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 1/3] 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 Date: Fri, 9 Oct 2026 16:32:00 +0000 Subject: [PATCH 2/3] biom-format: carry forward riscv64 patches to 2.1.18 Nightly version bump omitted the patches/biom-format/ 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 +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 From 7a217d457401f2322da7cc65c0f25644f33dac70 Mon Sep 17 00:00:00 2001 From: Ludovic Henry Date: Sat, 10 Oct 2026 07:50:52 +0000 Subject: [PATCH 3/3] biom-format: drop the np.in1d -> np.isin patch for 2.1.18 Upstream 2.1.18 already replaced np.in1d with np.isin in Table.from_hdf5's id subsetting (biocore/biom-format#1003, landed in 20ace60, listed in the 2.1.18 ChangeLog), so the carried-forward patch no longer applies and has nothing left to change; no other np.in1d use remains in the 2.1.18 tree. 2.1.17 keeps its patch. With no patches left for 2.1.18, skip the apply step when the version has no patch directory, as build-fastparquet.yml does. --- .github/workflows/build-biom-format.yml | 1 + ...le-use-np.isin-numpy-removed-np.in1d.patch | 31 ------------------- 2 files changed, 1 insertion(+), 31 deletions(-) delete mode 100644 patches/biom-format/2.1.18/0001-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 3b2a71a4b74..652a9e493e4 100644 --- a/.github/workflows/build-biom-format.yml +++ b/.github/workflows/build-biom-format.yml @@ -75,6 +75,7 @@ jobs: persist-credentials: false - name: Apply patches + if: hashFiles(format('python-wheels/patches/biom-format/{0}/*.patch', env.BIOM_FORMAT_VERSION)) != '' run: git apply -v python-wheels/patches/biom-format/${{ env.BIOM_FORMAT_VERSION }}/*.patch - name: Build wheels 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 deleted file mode 100644 index 8d7d950171a..00000000000 --- a/patches/biom-format/2.1.18/0001-table-use-np.isin-numpy-removed-np.in1d.patch +++ /dev/null @@ -1,31 +0,0 @@ -From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001 -From: Ludovic Henry -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