hydride: Add version 1.2.3

.github/workflows/build-hydride.yml

@@ -0,0 +1,111 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# Based on upstream's CI:
+#   https://github.com/biotite-dev/hydride/blob/v1.2.3/.github/workflows/test_and_deploy.yml
+name: Build hydride wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'Version glob to (re)build; empty builds every version of docs/packages/hydride.yaml not released yet'
+        required: false
+        default: ''
+  pull_request:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-hydride.yml'
+      - 'docs/packages/hydride.yaml'
+      - 'patches/hydride/**'
+  push:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-hydride.yml'
+      - 'docs/packages/hydride.yaml'
+      - 'patches/hydride/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read  # to fetch code (actions/checkout)
+
+env:
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+    with:
+      package: hydride
+      version: ${{ inputs.version }}
+
+  build_wheels:
+    needs: [setup]
+    if: needs.setup.outputs.versions != '[]'
+    name: Build hydride ${{ matrix.version }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 720
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+        # setup.py imports biotite at build time; biotite has no free-threaded wheel.
+        python: ["cp312", "cp313", "cp314"]
+    env:
+      HYDRIDE_VERSION: ${{ matrix.version }}
+
+    steps:
+      - name: Checkout hydride v${{ env.HYDRIDE_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: biotite-dev/hydride
+          ref: v${{ env.HYDRIDE_VERSION }}
+          persist-credentials: false
+
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Apply patches
+        run: git apply -v python-wheels/patches/hydride/${{ env.HYDRIDE_VERSION }}/*.patch
+
+      - name: Build and test wheels
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          CIBW_DEPENDENCY_VERSIONS: pinned
+          CIBW_ENVIRONMENT: PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+          CIBW_TEST_EXTRAS: test
+          CIBW_TEST_SOURCES: tests
+          CIBW_TEST_COMMAND: pytest tests --durations=50
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: hydride-${{ env.HYDRIDE_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish hydride ${{ matrix.version }}
+    needs: [setup, build_wheels]
+    if: needs.setup.outputs.versions != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    secrets:
+      app-private-key: ${{ secrets.RISEPROJECT_APP_PRIVATE_KEY }}
+    with:
+      artifact-pattern: hydride-${{ matrix.version }}-*-manylinux_riscv64

docs/packages/hydride.yaml

@@ -0,0 +1,6 @@
+package-name: hydride
+source-code: https://github.com/biotite-dev/hydride
+license: BSD-3-Clause
+versions:
+- version: 1.2.3
+  patched: true

patches/hydride/1.2.3/0001-Fix-setup-for-CCD-components-with-missing-coordinates.patch

@@ -0,0 +1,42 @@
+From bba37a77d314a02dce0e4f11fefd325455931a07 Mon Sep 17 00:00:00 2001
+From: Patrick Kunzmann <padix.key@gmail.com>
+Date: Thu, 25 Sep 2025 12:17:30 +0200
+Subject: [PATCH] Fix setup for CCD components with missing coordinates
+
+Upstream-Status: Backport [https://github.com/biotite-dev/hydride/commit/bba37a77d314a02dce0e4f11fefd325455931a07]
+
+setup.py compiles hydride's fragment library at build time by calling
+biotite.structure.info.residue() on every component of the Chemical
+Component Dictionary, skipping the ones it cannot load. The v1.2.3 tag
+only skips KeyError, but biotite >= 1.0 raises ValueError for a CCD
+component with missing coordinates (residue(allow_missing_coord=False)),
+so with the biotite 1.7.1 that build isolation pulls in from
+pypi.riseproject.dev the wheel build aborts in setup.py before any
+compiler runs. This is not riscv64-specific: any v1.2.3 build against a
+current biotite fails the same way.
+
+Upstream fixed it in bba37a7, which is on the v1.2.4 tag; that tag still
+declares __version__ = "1.2.3" and was never uploaded to PyPI, so 1.2.3
+remains the latest release and this one-line change is carried onto it.
+
+---
+ setup.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index e854b94..141f6c0 100644
+--- a/setup.py
++++ b/setup.py
+@@ -148,7 +148,8 @@ if not isfile(fragment_file_path):
+                 print(f"Compiling fragment library... ({i}/{len(mol_names)})", end="\r")
+             try:
+                 mol = info.residue(mol_name)
+-            except KeyError:
++            except ValueError:
++                # Molecule has missing coordinates
+                 continue
+             std_fragment_library.add_molecule(mol)
+     print("Compiling fragment library... Done" + " " * 20)
+-- 
+2.43.0
+

patches/hydride/1.2.3/0002-relax-cast-biotite-CellList-inputs-outputs-for-biotite-1.7.patch

@@ -0,0 +1,56 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Wed, 14 Oct 2026 12:00:00 +0000
+Subject: [PATCH] relax: cast biotite CellList inputs/outputs for biotite 1.7
+
+Upstream-Status: Issue [https://github.com/biotite-dev/hydride/issues/29]
+
+biotite 1.7 reimplemented structure.CellList in Rust, which changed two
+things MinimumFinder.__init__ relies on:
+
+- CellList.get_atoms() now returns int64 indices, so assigning the
+  result to the `cdef int32[:,:] adj_indices` memoryview raises
+  "ValueError: Buffer dtype mismatch, expected 'int32' but got 'long'"
+  for every relax_hydrogen() call (hydride issues #29 and #30).
+- CellList(..., periodic=True, box=...) only accepts a float32 box; the
+  float64 np.identity(3)-style boxes callers pass raise
+  "TypeError: 'ndarray' object cannot be cast as 'ndarray'".
+
+Cast the box to float32 and the returned indices to int32 at the call
+site. With biotite 1.7.1 (the only biotite on pypi.riseproject.dev) the
+unpatched wheel fails 141 of the 1327 tests on any architecture
+(reproduced on x86_64); with this patch they all pass. biotite 1.6.0
+and older already return int32 and accept a float32 box, so the casts
+are no-ops there.
+
+Signed-off-by: Ludovic Henry <git@ludovic.dev>
+---
+ src/hydride/relax.pyx | 5 +++--
+ 1 file changed, 3 insertions(+), 2 deletions(-)
+
+diff --git a/src/hydride/relax.pyx b/src/hydride/relax.pyx
+index 3c937bd..6c94593 100644
+--- a/src/hydride/relax.pyx
++++ b/src/hydride/relax.pyx
+@@ -218,7 +218,8 @@ class MinimumFinder:
+             )
+         else:
+             cell_list = struc.CellList(
+-                atoms, cell_size=force_cutoff, periodic=True, box=self._box
++                atoms, cell_size=force_cutoff, periodic=True,
++                box=np.asarray(self._box, dtype=np.float32)
+             )
+         relevant_mask = (np.asarray(groups) != -1)
+         cdef int32[:] relevant_indices = np.where(relevant_mask)[0] \
+@@ -226,7 +227,7 @@ class MinimumFinder:
+         cdef int32[:,:] adj_indices = cell_list.get_atoms(
+             atoms.coord[np.asarray(relevant_indices)],
+             radius=force_cutoff
+-        )
++        ).astype(np.int32, copy=False)
+
+
+         cdef int32[:,:] bond_indices = atoms.bonds.get_all_bonds()[0]
+-- 
+2.43.0
+