Fixed showmsg() bug in pybind11 based version. (#466)

* Fixed showmsg() bug in pybind11 based version. The newer implementation of showmsg() shows the outgoing messages with misdirected arrows. Fixed now. * Added newer version of pybind11 * Swapped clocks for channel and compartment to fix #467 * This actually fixes scheduling for channels and compartments #467 The previous commit only updated the docs. This one modifies the actual tick assignments. Now electrical compartments are scheduled on ticks 2 and 3 and channels (all derived from ChanBase) on 4. * Minor fix for compiler warning on loop var creating copy from const * Removed CMake generated compile command. the compile command file is generated by cmake in each build environment and should not be part of the repo.
BhallaLab · Mar 8, 2024 · 8b37d2d · 8b37d2d
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diff --git a/external/pybind11/.appveyor.yml b/external/pybind11/.appveyor.yml
@@ -1,70 +1,35 @@
 version: 1.0.{build}
 image:
 - Visual Studio 2017
-- Visual Studio 2015
 test: off
 skip_branch_with_pr: true
 build:
   parallel: true
 platform:
-- x64
 - x86
 environment:
   matrix:
   - PYTHON: 36
-    CPP: 14
     CONFIG: Debug
-  - PYTHON: 27
-    CPP: 14
-    CONFIG: Debug
-  - CONDA: 36
-    CPP: latest
-    CONFIG: Release
-matrix:
-  exclude:
-    - image: Visual Studio 2015
-      platform: x86
-    - image: Visual Studio 2015
-      CPP: latest
-    - image: Visual Studio 2017
-      CPP: latest
-      platform: x86
 install:
 - ps: |
-    if ($env:PLATFORM -eq "x64") { $env:CMAKE_ARCH = "x64" }
-    if ($env:APPVEYOR_JOB_NAME -like "*Visual Studio 2017*") {
-      $env:CMAKE_GENERATOR = "Visual Studio 15 2017"
-      $env:CMAKE_INCLUDE_PATH = "C:\Libraries\boost_1_64_0"
-      $env:CXXFLAGS = "-permissive-"
-    } else {
-      $env:CMAKE_GENERATOR = "Visual Studio 14 2015"
-    }
-    if ($env:PYTHON) {
-      if ($env:PLATFORM -eq "x64") { $env:PYTHON = "$env:PYTHON-x64" }
-      $env:PATH = "C:\Python$env:PYTHON\;C:\Python$env:PYTHON\Scripts\;$env:PATH"
-      python -W ignore -m pip install --upgrade pip wheel
-      python -W ignore -m pip install pytest numpy --no-warn-script-location
-    } elseif ($env:CONDA) {
-      if ($env:CONDA -eq "27") { $env:CONDA = "" }
-      if ($env:PLATFORM -eq "x64") { $env:CONDA = "$env:CONDA-x64" }
-      $env:PATH = "C:\Miniconda$env:CONDA\;C:\Miniconda$env:CONDA\Scripts\;$env:PATH"
-      $env:PYTHONHOME = "C:\Miniconda$env:CONDA"
-      conda --version
-      conda install -y -q pytest numpy scipy
-    }
+    $env:CMAKE_GENERATOR = "Visual Studio 15 2017"
+    if ($env:PLATFORM -eq "x64") { $env:PYTHON = "$env:PYTHON-x64" }
+    $env:PATH = "C:\Python$env:PYTHON\;C:\Python$env:PYTHON\Scripts\;$env:PATH"
+    python -W ignore -m pip install --upgrade pip wheel
+    python -W ignore -m pip install pytest numpy --no-warn-script-location pytest-timeout
 - ps: |
-    Start-FileDownload 'http://bitbucket.org/eigen/eigen/get/3.3.3.zip'
-    7z x 3.3.3.zip -y > $null
-    $env:CMAKE_INCLUDE_PATH = "eigen-eigen-67e894c6cd8f;$env:CMAKE_INCLUDE_PATH"
+    Start-FileDownload 'https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.zip'
+    7z x eigen-3.3.7.zip -y > $null
+    $env:CMAKE_INCLUDE_PATH = "eigen-3.3.7;$env:CMAKE_INCLUDE_PATH"
 build_script:
 - cmake -G "%CMAKE_GENERATOR%" -A "%CMAKE_ARCH%"
-    -DPYBIND11_CPP_STANDARD=/std:c++%CPP%
+    -DCMAKE_CXX_STANDARD=14
     -DPYBIND11_WERROR=ON
     -DDOWNLOAD_CATCH=ON
     -DCMAKE_SUPPRESS_REGENERATION=1
     .
 - set MSBuildLogger="C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
 - cmake --build . --config %CONFIG% --target pytest -- /m /v:m /logger:%MSBuildLogger%
 - cmake --build . --config %CONFIG% --target cpptest -- /m /v:m /logger:%MSBuildLogger%
-- if "%CPP%"=="latest" (cmake --build . --config %CONFIG% --target test_cmake_build -- /m /v:m /logger:%MSBuildLogger%)
 on_failure: if exist "tests\test_cmake_build" type tests\test_cmake_build\*.log*
diff --git a/external/pybind11/.clang-format b/external/pybind11/.clang-format
@@ -0,0 +1,38 @@
+---
+# See all possible options and defaults with:
+# clang-format --style=llvm --dump-config
+BasedOnStyle: LLVM
+AccessModifierOffset: -4
+AllowShortLambdasOnASingleLine: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+BreakBeforeBinaryOperators: All
+BreakConstructorInitializers: BeforeColon
+ColumnLimit: 99
+CommentPragmas: 'NOLINT:.*|^ IWYU pragma:'
+IncludeBlocks: Regroup
+IndentCaseLabels: true
+IndentPPDirectives: AfterHash
+IndentWidth: 4
+Language: Cpp
+SpaceAfterCStyleCast: true
+Standard: Cpp11
+StatementMacros: ['PyObject_HEAD']
+TabWidth: 4
+IncludeCategories:
+  - Regex:           '<pybind11/.*'
+    Priority:        -1
+  - Regex:           'pybind11.h"$'
+    Priority:        1
+  - Regex:           '^".*/?detail/'
+    Priority:        1
+    SortPriority:    2
+  - Regex:           '^"'
+    Priority:        1
+    SortPriority:    3
+  - Regex:           '<[[:alnum:]._]+>'
+    Priority:        4
+  - Regex:           '.*'
+    Priority:        5
+...
diff --git a/external/pybind11/.clang-tidy b/external/pybind11/.clang-tidy
@@ -0,0 +1,77 @@
+FormatStyle: file
+
+Checks: |
+  *bugprone*,
+  *performance*,
+  clang-analyzer-optin.cplusplus.VirtualCall,
+  clang-analyzer-optin.performance.Padding,
+  cppcoreguidelines-init-variables,
+  cppcoreguidelines-prefer-member-initializer,
+  cppcoreguidelines-pro-type-static-cast-downcast,
+  cppcoreguidelines-slicing,
+  google-explicit-constructor,
+  llvm-namespace-comment,
+  misc-definitions-in-headers,
+  misc-misplaced-const,
+  misc-non-copyable-objects,
+  misc-static-assert,
+  misc-throw-by-value-catch-by-reference,
+  misc-uniqueptr-reset-release,
+  misc-unused-parameters,
+  modernize-avoid-bind,
+  modernize-loop-convert,
+  modernize-make-shared,
+  modernize-redundant-void-arg,
+  modernize-replace-auto-ptr,
+  modernize-replace-disallow-copy-and-assign-macro,
+  modernize-replace-random-shuffle,
+  modernize-shrink-to-fit,
+  modernize-use-auto,
+  modernize-use-bool-literals,
+  modernize-use-default-member-init,
+  modernize-use-emplace,
+  modernize-use-equals-default,
+  modernize-use-equals-delete,
+  modernize-use-noexcept,
+  modernize-use-nullptr,
+  modernize-use-override,
+  modernize-use-using,
+  readability-avoid-const-params-in-decls,
+  readability-braces-around-statements,
+  readability-const-return-type,
+  readability-container-size-empty,
+  readability-delete-null-pointer,
+  readability-else-after-return,
+  readability-implicit-bool-conversion,
+  readability-inconsistent-declaration-parameter-name,
+  readability-make-member-function-const,
+  readability-misplaced-array-index,
+  readability-non-const-parameter,
+  readability-qualified-auto,
+  readability-redundant-function-ptr-dereference,
+  readability-redundant-smartptr-get,
+  readability-redundant-string-cstr,
+  readability-simplify-subscript-expr,
+  readability-static-accessed-through-instance,
+  readability-static-definition-in-anonymous-namespace,
+  readability-string-compare,
+  readability-suspicious-call-argument,
+  readability-uniqueptr-delete-release,
+  -bugprone-easily-swappable-parameters,
+  -bugprone-exception-escape,
+  -bugprone-reserved-identifier,
+  -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
+  value:           true
+- key:             performance-unnecessary-value-param.AllowedTypes
+  value:           'exception_ptr$;'
+- key:             readability-implicit-bool-conversion.AllowPointerConditions
+  value:           true
+
+HeaderFilterRegex: 'pybind11/.*h'
diff --git a/external/pybind11/.cmake-format.yaml b/external/pybind11/.cmake-format.yaml
@@ -0,0 +1,73 @@
+parse:
+  additional_commands:
+    pybind11_add_module:
+      flags:
+        - THIN_LTO
+        - MODULE
+        - SHARED
+        - NO_EXTRAS
+        - EXCLUDE_FROM_ALL
+        - SYSTEM
+
+format:
+  line_width: 99
+  tab_size: 2
+
+  # If an argument group contains more than this many sub-groups
+  # (parg or kwarg groups) then force it to a vertical layout.
+  max_subgroups_hwrap: 2
+
+  # If a positional argument group contains more than this many
+  # arguments, then force it to a vertical layout.
+  max_pargs_hwrap: 6
+
+  # If a cmdline positional group consumes more than this many
+  # lines without nesting, then invalidate the layout (and nest)
+  max_rows_cmdline: 2
+  separate_ctrl_name_with_space: false
+  separate_fn_name_with_space: false
+  dangle_parens: false
+
+  # If the trailing parenthesis must be 'dangled' on its on
+  # 'line, then align it to this reference: `prefix`: the start'
+  # 'of the statement,  `prefix-indent`: the start of the'
+  # 'statement, plus one indentation  level, `child`: align to'
+  # the column of the arguments
+  dangle_align: prefix
+  # If the statement spelling length (including space and
+  # parenthesis) is smaller than this amount, then force reject
+  # nested layouts.
+  min_prefix_chars: 4
+
+  # If the statement spelling length (including space and
+  # parenthesis) is larger than the tab width by more than this
+  # amount, then force reject un-nested layouts.
+  max_prefix_chars: 10
+
+  # If a candidate layout is wrapped horizontally but it exceeds
+  # this many lines, then reject the layout.
+  max_lines_hwrap: 2
+
+  line_ending: unix
+
+  # Format command names consistently as 'lower' or 'upper' case
+  command_case: canonical
+
+  # Format keywords consistently as 'lower' or 'upper' case
+  # unchanged is valid too
+  keyword_case: 'upper'
+
+  # A list of command names which should always be wrapped
+  always_wrap: []
+
+  # If true, the argument lists which are known to be sortable
+  # will be sorted lexicographically
+  enable_sort: true
+
+  # If true, the parsers may infer whether or not an argument
+  # list is sortable (without annotation).
+  autosort: false
+
+# Causes a few issues - can be solved later, possibly.
+markup:
+  enable_markup: false
diff --git a/external/pybind11/.codespell-ignore-lines b/external/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) {
diff --git a/external/pybind11/.gitattributes b/external/pybind11/.gitattributes
@@ -0,0 +1 @@
+docs/*.svg binary
diff --git a/external/pybind11/.github/CODEOWNERS b/external/pybind11/.github/CODEOWNERS
@@ -0,0 +1,9 @@
+*.cmake @henryiii
+CMakeLists.txt @henryiii
+*.yml @henryiii
+*.yaml @henryiii
+/tools/ @henryiii
+/pybind11/ @henryiii
+noxfile.py @henryiii
+.clang-format @henryiii
+.clang-tidy @henryiii