ensembl-utils 0.1.1__py3-none-any.whl

ensembl/utils/__init__.py

@@ -0,0 +1,27 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Ensembl Python general-purpose utils library."""
+
+__version__ = "0.1.1"
+
+__all__ = [
+    "StrPath",
+]
+
+import os
+from typing import Union
+
+
+StrPath = Union[str, os.PathLike]

ensembl/utils/archive.py

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Utils for common IO operations over archive files, e.g. tar or gzip."""
+
+__all__ = [
+    "SUPPORTED_ARCHIVE_FORMATS",
+    "open_gz_file",
+    "extract_file",
+]
+
+from contextlib import contextmanager
+import gzip
+from pathlib import Path
+import shutil
+from typing import Generator, TextIO
+
+from ensembl.utils import StrPath
+from ensembl.utils.argparse import ArgumentParser
+
+
+def _unpack_gz_files(src_file: StrPath, dst_dir: StrPath) -> None:
+    """Unpacks `src_file` to `dst_dir`.
+
+    Args:
+        src_file: File path to unpack (with ".gz" extension).
+        dst_dir: Directory path to unpack the file into.
+
+    """
+    # Remove '.gz' extension to create the destination file name
+    dst_file = Path(dst_dir) / Path(src_file).stem
+    with gzip.open(src_file, "rb") as f_in:
+        with dst_file.open("wb") as f_out:
+            shutil.copyfileobj(f_in, f_out)
+
+
+shutil.register_unpack_format("gzip", [".gz"], _unpack_gz_files, description="GZIP file")
+
+# Each registered format is a tuple (name, extensions, description)
+SUPPORTED_ARCHIVE_FORMATS = [ext for elem in shutil.get_unpack_formats() for ext in elem[1]]
+
+
+@contextmanager
+def open_gz_file(file_path: StrPath) -> Generator[TextIO, None, None]:
+    """Yields an open file object, even if the file is compressed with gzip.
+
+    The file is expected to contain a text, and this can be used with the usual "with".
+
+    Args:
+        file_path: A (single) file path to open.
+
+    """
+    src_file = Path(file_path)
+    if src_file.suffix == ".gz":
+        with gzip.open(src_file, "rt") as fh:
+            yield fh
+    else:
+        with src_file.open("rt") as fh:
+            yield fh
+
+
+def extract_file(src_file: StrPath, dst_dir: StrPath) -> None:
+    """Extracts the `src_file` into `dst_dir`.
+
+    If the file is not an archive, it will be copied to `dst_dir`. `dst_dir` will be created if it
+    does not exist.
+
+    Args:
+        src_file: Path to the file to unpack.
+        dst_dir: Path to the folder where to extract the file.
+
+    """
+    src_file = Path(src_file)
+    extensions = {"".join(src_file.suffixes[i:]) for i in range(0, len(src_file.suffixes))}
+
+    if extensions.intersection(SUPPORTED_ARCHIVE_FORMATS):
+        shutil.unpack_archive(src_file, dst_dir)
+    else:
+        # Replicate the functionality of shutil.unpack_archive() by creating `dst_dir`
+        Path(dst_dir).mkdir(parents=True, exist_ok=True)
+        shutil.copy(src_file, dst_dir)
+
+
+def extract_file_cli() -> None:
+    """Entry-point for the `extract_file` method"""
+    parser = ArgumentParser(description="Extracts file to the given location.")
+    parser.add_argument_src_path("--src_file", required=True, help="Path to the file to unpack")
+    parser.add_argument_dst_path(
+        "--dst_dir", default=Path.cwd(), help="Path to the folder where to extract the file"
+    )
+    args = parser.parse_args()
+    extract_file(args.src_file, args.dst_dir)

ensembl/utils/argparse.py

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Provide an extended version of `argparse.ArgumentParser` with additional functionality.
+
+Examples:
+
+    >>> from pathlib import Path
+    >>> from ensembl.util.argparse import ArgumentParser
+    >>> parser = ArgumentParser(description="Tool description")
+    >>> parser.add_argument_src_path("--src_file", required=True, help="Path to source file")
+    >>> parser.add_server_arguments(help="Server to connect to")
+    >>> args = parser.parse_args()
+    >>> args
+    Namespace(host='myserver', port=3826, src_file=PosixPath('/path/to/src_file.txt'),
+    url=URL('mysql://username@myserver:3826'), user='username')
+
+"""
+
+__all__ = [
+    "ArgumentParser",
+]
+
+import argparse
+import os
+from pathlib import Path
+
+from sqlalchemy.engine import make_url, URL
+
+from ensembl.utils import StrPath
+
+
+class ArgumentParser(argparse.ArgumentParser):
+    """Extends `argparse.ArgumentParser` with additional methods and functionality.
+
+    The default behaviour of the help text will be to display the default values on every non-required
+    argument, i.e. optional arguments with `required=False`.
+
+    """
+
+    def __init__(self, *args, **kwargs) -> None:
+        """Extends the base class to include the information about default argument values by default."""
+        super().__init__(*args, **kwargs)
+        self.formatter_class = argparse.ArgumentDefaultsHelpFormatter
+        self.__server_groups: list[str] = []
+
+    def _validate_src_path(self, src_path: StrPath) -> Path:
+        """Returns the path if exists and it is readable, raises an error through the parser otherwise.
+
+        Args:
+            src_path: File or directory path to check.
+
+        """
+        src_path = Path(src_path)
+        if not src_path.exists():
+            self.error(f"'{src_path}' not found")
+        elif not os.access(src_path, os.R_OK):
+            self.error(f"'{src_path}' not readable")
+        return src_path
+
+    def _validate_dst_path(self, dst_path: StrPath, exists_ok: bool = False) -> Path:
+        """Returns the path if it is writable, raises an error through the parser otherwise.
+
+        Args:
+            dst_path: File or directory path to check.
+            exists_ok: Do not raise an error during parsing if the destination path already exists.
+
+        """
+        dst_path = Path(dst_path)
+        if dst_path.exists():
+            if os.access(dst_path, os.W_OK):
+                if exists_ok:
+                    return dst_path
+                self.error(f"'{dst_path}' already exists")
+            else:
+                self.error(f"'{dst_path}' is not writable")
+        # Check if the first parent directory that exists is writable
+        for parent_path in dst_path.parents:
+            if parent_path.exists():
+                if not os.access(parent_path, os.W_OK):
+                    self.error(f"'{dst_path}' is not writable")
+                break
+        return dst_path
+
+    def add_argument(self, *args, **kwargs) -> None:  # type: ignore[override]
+        """Extends the parent function by excluding the default value in the help text when not provided.
+
+        Only applied to required arguments without a default value, i.e. positional arguments or optional
+        arguments with `required=True`.
+
+        """
+        if kwargs.get("required", False):
+            kwargs.setdefault("default", argparse.SUPPRESS)
+        super().add_argument(*args, **kwargs)
+
+    def add_argument_src_path(self, *args, **kwargs) -> None:
+        """Adds `pathlib.Path` argument, checking if it exists and it is readable at parsing time.
+
+        If "metavar" is not defined, it is added with "PATH" as value to improve help text readability.
+
+        """
+        kwargs.setdefault("metavar", "PATH")
+        kwargs["type"] = self._validate_src_path
+        self.add_argument(*args, **kwargs)
+
+    def add_argument_dst_path(self, *args, exists_ok: bool = True, **kwargs) -> None:
+        """Adds `pathlib.Path` argument, checking if it is writable at parsing time.
+
+        If "metavar" is not defined it is added with "PATH" as value to improve help text readability.
+
+        Args:
+            exists_ok: Do not raise an error if the destination path already exists.
+
+        """
+        kwargs.setdefault("metavar", "PATH")
+        kwargs["type"] = lambda x: self._validate_dst_path(x, exists_ok)
+        self.add_argument(*args, **kwargs)
+
+    def add_argument_url(self, *args, **kwargs) -> None:
+        """Adds `sqlalchemy.engine.URL` argument.
+
+        If "metavar" is not defined it is added with "URI" as value to improve help text readability.
+
+        """
+        kwargs.setdefault("metavar", "URI")
+        kwargs["type"] = make_url
+        self.add_argument(*args, **kwargs)
+
+    # pylint: disable=redefined-builtin
+    def add_server_arguments(self, prefix: str = "", include_database: bool = False, help: str = "") -> None:
+        """Adds the usual set of arguments needed to connect to a server, i.e. `--host`, `--port`, `--user`
+        and `--password` (optional).
+
+        Note that the parser will assume this is a MySQL server.
+
+        Args:
+            prefix: Prefix to add the each argument, e.g. if prefix is `src_`, the arguments will be
+                `--src_host`, etc.
+            include_database: Include `--database` argument.
+            help: Description message to include for this set of arguments.
+
+        """
+        group = self.add_argument_group(f"{prefix}server connection arguments", description=help)
+        group.add_argument(f"--{prefix}host", required=True, metavar="HOST", help="host name")
+        group.add_argument(f"--{prefix}port", required=True, type=int, metavar="PORT", help="port number")
+        group.add_argument(f"--{prefix}user", required=True, metavar="USER", help="user name")
+        group.add_argument(f"--{prefix}password", metavar="PWD", help="host password")
+        if include_database:
+            group.add_argument(f"--{prefix}database", required=True, metavar="NAME", help="database name")
+        self.__server_groups.append(prefix)
+
+    def add_log_arguments(self, add_log_file: bool = False) -> None:
+        """Adds the usual set of arguments required to set and initialise a logging system.
+
+        The current set includes a mutually exclusive group for the default logging level: `--verbose`,
+        `--debug` or `--log LEVEL`.
+
+        Args:
+            add_log_file: Add arguments to allow storing messages into a file, i.e. `--log_file` and
+                `--log_file_level`.
+
+        """
+        # Define the list of log levels available
+        log_levels = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
+        # NOTE: from 3.11 this list can be changed to: logging.getLevelNamesMapping().keys()
+        # Create logging arguments group
+        group = self.add_argument_group("logging arguments")
+        # Add 3 mutually exclusive options to set the logging level
+        subgroup = group.add_mutually_exclusive_group()
+        subgroup.add_argument(
+            "-v",
+            "--verbose",
+            action="store_const",
+            const="INFO",
+            dest="log_level",
+            help="verbose mode, i.e. 'INFO' log level",
+        )
+        subgroup.add_argument(
+            "--debug",
+            action="store_const",
+            const="DEBUG",
+            dest="log_level",
+            help="debugging mode, i.e. 'DEBUG' log level",
+        )
+        subgroup.add_argument(
+            "--log",
+            choices=log_levels,
+            type=str.upper,
+            default="WARNING",
+            metavar="LEVEL",
+            dest="log_level",
+            help="level of the events to track: %(choices)s",
+        )
+        subgroup.set_defaults(log_level="WARNING")
+        if add_log_file:
+            # Add log file-related arguments
+            group.add_argument(
+                "--log_file",
+                type=lambda x: self._validate_dst_path(x, exists_ok=True),
+                metavar="PATH",
+                default=None,
+                help="log file path",
+            )
+            group.add_argument(
+                "--log_file_level",
+                choices=log_levels,
+                type=str.upper,
+                default="DEBUG",
+                metavar="LEVEL",
+                help="level of the events to track in the log file: %(choices)s",
+            )
+
+    def parse_args(self, *args, **kwargs) -> argparse.Namespace:  # type: ignore[override]
+        """Extends the parent function by adding a new URL argument for every server group added.
+
+        The type of this new argument will be `sqlalchemy.engine.URL`. It also logs all the parsed
+        arguments for debugging purposes when logging arguments have been added.
+
+        """
+        arguments = super().parse_args(*args, **kwargs)
+        # Build and add an sqlalchemy.engine.URL object for every server group added
+        for prefix in self.__server_groups:
+            # Raise an error rather than overwriting when the URL argument is already present
+            if f"{prefix}url" in arguments:
+                self.error(f"argument '{prefix}url' is already present")
+            server_url = URL.create(
+                "mysql",
+                getattr(arguments, f"{prefix}user"),
+                getattr(arguments, f"{prefix}password"),
+                getattr(arguments, f"{prefix}host"),
+                getattr(arguments, f"{prefix}port"),
+                getattr(arguments, f"{prefix}database", None),
+            )
+            setattr(arguments, f"{prefix}url", server_url)
+        return arguments

ensembl/utils/logging.py

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Easy initialisation functionality to set an event logging system.
+
+Examples:
+
+    >>> import logging, pathlib
+    >>> from ensembl.utils.logging import init_logging
+    >>> logfile = pathlib.Path("test.log")
+    >>> init_logging("INFO", logfile, "DEBUG")
+    >>> logging.info("This message is written in both stderr and the log file")
+    >>> logging.debug("This message is only written in the log file")
+
+"""
+
+__all__ = [
+    "LogLevel",
+    "init_logging",
+    "init_logging_with_args",
+]
+
+import argparse
+import logging
+from typing import Optional, Union
+
+from ensembl.utils import StrPath
+
+
+LogLevel = Union[int, str]
+
+
+def init_logging(
+    log_level: LogLevel = "WARNING",
+    log_file: Optional[StrPath] = None,
+    log_file_level: LogLevel = "DEBUG",
+    msg_format: str = "%(asctime)s\t%(levelname)s\t%(message)s",
+    date_format: str = r"%Y-%m-%d_%H:%M:%S",
+) -> None:
+    """Initialises the logging system.
+
+    By default, all the log messages corresponding to `log_level` (and above) will be printed in the
+    standard error. If `log_file` is provided, all messages of `log_file_level` level (and above) will
+    be written into the provided file.
+
+    Args:
+        log_level: Minimum logging level for the standard error.
+        log_file: Logging file where to write logging messages besides the standard error.
+        log_file_level: Minimum logging level for the logging file.
+        msg_format: A format string for the logged output as a whole. More information:
+            https://docs.python.org/3/library/logging.html#logrecord-attributes
+        date_format: A format string for the date/time portion of the logged output. More information:
+            https://docs.python.org/3/library/logging.html#logging.Formatter.formatTime
+
+    """
+    # Configure the basic logging system, setting the root logger to the minimum log level available
+    # to avoid filtering messages in any handler due to "parent delegation". Also close and remove any
+    # existing handlers before setting this configuration.
+    logging.basicConfig(format=msg_format, datefmt=date_format, level="DEBUG", force=True)
+    # Set the correct log level of the new StreamHandler (by default it is set to NOTSET)
+    logging.root.handlers[0].setLevel(log_level)
+    if log_file:
+        # Create the log file handler and add it to the root logger
+        formatter = logging.Formatter(msg_format, datefmt=date_format)
+        file_handler = logging.FileHandler(log_file)
+        file_handler.setLevel(log_file_level)
+        file_handler.setFormatter(formatter)
+        logging.root.addHandler(file_handler)
+
+
+def init_logging_with_args(args: argparse.Namespace) -> None:
+    """Processes the Namespace object provided to call `init_logging()` with the correct arguments.
+
+    Args:
+        args: Namespace populated by an argument parser.
+
+    """
+    args_dict = vars(args)
+    log_args = {x: args_dict[x] for x in ["log_level", "log_file", "log_file_level"] if x in args_dict}
+    init_logging(**log_args)

ensembl/utils/rloader.py

@@ -0,0 +1,92 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Allow to seamlessly load / read the content of a remote file as if it was located locally."""
+
+__all__ = ["RemoteFileLoader"]
+
+import configparser
+import json
+import logging
+from io import StringIO
+from typing import Optional, Any
+
+import dotenv
+import requests
+import requests.exceptions
+import yaml
+
+
+logger = logging.getLogger(__name__)
+
+
+class RemoteFileLoader:
+    """Loads remote files, allowing specific format parsing options.
+
+    Args:
+        parser: Parser to use for this object. Default: `None` (no format-specific parsing done).
+
+    Attributes:
+        available_formats: File formats with ad-hoc parsers available.
+        parser: Parser selected for this object.
+
+    """
+
+    available_formats: set[str] = {"yaml", "ini", "env", "json"}
+    parser: Optional[str] = None
+
+    def __init__(self, parser: Optional[str] = None) -> None:
+        if parser in self.available_formats:
+            self.parser = parser
+
+    def __parse(self, content: str) -> Any:
+        if self.parser == "yaml":
+            return yaml.load(content, yaml.SafeLoader)
+        if self.parser == "ini":
+            config = configparser.ConfigParser()
+            try:
+                config.read_string(content)
+            except configparser.MissingSectionHeaderError:
+                content = "[DEFAULT]\n" + content
+                config.read_string(content)
+            return config
+        if self.parser == "env":
+            return dotenv.dotenv_values(stream=StringIO(content))
+        if self.parser == "json":
+            return json.loads(content)
+        # Only return content, no parsing
+        return content
+
+    def r_open(self, url: str) -> Any:
+        """Returns the parsed remote file from the given URL.
+
+        Args:
+            url: URL of the remote file to fetch.
+
+        Raises:
+            requests.exception.HTTPError: If loading or requesting the given URL returned an error.
+            requests.exception.Timeout: If a timeout was raised whilst requesting the given URL.
+
+        """
+        try:
+            r = requests.get(url, timeout=120)
+            if r.status_code == 200:
+                return self.__parse(r.text)
+            raise requests.exceptions.HTTPError(response=r)
+        except requests.exceptions.HTTPError as ex:
+            logger.exception(f"Error with request to {url}: {ex}")
+            raise ex
+        except requests.exceptions.Timeout as ex:
+            logger.exception(f"Request timed out {url}: {ex}")
+            raise ex

ensembl_utils-0.1.1.dist-info/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+
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+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
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+      direction or management of such entity, whether by contract or
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+
+      "You" (or "Your") shall mean an individual or Legal Entity
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ensembl_utils-0.1.1.dist-info/METADATA

@@ -0,0 +1,82 @@
+Metadata-Version: 2.1
+Name: ensembl-utils
+Version: 0.1.1
+Summary: Ensembl Python general-purpose utils
+Author-email: Ensembl <dev@ensembl.org>
+License: Apache License 2.0
+Project-URL: homepage, https://www.ensembl.org
+Project-URL: repository, https://github.com/Ensembl/ensembl-utils
+Keywords: ensembl,python,utils
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: python-dotenv >=0.19.2
+Requires-Dist: pyyaml ~=6.0
+Requires-Dist: requests >=2.22.0
+Requires-Dist: sqlalchemy ~=1.4.0
+Provides-Extra: build
+Requires-Dist: build ; extra == 'build'
+Requires-Dist: setuptools ; extra == 'build'
+Requires-Dist: setuptools-scm ; extra == 'build'
+Requires-Dist: wheel ; extra == 'build'
+Provides-Extra: cicd
+Requires-Dist: black ; extra == 'cicd'
+Requires-Dist: coverage ; extra == 'cicd'
+Requires-Dist: genbadge[coverage] ; extra == 'cicd'
+Requires-Dist: mypy ; extra == 'cicd'
+Requires-Dist: pylint ; extra == 'cicd'
+Requires-Dist: pytest ; extra == 'cicd'
+Requires-Dist: pytest-dependency ; extra == 'cicd'
+Requires-Dist: requests-mock >=1.8.0 ; extra == 'cicd'
+Requires-Dist: types-pyyaml ; extra == 'cicd'
+Requires-Dist: types-requests ; extra == 'cicd'
+Provides-Extra: docs
+Requires-Dist: mkdocs >=1.5.3 ; extra == 'docs'
+Requires-Dist: mkdocs-autorefs ; extra == 'docs'
+Requires-Dist: mkdocs-coverage ; extra == 'docs'
+Requires-Dist: mkdocs-gen-files ; extra == 'docs'
+Requires-Dist: mkdocs-literate-nav ; extra == 'docs'
+Requires-Dist: mkdocs-material ; extra == 'docs'
+Requires-Dist: mkdocs-material-extensions ; extra == 'docs'
+Requires-Dist: mkdocs-section-index ; extra == 'docs'
+Requires-Dist: mkdocstrings ; extra == 'docs'
+Requires-Dist: mkdocstrings-python ; extra == 'docs'
+
+# Ensembl Python general-purpose utils
+
+[![License](https://img.shields.io/badge/license-Apache_2.0-blue.svg)](https://github.com/Ensembl/ensembl-utils/blob/main/LICENSE)
+[![Coverage](https://ensembl.github.io/ensembl-utils/coverage/coverage-badge.svg)](https://ensembl.github.io/ensembl-utils/coverage)
+[![CI](https://github.com/Ensembl/ensembl-utils/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/Ensembl/ensembl-utils/actions/workflows/ci.yml)
+
+Centralise generic Python utils used by other project within Ensembl design to facilitate frequent tasks such as input file path checks, archive files IO manipulation or logging setup, among others.
+
+For more information, please consult this repository's [GitHub pages](https://ensembl.github.io/ensembl-utils/).
+
+## Getting Started
+
+### Basic installation
+
+This library is publicly available in [pypi.org](https://pypi.org) so it can be easily installed with your favourite Python dependency and packaging management, e.g.
+```bash
+pip install ensembl-utils
+```
+
+### Installing the development environment (with Python `venv`)
+
+If you want to install this library in editable mode, we suggest you to do so via Python's virtual environment module ([venv](https://docs.python.org/3/library/venv.html)):
+```bash
+python -m venv <VIRTUAL_ENVIRONMENT_NAME>
+source <VIRTUAL_ENVIRONMENT_NAME>/bin/activate
+git clone https://github.com/Ensembl/ensembl-utils.git
+cd ensembl-utils
+pip install -e .[cicd,dev,doc]
+```

ensembl_utils-0.1.1.dist-info/NOTICE

@@ -0,0 +1,5 @@
+Ensembl
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
+
+This product includes software developed at:
+- EMBL-European Bioinformatics Institute

ensembl_utils-0.1.1.dist-info/RECORD

@@ -0,0 +1,12 @@
+ensembl/utils/__init__.py,sha256=sCcfd60bFWeSiHOqf_DTJdaInZBDrjtibQ-uHs2zfXY,832
+ensembl/utils/archive.py,sha256=Nn_SPdsJEfBGWBZqqznP-hnrH8-HUn90TvcuiVGmj0s,3563
+ensembl/utils/argparse.py,sha256=p-0PrpGyCdufMHx4v9UVsSbBBnHlRWodb9iOwNvmPrw,10194
+ensembl/utils/logging.py,sha256=IJUolUDK7qk3lyFfEFnJPtP6FVxwM0yEKdX56U190E0,3664
+ensembl/utils/rloader.py,sha256=jNLt9jkHcD1R5s0l0zovvzJAr62uK6gNEvowIBdSwXw,3150
+ensembl_utils-0.1.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ensembl_utils-0.1.1.dist-info/METADATA,sha256=W8EF9M4KoZc9BD4MwwcptrERdqo_v6S0RA_QedFHon8,3646
+ensembl_utils-0.1.1.dist-info/NOTICE,sha256=KHSQKu-izGR6AEiAg6YL3lA2tzDM5yWvhWEKxA_R66A,156
+ensembl_utils-0.1.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+ensembl_utils-0.1.1.dist-info/entry_points.txt,sha256=cN_m77zJZRLZHxqvF7CCdWawyBsPplDUUtBGG_WNlko,72
+ensembl_utils-0.1.1.dist-info/top_level.txt,sha256=dUgAetY5ISlvzCun8T6ZjOtrtyC-ULeGQOJL7Bx7n0g,8
+ensembl_utils-0.1.1.dist-info/RECORD,,

ensembl_utils-0.1.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.43.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

ensembl_utils-0.1.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+extract_file = ensembl.utils.archive:extract_file_cli

ensembl_utils-0.1.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+ensembl