From f305b92c2bbb79c78bba3850ac60e9ab57738e16 Mon Sep 17 00:00:00 2001
From: Ludovic Henry <git@ludovic.dev>
Date: Fri, 11 Sep 2026 19:08:42 +0200
Subject: [PATCH 1/2] biom-format: add build-biom-format.yml for riscv64 wheels

---
 .github/workflows/build-biom-format.yml | 89 +++++++++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 .github/workflows/build-biom-format.yml

diff --git a/.github/workflows/build-biom-format.yml b/.github/workflows/build-biom-format.yml
new file mode 100644
index 00000000000..57f3df0a41a
--- /dev/null
+++ b/.github/workflows/build-biom-format.yml
@@ -0,0 +1,89 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# This workflow is based on: https://github.com/biocore/biom-format/blob/2.1.17/.github/workflows/wheels.yml
+name: Build biom-format wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'biom-format version to build (git tag, e.g. 2.1.17)'
+        required: true
+        default: '2.1.17'
+  pull_request:
+    paths:
+      - '.github/workflows/build-biom-format.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ inputs.version || '2.1.17' }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read  # to fetch code (actions/checkout)
+
+env:
+  # `inputs.version` is empty on pull_request events; default to 2.1.17 there.
+  BIOM_FORMAT_VERSION: ${{ inputs.version || '2.1.17' }}
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+
+  build_wheels:
+    needs: [setup]
+    name: Build biom-format ${{ inputs.version || '2.1.17' }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["cp312", "cp313", "cp314", "cp314t"]
+        include:
+          # pandas (a hard runtime requirement) publishes no cp314t wheel on
+          # any platform or index, so the wheel itself builds fine but can't
+          # be installed for testing under cp314t; skip only the test phase.
+          - python: "cp314t"
+            test_skip: "*"
+
+    steps:
+      - name: Checkout biom-format ${{ env.BIOM_FORMAT_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: biocore/biom-format
+          ref: ${{ env.BIOM_FORMAT_VERSION }}
+          persist-credentials: false
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          # numpy/scipy/pandas/h5py are build/runtime deps we ship on the
+          # registry; pin resolution to our wheels so pip doesn't instead pick
+          # PyPI's newer sdist-only releases (gotcha 84). cython has no
+          # riscv64 wheel on the registry but compiles from sdist in seconds,
+          # so it's left free to build.
+          CIBW_ENVIRONMENT: >-
+            PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+            PIP_ONLY_BINARY=numpy,scipy,pandas,h5py
+          CIBW_TEST_SKIP: ${{ matrix.test_skip }}
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: biom-format-${{ env.BIOM_FORMAT_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish biom-format ${{ inputs.version || '2.1.17' }}
+    needs: [setup, build_wheels]
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    with:
+      artifact-pattern: biom-format-${{ inputs.version || '2.1.17' }}-*-manylinux_riscv64

From fe5123e1c3ee9139e14bbccb009196953165a9ea Mon Sep 17 00:00:00 2001
From: Ludovic Henry <git@ludovic.dev>
Date: Fri, 11 Sep 2026 19:31:47 +0200
Subject: [PATCH 2/2] biom-format: patch table.py to use np.isin, numpy removed
 np.in1d

np.in1d was deprecated since numpy 1.25 and removed entirely by the numpy
our registry ships; np.isin is its documented drop-in replacement. Real
compatibility fix, not riscv64-specific -- any user installing this wheel
against a current numpy hits the same AttributeError.
---
 .github/workflows/build-biom-format.yml       |  9 ++++++
 ...le-use-np.isin-numpy-removed-np.in1d.patch | 31 +++++++++++++++++++
 2 files changed, 40 insertions(+)
 create mode 100644 patches/biom-format/2.1.17/0001-table-use-np.isin-numpy-removed-np.in1d.patch

diff --git a/.github/workflows/build-biom-format.yml b/.github/workflows/build-biom-format.yml
index 57f3df0a41a..9b65254c91f 100644
--- a/.github/workflows/build-biom-format.yml
+++ b/.github/workflows/build-biom-format.yml
@@ -55,6 +55,15 @@ jobs:
           ref: ${{ env.BIOM_FORMAT_VERSION }}
           persist-credentials: false
 
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Apply patches
+        run: git apply -v python-wheels/patches/biom-format/${{ env.BIOM_FORMAT_VERSION }}/*.patch
+
       - name: Build wheels
         uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
         with:
diff --git a/patches/biom-format/2.1.17/0001-table-use-np.isin-numpy-removed-np.in1d.patch b/patches/biom-format/2.1.17/0001-table-use-np.isin-numpy-removed-np.in1d.patch
new file mode 100644
index 00000000000..8d7d950171a
--- /dev/null
+++ b/patches/biom-format/2.1.17/0001-table-use-np.isin-numpy-removed-np.in1d.patch
@@ -0,0 +1,31 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Fri, 11 Sep 2026 17:30:00 +0200
+Subject: [PATCH] table: use np.isin, numpy removed np.in1d
+
+np.in1d was deprecated since numpy 1.25 and removed entirely by the numpy
+our registry ships; np.isin is its documented drop-in replacement (identical
+signature/semantics for this 1-D membership-test usage), so this is a real
+compatibility fix, not riscv64-specific -- any user installing this wheel
+against a current numpy hits the same AttributeError.
+
+Upstream-Status: To upstream [not yet submitted; needs a biom-format maintainer decision on the minimum supported numpy version]
+---
+ biom/table.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/biom/table.py b/biom/table.py
+index 0000000..0000000 100644
+--- a/biom/table.py
++++ b/biom/table.py
+@@ -4234,7 +4234,7 @@ class Table(object):
+                 else:
+                     desired_ids = np.asarray(desired_ids)
+                     # Get the index of the source ids to include
+-                    idx = np.in1d(source_ids, desired_ids)
++                    idx = np.isin(source_ids, desired_ids)
+                     # Retrieve only the ids that we are interested on
+                     ids = source_ids[idx]
+                     # Check that all desired ids have been found on source ids
+--
+2.43.0