From ac19bbdd50699e20808c05fa3af281a970bb2321 Mon Sep 17 00:00:00 2001 From: Silvano Cirujano Cuesta Date: Thu, 9 Nov 2023 01:25:46 +0100 Subject: [PATCH 1/7] test: test on python 3.12 Signed-off-by: Silvano Cirujano Cuesta --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 25448b2..c26b17c 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -32,7 +32,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ "3.11", "3.8" ] + python-version: [ "3.12", "3.11", "3.8" ] steps: From 7f02b39de870bbb4e66d89dce2738ebf30740e2a Mon Sep 17 00:00:00 2001 From: Silvano Cirujano Cuesta Date: Thu, 9 Nov 2023 09:26:12 +0100 Subject: [PATCH 2/7] chore: ensure pkg caches are python version specific In order to catch dependency issues with greenlet on python 3.12 caches should be Python version dependent. Signed-off-by: Silvano Cirujano Cuesta --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index c26b17c..ef7b451 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -65,7 +65,7 @@ jobs: uses: actions/cache@v3 with: path: .venv - key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }} + key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-${{ matrix.python-version }} #---------------------------------------------- # install dependencies if cache does not exist From d0c339a6cc16fae51fde5e923a071d8a7d29c30a Mon Sep 17 00:00:00 2001 From: Silvano Cirujano Cuesta Date: Mon, 6 Nov 2023 09:52:18 +0100 Subject: [PATCH 3/7] chore: add support for python 3.12 Upgrading greenlet, pyYAML and typing_extensions versions to have support for Python v3.12. See here for more information: https://github.com/python-greenlet/greenlet/issues/323 Closes #45 Signed-off-by: Silvano Cirujano Cuesta --- poetry.lock | 219 ++++++++++++++++++++++++------------------------- pyproject.toml | 1 + 2 files changed, 109 insertions(+), 111 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1927577..d6ca1eb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -500,77 +500,74 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>= [[package]] name = "greenlet" -version = "2.0.1" +version = "3.0.1" description = "Lightweight in-process concurrent programming" category = "dev" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" -files = [ - {file = "greenlet-2.0.1-cp27-cp27m-macosx_10_14_x86_64.whl", hash = "sha256:9ed358312e63bf683b9ef22c8e442ef6c5c02973f0c2a939ec1d7b50c974015c"}, - {file = "greenlet-2.0.1-cp27-cp27m-manylinux2010_x86_64.whl", hash = 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a/src/prefixmaps/ingest/ingest_bioregistry.py b/src/prefixmaps/ingest/ingest_bioregistry.py index eadcfb5..e5d4684 100644 --- a/src/prefixmaps/ingest/ingest_bioregistry.py +++ b/src/prefixmaps/ingest/ingest_bioregistry.py @@ -68,10 +68,10 @@ def from_bioregistry(upper=False, canonical_idorg=True, filter_dubious=True) -> "ols", "n2t", ] - records = bioregistry.get_extended_prefix_map( + converter = bioregistry.get_converter( uri_prefix_priority=priority, prefix_priority=prefix_priority ) - for record in tqdm(records): + for record in tqdm(converter.records): if record.prefix in SKIP: continue if filter_dubious and not NAMESPACE_RE.match(record.uri_prefix):