Release 2026.1.0

.github/workflows/pr.yaml

@@ -45,6 +45,7 @@ jobs:
       SIRE_SILENT_PHONEHOME: 1
       SIRE_EMLE: 1
       REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
+      SIRE_REMOTE: "https://github.com/${{ github.event.pull_request.head.repo.full_name || github.repository }}.git"
     steps:
       #
       - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+repos:
+  # General file quality checks (Python source files only)
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        files: ^(src|tests|wrapper)/
+        types: [python]
+      - id: end-of-file-fixer
+        files: ^(src|tests|wrapper)/
+        types: [python]
+      - id: check-added-large-files
+        args: [--maxkb=1000]
+      - id: check-merge-conflict
+
+  # Python formatting and linting (src/, tests/, and wrapper/ Python files)
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.4
+    hooks:
+      # Run the formatter
+      - id: ruff-format
+        files: ^(src|tests|wrapper)/
+      # Run the linter (auto-fix but don't block commits)
+      - id: ruff
+        files: ^(src|tests|wrapper)/
+        args: [--fix, --exit-zero]
+
+  # C++ formatting (corelib/ and wrapper/ only)
+  # Runs clang-format only on files staged for commit, so the codebase
+  # drifts gradually toward the .clang-format standard rather than
+  # requiring a blanket one-time reformatting pass.
+  # NOTE: do NOT run 'pre-commit run --all-files' for C++ — use per-file
+  # formatting instead to preserve the drift-based approach.
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v22.1.3
+    hooks:
+      - id: clang-format
+        files: ^(corelib|wrapper)/.*\.(cpp|h|hpp)$

README.rst

@@ -166,6 +166,22 @@ Developers guide
 Please `visit the website <https://sire.openbiosim.org>`__ for information on how to
 develop applications using sire.
 
+The repository uses `pre-commit <https://pre-commit.com>`__ to enforce
+consistent code style. After setting up your development environment, install
+the hooks with:
+
+.. code-block:: bash
+
+    pre-commit install
+
+Python code in ``src/``, ``tests/``, and ``wrapper/`` is formatted with
+`ruff <https://docs.astral.sh/ruff/>`__; C++ code in ``corelib/`` and
+``wrapper/`` is formatted with
+`clang-format <https://clang.llvm.org/docs/ClangFormat.html>`__ using the
+``.clang-format`` file in the repository root. The C++ formatter runs only
+on files staged for commit, allowing the codebase to drift gradually toward
+a consistent style without a blanket one-time reformatting.
+
 GitHub actions
 --------------
 Since sire is quite large, a build can take quite long and might not be neccessary

actions/generate_recipe.py

@@ -91,11 +91,20 @@ def get_git_info(srcdir):
     """Get the git remote URL and branch/tag."""
     gitdir = os.path.join(srcdir, ".git")
 
-    remote = run_cmd(
-        f"git --git-dir={gitdir} --work-tree={srcdir} config --get remote.origin.url"
-    )
-    if not remote.endswith(".git"):
-        remote += ".git"
+    # For PR builds from external forks the checkout remote points to the base
+    # repo, not the fork.  The workflow sets SIRE_REMOTE to the fork's clone
+    # URL so that rattler-build fetches from the right place.
+    env_remote = os.environ.get("SIRE_REMOTE")
+    if env_remote:
+        remote = env_remote
+        if not remote.endswith(".git"):
+            remote += ".git"
+    else:
+        remote = run_cmd(
+            f"git --git-dir={gitdir} --work-tree={srcdir} config --get remote.origin.url"
+        )
+        if not remote.endswith(".git"):
+            remote += ".git"
 
     branch = run_cmd(
         f"git --git-dir={gitdir} --work-tree={srcdir} rev-parse --abbrev-ref HEAD"

corelib/CMakeLists.txt

@@ -649,6 +649,9 @@ elseif (MSVC)
     add_compile_options("/EHsc")
     add_compile_options("/permissive-")
     add_compile_options("/Zc:twoPhase-")
+    # Provide stdext::make_checked_array_iterator stub for MSVC 14.38+ where it was removed.
+    # Qt5's qvector.h uses it unconditionally on MSVC, so force-include a polyfill.
+    add_compile_options("/FI${CMAKE_CURRENT_SOURCE_DIR}/build/cmake/stdext_compat.h")
     message( STATUS "Compiling with MSVC" )
     set( SIRE_COMPILER "MSVC" )
 

corelib/build/cmake/stdext_compat.h

@@ -0,0 +1,22 @@
+#pragma once
+// stdext::make_checked_array_iterator and make_unchecked_array_iterator were
+// removed in MSVC 14.38 (VS 2022 17.8). Qt5's qcompilerdetection.h maps
+// QT_MAKE_CHECKED_ARRAY_ITERATOR and QT_MAKE_UNCHECKED_ARRAY_ITERATOR to these
+// functions unconditionally on MSVC, so provide no-op stubs.
+#if defined(__cplusplus) && defined(_MSC_VER) && _MSC_VER >= 1938
+#include <cstddef>
+namespace stdext
+{
+    template <typename T>
+    T *make_checked_array_iterator(T *ptr, std::size_t, std::size_t index = 0)
+    {
+        return ptr + index;
+    }
+
+    template <typename T>
+    T *make_unchecked_array_iterator(T *ptr)
+    {
+        return ptr;
+    }
+}
+#endif