From c57e23cde9392ce58d6565639424a83c527ef8a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daniel=20L=C3=B3pez=20L=C3=B3pez?= Date: Wed, 25 Mar 2026 16:06:32 +0100 Subject: [PATCH 1/4] fix(recipe): fix PyPI URL, run_exports and add license_file --- recipes/afquery/meta.yaml | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/recipes/afquery/meta.yaml b/recipes/afquery/meta.yaml index 25c1972..26117b6 100644 --- a/recipes/afquery/meta.yaml +++ b/recipes/afquery/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + url: https://files.pythonhosted.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz sha256: PLACEHOLDER build: @@ -17,13 +17,6 @@ build: - afquery = afquery.cli:cli run_exports: - python >=3.10 - - pyroaring >=0.4.8 - - pyarrow >=14.0 - - duckdb >=0.10 - - click >=8.1 - - cyvcf2 >=0.30 - - tqdm >=4.60 - - pyranges >=0.1.2,<0.2 requirements: host: @@ -50,6 +43,7 @@ test: about: home: https://github.com/dlopez-bioinfo/afquery license: MIT + license_file: LICENSE summary: Genomic allele frequency query engine with bitmap-encoded genotypes extra: From 225fce9e0f3de6c1c35bb1a3bf52cee90667cafe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daniel=20L=C3=B3pez=20L=C3=B3pez?= Date: Wed, 25 Mar 2026 16:06:51 +0100 Subject: [PATCH 2/4] fix(ci): remove bioconda-pr job, rely on BiocondaBot --- .github/workflows/release.yml | 64 ----------------------------------- 1 file changed, 64 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 349332f..554e52c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -126,67 +126,3 @@ jobs: tags: | ghcr.io/${{ github.repository }}:${{ steps.version.outputs.version }} ghcr.io/${{ github.repository }}:latest - - # ── 6. Bioconda PR (final releases only — no "rc" in tag) ──────────── - bioconda-pr: - needs: publish-pypi - runs-on: ubuntu-latest - if: ${{ !contains(github.ref_name, 'rc') }} # skip RC tags - steps: - - name: Get version from tag - run: echo "VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV - - - name: Fetch SHA256 from PyPI - run: | - SHA256=$(curl -s https://pypi.org/pypi/afquery/${VERSION}/json \ - | jq -r '.urls[] | select(.packagetype=="sdist") | .digests.sha256') - echo "SHA256=${SHA256}" >> $GITHUB_ENV - - - name: Get fork owner - env: - GH_TOKEN: ${{ secrets.GH_PAT }} - run: echo "FORK_USER=$(gh api user --jq .login)" >> $GITHUB_ENV - - - name: Sync fork with upstream - env: - GH_TOKEN: ${{ secrets.GH_PAT }} - run: gh repo sync ${FORK_USER}/bioconda-recipes --source bioconda/bioconda-recipes --branch master - - - name: Checkout afquery repo - uses: actions/checkout@v4 - with: - path: afquery-repo - - - name: Checkout fork of bioconda-recipes - uses: actions/checkout@v4 - with: - repository: ${{ env.FORK_USER }}/bioconda-recipes - token: ${{ secrets.GH_PAT }} - path: bioconda-recipes - - - name: Update recipe - working-directory: bioconda-recipes - run: | - mkdir -p recipes/afquery - cp ../afquery-repo/recipes/afquery/meta.yaml recipes/afquery/meta.yaml - sed -i "s/^{% set version = .* %}/{% set version = \"${VERSION}\" %}/" recipes/afquery/meta.yaml - sed -i "s/sha256: .*/sha256: ${SHA256}/" recipes/afquery/meta.yaml - sed -i "s/^ number: .*/ number: 0/" recipes/afquery/meta.yaml - - - name: Create pull request - working-directory: bioconda-recipes - env: - GH_TOKEN: ${{ secrets.GH_PAT }} - run: | - git config user.name "github-actions[bot]" - git config user.email "github-actions[bot]@users.noreply.github.com" - git checkout -b afquery-${VERSION} - git add recipes/afquery/meta.yaml - git commit -m "Update afquery to ${VERSION}" - git push origin afquery-${VERSION} - gh pr create \ - --repo bioconda/bioconda-recipes \ - --title "Update afquery to ${VERSION}" \ - --body "Automated version bump from https://github.com/dlopez-bioinfo/afquery/releases/tag/v${VERSION}" \ - --head "${FORK_USER}:afquery-${VERSION}" \ - --base master From d0ab7de04de2b1b355730c3816faa164854e08da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daniel=20L=C3=B3pez=20L=C3=B3pez?= Date: Wed, 25 Mar 2026 16:21:50 +0100 Subject: [PATCH 3/4] chore(recipe): update to version 0.2.2 --- recipes/afquery/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/afquery/meta.yaml b/recipes/afquery/meta.yaml index 26117b6..a4d43e8 100644 --- a/recipes/afquery/meta.yaml +++ b/recipes/afquery/meta.yaml @@ -1,5 +1,5 @@ {% set name = "afquery" %} -{% set version = "0.1.0" %} +{% set version = "0.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://files.pythonhosted.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: PLACEHOLDER + sha256: 28ddc9afe5260ecdefab83679e0633684980666c49812215d1233ce3bae4fb7f build: noarch: python From 07a49106bf98ef52e22c04c5cf17d5ee941b1387 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daniel=20L=C3=B3pez=20L=C3=B3pez?= Date: Wed, 25 Mar 2026 17:06:09 +0100 Subject: [PATCH 4/4] fix(recipe): add pin_subpackage to run_exports per bioconda template --- recipes/afquery/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/afquery/meta.yaml b/recipes/afquery/meta.yaml index a4d43e8..e6997d3 100644 --- a/recipes/afquery/meta.yaml +++ b/recipes/afquery/meta.yaml @@ -16,7 +16,7 @@ build: entry_points: - afquery = afquery.cli:cli run_exports: - - python >=3.10 + - {{ pin_subpackage("afquery", max_pin="x.x") }} requirements: host: