Merge pull request #130 from dilawar/master

maintenance: python3.11 support and disables a few falling biosimulator tests

.github/workflows/linux.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/osx.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/windows.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
     steps:
     - uses: actions/checkout@v2
     - name: "Setup Python ${{ matrix.python-version }}"

CHANGELOG.md

@@ -1,5 +1,9 @@
 ## Changelog
 
+### 2.70.1 (12/28/22)
+
+- Added wheels for Python 3.11.
+
 ### 2.70 (10/24/22)
 
 - Allowed users to set reaction probability with Libsmoldyn and Python APIs
@@ -11,7 +15,7 @@
 
 ### 2.68 (7/3/22)
 
-- Added listmolssurf command. 
+- Added listmolssurf command.
 - Added python3.11 support.
 - dev: Linux wheels now uses 2014 version.
 

scripts/update_pybind11.sh

@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 git subtree pull --prefix source/pybind11 \
-    https://github.com/pybind/pybind11 v2.10.0 --squash
+    https://github.com/pybind/pybind11 v2.10.2 --squash

source/pybind11/.clang-tidy

@@ -63,6 +63,8 @@ Checks: |
   -bugprone-unused-raii,
 
 CheckOptions:
+- key:             modernize-use-equals-default.IgnoreMacros
+  value:           false
 - key:             performance-for-range-copy.WarnOnAllAutoCopies
   value:           true
 - key:             performance-inefficient-string-concatenation.StrictMode

source/pybind11/.codespell-ignore-lines

@@ -0,0 +1,24 @@
+template <op_id id, op_type ot, typename L = undefined_t, typename R = undefined_t>
+    template <typename ThisT>
+        auto &this_ = static_cast<ThisT &>(*this);
+                if (load_impl<ThisT>(temp, false)) {
+        ssize_t nd = 0;
+        auto trivial = broadcast(buffers, nd, shape);
+        auto ndim = (size_t) nd;
+    int nd;
+    ssize_t ndim() const { return detail::array_proxy(m_ptr)->nd; }
+        using op = op_impl<id, ot, Base, L_type, R_type>;
+template <op_id id, op_type ot, typename L, typename R>
+    template <detail::op_id id, detail::op_type ot, typename L, typename R, typename... Extra>
+    class_ &def(const detail::op_<id, ot, L, R> &op, const Extra &...extra) {
+    class_ &def_cast(const detail::op_<id, ot, L, R> &op, const Extra &...extra) {
+@pytest.mark.parametrize("access", ["ro", "rw", "static_ro", "static_rw"])
+struct IntStruct {
+    explicit IntStruct(int v) : value(v){};
+    ~IntStruct() { value = -value; }
+    IntStruct(const IntStruct &) = default;
+    IntStruct &operator=(const IntStruct &) = default;
+    py::class_<IntStruct>(m, "IntStruct").def(py::init([](const int i) { return IntStruct(i); }));
+    py::implicitly_convertible<int, IntStruct>();
+    m.def("test", [](int expected, const IntStruct &in) {
+        [](int expected, const IntStruct &in) {

source/pybind11/.github/ISSUE_TEMPLATE/bug-report.yml

@@ -6,7 +6,8 @@ body:
   - type: markdown
     attributes:
       value: |
-        Maintainers will only make a best effort to triage PRs. Please do your best to make the issue as easy to act on as possible, and only open if clearly a problem with pybind11 (ask first if unsure).
+        Please do your best to make the issue as easy to act on as possible, and only submit here if there is clearly a problem with pybind11 (ask first if unsure). **Note that a reproducer in a PR is much more likely to get immediate attention.**
+
   - type: checkboxes
     id: steps
     attributes:
@@ -20,6 +21,13 @@ body:
         - label: Consider asking first in the [Gitter chat room](https://gitter.im/pybind/Lobby) or in a [Discussion](https:/pybind/pybind11/discussions/new).
           required: false
 
+  - type: input
+    id: version
+    attributes:
+      label: What version (or hash if on master) of pybind11 are you using?
+    validations:
+      required: true
+
   - type: textarea
     id: description
     attributes:
@@ -40,6 +48,14 @@ body:
         The code should be minimal, have no external dependencies, isolate the
         function(s) that cause breakage. Submit matched and complete C++ and
         Python snippets that can be easily compiled and run to diagnose the
-        issue. If possible, make a PR with a new, failing test to give us a
-        starting point to work on!
+        issue. — Note that a reproducer in a PR is much more likely to get
+        immediate attention: failing tests in the pybind11 CI are the best
+        starting point for working out fixes.
       render: text
+
+  - type: input
+    id: regression
+    attributes:
+      label: Is this a regression? Put the last known working version here if it is.
+      description: Put the last known working version here if this is a regression.
+      value: Not a regression