playing with gfortran static build

PySCeS · May 22, 2020 · 5af2cff · 5af2cff
1 parent d8cb40a
commit 5af2cff
Show file tree

Hide file tree

Showing 5 changed files with 84 additions and 40 deletions.
diff --git a/packaging/conda/VS2019_gfortran8_build.md b/packaging/conda/VS2019_gfortran8_build.md
@@ -0,0 +1,36 @@
+Building with VS 2019-C++  and MINGW64-gfortran 8.1
+
+* It appears that for newer Pythons one should use Visual C++ as a compiler, rather than MINGW64-GCC.
+* For newer versions of numpy, you apparently need a recent version of MINGW64-gfortran. The one that comes with Anaconda (as part of the mingw package) is 4.7.0 which does not work!
+
+Here is how I have managed to build a wheel for Python 3.7 that seems to work:
+
+* I have Visual Studio 2017 installed for C++ stuff, however, the VS build tools are available for free. Try here for download details: https://wiki.python.org/moin/WindowsCompilers>
+** Anaconda might also have the VC build tools (package vc) but I have never used it.
+* Create a conda environment: conda create -n "pscbuild" python=3.7 ipython pip wheel numpy scipy matplotlib
+** Alternatively, if using an existing environment, make sure the Anaconda mingw package is not installed (remove it now)
+* I unpacked MINGW64 that I obtained here (https://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Personal%20Builds/mingw-builds/8.1.0/threads-posix/seh/x86_64-8.1.0-release-posix-seh-rt_v6-rev0.7z/download) based on the information I found here (https://stackoverflow.com/questions/48826283/compile-fortran-module-with-f2py-and-python-3-6-on-windows-10)
+* In a terminal I then activated the conda environment and added the new GCC to the path (making sure there was no existing gcc)
+** conda activate pscbuild
+** path=c:\tools\mingw64\bin;%path%
+* Build/install PySCeS with python setup.py build --compiler=msvc --fcompiler=gfortran install bdist_wheel
+
+For conda build we need the following:
+
+* Open a VS2015 terminal (v10) and change to your build directory
+** path=c:\tools\mingw64\bin;%path%
+** path="c:\Program Files (x86)\Windows Kits\10\bin\10.0.18362.0\x64";%path%
+* 3.6 <= Python < 3.8
+** conda build --python 3.6 --numpy 1.15 .
+** conda build --python 3.7 --numpy 1.15 .
+* Python >= 3.8
+** conda build --python 3.8 --numpy 1.18 .
+
+* cleanup and upload
+** conda build purge
+** conda clean --all
+** anaconda upload -u pysces-builds\*
+
+
+
+Brett 2020
diff --git a/packaging/conda/bld.bat b/packaging/conda/bld.bat
@@ -1,4 +1,4 @@
-copy ..\_h_env\libs\libpython27.dll.a ..\_h_env\libs\libpython27.a
-copy ..\_h_env\libs\libmsvcr90.dll.a ..\_h_env\libs\libmsvcr90.a
-"%PYTHON%" setup.py build --compiler=mingw32 install --record=record.txt
+::copy ..\_h_env\libs\libpython27.dll.a ..\_h_env\libs\libpython27.a
+::copy ..\_h_env\libs\libmsvcr90.dll.a ..\_h_env\libs\libmsvcr90.a
+"%PYTHON%" setup.py build --compiler=msvc --fcompiler=gfortran install --record=record.txt
 if errorlevel 1 exit 1
diff --git a/packaging/conda/conda_build.txt b/packaging/conda/conda_build.txt
@@ -1,26 +1,18 @@
-Open an anaconda prompt
+Open a VS2015 build prompt
 
-cd to conda build files
+path=c:\tools\mingw64\bin;%path%
+path="c:\Program Files (x86)\Windows Kits\10\bin\10.0.18362.0\x64";%path%
 
-Optional: update build version and SVN information in meta.yaml
- conda update conda
- conda update conda-build
+Run to build
+  conda build -c sbmlteam --python 3.6 --numpy 1.15 .
+  conda build -c sbmlteam --python 3.7 --numpy 1.15 .
 
-Run to build (note the upload command path e.g. anaconda upload C:\Anaconda\conda-bld\win-64\pysces-0.9.5-py27hd5793fb_1.tar.bz2):
- conda build -c sbmlteam .
-
-New hacks to workaround conda-build enhancements in 2019.1
- conda update conda-build
- conda clean --all
- conda build --numpy 1.15 --python 2.7 -c sbmlteam .
- conda build --numpy 1.15 --python 3.6 -c sbmlteam .
- conda build --numpy 1.15 --python 3.7 -c sbmlteam .
  conda clean --all
  conda build purge
 
- anaconda upload -u pysces C:\Anaconda\conda-bld\win-64\pysces-0.9.7-py27_2.tar.bz2
- anaconda upload -u pysces C:\Anaconda\conda-bld\win-64\pysces-0.9.7-py36_2.tar.bz2
- anaconda upload -u pysces C:\Anaconda\conda-bld\win-64\pysces-0.9.7-py37_2.tar.bz2
+ anaconda upload -u pysces 
+ anaconda upload -u pysces c:\Anaconda3\conda-bld\win-64\pysces-0.9.8-py37h6ebd63d_1.tar.bz2
+
 
 
 NOTES:

diff --git a/packaging/conda/meta.yaml b/packaging/conda/meta.yaml
@@ -4,6 +4,7 @@ package:
 
 source:
   git_url: https://github.com/PySCeS/pysces.git
+#  path: pysces-src
 
 build:
   number: 1
@@ -13,24 +14,20 @@ requirements:
   build:
     - python
     - setuptools
-    - numpy=1.15
+    - numpy
     - libpython
-    - mingw
     - scipy
     - matplotlib
     - nose
   run:
     - python
     - setuptools
-    - numpy>=1.15
+    - numpy
     - libpython
     - scipy
     - matplotlib
-    - nose  
-    - python-libsbml
-
+    - nose
 
-
 about:
   home: http://pysces.sourceforge.net
   license: BSD

diff --git a/setup.py b/setup.py
@@ -20,9 +20,11 @@
 from __future__ import absolute_import
 
 __doc__ = "PySCeS: the Python Simulator for Cellular Systems setup file"
-__version__ = '0.9.8post1'
+__version__ = '0.9.8'
 
 import os, re
+import sysconfig
+
 import fileinput
 import shutil
 try:
@@ -176,10 +178,26 @@ def writeConfig(local_path, config={}):
 #PySCeS modules
 mymodules = []
 
+# extra compile args for FORTRAN code that should meand that gfortran libraries are statically compiled into the pyd
+if os.sys.platform == 'win32':
+    #extra_f77_compile_args = ["-static-libgcc", "-static-libgfortran"]
+    extra_f77_compile_args = ["-static", "-static-libgcc", "-static-libgfortran"]
+else:
+    extra_f77_compile_args = []
+
+print('extra_f77_compile_args: ', extra_f77_compile_args)
+
+
 if pitcon:
     print('\nBuilding pitcon')
     extpath = os.path.join('pysces', 'pitcon')
-    pitcon = Extension('pysces.pitcon.pitcon',[os.path.join(extpath,'pitcon.pyf'),os.path.join(extpath,'pcon61subd.f'),os.path.join(extpath,'dpcon61.f'),os.path.join(extpath,'dpcon61w.f')])
+    pitcon = Extension('pysces.pitcon.pitcon', sources=[os.path.join(extpath,'pitcon.pyf'),
+                                                        os.path.join(extpath,'pcon61subd.f'),
+                                                        os.path.join(extpath,'dpcon61.f'),
+                                                        os.path.join(extpath,'dpcon61w.f')],
+                                               extra_f77_compile_args=extra_f77_compile_args
+
+                       )
     mymodules.append(pitcon)
     #mydata_files.append((os.path.join('pysces','pitcon'), [os.path.join(local_path, 'pysces', 'pitcon','readme.txt'), os.path.join(local_path, 'pysces', 'pitcon','readme.txt')]))
 else:
@@ -198,11 +216,13 @@ def writeConfig(local_path, config={}):
         ##  elif os.sys.byteorder == 'big':
             ##  shutil.copyfile(os.path.join(extpath,'nleq2_big.f'), os.path.join(extpath,'nleq2.f'))
     extpath = os.path.join('pysces', 'nleq2')
-    nleq2 = Extension('pysces.nleq2.nleq2',[os.path.join(extpath,'nleq2.pyf'),\
-            os.path.join(extpath,'nleq2.f'), os.path.join(extpath,'linalg_nleq2.f'),\
-            os.path.join(extpath,'zibmon.f'), os.path.join(extpath,'zibsec.f'),\
-            os.path.join(extpath,'zibconst.f'), os.path.join(extpath,'wnorm.f')
-            ])
+    nleq2 = Extension('pysces.nleq2.nleq2', sources=[os.path.join(extpath,'nleq2.pyf'),
+                                                     os.path.join(extpath,'nleq2.f'),
+                                                     os.path.join(extpath,'linalg_nleq2.f'),
+                                                     os.path.join(extpath,'zibmon.f'), os.path.join(extpath,'zibsec.f'),
+                                                     os.path.join(extpath,'zibconst.f'), os.path.join(extpath,'wnorm.f')],
+                                            extra_f77_compile_args=extra_f77_compile_args
+                      )
     mymodules.append(nleq2)
     mypackages.append('pysces.nleq2')
 else:
@@ -215,9 +235,9 @@ def writeConfig(local_path, config={}):
 # Data files to copy
 mydata_files.append((os.path.join('pysces'), [os.path.join('pysces','pyscfg.ini')]))
 mydata_files.append(('',[os.path.join('pysces','pysces.pth')]))
-mydata_files.append((os.path.join('pysces','docs'), [os.path.join('pysces','docs','userguide.pdf')]))
+#mydata_files.append((os.path.join('pysces','docs'), [os.path.join('pysces','docs','userguide.pdf')]))  # bgoli2020: does not exist anymore
 mydata_files.append((os.path.join('pysces','examples'), [os.path.join('pysces','examples',examplefile) for examplefile in os.listdir(os.path.join(local_path,'pysces','examples'))]))
-##not sure if this is necessary anymore, removed to test
+## not sure if this is necessary anymore now that I am using static gfortran linking
 if os.sys.platform == 'win32':
     mydata_files.append((os.path.join('pysces','win32'), [os.path.join('pysces','win32','libquadmath-0.dll'), os.path.join('pysces','win32','libgfortran-3.dll'),\
     os.path.join('pysces','win32','libgcc_s_seh-1.dll'), os.path.join('pysces','win32','libwinpthread-1.dll')]))
@@ -248,13 +268,12 @@ def writeConfig(local_path, config={}):
     maintainer = "Brett G. Olivier",
     maintainer_email = "bgoli@users.sourceforge.net",
     url = "http://pysces.sourceforge.net",
-    download_url = "http://pysces.sourceforge.net/download.html",
+    download_url = "https://pypi.org/project/pysces/#files",
     license = "New BSD style",
     keywords = "computational systems biology, modelling, simulation, systems biology" ,
     zip_safe = False,
-    #requires = ['numpy','scipy','matplotlib'],
-    install_requires = ['numpy','scipy','matplotlib','python-libsbml','nose'],
-    platforms = ["Windows", "Linux", "macOS"],
+    install_requires = ['numpy','scipy','matplotlib','nose'],
+    platforms = ["Windows", "POSIX", "Max OSX"],
     classifiers = [
     'Development Status :: 5 - Production/Stable',
     'Development Status :: 6 - Mature',