Merge pull request #1628 from borglab/python-updates

.github/scripts/python.sh

@@ -39,8 +39,6 @@ function install_dependencies()
   if [ "${GTSAM_WITH_TBB:-OFF}" == "ON" ]; then
     install_tbb
   fi
-
-  $PYTHON -m pip install -r $GITHUB_WORKSPACE/python/requirements.txt
 }
 
 function build()

.github/workflows/build-python.yml

@@ -109,10 +109,13 @@ jobs:
         with:
           swap-size-gb: 6
 
-      - name: Install Dependencies
+      - name: Install System Dependencies
         run: |
           bash .github/scripts/python.sh -d
 
+      - name: Install Python Dependencies
+        run: python$PYTHON_VERSION -m pip install -r python/dev_requirements.txt
+
       - name: Build
         run: |
           bash .github/scripts/python.sh -b

docker/ubuntu-gtsam-python/Dockerfile

@@ -6,9 +6,6 @@ FROM borglab/ubuntu-gtsam:bionic
 # Install pip
 RUN apt-get install -y python3-pip python3-dev
 
-# Install python wrapper requirements
-RUN python3 -m pip install -U -r /usr/src/gtsam/python/requirements.txt
-
 # Run cmake again, now with python toolbox on
 WORKDIR /usr/src/gtsam/build
 RUN cmake \

python/CMakeLists.txt

@@ -1,3 +1,4 @@
+set(PROJECT_PYTHON_SOURCE_DIR ${PROJECT_SOURCE_DIR}/python)
 set(GTSAM_PYTHON_BUILD_DIRECTORY ${PROJECT_BINARY_DIR}/python)
 
 if (NOT GTSAM_BUILD_PYTHON)
@@ -6,11 +7,11 @@ endif()
 
 # Generate setup.py.
 file(READ "${PROJECT_SOURCE_DIR}/README.md" README_CONTENTS)
-configure_file(${PROJECT_SOURCE_DIR}/python/setup.py.in
+configure_file(${PROJECT_PYTHON_SOURCE_DIR}/setup.py.in
                 ${GTSAM_PYTHON_BUILD_DIRECTORY}/setup.py)
 
 # Supply MANIFEST.in for older versions of Python
-file(COPY ${PROJECT_SOURCE_DIR}/python/MANIFEST.in
+file(COPY ${PROJECT_PYTHON_SOURCE_DIR}/MANIFEST.in
      DESTINATION ${GTSAM_PYTHON_BUILD_DIRECTORY})
 
 set(WRAP_BUILD_TYPE_POSTFIXES ${GTSAM_BUILD_TYPE_POSTFIXES})
@@ -99,7 +100,7 @@ pybind_wrap(${GTSAM_PYTHON_TARGET} # target
             "gtsam" # module_name
             "gtsam" # top_namespace
             "${ignore}" # ignore_classes
-            ${PROJECT_SOURCE_DIR}/python/gtsam/gtsam.tpl
+            ${PROJECT_PYTHON_SOURCE_DIR}/gtsam/gtsam.tpl
             gtsam # libs
             "gtsam;gtsam_header" # dependencies
             ${GTSAM_ENABLE_BOOST_SERIALIZATION} # use_boost_serialization
@@ -178,7 +179,7 @@ if(GTSAM_UNSTABLE_BUILD_PYTHON)
             "gtsam_unstable" # module_name
             "gtsam" # top_namespace
             "${ignore}" # ignore_classes
-            ${PROJECT_SOURCE_DIR}/python/gtsam_unstable/gtsam_unstable.tpl
+            ${PROJECT_PYTHON_SOURCE_DIR}/gtsam_unstable/gtsam_unstable.tpl
             gtsam_unstable # libs
             "gtsam_unstable;gtsam_unstable_header" # dependencies
             ${GTSAM_ENABLE_BOOST_SERIALIZATION} # use_boost_serialization

python/README.md

@@ -16,7 +16,7 @@ For instructions on updating the version of the [wrap library](https://github.co
 - This wrapper needs `pyparsing(>=2.4.2)`, and `numpy(>=1.11.0)`. These can be installed as follows:
 
   ```bash
-  pip install -r <gtsam_folder>/python/requirements.txt
+  pip install -r <gtsam_folder>/python/dev_requirements.txt
   ```
 
 ## Install

python/dev_requirements.txt

@@ -0,0 +1,2 @@
+-r requirements.txt
+pyparsing>=2.4.2

python/requirements.txt

@@ -1,2 +1 @@
 numpy>=1.11.0
-pyparsing>=2.4.2

python/setup.py.in

@@ -1,19 +1,17 @@
 """Setup file to install the GTSAM package."""
 
-try:
-    from setuptools import setup, find_packages
-except ImportError:
-    from distutils.core import setup, find_packages
+from setuptools import setup, find_namespace_packages
 
-packages = find_packages(where=".")
+packages = find_namespace_packages(
+    where=".",
+    exclude=('build', 'build.*', 'CMakeFiles', 'CMakeFiles.*',
+             'gtsam.notebooks', '*.preamble', '*.specializations', 'dist'))
 print("PACKAGES: ", packages)
 
 package_data = {
     '': [
         "./*.so",
-        "./*.dll",
-        "Data/*"  # Add the data files to the package
-        "Data/**/*"  # Add the data files in subdirectories
+        "./*.dll"
     ]
 }
 
@@ -41,7 +39,6 @@ setup(
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'License :: OSI Approved :: BSD License',
-        'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 3',
     ],
     packages=packages,

wrap/.gitignore

@@ -5,6 +5,8 @@ __pycache__/
 *dist*
 *.egg-info
 
+**/.DS_Store
+
 # Files related to code coverage stats
 **/.coverage
 

wrap/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

wrap/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) {

wrap/pybind11/.github/CONTRIBUTING.md

@@ -235,8 +235,8 @@ directory inside your pybind11 git clone. Files will be modified in place,
 so you can use git to monitor the changes.
 
 ```bash
-docker run --rm -v $PWD:/mounted_pybind11 -it silkeh/clang:13
-apt-get update && apt-get install -y python3-dev python3-pytest
+docker run --rm -v $PWD:/mounted_pybind11 -it silkeh/clang:15-bullseye
+apt-get update && apt-get install -y git python3-dev python3-pytest
 cmake -S /mounted_pybind11/ -B build -DCMAKE_CXX_CLANG_TIDY="$(which clang-tidy);--use-color" -DDOWNLOAD_EIGEN=ON -DDOWNLOAD_CATCH=ON -DCMAKE_CXX_STANDARD=17
 cmake --build build -j 2
 ```

wrap/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