diff --git a/CHANGELOG.md b/CHANGELOG.md index d66179d..748cc79 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/), and this +## 1.6.7 - 2024-10-xx + +### Fixes + +- Populate `additional_data` (if column exists) on `gn_meta.t_datasets`, `gn_meta.t_acquisition_frameworks` and `gn_synthese.t_sources`,fix #87 +- Replace module `pkg_resouces` by native `importlib`, fix #88 + ## 1.6.6 - 2024-08-20 ### Fixes diff --git a/gn2pg/__init__.py b/gn2pg/__init__.py index 84ef717..b3d2959 100644 --- a/gn2pg/__init__.py +++ b/gn2pg/__init__.py @@ -7,17 +7,18 @@ from pathlib import Path import coloredlogs -from pkg_resources import DistributionNotFound, get_distribution + +from importlib.metadata import version from gn2pg import metadata try: DIST_NAME = "gn2pg_client" - __version__ = get_distribution(DIST_NAME).version -except DistributionNotFound: # pragma: no cover + __version__ = version(DIST_NAME) +except : # pragma: no cover __version__ = metadata.VERSION finally: - del get_distribution, DistributionNotFound + del version __author__ = metadata.AUTHORS_STRING __license__ = metadata.LICENSE diff --git a/gn2pg/data/__init__.py b/gn2pg/data/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/gn2pg/helpers.py b/gn2pg/helpers.py index ca29e6d..62bbb48 100644 --- a/gn2pg/helpers.py +++ b/gn2pg/helpers.py @@ -10,7 +10,7 @@ from pathlib import Path from subprocess import call -import pkg_resources +import importlib.resources from gn2pg import _ from gn2pg.download import Data @@ -22,20 +22,24 @@ sh_col = BColors() - def init(file: str) -> None: """Init config file from template Args: - file (str): [description] + file (str): The name of the configuration file to create. """ - - toml_src = pkg_resources.resource_filename(__name__, "data/gn2pgconfig.toml") + + # Get the path to the template file + toml_src = importlib.resources.files(__name__).joinpath("data", "gn2pgconfig.toml") + toml_dst = str(ENVDIR / file) + + # Check if the destination file already exists if Path(toml_dst).is_file(): ENVDIR.mkdir(exist_ok=True) logger.info(_("Conf directory %s created"), str(ENVDIR)) logger.warning(_("%s file already exists"), toml_dst) + overwrite = input( _( f"{sh_col.color('header')}Would you like to overwrite file " @@ -44,16 +48,18 @@ def init(file: str) -> None: f"/[{sh_col.color('bold')}n{sh_col.color('endc')}]o) ? " ) ) + if overwrite.lower() == "n": logger.warning(_("File %s will be preserved"), toml_dst) sys.exit(0) else: logger.warning(_("file %s will be overwritten"), toml_dst) + logger.info(_("Creating TOML configuration file %s, from %s"), toml_dst, toml_src) shutil.copyfile(toml_src, toml_dst) logger.info(_("Please edit %s before running the script"), toml_dst) sys.exit(0) - + def edit(file: str) -> None: """Open editor to edit config file diff --git a/gn2pg/store_postgresql.py b/gn2pg/store_postgresql.py index 604fbe2..99790d8 100644 --- a/gn2pg/store_postgresql.py +++ b/gn2pg/store_postgresql.py @@ -7,8 +7,8 @@ from datetime import datetime from pathlib import Path from typing import Any, Optional +import importlib.resources -import pkg_resources from sqlalchemy import ( Column, DateTime, @@ -287,7 +287,7 @@ def custom_script(self, script: str = "to_gnsynthese") -> None: logger.info(_("Start to execute %s script"), script) conn = self._db.connect() if script == "to_gnsynthese": - file = pkg_resources.resource_filename(__name__, "data/to_gnsynthese.sql") + file = importlib.resources.files(__name__).joinpath("data", "to_gnsynthese.sql") logger.info( _("You choosed to use internal to_gnsynthese.sql script in schema %s"), self._db_schema, diff --git a/poetry.lock b/poetry.lock index 6ae6583..5402dad 100644 --- a/poetry.lock +++ b/poetry.lock @@ -112,13 +112,13 @@ files = [ [[package]] name = "certifi" -version = "2024.7.4" +version = "2024.8.30" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, - {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, + {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, + {file = 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