Merge remote-tracking branch 'greengroup/repackage'

This moves files into new pydas package, and means that software
using this library will need to be modified slightly:

    -from pydas import DASSL
    +from pydas.dassl import DASSL

It also removes DASPK2 and adds DASPK3.1, which allows
sensitivity analysis.

See
jwallen/PyDAS#11
jwallen/PyDAS#12

Author: rwest

.gitignore

@@ -32,3 +32,6 @@ make.inc
 /.project
 /.pydevproject
 /.settings
+
+# DASPK3.1 source files
+daspk31/*

Makefile

@@ -10,42 +10,49 @@ CYTHON_FLAGS=--inplace
 
 -include make.inc
 
-.PHONY: DASSL DASPK DASPK31 DASKR cython clean 
+.PHONY: DASSL DASPK31 DASKR cython clean 
 
-all: DASSL DASPK DASKR cython
+all: DASSL DASPK31 DASKR cython
 
-daspk: DASPK31 cython-daspk
+dassl: DASSL cython
 
-cython-daspk:
-	python setup.py build_ext daspk $(CYTHON_FLAGS)
+daspk: DASPK31 cython
 
-cython: DASSL DASPK DASKR pydas.pyx
+cython:
+ifeq (,$$(wildcard daspk31/solver/ddaspk.o))
+	# DASPK3.1 was not compiled. Cythonize the wrapper for only DASSL.
 	python setup.py build_ext $(CYTHON_FLAGS)
+else
+	# Cythonize both DASSL and DASPK3.1 wrappers
+	python setup.py build_ext daspk $(CYTHON_FLAGS)
+endif
+
 
-install: DASSL DASPK DASKR cython
+install: DASSL DASPK31 DASKR cython
+ifeq (,$$(wildcard pydas/daspk.so))
+	# the file "pydas/daspk.so" does not exist, so don't install daspk
 	python setup.py install
+	@echo "NOTE: Installed without DASPK, because it had not been compiled."
+else
+	# the file "pydas/daspk.so" does exist, so install daspk
+	python setup.py daspk install
+endif
 
 DASSL:
 	$(MAKE) -C dassl F77=$(F77)
 
-DASPK:
-	$(MAKE) -C daspk F77=$(F77)
-
 DASPK31:
 	$(MAKE) -C daspk31 F77=$(F77)
 
 DASKR:
 	$(MAKE) -C daskr F77=$(F77)
 
-clean: clean-DASSL clean-DASPK clean-DASPK31 clean-DASKR clean-cython
+clean: clean-DASSL clean-DASPK31 clean-DASKR clean-cython
 	rm -rf build
 
 clean-DASSL:
 	$(MAKE) -C dassl clean
 
-clean-DASPK:
-	$(MAKE) -C daspk clean
-
 clean-DASPK31:
 	$(MAKE) -C daspk31 clean
 
@@ -54,20 +61,16 @@ clean-DASKR:
 
 clean-cython:
 	python setup.py clean $(CLEAN_FLAGS)
-	rm -f *.so *.pyc *.c
+	rm -f pydas/*.so pydas/*.pyc pydas/*.c pydas/*.html
 
 help:
 	@echo ""
 	@echo "This makefile can be used to build PyDAS and its dependencies."
 	@echo ""
 	@echo "Typing \`make\` with no arguments will compile all three DAE solvers (DASSL,"
-	@echo "DASPK, and DASKR) to static libraries and compile the PyDAS Python modules"
-	@echo "that provide the Python interface to these solvers."
-	@echo ""
-	@echo "Typing \`make daspk\` after typing \`make\` will then additionally compile 
-	@echo "the optional DASPK 3.1 solver as well as the cython module pydaspk associated with it."
-	@echo "The DASPK 3.1 fortran source files must first be downloaded externally and placed"
-	@echo "in the daspk31 folder."
+	@echo "DASPK3.1, and DASKR) to static libraries and compile the PyDAS Python modules"
+	@echo "that provide the Python interface to these solvers. Note that one must agree"
+	@echo "to download the DASPK3.1 source code externally to compile the DASPK wrapper."
 	@echo ""
 	@echo "Typing \`make clean\` will delete all of the intermediate build files,"
 	@echo "compiled libraries, and compiled Python modules for all three DAE solvers and"
@@ -77,10 +80,9 @@ help:
 	@echo "<target> is one of:"
 	@echo ""
 	@echo "    DASSL    to compile the DASSL solver"
-	@echo "    DASPK    to compile the DASPK solver"   
 	@echo "    DASPK31    to compile the DASPK31 solver"   
 	@echo "    DASKR    to compile the DASKR solver"
 	@echo "    cython   to compile the PyDAS Python wrapper module for DASSL"
-	@echo "    cython-daspk   to compile the PyDAS Python wrapper module for both DASSL and DASPK3.1"
+	@echo "             and DASPK3.1 (if it was compiled)"
 	@echo ""
 

README.rst

@@ -7,12 +7,19 @@ Introduction
 
 PyDAS provides a means for Python code to utilize several notable Fortran-based
 differential algebraic system solvers from Python code. The solvers made
-available -- DASSL, DASPK, and DASKR -- are all publicly-available from 
+available -- DASSL and DASKR -- are all publicly-available from 
 `Netlib <http://www.netlib.org/ode/>`_, and are distributed with PyDAS. PyDAS
 provides a Python extension type for each solver, which in turn provides a
 Pythonic means of setting the solver options, providing residual and jacobian
 functions, and running the solver.
 
+In addition, PyDAS also provides a wrapper to the DASPK3.1 solver, which
+has native sensitivity analysis. The source code for DASPK3.1 is subject to
+copyright restrictions but is available for research purposes. Due to these
+restrictions, it is up to the user to download these source files manually 
+(or agree to download them during the prompt given when compiling the wrappers).
+Please see the README file inside the daspk31/ folder for more details.  
+
 The DASSL, DASPK, and DASKR solvers are all substantially more robust than
 VODE, the solver used within the ODE solver functionality provided by 
 `SciPy <http://www.scipy.org/>`_.
@@ -71,41 +78,52 @@ Installation
 
 .. note:: 
 
-    Currently only the DASSL solver has been wrapped. The installation 
-    scripts therefore only build and install the DASSL wrapper by default.
+    Currently only the DASSL and DASPK3.1 solvers have been wrapped. 
+    The installation scripts build and install the DASSL wrapper and the
+    DASPK wrapper (unless the DASPK3.1 fortran code was not compiled.)
 
 Windows
 -------
 
-The provided batch scripts will compile all of the solvers and the PyDAS
-wrapper code. These scripts presume that you have the 32-bit version of the
+The provided make.bat batch script will compile the DASSL solver and the PyDAS
+wrapper code. Use the make_daspk.bat script to compile the DASPK3.1 solver and the
+DASPK wrapper code.  Make sure you have manually downloaded the DASPK3.1 source
+files into the daspk31 folder.  See the daspk31/README file for more details.
+These scripts presume that you have the 32-bit version of the
 MinGW C and Fortran compilers installed. Once you have run the batch script,
 you can install PyDAS into your Python packages if you desire by running the
 following command from the base package directory:
 
     > python setup.py install
 
+Use the following command if you want to install both the DASSL and DASPK wrappers:
+
+    > python setup.py daspk install 
+
 Linux
 -----
 
-A Makefile has been provided that can be used to compile all of the solvers
-and the PyDAS wrapper code. To use, invoke the following command from the
+A Makefile has been provided that can be used to compile the DASSL solver and
+DASSL wrapper code. To use, invoke the following command from the
 base package directory::
 
     $ make
 
 This command will build PyDAS in-place, rather than installing it to your
-Python package directory. If you wish to formall install PyDAS, run the
+Python package directory.
+
+If you wish to formally install PyDAS, run the
 following command from the base package directory after the ``make`` command
 (you may need root privileges for this)::
 
-    $ python setup.py install
+    $ make install
 
 You may wish to write a file `make.inc` that sets certain variables used by
 the Makefiles (e.g. the Fortran compiler). An example of such a file, 
 `make.inc.example`, has been provided.
 
 
+
 Mac OS X
 --------
 
@@ -115,15 +133,14 @@ Homebrew (http://brew.sh) is an easy way to get gfortran::
 
 But your system may still not be able to find the correct `libgfortran.a` library file
 (see https://github.com/mxcl/homebrew/issues/8539 ). Also, there are some problems
-linking with `clang`, so you need to make it link with `gcc`. This one-liner should
+linking with `clang`, so you need to make it link with `gcc`. This should
 build and install, assuming you have NumPy, Cython, etc. all set up::
 
-    $ LIBRARY_PATH=/usr/local/lib/gcc LDSHARED='gcc -bundle -undefined dynamic_lookup -arch x86_64' make F77=gfortran install
-
-Or perhaps, with a newer version of Homebrew / Python / gfortran / NumPy / Cython, it will be a simple::
-
-    $ LIBRARY_PATH=/usr/local/Cellar/gfortran/4.8.0/gfortran/lib make F77=gfortran
+    $ export LIBRARY_PATH=$(dirname $(gfortran -print-libgcc-file-name))
+    $ make
+    $ make install
 
+Although at one stage it also required ``LDSHARED='gcc -bundle -undefined dynamic_lookup -arch x86_64'``.
 It seems to keep on changing. If you have difficulty, check the
 `issue tracker <https://github.com/jwallen/PyDAS/issues/>`_, and if you solve
 your difficulty, please share your successful approach.