From 7215b4263e501229bd2713bacad6cdb5ed3a0a14 Mon Sep 17 00:00:00 2001
From: "riseproject-dev[bot]"
 <330740410+riseproject-dev[bot]@users.noreply.github.com>
Date: Tue, 6 Oct 2026 08:41:31 +0000
Subject: [PATCH 1/2] biom-format: Add version 2.1.18

Signed-off-by: riseproject-dev[bot] <330740410+riseproject-dev[bot]@users.noreply.github.com>
---
 docs/packages/biom-format.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/packages/biom-format.yaml b/docs/packages/biom-format.yaml
index 890711af5c9..5092ded9517 100644
--- a/docs/packages/biom-format.yaml
+++ b/docs/packages/biom-format.yaml
@@ -18,3 +18,4 @@ versions:
   - filename: biom_format-2.1.17-cp314-cp314t-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl
     sha256: ba7cc51fec0abef70286e9bfd4e657b69bcd603052f4e297d7fb957b51135304
     requires-python: '>=3.9'
+- version: 2.1.18

From 084d205f52d0df38c91ec7fba5100918076d9c83 Mon Sep 17 00:00:00 2001
From: Ludovic Henry <git@ludovic.dev>
Date: Fri, 9 Oct 2026 16:32:00 +0000
Subject: [PATCH 2/2] biom-format: carry forward riscv64 patches to 2.1.18

Nightly version bump omitted the patches/biom-format/<version> directory for
2.1.18, so the build's unconditional `git apply .../*.patch` step
failed with "No such file or directory" before any build/test ran.
Copied forward the same patch set from 2.1.17 (unchanged since then).
---
 ...le-use-np.isin-numpy-removed-np.in1d.patch | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 patches/biom-format/2.1.18/0001-table-use-np.isin-numpy-removed-np.in1d.patch

diff --git a/patches/biom-format/2.1.18/0001-table-use-np.isin-numpy-removed-np.in1d.patch b/patches/biom-format/2.1.18/0001-table-use-np.isin-numpy-removed-np.in1d.patch
new file mode 100644
index 00000000000..8d7d950171a
--- /dev/null
+++ b/patches/biom-format/2.1.18/0001-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