mutcleaner 0.1.0.post1.dev40__tar.gz → 0.3.0__tar.gz

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mutcleaner
-Version: 0.1.0.post1.dev40
+Version: 0.3.0
 Summary: An efficient framework for cleaning, standardizing, and processing biological mutation data.
 Author: Yuxiang Tang, Ziyu Shi
 License-Expression: BSD-3-Clause
@@ -234,6 +234,11 @@ See the [Data Cleaners Usage Guide](https://xulab-research.github.io/MutCleaner/
       <td><a href="https://doi.org/10.1038/s41586-021-03807-6">SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape</a></td>
       <td><a href="https://huggingface.co/datasets/xulab-research/MutCleaner/blob/main/RBD_Antibody_Dataset/SARS-CoV-2-RBD_MAP_Vir_mAbs.csv">SARS-CoV-2-RBD_MAP_Vir_mAbs.csv</a></td>
     </tr>
+    <tr>
+      <td>Chitosanase Dataset</td>
+      <td>None</td>
+      <td><a href="https://huggingface.co/datasets/xulab-research/MutCleaner/blob/main/Chitosanase_Dataset/Chitosanase_Dataset.csv">Chitosanase_Dataset.csv</a></td>
+    </tr>
   </tbody>
 </table>
 

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/README.md

@@ -188,6 +188,11 @@ See the [Data Cleaners Usage Guide](https://xulab-research.github.io/MutCleaner/
       <td><a href="https://doi.org/10.1038/s41586-021-03807-6">SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape</a></td>
       <td><a href="https://huggingface.co/datasets/xulab-research/MutCleaner/blob/main/RBD_Antibody_Dataset/SARS-CoV-2-RBD_MAP_Vir_mAbs.csv">SARS-CoV-2-RBD_MAP_Vir_mAbs.csv</a></td>
     </tr>
+    <tr>
+      <td>Chitosanase Dataset</td>
+      <td>None</td>
+      <td><a href="https://huggingface.co/datasets/xulab-research/MutCleaner/blob/main/Chitosanase_Dataset/Chitosanase_Dataset.csv">Chitosanase_Dataset.csv</a></td>
+    </tr>
   </tbody>
 </table>
 

mutcleaner-0.3.0/doc/changelog/CHANGELOG_0.2.0.md

@@ -0,0 +1,26 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.2.0] - 2026-06-02
+
+### Added
+
+- Added ACE2-RBD & Antibody-RBD cleaner-related files for the data preprocessing workflow. ([#5](https://github.com/xulab-research/MutCleaner/pull/5)) by @Lodaisthirsty
+
+### Other Changes
+
+- Make the records in the dataset more detailed. ([#2](https://github.com/xulab-research/MutCleaner/pull/2)) by @Lodaisthirsty
+
+### Contributors
+
+A total of 2 people contributed to this release. People with a "+" by their names contributed a patch for the first time.
+
+- Yancheng Shi +
+- Ziyu Shi
+
+
+**Full Changelog**: [v0.1.0..v0.2.0](https://github.com/xulab-research/MutCleaner/compare/v0.1.0..v0.2.0)

mutcleaner-0.3.0/doc/changelog/CHANGELOG_0.3.0.md

@@ -0,0 +1,23 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.3.0] - 2026-06-02
+
+### Other Changes
+
+- Chitosanase ([#6](https://github.com/xulab-research/MutCleaner/pull/6)) by @MnZnYang
+
+### Contributors
+
+A total of 3 people contributed to this release. People with a "+" by their names contributed a patch for the first time.
+
+- Mengxin Yang +
+- Ziyu Shi
+- yukiko-shi
+
+
+**Full Changelog**: [v0.2.0..v0.3.0](https://github.com/xulab-research/MutCleaner/compare/v0.2.0..v0.3.0)

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/doc/source/conf.py

@@ -7,7 +7,7 @@ sys.path.insert(0, f"{project_root}")
 project = "mutcleaner"
 copyright = "2026, Ziyu Shi, Yuxiang Tang"
 author = "Yuxiang Tang and Ziyu Shi"
-release = "0.1.0"
+release = "0.3.0"
 
 extensions = [
     "sphinx.ext.autodoc",

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/doc/source/user_guide/overview.md

@@ -13,3 +13,5 @@ This guide provides usage examples for data cleaning modules organized by datase
 - [**CTXM Epistasis Dataset**](supported_datasets.md#ctxm-epistasis-dataset): A large-scale pairwise deep mutational scanning dataset of the CTX-M-14 β-lactamase active site, covering 49,096 double mutants across 17 active-site residues. Fitness measurements were obtained from functional selection under ampicillin and cefotaxime, providing substrate-dependent fitness landscapes for studying epistasis, compensatory mutations, and antibiotic resistance prediction.
 - [**RBD-ACE2 Dataset**](supported_datasets.md#rbd-ace2-dataset): SARS-CoV-2 RBD sequences with ACE2 binding affinity scores, labeled by `log10Ka` where higher values indicate stronger ACE2 binding affinity.
 - [**RBD-Antibody Dataset**](supported_datasets.md#rbd-antibody-dataset): SARS-CoV-2 RBD antibody escape data with mutation-level antibody escape scores.
+- [**Chitosanase Dataset**](supported_datasets.md#chitosanase-dataset): Wet-lab generated chitosanase mutation dataset containing wild-type protein sequences, amino acid mutation annotations, and experimentally measured melting temperatures (Tm). The Tm value serves as the label for protein thermostability prediction and mutation effect analysis.
+

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/doc/source/user_guide/supported_datasets.md

@@ -849,3 +849,60 @@ Alternatively, you can download it from
 ### Advanced Settings
 
 See {py:class}`mutcleaner.cleaners.RBDAntibodyCleanerConfig` for details.
+
+
+## Chitosanase Dataset
+
+### Basic Usage
+
+You can download the source file directly by running (see {py:func}`mutcleaner.utils.download_chitosanase_source_file` for details):
+```python
+import pickle
+from pathlib import Path
+from mutcleaner import download_chitosanase_source_file
+from mutcleaner.cleaners import (
+    create_chitosanase_cleaner,
+    clean_chitosanase_dataset,
+)
+
+
+def main():
+    # Prepare data
+    raw_data_dir = Path("raw_dataset/Chitosanase_Dataset")
+    download_chitosanase_source_file(raw_data_dir, overwrite=True)
+
+    # File settings
+    for dataset_filepath in sorted(raw_data_dir.glob("*.csv")):
+        artifact_path = Path(f"logs/Chitosanase_Dataset/artifacts.pkl")
+        artifact_csv_dir = Path(f"logs/Chitosanase_Dataset")
+
+        artifact_csv_dir.mkdir(parents=True, exist_ok=True)
+
+        # Clean data
+        chitosanase_cleaning_pipeline = create_chitosanase_cleaner(dataset_filepath)
+        chitosanase_cleaning_pipeline, chitosanase_dataset = clean_chitosanase_dataset(chitosanase_cleaning_pipeline)
+
+        # Save data
+        chitosanase_dataset.save(f"cleaned_dataset/cleaned_Chitosanase_Dataset")
+        chitosanase_cleaning_pipeline.save_artifacts(artifact_path)
+
+        # open the pickle file
+        with open(artifact_path, "rb") as file:
+            artifacts = pickle.load(file)
+
+        for artifact_name, artifact_df in artifacts.items():
+            artifact_df.to_csv(f"{artifact_csv_dir}/{artifact_name}.csv", index=False)
+
+
+if __name__ == "__main__":
+    import multiprocessing
+
+    multiprocessing.freeze_support()
+    main()
+
+
+```
+
+### Advanced Settings
+
+See {py:class}`mutcleaner.cleaners.ChitosanaseCleanerConfig` for details.

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/mutcleaner/__init__.py

@@ -5,7 +5,7 @@ MutCleaner: An efficient framework for cleaning, standardizing, and processing b
 
 __author__ = "Yuxiang Tang and Ziyu Shi"
 
-__version__ = "0.1.0"
+__version__ = "0.3.0"
 
 from .core import (
     # Alphabet
@@ -38,6 +38,7 @@ from .cleaners import (
     trpb_cleaner,
     antitoxin_pard3_cleaner,
     rbd_ace2_cleaner,
+    chitosanase_cleaner,
 )
 
 from .utils import (
@@ -55,4 +56,5 @@ from .utils import (
     download_antitoxin_pard3_source_file,
     download_rbd_antibody_source_file,
     download_rbd_ace2_source_file,
+    download_chitosanase_source_file,
 )

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/mutcleaner/cleaners/__init__.py

@@ -56,6 +56,12 @@ from .rbd_antibody_cleaner import (
     create_rbd_antibody_cleaner,
 )
 
+from .chitosanase_cleaner import (
+    ChitosanaseCleanerConfig,
+    create_chitosanase_cleaner,
+    clean_chitosanase_dataset,
+)
+
 __all__ = [
     "CDNAProteolysisCleanerConfig",
     "create_cdna_proteolysis_cleaner",
@@ -87,6 +93,9 @@ __all__ = [
     "RBDACE2CleanerConfig",
     "create_rbd_ace2_cleaner",
     "clean_rbd_ace2_dataset",
+    "ChitosanaseCleanerConfig",
+    "create_chitosanase_cleaner",
+    "clean_chitosanase_dataset",
     "RBDAntibodyCleanerConfig",
     "create_rbd_antibody_cleaner",
     "clean_rbd_antibody_dataset",

mutcleaner-0.3.0/mutcleaner/cleaners/chitosanase_cleaner.py

@@ -0,0 +1,220 @@
+from __future__ import annotations
+
+import logging
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import numpy as np
+
+from .base_config import BaseCleanerConfig
+from .basic_cleaners import (
+    add_columns,
+    apply_mutations_to_sequences,
+    convert_data_types,
+    convert_to_mutation_dataset_format,
+    extract_and_rename_columns,
+    filter_and_clean_data,
+    subtract_labels_by_wt,
+)
+from .chitosanase_custom_cleaners import parse_chitosanase_raw_file
+from ..core.dataset import MutationDataset
+from ..core.pipeline import Pipeline, create_pipeline
+
+if TYPE_CHECKING:
+    from typing import Any, Dict, List, Optional, Tuple, Union
+
+__all__ = [
+    "ChitosanaseCleanerConfig",
+    "create_chitosanase_cleaner",
+    "clean_chitosanase_dataset",
+]
+
+
+def __dir__() -> List[str]:
+    return __all__
+
+
+# Create module logger
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class ChitosanaseCleanerConfig(BaseCleanerConfig):
+    """Configuration for the Chitosanase cleaning pipeline.
+
+    Holds dataset-specific defaults for the Chitosanase pipeline. The
+    pipeline expects each raw input file to contain a CSV block followed by
+    a WT sequence separated by ``wt_separator``.
+
+    Attributes
+    ----------
+    infer_mut_workers : int
+        Number of workers used when inferring/applying mutations (default 16).
+    pipeline_name : str
+        Human-readable pipeline name used in logs and artifacts.
+    wt_separator : str
+        Token that separates CSV block and WT sequence in raw files.
+    column_mapping : Dict[str, str]
+        Mapping from raw Chitosanase columns to pipeline column names.
+    columns_to_add : Dict[str, Any]
+        Constant columns to attach during preprocessing.
+    """
+
+    infer_mut_workers: int = 16
+    pipeline_name: str = "Chitosanase"
+    wt_separator: str = '">wt'
+    column_mapping: dict[str, str] = field(
+        default_factory=lambda: {
+            "aa_mut": "mut_info",
+            "Tm": "label",
+            "wt_seq": "sequence",
+        }
+    )
+    columns_to_add: dict[str, Any] = field(
+        default_factory=lambda: {
+            "name": "Chitosanase",
+        }
+    )
+
+    def validate(self) -> None:
+        super().validate()
+
+
+def create_chitosanase_cleaner(
+    dataset_or_path: Optional[Union[str, Path]] = None,
+    config: Optional[Union[ChitosanaseCleanerConfig, Dict[str, Any], str, Path]] = None,
+) -> Pipeline:
+    """Create a configured Pipeline for cleaning Chitosanase raw files.
+
+    Parameters
+    ----------
+    dataset_or_path : Optional[Union[str, Path]]
+        Path to a raw Chitosanase input file (or a DataFrame for programmatic
+        callers). Raw files must contain a CSV block followed by the WT
+        sequence separated by the configured ``wt_separator``.
+    config : Optional[Union[ChitosanaseCleanerConfig, Dict[str, Any], str, Path]]
+        Pipeline configuration. Accepts a `ChitosanaseCleanerConfig` instance,
+        a dict of overrides merged with defaults, or a path to a JSON
+        configuration file.
+
+    Returns
+    -------
+    Pipeline
+        A :class:`Pipeline` instance ready for execution via
+        ``pipeline.execute()``.
+
+    Examples
+    --------
+    >>> pipeline = create_chitosanase_cleaner("/path/to/Chitosanase_Dataset.csv")
+    >>> pipeline.execute()
+    """
+    # Handle config
+    if config is None:
+        final_config = ChitosanaseCleanerConfig()
+    elif isinstance(config, ChitosanaseCleanerConfig):
+        final_config = config
+    elif isinstance(config, dict):
+        final_config = ChitosanaseCleanerConfig().merge(config)
+    elif isinstance(config, (str, Path)):
+        final_config = ChitosanaseCleanerConfig.from_json(config)
+    else:
+        raise TypeError(f"config has invalid type: {type(config)}")
+
+    if dataset_or_path is None:
+        raise TypeError("dataset_or_path must be a Chitosanase file path")
+
+    try:
+        pipeline = create_pipeline(dataset_or_path, final_config.pipeline_name)
+        mutation_column = final_config.column_mapping.get("aa_mut", "aa_mut")
+        label_column = final_config.column_mapping.get("Tm", "Tm")
+        sequence_column = final_config.column_mapping.get("wt_seq", "wt_seq")
+
+        # Add cleaning steps
+        pipeline = (
+            pipeline.delayed_then(parse_chitosanase_raw_file, wt_separator=final_config.wt_separator)
+            .delayed_then(filter_and_clean_data, drop_na_columns=["Tm"])
+            .delayed_then(convert_data_types, type_conversions={"Tm": np.float32})
+            .delayed_then(
+                extract_and_rename_columns,
+                column_mapping={
+                    "aa_mut": mutation_column,
+                    "Tm": label_column,
+                    "wt_seq": sequence_column,
+                },
+            )
+            .delayed_then(
+                add_columns,
+                columns_to_add=final_config.columns_to_add,
+            )
+            .delayed_then(
+                subtract_labels_by_wt,
+                name_column="name",
+                label_columns=label_column,
+                mutation_column=mutation_column,
+                wt_identifier="WT",
+                in_place=True,
+                drop_wt_row=True,
+            )
+            .delayed_then(
+                apply_mutations_to_sequences,
+                sequence_column=sequence_column,
+                mutation_column=mutation_column,
+                sequence_type="protein",
+                is_zero_based=False,
+                num_workers=final_config.infer_mut_workers,
+            )
+            .delayed_then(
+                convert_to_mutation_dataset_format,
+                name_column="name",
+                mutation_column=mutation_column,
+                sequence_column=sequence_column,
+                mutated_sequence_column="mut_seq",
+                label_column=label_column,
+                is_zero_based=False,
+            )
+        )
+        return pipeline
+    except Exception as e:
+        logger.error(f"Error in creating Chitosanase cleaning pipeline: {str(e)}")
+        raise RuntimeError(f"Error in creating Chitosanase cleaning pipeline: {str(e)}")
+
+
+def clean_chitosanase_dataset(
+    pipeline: Pipeline,
+) -> Tuple[Pipeline, MutationDataset]:
+    """Run the Chitosanase pipeline and return the formatted dataset.
+
+    Executes the provided :class:`Pipeline`, converts the pipeline output
+    into a :class:`MutationDataset`, and returns both the executed pipeline
+    and the dataset. Pipeline artifacts and diagnostics may be saved with
+    ``pipeline.save_artifacts(path)`` by the caller.
+
+    Parameters
+    ----------
+    pipeline : Pipeline
+        The configured Chitosanase cleaning pipeline to execute.
+
+    Returns
+    -------
+    Tuple[Pipeline, MutationDataset]
+        - The executed :class:`Pipeline`.
+        - The resulting :class:`MutationDataset` built from the formatted
+          DataFrame emitted by the pipeline.
+
+    Examples
+    --------
+    >>> pipeline = create_chitosanase_cleaner("/path/to/file.csv")
+    >>> pipeline, dataset = clean_chitosanase_dataset(pipeline)
+    """
+    try:
+        pipeline.execute()
+
+        formatted_df, ref_dict = pipeline.data
+        chitosanase_dataset = MutationDataset.from_dataframe(formatted_df, reference_sequences=ref_dict)
+
+        logger.info(f"Successfully cleaned Chitosanase dataset: " f"{len(formatted_df)} mutations from {len(ref_dict)} proteins")
+        return pipeline, chitosanase_dataset
+    except Exception as e:
+        logger.error(f"Error in running Chitosanase cleaning pipeline: {str(e)}")
+        raise RuntimeError(f"Error in running Chitosanase cleaning pipeline: {str(e)}")

mutcleaner-0.3.0/mutcleaner/cleaners/chitosanase_custom_cleaners.py

@@ -0,0 +1,69 @@
+from __future__ import annotations
+
+import io
+from pathlib import Path
+import pandas as pd
+from typing import TYPE_CHECKING
+
+from ..core.pipeline import pipeline_step
+
+if TYPE_CHECKING:
+    from typing import List
+
+__all__ = ["parse_chitosanase_raw_file"]
+
+
+def __dir__() -> List[str]:
+    return __all__
+
+
+@pipeline_step
+def parse_chitosanase_raw_file(file_path: str | Path, wt_separator: str = '">wt') -> pd.DataFrame:
+    """Parse a raw Chitosanase input file and return the raw DataFrame.
+
+    The raw file contains a CSV block followed by a wild-type sequence.
+    This step only reads the file, splits the two blocks, parses the CSV into
+    a DataFrame, and attaches the WT sequence as a constant column so that the
+    downstream pipeline steps can do the actual cleaning and formatting.
+
+    Parameters
+    ----------
+    file_path : str | pathlib.Path
+        Path to the raw Chitosanase input file. The file should contain a
+        CSV section then the WT sequence separated by ``wt_separator``.
+    wt_separator : str, optional
+        Substring that separates CSV and WT sequence blocks (default '\">wt').
+
+    Returns
+    -------
+    pd.DataFrame
+        Raw DataFrame parsed from the CSV block. It keeps the original input
+        columns and adds ``wt_seq`` so downstream pipeline steps can create
+        the sequence-related columns.
+
+    Raises
+    ------
+    ValueError
+        If the expected WT separator is not found.
+
+    Examples
+    --------
+    >>> from pathlib import Path
+    >>> df = parse_chitosanase_raw_file(Path("/path/to/Chitosanase_Dataset.csv"))
+    >>> sorted(df.columns)
+    ['Tm', 'aa_mut', 'wt_seq']
+    """
+    with open(file_path, "r") as f:
+        raw_text = f.read()
+
+    if wt_separator in raw_text:
+        parts = raw_text.split(wt_separator)
+        csv_text = parts[0].strip()
+        wt_seq = parts[1].replace('"', "").replace(",", "").strip()
+        wt_seq = "".join(wt_seq.split())
+    else:
+        raise ValueError(f"Cannot find WT sequence separator '{wt_separator}' in the expected format.")
+
+    df = pd.read_csv(io.StringIO(csv_text))
+    df["wt_seq"] = wt_seq
+    return df

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/mutcleaner/utils/__init__.py

@@ -18,6 +18,7 @@ from .raw_data_downloader import (
     download_antitoxin_pard3_source_file,
     download_rbd_antibody_source_file,
     download_rbd_ace2_source_file,
+    download_chitosanase_source_file
 )
 
 # fmt: off
@@ -36,4 +37,5 @@ __all__ = [
     "download_antitoxin_pard3_source_file",
     "download_rbd_antibody_source_file",
     "download_rbd_ace2_source_file",
+    "download_chitosanase_source_file"
 ]

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/mutcleaner/utils/data_source.py

@@ -293,6 +293,15 @@ DATASETS = {
             },
         },
     },
+    "Chitosanase Dataset": {
+        "paper_title": "Chitosanase_dataset",
+        "official_doi": None,
+        "files": ["Chitosanase_Dataset.csv"],
+        "huggingface_repos": [
+            "datasets/xulab-research/MutCleaner/resolve/main/Chitosanase_Dataset/Chitosanase_Dataset.csv?download=true",
+        ],
+        "file_name": ["Chitosanase_Dataset.csv"],
+    },
 }
 
 
@@ -320,6 +329,7 @@ def list_datasets_with_built_in_cleaners() -> None:
     - CTXM Epistasis Dataset
     - RBD Antibody Dataset
     - RBD ACE2 Dataset
+    - Chitosanase Dataset
     """
     print("Public datasets with ready-to-use cleaning pipelines:")
     for key, info in DATASETS.items():

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/mutcleaner/utils/raw_data_downloader.py

@@ -747,3 +747,23 @@ def download_rbd_ace2_source_file(
         overwrite=overwrite,
         sub_dataset=sub_dataset,
     )
+
+
+def download_chitosanase_source_file(dir: str, *, overwrite: bool = False) -> Dict[str, str]:
+    """
+    Download the source file for Chitosanase Dataset from the original source.
+
+    Parameters
+    ----------
+    dir : str
+        The target directory where the file will be saved
+    overwrite : bool, default=False
+        Whether to overwrite the file if it already exists. Default is False.
+
+    Returns
+    -------
+    Dict[str, str]
+        key: file name,
+        value: file path pointing to Chitosanase Dataset source file
+    """
+    return download_source_file_from_huggingface("Chitosanase Dataset", dir, overwrite=overwrite)

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/mutcleaner.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mutcleaner
-Version: 0.1.0.post1.dev40
+Version: 0.3.0
 Summary: An efficient framework for cleaning, standardizing, and processing biological mutation data.
 Author: Yuxiang Tang, Ziyu Shi
 License-Expression: BSD-3-Clause
@@ -234,6 +234,11 @@ See the [Data Cleaners Usage Guide](https://xulab-research.github.io/MutCleaner/
       <td><a href="https://doi.org/10.1038/s41586-021-03807-6">SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape</a></td>
       <td><a href="https://huggingface.co/datasets/xulab-research/MutCleaner/blob/main/RBD_Antibody_Dataset/SARS-CoV-2-RBD_MAP_Vir_mAbs.csv">SARS-CoV-2-RBD_MAP_Vir_mAbs.csv</a></td>
     </tr>
+    <tr>
+      <td>Chitosanase Dataset</td>
+      <td>None</td>
+      <td><a href="https://huggingface.co/datasets/xulab-research/MutCleaner/blob/main/Chitosanase_Dataset/Chitosanase_Dataset.csv">Chitosanase_Dataset.csv</a></td>
+    </tr>
   </tbody>
 </table>
 

{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.3.0}/mutcleaner.egg-info/SOURCES.txt

@@ -9,6 +9,8 @@ doc/make.bat
 doc/requirements.in
 doc/requirements.txt
 doc/changelog/CHANGELOG_0.1.0.md
+doc/changelog/CHANGELOG_0.2.0.md
+doc/changelog/CHANGELOG_0.3.0.md
 doc/source/conf.py
 doc/source/index.rst
 doc/source/_static/custom.css
@@ -32,6 +34,8 @@ mutcleaner/cleaners/base_config.py
 mutcleaner/cleaners/basic_cleaners.py
 mutcleaner/cleaners/cdna_proteolysis_cleaner.py
 mutcleaner/cleaners/cdna_proteolysis_custom_cleaners.py
+mutcleaner/cleaners/chitosanase_cleaner.py
+mutcleaner/cleaners/chitosanase_custom_cleaners.py
 mutcleaner/cleaners/ctxm_cleaner.py
 mutcleaner/cleaners/ddg_dtm_cleaners.py
 mutcleaner/cleaners/human_domainome_custom_cleaners.py

mutcleaner-0.3.0/tools/release.sh

@@ -0,0 +1,102 @@
+#!/bin/bash
+set -euo pipefail
+
+VERSION=${1:-}
+
+if [ -z "$VERSION" ]; then
+    echo "Usage: ./tools/release.sh 0.3.0"
+    exit 1
+fi
+
+if [ -z "${GITHUB_TOKEN:-}" ]; then
+    echo "Error: Please set GITHUB_TOKEN"
+    exit 1
+fi
+
+if [ "$(git branch --show-current)" != "main" ]; then
+    echo "Error: release must be run from main branch"
+    exit 1
+fi
+
+if [ -n "$(git status --porcelain)" ]; then
+    echo "Error: working tree is not clean"
+    git status --short
+    exit 1
+fi
+
+echo "Starting release v$VERSION"
+echo "========================================"
+
+echo "[1/9] Pulling latest main..."
+git pull --ff-only origin main
+
+echo "[2/9] Running tests..."
+pytest tests/ -v
+
+if grep -q '^version = ' pyproject.toml; then
+    sed -i -E "s/^version = \".*\"/version = \"$VERSION\"/" pyproject.toml
+else
+    echo "pyproject.toml uses dynamic version; package version will come from tag v$VERSION"
+fi
+
+if grep -q '^__version__ = ' mutcleaner/__init__.py; then
+    sed -i -E "s/^__version__ = \".*\"/__version__ = \"$VERSION\"/" mutcleaner/__init__.py
+fi
+
+if grep -q '^release = ' doc/source/conf.py; then
+    sed -i -E "s/^release = \".*\"/release = \"$VERSION\"/" doc/source/conf.py
+fi
+
+echo "[4/9] Generating changelog..."
+LAST_TAG=$(git describe --tags --abbrev=0)
+CHANGELOG="doc/changelog/CHANGELOG_$VERSION.md"
+
+python tools/changelog.py \
+    "$GITHUB_TOKEN" \
+    "xulab-research/MutCleaner" \
+    "$LAST_TAG..HEAD" \
+    --template keepachangelog \
+    --output "$CHANGELOG"
+
+sed -i "s/## \[HEAD\]/## [$VERSION]/" "$CHANGELOG"
+sed -i "s/$LAST_TAG..HEAD/$LAST_TAG..v$VERSION/g" "$CHANGELOG"
+
+echo "[5/9] Committing release changes..."
+git add pyproject.toml mutcleaner/__init__.py doc/source/conf.py "$CHANGELOG"
+git commit -m "chore: release v$VERSION"
+
+echo "[6/9] Creating local tag..."
+git tag -a "v$VERSION" -m "Release v$VERSION"
+
+echo "[7/9] Building distribution..."
+rm -rf dist/ build/ *.egg-info
+python -m build
+
+python - <<EOF
+from pathlib import Path
+
+version = "$VERSION"
+files = [p.name for p in Path("dist").iterdir()]
+if not files or any(version not in f for f in files):
+    raise SystemExit(f"Unexpected dist files: {files}")
+print("\\n".join(files))
+EOF
+
+echo "[8/9] Checking distribution..."
+twine check dist/*
+
+echo "[9/9] Pushing and uploading..."
+git push origin main
+git push origin "v$VERSION"
+twine upload dist/*
+
+echo "========================================"
+echo "Release v$VERSION completed!"
+echo ""
+echo "Next steps:"
+echo "1. Create GitHub Release:"
+echo "   https://github.com/xulab-research/MutCleaner/releases/new?tag=v$VERSION"
+echo "2. Verify PyPI:"
+echo "   https://pypi.org/project/mutcleaner/$VERSION/"
+echo "3. Verify docs:"
+echo "   https://xulab-research.github.io/MutCleaner/"

mutcleaner-0.1.0.post1.dev40/tools/release.sh

@@ -1,65 +0,0 @@
-#!/bin/bash
-set -e
-
-VERSION=$1
-if [ -z "$VERSION" ]; then
-    echo "Usage: ./tools/release.sh 0.5.0"
-    exit 1
-fi
-
-echo "Starting release process for v$VERSION"
-echo "========================================"
-
-if [ -z "$GITHUB_TOKEN" ]; then
-    echo "Error: Please set GITHUB_TOKEN"
-    exit 1
-fi
-
-echo "[1/8] Running tests..."
-pytest tests/ -v
-
-
-echo "[2/8] Updating version to $VERSION..."
-OLD_VERSION=$(grep 'version = ' pyproject.toml | head -1 | sed 's/.*"\(.*\)".*/\1/')
-sed -i "s/version = \"$OLD_VERSION\"/version = \"$VERSION\"/" pyproject.toml
-sed -i "s/__version__ = \"$OLD_VERSION\"/__version__ = \"$VERSION\"/" mutcleaner/__init__.py
-sed -i "s/release = \"$OLD_VERSION\"/release = \"$VERSION\"/" doc/source/conf.py
-
-echo "[3/8] Generating CHANGELOG..."
-LAST_TAG=$(git describe --tags --abbrev=0)
-
-python tools/changelog.py \
-    "$GITHUB_TOKEN" \
-    "xulab-research/MutCleaner" \
-    "$LAST_TAG..HEAD" \
-    --template keepachangelog \
-    --output "./doc/changelog/CHANGELOG_$1.md"
-
-echo "[4/8] Building distribution..."
-rm -rf dist/ build/
-python -m build
-
-echo "[5/8] Checking distribution..."
-twine check dist/*
-
-echo "[6/8] Committing changes..."
-git add pyproject.toml mutcleaner/__init__.py doc/source/conf.py "doc/changelog/CHANGELOG_$VERSION.md"
-git commit -m "chore: bump version to $VERSION"
-git push origin main
-
-echo "[7/8] Creating and pushing tag v$VERSION..."
-git tag -a "v$VERSION" -m "Release v$VERSION"
-git push origin "v$VERSION"
-
-
-echo "[8/8] Uploading to PyPI..."
-twine upload dist/*
-
-echo "========================================"
-echo "Release v$VERSION completed!"
-echo ""
-echo "Next steps:"
-echo "1. Create GitHub Release at:"
-echo "   https://github.com/xulab-research/MutCleaner/releases/new?tag=v$VERSION"
-echo "2. Verify PyPI: https://pypi.org/project/mutcleaner/$VERSION/"
-echo "3. Verify docs: https://xulab-research.github.io/MutCleaner/"