From cff903bbe9fdf7eece2c9ceb5b67ee3acc1a5422 Mon Sep 17 00:00:00 2001 From: jtb Date: Sat, 25 Nov 2023 15:38:24 -0600 Subject: [PATCH] feat: switched from using typer to just argparse This project originally used typer because of some of the limited features of the argparse library. Now argparse has acceptable features so this push replaces all of the typer dependencies with argparse. --- drive/cluster/cluster.py | 3 + drive/drive.py | 323 ++++++++----- drive/filters/filter.py | 13 +- drive/log | 2 +- drive/models/__init__.py | 1 - drive/models/choices.py | 23 - drive/utilities/callbacks/__init__.py | 2 +- drive/utilities/callbacks/callbacks.py | 104 ++--- poetry.lock | 608 ++++--------------------- pyproject.toml | 9 +- 10 files changed, 354 insertions(+), 734 deletions(-) delete mode 100644 drive/models/choices.py diff --git a/drive/cluster/cluster.py b/drive/cluster/cluster.py index 0a837d1..54697ff 100644 --- a/drive/cluster/cluster.py +++ b/drive/cluster/cluster.py @@ -77,6 +77,9 @@ def random_walk(self, graph: ig.Graph) -> ig.VertexClustering: result of the random walk cluster. This object has information about clusters and membership """ + logger.debug( + f"Performing the community walktrap algorithm with a random walk step size of: {self.random_walk_step_size}" + ) ibd_walktrap = ig.Graph.community_walktrap( graph, weights="cm", steps=self.random_walk_step_size diff --git a/drive/drive.py b/drive/drive.py index 80f2d43..87d12c7 100755 --- a/drive/drive.py +++ b/drive/drive.py @@ -2,19 +2,45 @@ import re from datetime import datetime from pathlib import Path +import argparse from typing import Optional +from rich_argparse import RichHelpFormatter -import typer import drive.factory as factory from drive.cluster import ClusterHandler, cluster from drive.filters import IbdFilter from drive.log import CustomLogger -from drive.models import Data, FormatTypes, Genes, OverlapOptions, create_indices -from drive.utilities.callbacks import check_input_exists, check_json_path +from drive.models import Data, Genes, create_indices +from drive.utilities.callbacks import CheckInputExist from drive.utilities.parser import PhenotypeFileParser, load_phenotype_descriptions -app = typer.Typer(add_completion=False) + +def find_json_file() -> Path: + """Method to find the default config file if the user does not provide one + + Returns + ------- + Path + returns the path to the json file + + Raises + ------ + FileNotFoundError + Raises a FileNotFoundError if the program can not locate a json file and the + user does not provide the path to a file + """ + + src_dir = Path(__file__).parent + + config_path = src_dir / "config.json" + + if not config_path.exists(): + raise FileNotFoundError( + f"Expected the user to either pass a configuration file path or for the config.json file to be present in the program root directory at {config_path}." # noqa: E501 + ) + + return config_path def split_target_string(chromo_pos_str: str) -> Genes: @@ -60,149 +86,204 @@ def split_target_string(chromo_pos_str: str) -> Genes: return Genes(*integer_split_str) -@app.command() -def main( - input_file: Path = typer.Option( - ..., "-i", "--input", help="IBD input file", callback=check_input_exists - ), - ibd_format: FormatTypes = typer.Option( - FormatTypes.HAPIBD.value, - "-f", +def main() -> None: + parser = argparse.ArgumentParser( + description=" Distant Relatedness for Identification and Variant Evaluation (DRIVE) is a novel approach to IBD-based genotype inference used to identify shared chromosomal segments in dense genetic arrays", + formatter_class=RichHelpFormatter, + ) + + parser.add_argument( + "--input", + "-i", + type=Path, + help="IBD input file from ibd detection software", + required=True, + action=CheckInputExist, + ) + + parser.add_argument( "--format", - help="IBD file format. Allowed values are hapibd, ilash, germline, rapid", - ), - target: str = typer.Option( - ..., - "-t", + "-f", + default="hapibd", + type=str, + help="IBD program used to detect segments. Allowed values are hapibd, ilash, germline, rapid. Program expects for value to be lowercase. (default: %(default)s)", + choices=["hapibd", "ilash", "germline", "rapid"], + ) + + parser.add_argument( "--target", + "-t", + type=str, help="Target region or position, chr:start-end or chr:pos", - ), - output: Path = typer.Option(..., "-o", "--output", help="output file prefix"), - min_cm: int = typer.Option( - 3, "-m", "--min-cm", help="minimum centimorgan threshold." - ), - step: int = typer.Option(3, "-k", "--step", help="steps for random walk"), - max_check: int = typer.Option( - 5, + required=True, + ) + + parser.add_argument( + "--output", + "-o", + type=Path, + help="output file prefix. The program will append .drive_networks.txt to the filename provided", + required=True, + ) + + parser.add_argument( + "--min-cm", + "-m", + default=3, + type=int, + help="minimum centimorgan threshold. The program expects this to be an integer value. (default: %(default)s)", + ) + + parser.add_argument( + "--step", + "-k", + default=3, + type=int, + help="Minimum required number of steps for the community walktrap algorithm.(default: %(default)s)", + ) + + parser.add_argument( "--max-recheck", - help="Maximum number of times to re-perform the clustering. This value will not be used if the flag --no-recluster is used.", # noqa: E501 - ), - case_file: Optional[Path] = typer.Option( - None, - "-c", + default=5, + type=int, + help="Maximum number of times to re-perform the clustering. This value will not be used if the flag --no-recluster is used.(default: %(default)s)", # noqa: E501 + ) + + parser.add_argument( "--cases", - help="A file containing individuals who are cases. This file expects for there to be two columns. The first column will have individual ids and the second has status where cases are indicated by a 1 and control are indicated by a 0.", # noqa: E501 - ), - segment_overlap: OverlapOptions = typer.Option( - OverlapOptions.CONTAINS.value, + "-c", + type=Path, + help="A file containing individuals who are cases. This file expects for there to be two columns. The first column will have individual ids and the second has status where cases are indicated by a 1, control are indicated by a 0, and exclusions are indicated by NA.", # noqa: E501 + action=CheckInputExist, + ) + + parser.add_argument( "--segment-overlap", - help="Indicates if the user wants the gene to contain the whole target region or if it just needs to overlap the segment.", # noqa: E501 - ), - phenotype_description_file: Optional[Path] = typer.Option( - None, - "-d", + default="contains", + choices=["contains", "overlaps"], + type=str, + help="Indicates if the user wants the gene to contain the whole target region or if it just needs to overlap the segment. (default: %(default)s)", # noqa: E501 + ) + + parser.add_argument( "--descriptions", + "-d", + type=Path, help="tab delimited text file that has descriptions for each phecode. this file should have two columns called phecode and phenotype", # noqa: E501 - ), - max_network_size: int = typer.Option( - 30, "--max-network-size", help="maximum network size allowed" - ), - minimum_connected_thres: float = typer.Option( - 0.5, + ) + + parser.add_argument( + "--max-network-size", + default=30, + type=int, + help="maximum network size allowed if the user has allowed the recluster option. (default: %(default)s)", + ) + + parser.add_argument( "--min-connected-threshold", - help="minimum connectedness ratio required for the network", - ), - min_network_size: int = typer.Option( - 2, + default=0.5, + type=float, + help="minimum connectedness ratio required for the network. (default: %(default)s)", + ) + + parser.add_argument( "--min-network-size", - help="This argument sets the minimun network size that we allow. All networks smaller than this size will be filtered out. If the user wishes to keep all networks they can set this to 0", # noqa: E501 - ), - segment_dist_threshold: float = typer.Option( - 0.2, + default=2, + type=int, + help="This argument sets the minimun network size that we allow. All networks smaller than this size will be filtered out. If the user wishes to keep all networks they can set this to 0. (default: %(default)s)", # noqa: E501 + ) + + parser.add_argument( "--segment-distribution-threshold", - help="Threshold to filter the network length to remove hub individuals", - ), - hub_threshold: float = typer.Option( - 0.01, + default=0.2, + type=float, + help="Threshold to filter the network length to remove hub individuals. (default: %(default)s)", + ) + + parser.add_argument( "--hub-threshold", - help="Threshold to determine what percentage of hubs to keep", - ), - json_path: Path = typer.Option( - None, + default=0.01, + type=float, + help="Threshold to determine what percentage of hubs to keep. (default: %(default)s)", + ) + + parser.add_argument( "--json-config", "-j", + default=None, + type=Path, help="path to the json config file", - callback=check_json_path, - ), - recluster: bool = typer.Option( - True, + ) + + parser.add_argument( + "--recluster", + type=bool, + default=True, + action=argparse.BooleanOptionalAction, help="whether or not the user wishes the program to automically recluster based on things lik hub threshold, max network size and how connected the graph is. ", # noqa: E501 - ), - verbose: int = typer.Option( - 0, + ) + + parser.add_argument( "--verbose", "-v", + default=0, help="verbose flag indicating if the user wants more information", - count=True, - ), - log_to_console: bool = typer.Option( - False, + action="count", + ) + + parser.add_argument( "--log-to-console", + default=False, help="Optional flag to log to only the console or also a file", - is_flag=True, - ), - log_filename: str = typer.Option( - "drive.log", "--log-filename", help="Name for the log output file." - ), -) -> None: + action="store_true", + ) + + parser.add_argument( + "--log-filename", + default="drive.log", + type=str, + help="Name for the log output file. (default: %(default)s)", + ) + + args = parser.parse_args() + # getting the programs start time start_time = datetime.now() + # We need to make sure that there is a configuration file + json_config = args.json_config if args.json_config else find_json_file() + # creating and configuring the logger and then recording user inputs logger = CustomLogger.create_logger() - logger.configure(output.parent, log_filename, verbose, log_to_console) - # record the input parameters - logger.record_inputs( - ibd_file=input_file, - ibd_program_used=ibd_format, - gene_target_region=target, - output_prefix=output, - phenotype_description_file=phenotype_description_file, - phenotype_file=case_file, - minimum_centimorgan_threshold=min_cm, - random_walk_step_size=step, - max_recheck_times=max_check, - max_network_size=max_network_size, - minimum_connection_threshold=minimum_connected_thres, - min_network_size=min_network_size, - log_to_console=log_to_console, - log_filename=log_filename, - recluster=recluster, + logger.configure( + args.output.parent, args.log_filename, args.verbose, args.log_to_console ) - logger.debug(f"Parent directory for log files and output: {output.parent}") + # record the input parameters using a method from the logger object that + # takes the parser as an argument + logger.record_namespace(args) + + logger.debug(f"Parent directory for log files and output: {args.output.parent}") logger.info(f"Analysis start time: {start_time}") # we need to load in the phenotype descriptions file to get # descriptions of each phenotype - if phenotype_description_file: - logger.verbose( - f"Using the phenotype descriptions file at: {phenotype_description_file}" - ) - desc_dict = load_phenotype_descriptions(phenotype_description_file) + if args.descriptions: + logger.verbose(f"Using the phenotype descriptions file at: {args.descriptions}") + desc_dict = load_phenotype_descriptions(args.descriptions) else: logger.verbose("No phenotype descriptions provided") desc_dict = {} # if the user has provided a phenotype file then we will determine case/control/ # exclusion counts. Otherwise we return an empty dictionary - if case_file: - with PhenotypeFileParser(case_file) as phenotype_file: + if args.cases: + with PhenotypeFileParser(args.cases) as phenotype_file: phenotype_counts, cohort_ids = phenotype_file.parse_cases_and_controls() logger.info( - f"identified {len(phenotype_counts.keys())} phenotypes within the file {case_file}" # noqa: E501 + f"identified {len(phenotype_counts.keys())} phenotypes within the file {args.cases}" # noqa: E501 ) else: logger.info( @@ -212,21 +293,21 @@ def main( phenotype_counts = {} cohort_ids = [] - indices = create_indices(ibd_format.lower()) + indices = create_indices(args.format.lower()) logger.debug(f"created indices object: {indices}") ##target gene region or variant position - target_gene = split_target_string(target) + target_gene = split_target_string(args.target) logger.debug(f"Identified a target region: {target_gene}") - filter_obj: IbdFilter = IbdFilter.load_file(input_file, indices, target_gene) + filter_obj: IbdFilter = IbdFilter.load_file(args.input, indices, target_gene) # choosing the proper way to filter the ibd files - filter_obj.set_filter(segment_overlap) + filter_obj.set_filter(args.segment_overlap) - filter_obj.preprocess(min_cm, cohort_ids) + filter_obj.preprocess(args.min_cm, cohort_ids) # We need to invert the hapid_map dictionary so that the # integer mappings are keys and the values are the @@ -235,27 +316,27 @@ def main( # creating the object that will handle clustering within the networks cluster_handler = ClusterHandler( - minimum_connected_thres, - max_network_size, - max_check, - step, - min_network_size, - segment_dist_threshold, - hub_threshold, + args.min_connected_threshold, + args.max_network_size, + args.max_recheck, + args.step, + args.min_network_size, + args.segment_distribution_threshold, + args.hub_threshold, hapid_inverted, - recluster, + args.recluster, ) networks = cluster(filter_obj, cluster_handler, indices.cM_indx) # creating the data container that all the plugins can interact with - plugin_api = Data(networks, output, phenotype_counts, desc_dict) + plugin_api = Data(networks, args.output, phenotype_counts, desc_dict) logger.debug(f"Data container: {plugin_api}") # making sure that the output directory is created # This section will load in the analysis plugins and run each plugin - with open(json_path, encoding="utf-8") as json_config: + with open(json_config, encoding="utf-8") as json_config: config = json.load(json_config) factory.load_plugins(config["plugins"]) @@ -278,4 +359,4 @@ def main( if __name__ == "__main__": - app() + main() diff --git a/drive/filters/filter.py b/drive/filters/filter.py index 266afcb..4909a26 100644 --- a/drive/filters/filter.py +++ b/drive/filters/filter.py @@ -2,11 +2,10 @@ from dataclasses import dataclass, field from pathlib import Path from typing import Callable, Dict, Iterator, List, Optional, TypeVar - from pandas import DataFrame, concat, read_csv from drive.log import CustomLogger -from drive.models import FileIndices, Genes, OverlapOptions +from drive.models import FileIndices, Genes logger = CustomLogger.get_logger(__name__) @@ -15,7 +14,6 @@ T = TypeVar("T", bound="IbdFilter") -# def filter_ @dataclass class IbdFilter: ibd_file: Iterator[DataFrame] @@ -221,16 +219,17 @@ def _overlaps_filter(self, data_chunk: DataFrame, min_cm: int) -> DataFrame: & (data_chunk[self.indices.cM_indx] >= min_cm) ].copy() - def set_filter(self, filter_option: OverlapOptions) -> None: + def set_filter(self, filter_option: str) -> None: """Method to determine how the user wishes to filter the IBD segments file Parameters ---------- - filter_option : OverlapOptions - Enum that represents the user's choice for how to filter the ibd segments. + filter_option : str + string that represents the user's choice for how to filter the ibd segments. If the user chooses 'contains' the only segments that contain the entire region are kept. If the user chooses 'overlaps' then segments that overlap at all with the target region are kept.""" + if filter_option == "contains": logger.info("Identifying IBD segments that contain the target region") self.filter = self._contains_filter @@ -379,7 +378,6 @@ def _check_empty_dataframes(self) -> None: def preprocess( self, min_centimorgan: int, - target_overlap_style: OverlapOptions, cohort_ids: Optional[List[str]] = None, ) -> None: """Method that will filter the ibd file. @@ -395,6 +393,7 @@ def preprocess( Lists of ids that make up the cohort. The ibd_file will be filtered to only this list. """ + for chunk in self.ibd_file: cohort_restricted_chunk = self._filter_for_cohort(chunk, cohort_ids) diff --git a/drive/log b/drive/log index 3b5eec1..5fb8e93 160000 --- a/drive/log +++ b/drive/log @@ -1 +1 @@ -Subproject commit 3b5eec1b148a1a18f3e251bca2aa5c7715d16f68 +Subproject commit 5fb8e93d0bd309355480a09c322973c28f326720 diff --git a/drive/models/__init__.py b/drive/models/__init__.py index 7656549..5974860 100644 --- a/drive/models/__init__.py +++ b/drive/models/__init__.py @@ -1,4 +1,3 @@ -from .choices import FormatTypes, LogLevel, OverlapOptions from .data_container import Data, Data_Interface from .generate_indices import FileIndices, create_indices from .networks import Network, Network_Interface diff --git a/drive/models/choices.py b/drive/models/choices.py deleted file mode 100644 index 6026f3b..0000000 --- a/drive/models/choices.py +++ /dev/null @@ -1,23 +0,0 @@ -from enum import Enum - - -class LogLevel(str, Enum): - """Enum used to define the options for the log level in the cli""" - - INFO = 0 - DEBUG = 1 - - -class FormatTypes(str, Enum): - HAPIBD = "hapibd" - ILASH = "ilash" - GERMLINE = "germline" - RAPID = "rapid" - - -class OverlapOptions(str, Enum): - """Enum defining options for how the use wants to define - overlap with the gene region of interest. Values can be contains or overlaps""" - - CONTAINS = "contains" - OVERLAPS = "overlaps" diff --git a/drive/utilities/callbacks/__init__.py b/drive/utilities/callbacks/__init__.py index 7b79f6d..a69be9b 100644 --- a/drive/utilities/callbacks/__init__.py +++ b/drive/utilities/callbacks/__init__.py @@ -1 +1 @@ -from .callbacks import check_input_exists, check_json_path +from .callbacks import CheckInputExist diff --git a/drive/utilities/callbacks/callbacks.py b/drive/utilities/callbacks/callbacks.py index 0addfae..891aadb 100644 --- a/drive/utilities/callbacks/callbacks.py +++ b/drive/utilities/callbacks/callbacks.py @@ -1,62 +1,50 @@ from pathlib import Path +import argparse +import sys + + +class CheckInputExist(argparse.Action): + def __init__(self, option_strings, dest, nargs=None, **kwargs) -> None: + if nargs is not None: + raise ValueError("nargs not allowed") + super(CheckInputExist, self).__init__(option_strings, dest, **kwargs) + + def __call__( + self, + parser: argparse.ArgumentParser, + namespace: argparse.Namespace, + values: Path, + option_string: str = None, + ) -> None: + if values.exists(): + setattr(namespace, self.dest, values) + else: + print( + f"ERROR: The file, {values}, was not found. Please make sure that there is not a typo in the file name." + ) + sys.exit(1) -def check_input_exists(ibd_input_file: Path) -> Path: - """Callback that will check that the input ibd file exists - - Parameters - ---------- - ibd_input_file : Path - Path object to the input ibd file. This file should be gzipped - - Returns - ------- - Path - returns the Path object if it exists - - Raises - ------ - FileNotFoundError - If the ibd input file does not exist then the program will - immediately raise a FileNotFoundError - """ - if ibd_input_file.exists(): - return ibd_input_file - else: - raise FileNotFoundError(f"The file, {ibd_input_file}, was not found") - - -def check_json_path(json_path: Path) -> Path: - """Callback function that creates the json path string. If the user provides a value - then it uses the user provided value else it creates the path to the default file - - Parameters - ---------- - json_path : str - path to the json config file or an empty string - - Returns - ------- - Path - returns the Path object pointing to the file - - Raises - ------ - FileNotFoundError - If the config.json file does not exist at the specified path then this error is - raised - """ - - if json_path: - return json_path - else: - src_dir = Path(__file__).parent.parent.parent - - config_path = src_dir / "config.json" - - if not config_path.exists(): - raise FileNotFoundError( - f"Expected the user to either pass a configuration file path or for the config.json file to be present in the program root directory at {config_path}." # noqa: E501 - ) +# class CheckJsonPath(argparse.Action): + +# def __init__(self, option_strings, dest, nargs=None, **kwargs) -> None: +# if nargs is not None: +# raise ValueError("nargs not allowed") +# super(CheckJsonPath, self).__init__(option_strings, dest, **kwargs) + + +# def __call__(self, parser: argparse.ArgumentParser, namespace: argparse.Namespace, values: Path, option_string: str =None) -> None: +# print(f"This is the content in values: {values}") +# if values: +# setattr(namespace, self.dest, values) +# else: +# src_dir = Path(__file__).parent.parent.parent + +# config_path = src_dir / "config.json" + +# if not config_path.exists(): +# raise FileNotFoundError( +# f"Expected the user to either pass a configuration file path or for the config.json file to be present in the program root directory at {config_path}." # noqa: E501 +# ) - return config_path +# setattr(namespace, self.dest, config_path) diff --git a/poetry.lock b/poetry.lock index 1858a01..f66c085 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,313 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. - -[[package]] -name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" -optional = false -python-versions = ">=3.6" -files = [ - {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, - {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, -] - -[[package]] -name = "babel" -version = "2.12.1" -description = "Internationalization utilities" -optional = false -python-versions = ">=3.7" -files = [ - {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, - {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, -] - -[package.dependencies] -pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} - -[[package]] -name = "beautifulsoup4" -version = "4.12.2" -description = "Screen-scraping library" -optional = false -python-versions = ">=3.6.0" -files = [ - {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, - {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"}, -] - -[package.dependencies] -soupsieve = ">1.2" - -[package.extras] -html5lib = ["html5lib"] -lxml = ["lxml"] - -[[package]] -name = "certifi" -version = "2022.12.7" -description = "Python package for providing Mozilla's CA Bundle." -optional = false -python-versions = ">=3.6" -files = [ - {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"}, - {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"}, -] - -[[package]] -name = "charset-normalizer" -version = "3.1.0" -description = "The Real First Universal Charset Detector. 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= false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -2028,7 +1643,6 @@ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." category = "dev" - optional = false python-versions = "*" files = [ @@ -2040,9 +1654,7 @@ files = [ name = "soupsieve" version = "2.4.1" description = "A modern CSS selector implementation for Beautiful Soup." - category = "dev" - optional = false python-versions = ">=3.7" files = [ @@ -2055,7 +1667,6 @@ name = "sphinx" version = "6.2.1" description = "Python documentation generator" category = "dev" - optional = false python-versions = ">=3.8" files = [ @@ -2092,7 +1703,6 @@ name = "sphinx-autobuild" version = "2021.3.14" description = "Rebuild Sphinx documentation on changes, with live-reload in the browser." category = "dev" - optional = false python-versions = ">=3.6" files = [ @@ -2162,13 +1772,11 @@ sphinx = ">=1.8" code-style = ["pre-commit (==2.12.1)"] rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme", "sphinx-examples"] - [[package]] name = "sphinxcontrib-applehelp" version = "1.0.4" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" category = "dev" - optional = false python-versions = ">=3.8" files = [ @@ -2185,7 +1793,6 @@ name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." category = "dev" - optional = false python-versions = ">=3.5" files = [ @@ -2202,7 +1809,6 @@ name = "sphinxcontrib-htmlhelp" version = "2.0.1" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" category = "dev" - optional = false python-versions = ">=3.8" files = [ @@ -2234,7 +1840,6 @@ name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." category = "dev" - optional = false python-versions = ">=3.5" files = [ @@ -2251,7 +1856,6 @@ name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." category = "dev" - optional = false python-versions = ">=3.5" files = [ @@ -2303,7 +1907,6 @@ name = "texttable" version = "1.6.7" description = "module to create simple ASCII tables" category = "main" - optional = false python-versions = "*" files = [ @@ -2372,35 +1975,11 @@ files = [ docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] -[[package]] -name = "typer" -version = "0.7.0" -description = "Typer, build great CLIs. Easy to code. Based on Python type hints." -category = "main" -optional = false -python-versions = ">=3.6" -files = [ - {file = "typer-0.7.0-py3-none-any.whl", hash = "sha256:b5e704f4e48ec263de1c0b3a2387cd405a13767d2f907f44c1a08cbad96f606d"}, - {file = "typer-0.7.0.tar.gz", hash = "sha256:ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165"}, -] - -[package.dependencies] -click = ">=7.1.1,<9.0.0" -colorama = {version = ">=0.4.3,<0.5.0", optional = true, markers = "extra == \"all\""} -rich = {version = ">=10.11.0,<13.0.0", optional = true, markers = "extra == \"all\""} -shellingham = {version = ">=1.3.0,<2.0.0", optional = true, markers = "extra == \"all\""} - -[package.extras] -all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"] -dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] -doc = ["cairosvg (>=2.5.2,<3.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pillow (>=9.3.0,<10.0.0)"] -test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"] - [[package]] name = "typing-extensions" version = "4.1.1" description = "Backported and Experimental Type Hints for Python 3.6+" -category = "main" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2413,7 +1992,6 @@ name = "urllib3" version = "2.0.2" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "dev" - optional = false python-versions = ">=3.7" files = [ @@ -2428,7 +2006,6 @@ socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] [[package]] - name = "wcwidth" version = "0.2.6" description = "Measures the displayed width of unicode strings in a terminal" @@ -2445,7 +2022,6 @@ name = "zipp" version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "dev" - optional = false python-versions = ">=3.7" files = [ @@ -2459,7 +2035,5 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" - -python-versions = ">=3.8,<3.12" -content-hash = "2375d1ec9f15708be431c0246aea061dbd2c035a2b8c75b35ecc0f90c2e25527" - +python-versions = ">=3.9,<3.12" +content-hash = "f1f72f9dcb97490be54776ed8bfe9084df560f9e3020ebb557408b8a2b4f0b86" diff --git a/pyproject.toml b/pyproject.toml index 100581b..abd5131 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "drive-ibd" -version = "2.1.3" +version = "2.2.0" description = "cli tool to identify networks of individuals who share IBD segments overlapping loci of interest" authors = ["James Baker ", "Hung-Hsin Chen ", "Jennifer E. Below "] maintainers = ["James Baker ", "Hung-Hsin Chen "] @@ -11,7 +11,6 @@ keywords = ["python", "genetics", "identity by descent", "relatedness"] classifiers = [ "Development Status :: 5 - Production/Stable", "Operating System :: Unix", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", @@ -22,15 +21,15 @@ packages = [ ] [tool.poetry.scripts] -drive = 'drive.drive:app' +drive = 'drive.drive:main' [tool.poetry.dependencies] -python = ">=3.8,<3.12" -typer = {extras = ["all"], version = "^0.7.0"} +python = ">=3.9,<3.12" pandas = "^1.5.3" numpy = "^1.24.2" igraph = "^0.10.4" scipy = "^1.10.1" +rich-argparse = "^1.3.0" [tool.poetry.group.dev.dependencies]