From 2922d871be0aa9a41f1dd9cbfc464dddb869769c Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 07:47:39 +0100 Subject: [PATCH] Replace deprecated pkg_resources with importlib_resources --- CHANGELOG.md | 3 +- poetry.lock | 818 +++++++++++++++++++------------ preClinVar/demo/__init__.py | 35 +- preClinVar/resources/__init__.py | 8 +- pyproject.toml | 1 + 5 files changed, 515 insertions(+), 350 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ff5cee7..b30ab63 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,8 @@ - Updated version of external images in GitHub actions ### Fixed - Bump certifi from 2022.12.7 to 2023.7.22 -- Description of the response returned by dry run endpoint in README file +- Description of the response returned by dry run endpoint in README file +- Migrate from deprecated `pkg_resources` lib to `importlib_resources` ## [2.3.1] ### Fixed diff --git a/poetry.lock b/poetry.lock index bb95856..59f88df 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,83 +1,65 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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optional = false python-versions = ">=3.7" files = [ - {file = "uvicorn-0.18.2-py3-none-any.whl", hash = "sha256:c19a057deb1c5bb060946e2e5c262fc01590c6529c0af2c3d9ce941e89bc30e0"}, - {file = "uvicorn-0.18.2.tar.gz", hash = "sha256:cade07c403c397f9fe275492a48c1b869efd175d5d8a692df649e6e7e2ed8f4e"}, + {file = "uvicorn-0.18.3-py3-none-any.whl", hash = "sha256:0abd429ebb41e604ed8d2be6c60530de3408f250e8d2d84967d85ba9e86fe3af"}, + {file = "uvicorn-0.18.3.tar.gz", hash = "sha256:9a66e7c42a2a95222f76ec24a4b754c158261c4696e683b9dadc72b590e0311b"}, ] [package.dependencies] @@ -714,24 +888,24 @@ click = ">=7.0" h11 = ">=0.8" [package.extras] -standard = ["PyYAML (>=5.1)", "colorama (>=0.4)", "httptools (>=0.4.0)", "python-dotenv (>=0.13)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.0)"] +standard = ["colorama (>=0.4)", "httptools (>=0.4.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.0)"] [[package]] name = "zipp" -version = "3.8.0" +version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "zipp-3.8.0-py3-none-any.whl", hash = "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"}, - {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] [package.extras] -docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] -testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "0e8d3a4b70c90117a9fad7a0299fa155837dcf633f5653e3d3a2e1ee585d47ea" +content-hash = "b6e3362a8e2254decbc6c7c56c340ed32a69901b57dc24ad1b2fdc220afca855" diff --git a/preClinVar/demo/__init__.py b/preClinVar/demo/__init__.py index 9de6ee7..867fcee 100644 --- a/preClinVar/demo/__init__.py +++ b/preClinVar/demo/__init__.py @@ -1,4 +1,6 @@ -import pkg_resources +from importlib_resources import files + +BASE_PATH = "preClinVar.demo" ###### .csv files ###### casedata_old_csv = "CaseData_before_221121.csv" @@ -11,27 +13,14 @@ casedata_sv_csv = "CaseData_sv.csv" ###### Path to .csv files ###### -casedata_old_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", casedata_old_csv]) -) -variants_old_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_old_csv]) -) -casedata_snv_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", casedata_snv_csv]) -) -casedata_sv_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", casedata_sv_csv]) -) -variants_hgvs_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_hgvs_csv]) -) -variants_sv_breakpoints_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_sv_breakpoints_csv]) -) -variants_sv_range_coords_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_sv_range_coords_csv]) -) +casedata_old_csv_path = str(files(BASE_PATH).joinpath(casedata_old_csv)) +variants_old_csv_path = str(files(BASE_PATH).joinpath(variants_old_csv)) +casedata_snv_csv_path = str(files(BASE_PATH).joinpath(casedata_snv_csv)) +casedata_sv_csv_path = str(files(BASE_PATH).joinpath(casedata_sv_csv)) +variants_hgvs_csv_path = str(files(BASE_PATH).joinpath(variants_hgvs_csv)) +variants_sv_breakpoints_csv_path = str(files(BASE_PATH).joinpath(variants_sv_breakpoints_csv)) +variants_sv_range_coords_csv_path = str(files(BASE_PATH).joinpath(variants_sv_range_coords_csv)) + ###### Example of a json file submission ###### subm_json = "submission.json" -subm_json_path = pkg_resources.resource_filename("preClinVar", "/".join(["demo", subm_json])) +subm_json_path = str(files(BASE_PATH).joinpath(subm_json)) diff --git a/preClinVar/resources/__init__.py b/preClinVar/resources/__init__.py index 7270749..0ec0e52 100644 --- a/preClinVar/resources/__init__.py +++ b/preClinVar/resources/__init__.py @@ -1,10 +1,10 @@ -import pkg_resources +from importlib_resources import files + +BASE_PATH = "preClinVar.resources" ###### submission schema json file ###### subm_schema = "submission_schema.json" ###### Path to submission schema file ###### -subm_schema_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["resources", subm_schema]) -) +subm_schema_path = str(files(BASE_PATH).joinpath(subm_schema)) diff --git a/pyproject.toml b/pyproject.toml index 05d107f..5af4709 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,6 +15,7 @@ black = "^22.6.0" python-multipart = "^0.0.5" jsonschema = "^4.6.1" responses = "^0.21.0" +importlib-resources = "^6.1.1" [tool.poetry.dev-dependencies] pytest = "^7.1.2"