Fix for pybind11 and updates in github actions

.github/workflows/pymoose.yml

@@ -17,24 +17,43 @@ jobs:
           - os: macos-14
             brew: 20
     steps:
-    - uses: actions/checkout@v2
-    - if: ${{ matrix.apt }}
-      run: sudo apt-get install libhdf5-dev libgsl0-dev
-    - if: ${{ matrix.brew }}
-      run: |
-        brew install gsl
-        brew install hdf5      
-    - name: Set up Python ${{ matrix.python-version }}
-      shell: bash
-      run: |
-        "${SHELL}" <(curl -L micro.mamba.pm/install.sh)
-        micromamba self-update
-        micromamba create -n moose python=${{ matrix.python-version }} graphviz lxml cmake numpy matplotlib vpython hdf5 pytables doxygen -c conda-forge
-        eval "$(micromamba shell hook --shell bash)"
-        micromamba activate moose
-        pip install python-libsbml
-        pip install pyneuroml
-    - name: Build
-      run: |
-        pip install .
-
+      - name: mamba-setup
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: moose
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+            hdf5
+            graphviz
+            pytables
+            numpy
+            matplotlib
+            vpython
+            lxml
+            doxygen
+            setuptools
+            wheel
+      - name: Display Python version
+        run: |          
+          python -c "import sys; print(sys.version)"
+      - if: ${{ matrix.apt }}
+        run: sudo apt-get install libhdf5-dev libgsl0-dev graphviz-dev python3-lxml cmake doxygen
+      - if: ${{ matrix.brew }}
+        run: |
+          brew install gsl
+          brew install hdf5
+          brew install graphviz
+          brew install cmake
+          brew install doxygen
+      - name: install python module dependencies via pip
+        run: |
+          pip install pybind11[global]
+          pip install python-libsbml
+      - name: checkout
+        uses: actions/checkout@v4          
+      - name: build and install
+        run: |
+          pip install .
+          python -c "import moose; moose.le()"

CMakeLists.txt

@@ -9,14 +9,9 @@ include(CheckCXXCompiler.cmake)
 include(CheckIncludeFileCXX)
 
 # We find python executable here. Though mainly used inside pymoose. 
-# FIXME: When cmake 3.12 is widely available use the following:
-#   find_package(Python3 COMPONENTS Interpreter Numpy)
-#   set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
-set(Python_ADDITIONAL_VERSIONS 2.7)
-find_package(PythonInterp 3.5)
-if(NOT PYTHONINTERP_FOUND)
-  find_package(PythonInterp 2.7)
-endif()
+find_package(Python3 COMPONENTS Interpreter Numpy)
+set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
+find_package(PythonInterp 3.8)
 
 set(CMAKE_MACOSX_RPATH OFF)
 
@@ -321,14 +316,9 @@ endif( WITH_BOOST )
 # It can be easily done with `pip install pybind11`
 # See: https://pybind11.readthedocs.io/en/stable/installing.html
 # - Subha, Mon Apr 22 14:26:58 IST 2024
-
-# if(NOT WITH_LEGACY_BINDING)
-#     add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11)
-#     add_subdirectory(pybind11)
-# else()
-#     message(STATUS "Building legacy python binding.")
-#     add_subdirectory(pymoose)
-# endif()
+execute_process(COMMAND ${CMAKE_COMMAND} -E pybind11-config --cmakedir OUTPUT_VARIABLE pybind11_DIR OUTPUT_STRIP_TRAILING_WHITESPACE)
+find_package(pybind11 REQUIRED HINTS "${Python3_SITELIB}")
+add_subdirectory(pybind11)
 
 
 # always override debian default installation directory. It will be installed in

INSTALL.md

@@ -8,11 +8,12 @@ followings are installed.
 
 - gsl-1.16 or higher.
 - python-numpy
+- pybind11 (if the setup fails to find pybind11, try running `pip install pybind11[global]`)
 
 On Ubuntu-16.04 or higher, these dependencies can be installed with:
 
 ```
-sudo apt-get install python-pip python-numpy cmake libgsl-dev g++
+sudo apt-get install python-pip python-numpy cmake libgsl-dev g++ pybind11
 ```
 
 Now use `pip` to download and install `pymoose` from the [github repository](https://github.com/BhallaLab/moose-core).
@@ -83,10 +84,26 @@ Now you can import moose in a Python script or interpreter with the statement:
     >>> import moose
     >>> moose.test()   # will take time. Not all tests will pass.
 
+## Uninstall
+
+To uninstall moose, run
+
+    $ pip uninstall pymoose
+
+If you are building moose from source, make sure to get out of the source directory, or you may encounter a message like this:
+
+    Found existing installation: pymoose {version}
+    Can't uninstall 'pymoose'. No files were found to uninstall.
+
+
+
+
 # Notes
 
-SBML support is enabled by installing
+- SBML support is enabled by installing
 [python-libsbml](http://sbml.org/Software/libSBML/docs/python-api/libsbml-installation.html).
 Alternatively, it can be installed by using `python-pip`
 
     $ sudo pip install python-libsbml
+
+

pybind11/Finfo.cpp

@@ -9,10 +9,10 @@
 //
 // =====================================================================================
 
-#include "../external/pybind11/include/pybind11/pybind11.h"
-#include "../external/pybind11/include/pybind11/stl.h"
-#include "../external/pybind11/include/pybind11/numpy.h"
-#include "../external/pybind11/include/pybind11/functional.h"
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <pybind11/numpy.h>
+#include <pybind11/functional.h>
 
 namespace py = pybind11;
 

pybind11/MooseVec.cpp

@@ -13,9 +13,9 @@
 
 using namespace std;
 
-#include "../external/pybind11/include/pybind11/pybind11.h"
-#include "../external/pybind11/include/pybind11/numpy.h"
-#include "../external/pybind11/include/pybind11/stl.h"
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/stl.h>
 
 namespace py = pybind11;
 

pybind11/MooseVec.h

@@ -10,8 +10,8 @@
 #ifndef MOOSE_VEC_H
 #define MOOSE_VEC_H
 
-#include "../external/pybind11/include/pybind11/pybind11.h"
-#include "../external/pybind11/include/pybind11/numpy.h"
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
 namespace py = pybind11;
 
 class MooseVec

pybind11/helper.cpp

@@ -18,16 +18,16 @@
 #include <stdexcept>
 #include <csignal>
 
-#include "../external/pybind11/include/pybind11/functional.h"
-#include "../external/pybind11/include/pybind11/numpy.h"
-#include "../external/pybind11/include/pybind11/pybind11.h"
-#include "../external/pybind11/include/pybind11/stl.h"
+#include <pybind11/functional.h>
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
 
 namespace py = pybind11;
 
 // See
 // https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html#binding-stl-containers
-// #include "../external/pybind11/include/pybind11/stl_bind.h"
+// #include <pybind11/stl_bind.h>
 
 #include "../basecode/header.h"
 #include "../basecode/global.h"

pybind11/pymoose.cpp

@@ -19,9 +19,9 @@
 #include <functional>
 #include <chrono>
 
-#include "../external/pybind11/include/pybind11/pybind11.h"
-#include "../external/pybind11/include/pybind11/stl.h"
-#include "../external/pybind11/include/pybind11/numpy.h"
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <pybind11/numpy.h>
 
 namespace py = pybind11;
 using namespace std;

setup.py

@@ -28,7 +28,7 @@
 # See https://docs.python.org/3/library/distutils.html
 # setuptools is preferred over distutils. And we are supporting python3 only.
 from setuptools import setup, Extension, Command
-from setuptools.command.build_ext import build_ext as _build_ext
+from setuptools.command.build_ext import build_ext
 import subprocess
 
 # Global variables.
@@ -39,6 +39,7 @@
 
 if not os.path.exists(builddir_):
     os.makedirs(builddir_)
+
 
 numCores_ = multiprocessing.cpu_count()
 
@@ -49,18 +50,10 @@
 
 
 class CMakeExtension(Extension):
+    # Reference: https://martinopilia.com/posts/2018/09/15/building-python-extension.html
     def __init__(self, name, **kwargs):
         # don't invoke the original build_ext for this special extension
-        import tempfile
-
-        # Create a temp file to create a dummy target. This build raises an
-        # exception because sources are empty. With python3 we can fix it by
-        # passing `optional=True` to the argument. With python2 there is no
-        # getaway from it.
-        f = tempfile.NamedTemporaryFile(suffix='.cpp', delete=False)
-        f.write(b'int main() { return 1; }')
-        Extension.__init__(self, name, sources=[f.name], **kwargs)
-        f.close()
+        Extension.__init__(self, name, sources=[], **kwargs)
 
 
 class TestCommand(Command):
@@ -79,14 +72,14 @@ def run(self):
         os.chdir(sdir_)
 
 
-class build_ext(_build_ext):
+class cmake_build_ext(build_ext):
     user_options = [
         ('with-boost', None, 'Use Boost Libraries (OFF)'),
         ('with-gsl', None, 'Use Gnu Scienfific Library (ON)'),
         ('with-gsl-static', None, 'Use GNU Scientific Library (static library) (OFF)'),
         ('debug', None, 'Build moose in debugging mode (OFF)'),
         ('no-build', None, 'DO NOT BUILD. (for debugging/development)'),
-    ] + _build_ext.user_options
+    ] + build_ext.user_options
 
     def initialize_options(self):
         # Initialize options.
@@ -97,12 +90,12 @@ def initialize_options(self):
         self.no_build = 0
         self.cmake_options = {}
         #  super().initialize_options()
-        _build_ext.initialize_options(self)
+        build_ext.initialize_options(self)
 
     def finalize_options(self):
         # Finalize options.
         #  super().finalize_options()
-        _build_ext.finalize_options(self)
+        build_ext.finalize_options(self)
         self.cmake_options['PYTHON_EXECUTABLE'] = os.path.realpath(sys.executable)
         self.cmake_options['VERSION_MOOSE'] = version_
         if self.with_boost:
@@ -122,7 +115,7 @@ def run(self):
         for ext in self.extensions:
             self.build_cmake(ext)
         #  super().run()
-        _build_ext.run(self)
+        build_ext.run(self)
 
     def build_cmake(self, ext):
         global numCores_
@@ -175,7 +168,7 @@ def build_cmake(self, ext):
         ]
     },
     install_requires=['numpy', 'matplotlib', 'vpython', 'pybind11'],
-    extra_requires={'dev': ['coverage', 'pytest', 'pytest-cov']},
-    ext_modules=[CMakeExtension('dummy', optional=True)],
-    cmdclass={'build_ext': build_ext, 'test': TestCommand},
+    extra_require={'dev': ['coverage', 'pytest', 'pytest-cov']},
+    ext_modules=[CMakeExtension('_moose', optional=True)],
+    cmdclass={'build_ext': cmake_build_ext, 'test': TestCommand},
 )