From 7a4a07262358736b1032add50a83a3add7043b36 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Jul 2024 10:16:22 +0000 Subject: [PATCH 01/12] [DEPENDABOT]: Bump pandas from 1.5.3 to 2.2.2 Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.5.3 to 2.2.2. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.5.3...v2.2.2) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- poetry.lock | 107 ++++++++++++++++++++++++++++++++----------------- pyproject.toml | 2 +- 2 files changed, 71 insertions(+), 38 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1c4506e..d500483 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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def test_read_file(self, raw_data, tmpdir): + def setUp(self): # noqa: D102 + # Simple toy MS data containing float, list[float], str, int, and list[int] + self.raw_data = { + "scan_number": [1, 234, 5678], + "intensities": [ + [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": [ + [0, 1, 0, 0, 0, 0], + [0, 1, 0, 0, 0, 0], + [0, 0, 1, 0, 0, 0], + ], + "collision_energy_normed": [0.250827308624, 0.288798207462, 0.2887064038764], + } + self.temp_dir = Path(tempfile.mkdtemp()) + + def tearDown(self): # noqa: D102 + shutil.rmtree(self.temp_dir) + + def test_read_file(self): """Test read operation for a single dataset.""" - output_path = Path(tmpdir / "table.parquet") - pq.write_table(pa.Table.from_pydict(raw_data), output_path) + output_path = self.temp_dir / "table.parquet" + pq.write_table(pa.Table.from_pydict(self.raw_data), output_path) df = parquet.read_file(output_path) - output_path.unlink() - pd.testing.assert_frame_equal(df, pd.DataFrame(raw_data)) + pd.testing.assert_frame_equal(df, pd.DataFrame(self.raw_data)) - def test_write_file(self, raw_data, tmpdir): + def test_write_file(self): """Check write operation for a single dataset.""" - output_path = Path(tmpdir / "table.parquet") - df = pd.DataFrame(raw_data) + output_path = self.temp_dir / "table.parquet" + df = pd.DataFrame(self.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): + def test_read_write_partition(self): """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) + output_path = self.temp_dir / "partition" + df = pd.DataFrame(self.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): + def test_read_write_partition_integer_key(self): """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) + output_path = self.temp_dir / "partition" + df = pd.DataFrame(self.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): + def test_modify_partition(self): """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) + output_path = self.temp_dir / "partition" + df = pd.DataFrame(self.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") - shutil.rmtree(output_path) pd.testing.assert_frame_equal(read_df, df) - def test_write_not_implemented(self, raw_data, tmpdir): + def test_write_not_implemented(self): """Check whether write_file() raises a NotImplementedError if provided with an unsupported object.""" - with pytest.raises(NotImplementedError): + with self.assertRaises(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() + output_path = self.temp_dir / "table.parquet" + df = pd.DataFrame(self.raw_data).to_numpy() parquet.write_file(df, output_path) - output_path.unlink() - def test_read_write_partition_not_implemented(self, raw_data, tmpdir): + def test_read_write_partition_not_implemented(self): """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" - with pytest.raises(NotImplementedError): + with self.assertRaises(NotImplementedError): with suppress_type_checks() if "typeguard" in sys.modules else nullcontext(): - output_path = Path(tmpdir / "partition") - df = pd.DataFrame(raw_data).to_numpy() + output_path = self.temp_dir / "partition" + df = pd.DataFrame(self.raw_data).to_numpy() parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) - output_path.unlink() - - -@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, 0.0, -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": [ - [0, 1, 0, 0, 0, 0], - [0, 1, 0, 0, 0, 0], - [0, 0, 1, 0, 0, 0], - ], - "collision_energy_normed": [0.250827308624, 0.288798207462, 0.2887064038764], - } From 1b9194d2590f852e0506a59a64f536ab49bf121a Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 6 Aug 2024 14:35:12 +0000 Subject: [PATCH 03/12] refactor(parquet IO): drop unnecessary file format support Remove TODOs for sparse matrices, anndata matrices and HuggingFace datasets as their conversion from/to columnar format for serialization as Parquet files is context-dependent. Correspondingly remove tests for NotImplementedErrors as they are now redundant --- spectrum_io/file/parquet.py | 27 ++++++--------------------- tests/unit_tests/test_parquet.py | 16 ---------------- 2 files changed, 6 insertions(+), 37 deletions(-) diff --git a/spectrum_io/file/parquet.py b/spectrum_io/file/parquet.py index 8fc164f..b3837de 100644 --- a/spectrum_io/file/parquet.py +++ b/spectrum_io/file/parquet.py @@ -7,12 +7,7 @@ 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__) @@ -53,36 +48,26 @@ def read_partition(path: Pathlike, dataset_name: str) -> pd.DataFrame: return df -def write_file(data: Dataset, path: Pathlike) -> None: +def write_file(data: pd.DataFrame, 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 - - :raises NotImplementedError: if anything else but a Pandas DataFrame is used as the dataset """ - if isinstance(data, pd.DataFrame): - data.to_parquet(path) - else: - raise NotImplementedError + data.to_parquet(path) -def write_partition(datasets: List[Dataset], path: Pathlike, dataset_names: List[str]) -> None: +def write_partition(datasets: List[pd.DataFrame], path: Pathlike, dataset_names: List[str]) -> None: """ - Write several datasets to a Parquet dataset as a directory containing subdirectories partinioned by dataset name. + Write several datasets to a Parquet dataset as a directory containing subdirectories partitioned 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! - - :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)]) - table = pa.Table.from_pandas(df) - else: - raise NotImplementedError + df = pd.concat([dataset.assign(dataset=name) for dataset, name in zip(datasets, dataset_names)]) + table = pa.Table.from_pandas(df) if isinstance(path, str): path = Path(path) diff --git a/tests/unit_tests/test_parquet.py b/tests/unit_tests/test_parquet.py index 2b6fb82..b89f7c5 100644 --- a/tests/unit_tests/test_parquet.py +++ b/tests/unit_tests/test_parquet.py @@ -79,19 +79,3 @@ def test_modify_partition(self): 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): - """Check whether write_file() raises a NotImplementedError if provided with an unsupported object.""" - with self.assertRaises(NotImplementedError): - with suppress_type_checks() if "typeguard" in sys.modules else nullcontext(): - output_path = self.temp_dir / "table.parquet" - df = pd.DataFrame(self.raw_data).to_numpy() - parquet.write_file(df, output_path) - - def test_read_write_partition_not_implemented(self): - """Check whether write_partition() raises a NotImplementedError if provided with an unsupported object.""" - with self.assertRaises(NotImplementedError): - with suppress_type_checks() if "typeguard" in sys.modules else nullcontext(): - output_path = self.temp_dir / "partition" - df = pd.DataFrame(self.raw_data).to_numpy() - parquet.write_partition([df, df], output_path, ["dataset_1", "dataset_2"]) From e32967bde8dfa95c864eb9c197d111cfaee65fa5 Mon Sep 17 00:00:00 2001 From: Julius Schlensok Date: Tue, 6 Aug 2024 15:04:44 +0000 Subject: [PATCH 04/12] chore: remove unused parameter --- spectrum_io/raw/msraw.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/spectrum_io/raw/msraw.py b/spectrum_io/raw/msraw.py index 9157716..5d1fe2b 100644 --- a/spectrum_io/raw/msraw.py +++ b/spectrum_io/raw/msraw.py @@ -116,7 +116,6 @@ def read_mzml( source: Union[str, Path, List[Union[str, Path]]], ext: str = "mzml", package: str = "pyteomics", - search_type: str = "Maxquant", scanidx: Optional[List] = None, *args, **kwargs, @@ -128,7 +127,6 @@ def read_mzml( :param ext: file extension for searching a specified directory :param package: package for parsing the mzml file. Can eiter be "pymzml" or "pyteomics" :param scanidx: optional list of scan numbers to extract. if not specified, all scans will be extracted - :param search_type: type of the search (Maxquant, Mascot, Msfragger) :param args: additional positional arguments :param kwargs: additional keyword arguments :raises AssertionError: if package has an unexpected type From 362fc1dcb9bd6097b301ded0f404b3b32a62ac35 Mon Sep 17 00:00:00 2001 From: Fabian Basso Date: Thu, 8 Aug 2024 07:31:55 +0000 Subject: [PATCH 05/12] fixed filtering sequences properly --- spectrum_io/search_result/search_results.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/spectrum_io/search_result/search_results.py b/spectrum_io/search_result/search_results.py index 168648b..cf11f4d 100644 --- a/spectrum_io/search_result/search_results.py +++ b/spectrum_io/search_result/search_results.py @@ -22,9 +22,8 @@ def filter_valid_prosit_sequences(df: pd.DataFrame) -> pd.DataFrame: # retain only peptides that fall within [7, 30] length supported by Prosit df = df[(df["PEPTIDE_LENGTH"] <= 30) & (df["PEPTIDE_LENGTH"] >= 7)] # remove unsupported mods to exclude - unsupported_mods = [r"Acetyl \(Protein N\-term\)", "ac", r"\[[0-9]+\]", r"\+"] - exclude_mods_pattern = re.compile("|".join(unsupported_mods)) - df = df[~df["MODIFIED_SEQUENCE"].str.contains(exclude_mods_pattern)] + supported_pattern = re.compile("^(?:\[UNIMOD:\d+\]\-)?(?:[ACDEFGHIKLMNPQRSTVWY]+(?:\[UNIMOD:\d+\])?)*$") + df = df[df["MODIFIED_SEQUENCE"].str.contains(supported_pattern)] # remove non-canonical aas df = df[(~df["SEQUENCE"].str.contains("U|O"))] # remove precursor charges greater than 6 From b858357a1a31c2727a454b909504531e27659227 Mon Sep 17 00:00:00 2001 From: Fabian Basso Date: Thu, 8 Aug 2024 07:37:14 +0000 Subject: [PATCH 06/12] flake8 fix --- spectrum_io/search_result/search_results.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spectrum_io/search_result/search_results.py b/spectrum_io/search_result/search_results.py index cf11f4d..ea072bb 100644 --- a/spectrum_io/search_result/search_results.py +++ b/spectrum_io/search_result/search_results.py @@ -22,7 +22,7 @@ def filter_valid_prosit_sequences(df: pd.DataFrame) -> pd.DataFrame: # retain only peptides that fall within [7, 30] length supported by Prosit df = df[(df["PEPTIDE_LENGTH"] <= 30) & (df["PEPTIDE_LENGTH"] >= 7)] # remove unsupported mods to exclude - supported_pattern = re.compile("^(?:\[UNIMOD:\d+\]\-)?(?:[ACDEFGHIKLMNPQRSTVWY]+(?:\[UNIMOD:\d+\])?)*$") + supported_pattern = re.compile(r"^(?:\[UNIMOD:\d+\]\-)?(?:[ACDEFGHIKLMNPQRSTVWY]+(?:\[UNIMOD:\d+\])?)*$") df = df[df["MODIFIED_SEQUENCE"].str.contains(supported_pattern)] # remove non-canonical aas df = df[(~df["SEQUENCE"].str.contains("U|O"))] From acea115f381fead1bc0af3e077d3f016f627f3f2 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 8 Aug 2024 14:52:01 +0200 Subject: [PATCH 07/12] filter to required columns --- spectrum_io/search_result/search_results.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/spectrum_io/search_result/search_results.py b/spectrum_io/search_result/search_results.py index 168648b..43e2045 100644 --- a/spectrum_io/search_result/search_results.py +++ b/spectrum_io/search_result/search_results.py @@ -11,6 +11,20 @@ logger = logging.getLogger(__name__) +COLUMNS = [ + "RAW_FILE", + "SCAN_NUMBER", + "MODIFIED_SEQUENCE", + "PRECURSOR_CHARGE", + "MASS", + "SCORE", + "REVERSE", + "SEQUENCE", + "PEPTIDE_LENGTH", + "PROTEINS", +] + + def filter_valid_prosit_sequences(df: pd.DataFrame) -> pd.DataFrame: """ Filter valid Prosit sequences. @@ -124,8 +138,8 @@ def generate_internal( """ if out_path is None: # convert and return - return self.read_result(tmt_label, custom_mods=custom_mods) - + filtered_df = self.read_result(tmt_label, custom_mods=custom_mods) + return filtered_df[COLUMNS] if isinstance(out_path, str): out_path = Path(out_path) From bfc8eb406fa6f70db0b5d7c980bb444346148f20 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 8 Aug 2024 15:03:51 +0200 Subject: [PATCH 08/12] always filter columns --- spectrum_io/search_result/search_results.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/spectrum_io/search_result/search_results.py b/spectrum_io/search_result/search_results.py index cf4ec12..8df1175 100644 --- a/spectrum_io/search_result/search_results.py +++ b/spectrum_io/search_result/search_results.py @@ -37,7 +37,7 @@ def filter_valid_prosit_sequences(df: pd.DataFrame) -> pd.DataFrame: df = df[(df["PEPTIDE_LENGTH"] <= 30) & (df["PEPTIDE_LENGTH"] >= 7)] # remove unsupported mods to exclude supported_pattern = re.compile(r"^(?:\[UNIMOD:\d+\]\-)?(?:[ACDEFGHIKLMNPQRSTVWY]+(?:\[UNIMOD:\d+\])?)*$") - df = df[df["MODIFIED_SEQUENCE"].str.contains(supported_pattern)] + df = df[df["MODIFIED_SEQUENCE"].str.contains(supported_pattern)] # remove non-canonical aas df = df[(~df["SEQUENCE"].str.contains("U|O"))] # remove precursor charges greater than 6 @@ -149,7 +149,7 @@ def generate_internal( return csv.read_file(out_path) # convert, save and return - df = self.read_result(tmt_label, custom_mods=custom_mods) + df = self.read_result(tmt_label, custom_mods=custom_mods)[COLUMNS] csv.write_file(df, out_path) return df From f6be7fcd976e6124f59d0e9bc2ca757d146534ab Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 8 Aug 2024 15:38:42 +0200 Subject: [PATCH 09/12] simplified regex matching --- spectrum_io/search_result/search_results.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/spectrum_io/search_result/search_results.py b/spectrum_io/search_result/search_results.py index ea072bb..6377bc2 100644 --- a/spectrum_io/search_result/search_results.py +++ b/spectrum_io/search_result/search_results.py @@ -23,9 +23,8 @@ def filter_valid_prosit_sequences(df: pd.DataFrame) -> pd.DataFrame: df = df[(df["PEPTIDE_LENGTH"] <= 30) & (df["PEPTIDE_LENGTH"] >= 7)] # remove unsupported mods to exclude supported_pattern = re.compile(r"^(?:\[UNIMOD:\d+\]\-)?(?:[ACDEFGHIKLMNPQRSTVWY]+(?:\[UNIMOD:\d+\])?)*$") - df = df[df["MODIFIED_SEQUENCE"].str.contains(supported_pattern)] - # remove non-canonical aas - df = df[(~df["SEQUENCE"].str.contains("U|O"))] + df = df[df["MODIFIED_SEQUENCE"].str.match(supported_pattern)] + # remove precursor charges greater than 6 df = df[df["PRECURSOR_CHARGE"] <= 6] logger.info(f"#sequences after filtering for valid prosit sequences: {len(df.index)}") From 956e75bc8b94b9b57f3dab6f7e7ab163a6f61053 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 8 Aug 2024 15:45:48 +0200 Subject: [PATCH 10/12] only read MQ columns that are needed --- spectrum_io/search_result/maxquant.py | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/spectrum_io/search_result/maxquant.py b/spectrum_io/search_result/maxquant.py index 709746a..10ed7e3 100644 --- a/spectrum_io/search_result/maxquant.py +++ b/spectrum_io/search_result/maxquant.py @@ -71,7 +71,21 @@ def read_result( parsed_mods["^_"] = f"_{unimod_tag}-" logger.info("Reading msms.txt file") - self.results = pd.read_csv(self.path / "msms.txt", sep="\t") + self.results = pd.read_csv( + self.path / "msms.txt", + usecols=[ + "Raw file", + "Scan number", + "Modified sequence", + "Charge", + "Scan event number", + "Mass", # = Calculated Precursor mass; TODO get column with experimental Precursor mass instead + "Score", + "Reverse", + "Proteins", + ], + sep="\t", + ) logger.info("Finished reading msms.txt file") From 0c0f7e1dcadce0b7e84d158f336ba65ef4a09066 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 8 Aug 2024 15:46:48 +0200 Subject: [PATCH 11/12] Bump version from 0.6.0 to 0.6.1 --- .cookietemple.yml | 2 +- .github/release-drafter.yml | 4 ++-- cookietemple.cfg | 2 +- docs/conf.py | 4 ++-- pyproject.toml | 2 +- spectrum_io/__init__.py | 2 +- spectrum_io/__main__.py | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.cookietemple.yml b/.cookietemple.yml index 7dfbf33..e31dc4d 100644 --- a/.cookietemple.yml +++ b/.cookietemple.yml @@ -15,5 +15,5 @@ full_name: Mario Picciani email: mario.picciani@tum.de project_name: spectrum_io project_short_description: IO related functionalities for oktoberfest. -version: 0.6.0 +version: 0.6.1 license: MIT diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index 8f8af9b..96aaae2 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: "0.6.0 🌈" # <> -tag-template: 0.6.0 # <> +name-template: "0.6.1 🌈" # <> +tag-template: 0.6.1 # <> exclude-labels: - "skip-changelog" diff --git a/cookietemple.cfg b/cookietemple.cfg index bd1dee7..df3da30 100644 --- a/cookietemple.cfg +++ b/cookietemple.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.6.0 +current_version = 0.6.1 [bumpversion_files_whitelisted] init_file = spectrum_io/__init__.py diff --git a/docs/conf.py b/docs/conf.py index a4f6cae..8a6ddd6 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -52,9 +52,9 @@ # the built documents. # # The short X.Y version. -version = "0.6.0" +version = "0.6.1" # The full version, including alpha/beta/rc tags. -release = "0.6.0" +release = "0.6.1" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/pyproject.toml b/pyproject.toml index 4e5d056..d3dd879 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "spectrum_io" -version = "0.6.0" # <> +version = "0.6.1" # <> 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 0d10c7f..8a31418 100644 --- a/spectrum_io/__init__.py +++ b/spectrum_io/__init__.py @@ -5,7 +5,7 @@ __author__ = """The Oktoberfest development team (Wilhelmlab at Technical University of Munich)""" __copyright__ = f"Copyright {datetime.now():%Y}, Wilhelmlab at Technical University of Munich" __license__ = "MIT" -__version__ = "0.6.0" +__version__ = "0.6.1" import logging import logging.handlers diff --git a/spectrum_io/__main__.py b/spectrum_io/__main__.py index ecf8132..5d5fecc 100644 --- a/spectrum_io/__main__.py +++ b/spectrum_io/__main__.py @@ -5,7 +5,7 @@ @click.command() -@click.version_option(version="0.6.0", message=click.style("spectrum_io Version: 0.6.0")) +@click.version_option(version="0.6.1", message=click.style("spectrum_io Version: 0.6.1")) def main() -> None: """spectrum_io.""" From f77589bec88b8acb9ee1b42fd963203c69f71d85 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 8 Aug 2024 15:51:23 +0200 Subject: [PATCH 12/12] updating dependencies --- poetry.lock | 471 +++++++++++++++++++++++++---------------------- requirements.txt | 19 +- 2 files changed, 260 insertions(+), 230 deletions(-) diff --git a/poetry.lock b/poetry.lock index a9cd57c..aace8a1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "alabaster" @@ -75,13 +75,13 @@ trio = ["trio (>=0.23)"] [[package]] name = "attrs" -version = "24.1.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-24.1.0-py3-none-any.whl", hash = "sha256:377b47448cb61fea38533f671fba0d0f8a96fd58facd4dc518e3dac9dbea0905"}, - {file = "attrs-24.1.0.tar.gz", hash = "sha256:adbdec84af72d38be7628e353a09b6a6790d15cd71819f6e9d7b0faa8a125745"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] @@ -203,63 +203,78 @@ files = [ [[package]] name = "cffi" -version = "1.16.0" +version = "1.17.0" description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.8" files = [ - {file = 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