update pybind11, cmakelists with official cmake python3

cosmicrays · Jan 12, 2024 · a00c6a8 · a00c6a8
1 parent 0b0743f
commit a00c6a8
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -345,12 +345,12 @@ target_link_libraries(hermes ${HERMES_EXTRA_LIBRARIES})
 # Python
 # ----------------------------------------------------------------------------
 option(ENABLE_PYTHON "Create python library via Pybind11" OFF)
-include(FindPython)
-find_package(Python COMPONENTS Interpreter Development)
+include(FindPython3)
+find_package(Python3 COMPONENTS Interpreter Development)
 
-if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
-    include_directories(${PYTHON_INCLUDE_DIRS})
-    set(PYBIND11_PYTHON_VERSION ${PYTHON_DOT_VERSION}) 
+if(ENABLE_PYTHON AND Python3_Development_FOUND)
+    include_directories(${Python3_INCLUDE_DIRS})
+    set(PYBIND11_PYTHON_VERSION ${Python3_VERSION}) 
     add_subdirectory(lib/pybind11)
     # for PYBIND11_EXPAND_SIDE_EFFECTS in pybind11.h - temporary,
     #   should be removed after the fix lands to the upstream
@@ -381,8 +381,8 @@ if(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
         LINKER_LANGUAGE CXX)
     target_link_libraries(pyhermes PRIVATE hermes)
 
-    install(TARGETS pyhermes LIBRARY DESTINATION "${PYTHON_SITE_PACKAGES}")
-endif(ENABLE_PYTHON AND PYTHONLIBS_FOUND)
+    install(TARGETS pyhermes LIBRARY DESTINATION "${Python3_SITELIB}")
+endif(ENABLE_PYTHON AND Python3_Development_FOUND)
 
 # ------------------------------------------------------------------
 # Documentation

diff --git a/Dockerfile b/Dockerfile
@@ -23,6 +23,7 @@ USER ${NB_UID}
 
 # Install Python 3 packages
 RUN mamba install --yes \
+    'conda-forge::sphinx' \
     'healpy' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
@@ -32,13 +33,15 @@ RUN mamba install --yes \
 WORKDIR /tmp
 RUN git clone https://github.com/cosmicrays/hermes.git
 WORKDIR /tmp/hermes
-RUN conda init 
+ENV PATH /opt/conda/bin:$PATH
+RUN /bin/bash -c "source activate base"
 RUN mkdir build && \
     cd build && \
     CMAKE_PREFIX_PATH=${CONDA_DIR} cmake \
-         -DPython_EXECUTABLE=${CONDA_DIR}/bin/${PYTHON_VERSION} \
-         -DPython_INCLUDE_DIRS=${CONDA_DIR}/include/${PYTHON_VERSION} \
-         -DPython_LIBRARIES=${CONDA_DIR}/lib/${PYTHON_VERSION} \
+         -DPython3_EXECUTABLE=${CONDA_DIR}/bin/python${PYTHON_VERSION} \
+         -DPython3_INCLUDE_DIRS=${CONDA_DIR}/include/python${PYTHON_VERSION} \
+         -DPython3_LIBRARIES=${CONDA_DIR}/lib/python${PYTHON_VERSION} \
+         -DENABLE_PYTHON=On \
          -DCMAKE_INSTALL_PREFIX=${CONDA_DIR} \
          -DENABLE_TESTING=On .. && \
     make -j && \

diff --git a/lib/pybind11/.pre-commit-config.yaml b/lib/pybind11/.pre-commit-config.yaml
@@ -22,9 +22,47 @@ ci:
 exclude: ^tools/JoinPaths.cmake$
 
 repos:
+
+# Clang format the codebase automatically
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: "v17.0.6"
+  hooks:
+  - id: clang-format
+    types_or: [c++, c, cuda]
+
+# Ruff, the Python auto-correcting linter/formatter written in Rust
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.1.9
+  hooks:
+  - id: ruff
+    args: ["--fix", "--show-fixes"]
+  - id: ruff-format
+
+# Check static types with mypy
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: "v1.8.0"
+  hooks:
+  - id: mypy
+    args: []
+    exclude: ^(tests|docs)/
+    additional_dependencies:
+    - markdown-it-py<3 # Drop this together with dropping Python 3.7 support.
+    - nox
+    - rich
+    - types-setuptools
+
+# CMake formatting
+- repo: https://github.com/cheshirekow/cmake-format-precommit
+  rev: "v0.6.13"
+  hooks:
+  - id: cmake-format
+    additional_dependencies: [pyyaml]
+    types: [file]
+    files: (\.cmake|CMakeLists.txt)(.in)?$
+
 # Standard hooks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: "v4.3.0"
+  rev: "v4.5.0"
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -39,109 +77,38 @@ repos:
   - id: requirements-txt-fixer
   - id: trailing-whitespace
 
-# Upgrade old Python syntax
-- repo: https://github.com/asottile/pyupgrade
-  rev: "v3.2.0"
-  hooks:
-  - id: pyupgrade
-    args: [--py36-plus]
-
-# Nicely sort includes
-- repo: https://github.com/PyCQA/isort
-  rev: "5.10.1"
-  hooks:
-  - id: isort
-
-# Black, the code formatter, natively supports pre-commit
-- repo: https://github.com/psf/black
-  rev: "22.10.0" # Keep in sync with blacken-docs
-  hooks:
-  - id: black
-
 # Also code format the docs
 - repo: https://github.com/asottile/blacken-docs
-  rev: "v1.12.1"
+  rev: "1.16.0"
   hooks:
   - id: blacken-docs
     additional_dependencies:
-    - black==22.10.0 # keep in sync with black hook
+    - black==23.*
 
 # Changes tabs to spaces
 - repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: "v1.3.1"
+  rev: "v1.5.4"
   hooks:
   - id: remove-tabs
 
+# Avoid directional quotes
 - repo: https://github.com/sirosen/texthooks
-  rev: "0.4.0"
+  rev: "0.6.3"
   hooks:
   - id: fix-ligatures
   - id: fix-smartquotes
 
-# Autoremoves unused imports
-- repo: https://github.com/hadialqattan/pycln
-  rev: "v2.1.1"
-  hooks:
-  - id: pycln
-    stages: [manual]
-
 # Checking for common mistakes
 - repo: https://github.com/pre-commit/pygrep-hooks
-  rev: "v1.9.0"
+  rev: "v1.10.0"
   hooks:
-  - id: python-check-blanket-noqa
-  - id: python-check-blanket-type-ignore
-  - id: python-no-log-warn
-  - id: python-use-type-annotations
   - id: rst-backticks
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 
-# Automatically remove noqa that are not used
-- repo: https://github.com/asottile/yesqa
-  rev: "v1.4.0"
-  hooks:
-  - id: yesqa
-    additional_dependencies: &flake8_dependencies
-      - flake8-bugbear
-      - pep8-naming
-
-# Flake8 also supports pre-commit natively (same author)
-- repo: https://github.com/PyCQA/flake8
-  rev: "5.0.4"
-  hooks:
-  - id: flake8
-    exclude: ^(docs/.*|tools/.*)$
-    additional_dependencies: *flake8_dependencies
-
-# PyLint has native support - not always usable, but works for us
-- repo: https://github.com/PyCQA/pylint
-  rev: "v2.15.5"
-  hooks:
-  - id: pylint
-    files: ^pybind11
-
-# CMake formatting
-- repo: https://github.com/cheshirekow/cmake-format-precommit
-  rev: "v0.6.13"
-  hooks:
-  - id: cmake-format
-    additional_dependencies: [pyyaml]
-    types: [file]
-    files: (\.cmake|CMakeLists.txt)(.in)?$
-
-# Check static types with mypy
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: "v0.982"
-  hooks:
-  - id: mypy
-    args: []
-    exclude: ^(tests|docs)/
-    additional_dependencies: [nox, rich]
-
 # Checks the manifest for missing files (native support)
 - repo: https://github.com/mgedmin/check-manifest
-  rev: "0.48"
+  rev: "0.49"
   hooks:
   - id: check-manifest
     # This is a slow hook, so only run this if --hook-stage manual is passed
@@ -152,15 +119,15 @@ repos:
 # Use tools/codespell_ignore_lines_from_errors.py
 # to rebuild .codespell-ignore-lines
 - repo: https://github.com/codespell-project/codespell
-  rev: "v2.2.2"
+  rev: "v2.2.6"
   hooks:
   - id: codespell
     exclude: ".supp$"
-    args: ["-x", ".codespell-ignore-lines"]
+    args: ["-x.codespell-ignore-lines", "-Lccompiler"]
 
 # Check for common shell mistakes
 - repo: https://github.com/shellcheck-py/shellcheck-py
-  rev: "v0.8.0.4"
+  rev: "v0.9.0.6"
   hooks:
   - id: shellcheck
 
@@ -170,12 +137,12 @@ repos:
   - id: disallow-caps
     name: Disallow improper capitalization
     language: pygrep
-    entry: PyBind|Numpy|Cmake|CCache|PyTest
+    entry: PyBind|\bNumpy\b|Cmake|CCache|PyTest
     exclude: ^\.pre-commit-config.yaml$
 
-# Clang format the codebase automatically
-- repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: "v14.0.6"
+# PyLint has native support - not always usable, but works for us
+- repo: https://github.com/PyCQA/pylint
+  rev: "v3.0.3"
   hooks:
-  - id: clang-format
-    types_or: [c++, c, cuda]
+  - id: pylint
+    files: ^pybind11
diff --git a/lib/pybind11/.readthedocs.yml b/lib/pybind11/.readthedocs.yml
@@ -1,3 +1,20 @@
+# https://blog.readthedocs.com/migrate-configuration-v2/
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  apt_packages:
+    - librsvg2-bin
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/conf.py
+
 python:
-  version: 3
-requirements_file: docs/requirements.txt
+  install:
+  - requirements: docs/requirements.txt
+
+formats:
+  - pdf
diff --git a/lib/pybind11/CMakeLists.txt b/lib/pybind11/CMakeLists.txt
@@ -5,15 +5,25 @@
 # All rights reserved. Use of this source code is governed by a
 # BSD-style license that can be found in the LICENSE file.
 
-cmake_minimum_required(VERSION 3.4)
+# Propagate this policy (FindPythonInterp removal) so it can be detected later
+if(NOT CMAKE_VERSION VERSION_LESS "3.27")
+  cmake_policy(GET CMP0148 _pybind11_cmp0148)
+endif()
+
+cmake_minimum_required(VERSION 3.5)
 
-# The `cmake_minimum_required(VERSION 3.4...3.22)` syntax does not work with
+# The `cmake_minimum_required(VERSION 3.5...3.27)` syntax does not work with
 # some versions of VS that have a patched CMake 3.11. This forces us to emulate
 # the behavior using the following workaround:
-if(${CMAKE_VERSION} VERSION_LESS 3.22)
+if(${CMAKE_VERSION} VERSION_LESS 3.27)
   cmake_policy(VERSION ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION})
 else()
-  cmake_policy(VERSION 3.22)
+  cmake_policy(VERSION 3.27)
+endif()
+
+if(_pybind11_cmp0148)
+  cmake_policy(SET CMP0148 ${_pybind11_cmp0148})
+  unset(_pybind11_cmp0148)
 endif()
 
 # Avoid infinite recursion if tests include this as a subdirectory
@@ -82,9 +92,15 @@ if(CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR)
   set(pybind11_system "")
 
   set_property(GLOBAL PROPERTY USE_FOLDERS ON)
+  if(CMAKE_VERSION VERSION_LESS "3.18")
+    set(_pybind11_findpython_default OFF)
+  else()
+    set(_pybind11_findpython_default ON)
+  endif()
 else()
   set(PYBIND11_MASTER_PROJECT OFF)
   set(pybind11_system SYSTEM)
+  set(_pybind11_findpython_default OFF)
 endif()
 
 # Options
@@ -106,9 +122,18 @@ cmake_dependent_option(
   "Install pybind11 headers in Python include directory instead of default installation prefix"
   OFF "PYBIND11_INSTALL" OFF)
 
-cmake_dependent_option(PYBIND11_FINDPYTHON "Force new FindPython" OFF
+cmake_dependent_option(PYBIND11_FINDPYTHON "Force new FindPython" ${_pybind11_findpython_default}
                        "NOT CMAKE_VERSION VERSION_LESS 3.12" OFF)
 
+# Allow PYTHON_EXECUTABLE if in FINDPYTHON mode and building pybind11's tests
+# (makes transition easier while we support both modes).
+if(PYBIND11_MASTER_PROJECT
+   AND PYBIND11_FINDPYTHON
+   AND DEFINED PYTHON_EXECUTABLE
+   AND NOT DEFINED Python_EXECUTABLE)
+  set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+endif()
+
 # NB: when adding a header don't forget to also add it to setup.py
 set(PYBIND11_HEADERS
     include/pybind11/detail/class.h
@@ -126,11 +151,13 @@ set(PYBIND11_HEADERS
     include/pybind11/complex.h
     include/pybind11/options.h
     include/pybind11/eigen.h
+    include/pybind11/eigen/common.h
     include/pybind11/eigen/matrix.h
     include/pybind11/eigen/tensor.h
     include/pybind11/embed.h
     include/pybind11/eval.h
     include/pybind11/gil.h
+    include/pybind11/gil_safe_call_once.h
     include/pybind11/iostream.h
     include/pybind11/functional.h
     include/pybind11/numpy.h
@@ -139,7 +166,9 @@ set(PYBIND11_HEADERS
     include/pybind11/pytypes.h
     include/pybind11/stl.h
     include/pybind11/stl_bind.h
-    include/pybind11/stl/filesystem.h)
+    include/pybind11/stl/filesystem.h
+    include/pybind11/type_caster_pyobject_ptr.h
+    include/pybind11/typing.h)
 
 # Compare with grep and warn if mismatched
 if(PYBIND11_MASTER_PROJECT AND NOT CMAKE_VERSION VERSION_LESS 3.12)
@@ -275,7 +304,21 @@ if(PYBIND11_INSTALL)
 
   # pkg-config support
   if(NOT prefix_for_pc_file)
-    set(prefix_for_pc_file "${CMAKE_INSTALL_PREFIX}")
+    if(IS_ABSOLUTE "${CMAKE_INSTALL_DATAROOTDIR}")
+      set(prefix_for_pc_file "${CMAKE_INSTALL_PREFIX}")
+    else()
+      set(pc_datarootdir "${CMAKE_INSTALL_DATAROOTDIR}")
+      if(CMAKE_VERSION VERSION_LESS 3.20)
+        set(prefix_for_pc_file "\${pcfiledir}/..")
+        while(pc_datarootdir)
+          get_filename_component(pc_datarootdir "${pc_datarootdir}" DIRECTORY)
+          string(APPEND prefix_for_pc_file "/..")
+        endwhile()
+      else()
+        cmake_path(RELATIVE_PATH CMAKE_INSTALL_PREFIX BASE_DIRECTORY CMAKE_INSTALL_DATAROOTDIR
+                   OUTPUT_VARIABLE prefix_for_pc_file)
+      endif()
+    endif()
   endif()
   join_paths(includedir_for_pc_file "\${prefix}" "${CMAKE_INSTALL_INCLUDEDIR}")
   configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11.pc.in"