u001b[39m=\u001b[39;49mstorage_options,\n\u001b[1;32m 2615\u001b[0m )\n\u001b[1;32m 2617\u001b[0m \u001b[39m# Build dataset for splits\u001b[39;00m\n\u001b[1;32m 2618\u001b[0m keep_in_memory \u001b[39m=\u001b[39m (\n\u001b[1;32m 2619\u001b[0m keep_in_memory \u001b[39mif\u001b[39;00m keep_in_memory \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39melse\u001b[39;00m is_small_dataset(builder_instance\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39mdataset_size)\n\u001b[1;32m 2620\u001b[0m )\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1027\u001b[0m, in \u001b[0;36mDatasetBuilder.download_and_prepare\u001b[0;34m(self, output_dir, download_config, download_mode, verification_mode, ignore_verifications, try_from_hf_gcs, dl_manager, base_path, use_auth_token, file_format, max_shard_size, num_proc, storage_options, **download_and_prepare_kwargs)\u001b[0m\n\u001b[1;32m 1025\u001b[0m \u001b[39mif\u001b[39;00m num_proc \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m 1026\u001b[0m prepare_split_kwargs[\u001b[39m\"\u001b[39m\u001b[39mnum_proc\u001b[39m\u001b[39m\"\u001b[39m] \u001b[39m=\u001b[39m num_proc\n\u001b[0;32m-> 1027\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_download_and_prepare(\n\u001b[1;32m 1028\u001b[0m dl_manager\u001b[39m=\u001b[39;49mdl_manager,\n\u001b[1;32m 1029\u001b[0m verification_mode\u001b[39m=\u001b[39;49mverification_mode,\n\u001b[1;32m 1030\u001b[0m \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mprepare_split_kwargs,\n\u001b[1;32m 1031\u001b[0m \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mdownload_and_prepare_kwargs,\n\u001b[1;32m 1032\u001b[0m )\n\u001b[1;32m 1033\u001b[0m \u001b[39m# Sync info\u001b[39;00m\n\u001b[1;32m 1034\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39mdataset_size \u001b[39m=\u001b[39m \u001b[39msum\u001b[39m(split\u001b[39m.\u001b[39mnum_bytes \u001b[39mfor\u001b[39;00m split \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39minfo\u001b[39m.\u001b[39msplits\u001b[39m.\u001b[39mvalues())\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1122\u001b[0m, in \u001b[0;36mDatasetBuilder._download_and_prepare\u001b[0;34m(self, dl_manager, verification_mode, **prepare_split_kwargs)\u001b[0m\n\u001b[1;32m 1118\u001b[0m split_dict\u001b[39m.\u001b[39madd(split_generator\u001b[39m.\u001b[39msplit_info)\n\u001b[1;32m 1120\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[1;32m 1121\u001b[0m \u001b[39m# Prepare split will record examples associated to the split\u001b[39;00m\n\u001b[0;32m-> 1122\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_prepare_split(split_generator, \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mprepare_split_kwargs)\n\u001b[1;32m 1123\u001b[0m \u001b[39mexcept\u001b[39;00m \u001b[39mOSError\u001b[39;00m \u001b[39mas\u001b[39;00m e:\n\u001b[1;32m 1124\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mOSError\u001b[39;00m(\n\u001b[1;32m 1125\u001b[0m \u001b[39m\"\u001b[39m\u001b[39mCannot find data file. \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m 1126\u001b[0m \u001b[39m+\u001b[39m (\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmanual_download_instructions \u001b[39mor\u001b[39;00m \u001b[39m\"\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m 1127\u001b[0m \u001b[39m+\u001b[39m \u001b[39m\"\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39mOriginal error:\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39m\"\u001b[39m\n\u001b[1;32m 1128\u001b[0m \u001b[39m+\u001b[39m \u001b[39mstr\u001b[39m(e)\n\u001b[1;32m 1129\u001b[0m ) \u001b[39mfrom\u001b[39;00m \u001b[39mNone\u001b[39;00m\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:1882\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split\u001b[0;34m(self, split_generator, file_format, num_proc, max_shard_size)\u001b[0m\n\u001b[1;32m 1880\u001b[0m job_id \u001b[39m=\u001b[39m \u001b[39m0\u001b[39m\n\u001b[1;32m 1881\u001b[0m \u001b[39mwith\u001b[39;00m pbar:\n\u001b[0;32m-> 1882\u001b[0m \u001b[39mfor\u001b[39;00m job_id, done, content \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_prepare_split_single(\n\u001b[1;32m 1883\u001b[0m gen_kwargs\u001b[39m=\u001b[39mgen_kwargs, job_id\u001b[39m=\u001b[39mjob_id, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39m_prepare_split_args\n\u001b[1;32m 1884\u001b[0m ):\n\u001b[1;32m 1885\u001b[0m \u001b[39mif\u001b[39;00m done:\n\u001b[1;32m 1886\u001b[0m result \u001b[39m=\u001b[39m content\n", - "File \u001b[0;32m~/micromamba/envs/spectrum-io/lib/python3.10/site-packages/datasets/builder.py:2038\u001b[0m, in \u001b[0;36mArrowBasedBuilder._prepare_split_single\u001b[0;34m(self, gen_kwargs, fpath, file_format, max_shard_size, job_id)\u001b[0m\n\u001b[1;32m 2036\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39misinstance\u001b[39m(e, DatasetGenerationError):\n\u001b[1;32m 2037\u001b[0m \u001b[39mraise\u001b[39;00m\n\u001b[0;32m-> 2038\u001b[0m \u001b[39mraise\u001b[39;00m DatasetGenerationError(\u001b[39m\"\u001b[39m\u001b[39mAn error occurred while generating the dataset\u001b[39m\u001b[39m\"\u001b[39m) \u001b[39mfrom\u001b[39;00m \u001b[39me\u001b[39;00m\n\u001b[1;32m 2040\u001b[0m \u001b[39myield\u001b[39;00m job_id, \u001b[39mTrue\u001b[39;00m, (total_num_examples, total_num_bytes, writer\u001b[39m.\u001b[39m_features, num_shards, shard_lengths)\n", - "\u001b[0;31mDatasetGenerationError\u001b[0m: An error occurred while generating the dataset" - ] - } - ], - "source": [ - "ds = datasets.load_dataset(str(root_path))" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "input_test_file = Path.cwd().parent.parent.parent / \"oktoberfest/data/intensity_data.parquet\"\n", - "raw_data = {\n", - " \"intensities\": [\n", - " [4e-5, 0., -1., 0., 0., -1., 0.03, 0., -1., 0.4],\n", - " [.3, 0., -1., 1., 0., -1., 0.4, 0., -1., 0.05],\n", - " [.04, 0., 0., 0., 0., 0., 2e-3, 0., 0., .13]\n", - " ],\n", - " \"sequence\": [\"SVFLTFLR\", \"KTSQIFLAK\", \"SPVGRVTPKEWR\"],\n", - " \"precursor_charge_onehot\": [\n", - " [0, 1, 0, 0, 0, 0],\n", - " [0, 1, 0, 0, 0, 0],\n", - " [0, 0, 1, 0, 0, 0],\n", - " ],\n", - " \"collision_energy_normed\": [.25, .28, .28]\n", - "}" - ] - }, - { - "cell_type": "code", - "execution_count": 42, - "metadata": {}, - "outputs": [], - "source": [ - "output_path = Path.cwd() / \"temp\"\n", - "output_path.mkdir(exist_ok=True)\n", - "\n", - "df = pd.DataFrame(raw_data)\n", - "\n", - "#df2 = pd.concat([df, df], keys=['1', '2'], names=[\"dataset\", \"index\"])\n", - "df2 = pd.concat([df.assign(dataset='1'), df.assign(dataset='2')])\n", - "table = pa.Table.from_pandas(df2)\n", - "\n", - "pq.write_to_dataset(\n", - " table,\n", - " root_path=output_path,\n", - " partition_cols=[\"dataset\"],\n", - " existing_data_behavior=\"delete_matching\",\n", - ")" - ] - }, - { - "cell_type": "code", - "execution_count": 43, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "pyarrow.Table\n", - "intensities: list\n", - " child 0, item: double\n", - "sequence: string\n", - "precursor_charge_onehot: list\n", - " child 0, item: int64\n", - "collision_energy_normed: double\n", - "dataset: string\n", - "__index_level_0__: int64\n", - "----\n", - "intensities: [[[0.00004,0,-1,0,0,-1,0.03,0,-1,0.4],[0.3,0,-1,1,0,-1,0.4,0,-1,0.05],...,[0.3,0,-1,1,0,-1,0.4,0,-1,0.05],[0.04,0,0,0,0,0,0.002,0,0,0.13]]]\n", - "sequence: [[\"SVFLTFLR\",\"KTSQIFLAK\",\"SPVGRVTPKEWR\",\"SVFLTFLR\",\"KTSQIFLAK\",\"SPVGRVTPKEWR\"]]\n", - "precursor_charge_onehot: [[[0,1,0,0,0,0],[0,1,0,0,0,0],...,[0,1,0,0,0,0],[0,0,1,0,0,0]]]\n", - "collision_energy_normed: [[0.25,0.28,0.28,0.25,0.28,0.28]]\n", - "dataset: [[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"]]\n", - "__index_level_0__: [[0,1,2,0,1,2]]" - ] - }, - "execution_count": 43, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "table" - ] - }, - { - "cell_type": "code", - "execution_count": 44, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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intensitiessequenceprecursor_charge_onehotcollision_energy_normed
0[4e-05, 0.0, -1.0, 0.0, 0.0, -1.0, 0.03, 0.0, ...SVFLTFLR[0, 1, 0, 0, 0, 0]0.25
1[0.3, 0.0, -1.0, 1.0, 0.0, -1.0, 0.4, 0.0, -1....KTSQIFLAK[0, 1, 0, 0, 0, 0]0.28
2[0.04, 0.0, 0.0, 0.0, 0.0, 0.0, 0.002, 0.0, 0....SPVGRVTPKEWR[0, 0, 1, 0, 0, 0]0.28
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" - ], - "text/plain": [ - " intensities sequence \\\n", - "0 [4e-05, 0.0, -1.0, 0.0, 0.0, -1.0, 0.03, 0.0, ... SVFLTFLR \n", - "1 [0.3, 0.0, -1.0, 1.0, 0.0, -1.0, 0.4, 0.0, -1.... KTSQIFLAK \n", - "2 [0.04, 0.0, 0.0, 0.0, 0.0, 0.0, 0.002, 0.0, 0.... SPVGRVTPKEWR \n", - "\n", - " precursor_charge_onehot collision_energy_normed \n", - "0 [0, 1, 0, 0, 0, 0] 0.25 \n", - "1 [0, 1, 0, 0, 0, 0] 0.28 \n", - "2 [0, 0, 1, 0, 0, 0] 0.28 " - ] - }, - "execution_count": 44, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "dataset = pq.ParquetDataset(output_path, filters=[(\"dataset\", \"=\", '1')])\n", - "df = dataset.read().to_pandas().drop(\"dataset\", axis=1)\n", - "df#.to_pandas()\n", - "#read_df = read_partition(output_path, '1')\n", - "#pd.testing.assert_frame_equal(read_df, df)" - ] - }, - { - "cell_type": "code", - "execution_count": 64, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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intensitiessequenceprecursor_charge_onehotcollision_energy_aligned_normed
0[0.03713018032121684, 0.0, -1.0, 0.0, 0.0, -1....SVFLTFLR[0, 1, 0, 0, 0, 0]0.25
1[0.32880081359926777, 0.0, -1.0, 1.0, 0.0, -1....KTSQIFLAK[0, 1, 0, 0, 0, 0]0.28
2[0.03919235848040409, 0.0, 0.0, 0.0, 0.0, 0.0,...SPVGRVTPKEWR[0, 0, 1, 0, 0, 0]0.28
3[0.11537762755556774, 0.0, 0.0, 0.0, 0.0, 0.0,...SHIWPEYCSRALR[0, 0, 1, 0, 0, 0]0.30
4[0.003340655605539741, 0.0, 0.0, 0.00303169307...ELESQISELQEDLESERASR[0, 0, 1, 0, 0, 0]0.20
...............
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41588[0.036119027089409034, 0.0, 0.0, 0.0, 0.0, 0.0...AYVGLERFLAGLRDY[0, 0, 1, 0, 0, 0]0.35
41589[0.036547268719584185, 0.0, 0.0, 0.0, 0.0, 0.0...AACLLTKWTAGR[0, 0, 1, 0, 0, 0]0.23
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intensitiessequenceprecursor_charge_onehotcollision_energy_aligned_normed
datasetindex
10[0.03713018032121684, 0.0, -1.0, 0.0, 0.0, -1....SVFLTFLR[0, 1, 0, 0, 0, 0]0.25
1[0.32880081359926777, 0.0, -1.0, 1.0, 0.0, -1....KTSQIFLAK[0, 1, 0, 0, 0, 0]0.28
2[0.03919235848040409, 0.0, 0.0, 0.0, 0.0, 0.0,...SPVGRVTPKEWR[0, 0, 1, 0, 0, 0]0.28
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4[0.003340655605539741, 0.0, 0.0, 0.00303169307...ELESQISELQEDLESERASR[0, 0, 1, 0, 0, 0]0.20
..................
241587[0.12310221158139793, 0.0, 0.0, 0.0, 0.0, 0.0,...LKFEEITGVINPALDKYFPSDSGVR[0, 0, 1, 0, 0, 0]0.30
41588[0.036119027089409034, 0.0, 0.0, 0.0, 0.0, 0.0...AYVGLERFLAGLRDY[0, 0, 1, 0, 0, 0]0.35
41589[0.036547268719584185, 0.0, 0.0, 0.0, 0.0, 0.0...AACLLTKWTAGR[0, 0, 1, 0, 0, 0]0.23
41590[0.053176686541959346, -1.0, -1.0, 0.0, -1.0, ...SLEKLEIIPASQ[1, 0, 0, 0, 0, 0]0.30
41591[0.0, -1.0, -1.0, 0.0, -1.0, -1.0, 0.055506936...LVSEIDTGTLAQL[1, 0, 0, 0, 0, 0]0.20
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Refer to documentation # for a list of supported languages. diff --git a/pyproject.toml b/pyproject.toml index a4bf07d..bb71091 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "spectrum_io" -version = "0.4.4" # <> +version = "0.5.0" # <> description = "IO related functionalities for oktoberfest." authors = ["Wilhelmlab at Technical University of Munich"] license = "MIT" diff --git a/spectrum_io/__init__.py b/spectrum_io/__init__.py index 8130fd6..3c1c5b3 100644 --- a/spectrum_io/__init__.py +++ b/spectrum_io/__init__.py @@ -2,7 +2,7 @@ __author__ = "Mario Picciani" __email__ = "mario.picciani@tum.de" -__version__ = "0.4.4" +__version__ = "0.5.0" import logging import logging.handlers diff --git a/spectrum_io/__main__.py b/spectrum_io/__main__.py index 98dd70d..cf36531 100644 --- a/spectrum_io/__main__.py +++ b/spectrum_io/__main__.py @@ -5,7 +5,7 @@ @click.command() -@click.version_option(version="0.4.4", message=click.style("spectrum_io Version: 0.4.4")) +@click.version_option(version="0.5.0", message=click.style("spectrum_io Version: 0.5.0")) def main() -> None: """spectrum_io.""" From 2d8ec2c3e0d3168baaeadb856f7372a09534477f Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 8 Jul 2024 16:39:58 +0200 Subject: [PATCH 30/33] updated required spectrum_fundamentals version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index bb71091..bdbd302 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ pyarrow = ">=16.0.0" pymzml = "^2.5.0" pyteomics = "^4.3.3" lxml= '>=4.5.2,<6.0.0' -spectrum-fundamentals = ">=0.5.4,<0.6.0" +spectrum-fundamentals = ">=0.6.0,<0.7.0" alphatims = "^1.0.8" sortedcontainers = "^2.4.0" From 15ed5143b48a752e16494a176df55d355d07a940 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 8 Jul 2024 16:41:22 +0200 Subject: [PATCH 31/33] rm unnecessary setup.py --- setup.py | 46 ---------------------------------------------- 1 file changed, 46 deletions(-) delete mode 100644 setup.py diff --git a/setup.py b/setup.py deleted file mode 100644 index c9f7903..0000000 --- a/setup.py +++ /dev/null @@ -1,46 +0,0 @@ -from setuptools import setup - -packages = [ - "spectrum_io", - "spectrum_io.file", - "spectrum_io.raw", - "spectrum_io.search_result", - "spectrum_io.spectral_library", -] - -package_data = { - "": ["*"], - "spectrum_io.raw": ["utils/ThermoRawFileParser/*"], - "spectrum_io.spectral_library": ["dlib/*", "msp/*", "spectronaut/*"], -} - -install_requires = [ - "fundamentals @ " "git+ssh://git@gitlab.lrz.de/compmass/prosit/tools/fundamentals.git@develop", - "h5py>=3.3.0,<4.0.0", - "numpy>=1.21.0,<2.0.0", - "pandas>=1.3.0,<2.0.0", - "pymzml>=2.5.0,<3.0.0", - "pyteomics>=4.3.3", - "lxml>=4.5.2", -] - -setup_kwargs = { - "name": "prosit-io", - "version": "0.1.0", - "description": "Handle IO operations for Oktoberfest", - "long_description": None, - "author": "WassimG", - "author_email": "wassim.gabriel@tum.de", - "maintainer": None, - "maintainer_email": None, - "url": None, - "packages": packages, - "package_data": package_data, - "install_requires": install_requires, - "python_requires": ">=3.8,<4.0", -} - - -setup(**setup_kwargs) - -# This setup.py was autogenerated using poetry. From 2e3ff8eb355d3c654950fe32f266d85c1921a132 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Wed, 10 Jul 2024 09:56:27 +0200 Subject: [PATCH 32/33] fix poetry lock --- poetry.lock | 749 +++++++++++++++++++++++++++------------------------- 1 file changed, 386 insertions(+), 363 deletions(-) diff --git a/poetry.lock b/poetry.lock index bef1a65..1c4506e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -122,13 +122,13 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "bandit" -version = "1.7.8" +version = "1.7.9" description = "Security oriented static analyser for python code." optional = false python-versions = ">=3.8" files = [ - {file = "bandit-1.7.8-py3-none-any.whl", hash = "sha256:509f7af645bc0cd8fd4587abc1a038fc795636671ee8204d502b933aee44f381"}, - {file = "bandit-1.7.8.tar.gz", hash = "sha256:36de50f720856ab24a24dbaa5fee2c66050ed97c1477e0a1159deab1775eab6b"}, + {file = "bandit-1.7.9-py3-none-any.whl", hash = "sha256:52077cb339000f337fb25f7e045995c4ad01511e716e5daac37014b9752de8ec"}, + {file = "bandit-1.7.9.tar.gz", hash = "sha256:7c395a436743018f7be0a4cbb0a4ea9b902b6d87264ddecf8cfdc73b4f78ff61"}, ] [package.dependencies] @@ -192,13 +192,13 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "certifi" -version = "2024.6.2" +version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"}, - {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, + {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, + {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, ] [[package]] @@ -669,34 +669,34 @@ 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"jaraco.itertools", [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.11.0" -content-hash = "f81f7865699214a187651984ecd930f75f5c364890f55a25a553375b8c19faad" +content-hash = "7b58204c5231af5f95794d153ae7d47b82bea6e7369a3e683c3c4be18bd3f191" From 8cb9098859b653c2ce8888afb613f6fdff695d77 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 11 Jul 2024 12:42:55 +0200 Subject: [PATCH 33/33] updated to use new coverage report up/download v4 --- .github/workflows/run_tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index c21c447..2a323c4 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -116,15 +116,15 @@ jobs: run: nox --force-color --python=${{ matrix.python-version }} - name: Upload coverage data - if: always() && matrix.session == 'tests' - uses: actions/upload-artifact@v3 + if: always() && matrix.session == 'tests' && matrix.os == 'ubuntu-latest' + uses: actions/upload-artifact@v4 with: name: coverage-data path: ".coverage.*" - name: Upload documentation if: matrix.session == 'docs-build' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: docs path: docs/_build