updated todo

#TODO.org#

+* Todo list for the binary_c-python
+** Logging functionality:
+Idea is to be able to give a string via python that will be used in the through the libbinary_c.so so that log_every_timestep.c 
+
+** General:
+*** DONE Get a more reliable way of loading the default values (running a ./tbse echo or something?)
+    CLOSED: [2019-10-29 Tue 17:44]
+*** DONE make routine that reads out all the lines, splits them into pieces and reads out the correct key
+    CLOSED: [2019-10-29 Tue 17:43]
+*** TODO Put header and other source files in a dedicated directory
+*** TODO Use sphinx or read the docs for auto generation of documentation
+*** TODO Have the compiled files put into a build directory
+*** TODO add pythonpath thing to readme
+*** TODO make script that will set up binaryc automatically so that this can become an out of the box thing
+*** TODO Test the importing of this code from different places
+** Population ideas
+*** TODO Queuing system and some multiprocessing to run many systems
+*** TODO Consider rewriting the work that perl does

.#TODO.org

+david@david-Lenovo-IdeaPad-S340-14IWL.21326:1572369068
\ No newline at end of file

TODO.org

 * Todo list for the binary_c-python
----------------------
-** General:
-** DONE Get a more reliable way of loading the default values (running a ./tbse echo or something?)
-   CLOSED: [2019-10-29 Tue 17:44]
-
+** Logging functionality:
+Idea is to be able to give a string via python that will be used in the 
 
 
-** DONE make routine that reads out all the lines, splits them into pieces and reads out the correct key
-   CLOSED: [2019-10-29 Tue 17:43]
-** TODO Put header and other source files in a dedicated directory
-** TODO Use sphinx or read the docs for auto generation of documentation
-** TODO Have the compiled files put into a build directory
-** TODO add pythonpath thing to readme
-** TODO make script that will set up binaryc automatically so that this can become an out of the box thing
-** TODO Test the importing of this code from different places
+** General:
+*** DONE Get a more reliable way of loading the default values (running a ./tbse echo or something?)
+    CLOSED: [2019-10-29 Tue 17:44]
+*** DONE make routine that reads out all the lines, splits them into pieces and reads out the correct key
+    CLOSED: [2019-10-29 Tue 17:43]
+*** TODO Put header and other source files in a dedicated directory
+*** TODO Use sphinx or read the docs for auto generation of documentation
+*** TODO Have the compiled files put into a build directory
+*** TODO add pythonpath thing to readme
+*** TODO make script that will set up binaryc automatically so that this can become an out of the box thing
+*** TODO Test the importing of this code from different places
 ** Population ideas
 *** TODO Queuing system and some multiprocessing to run many systems
 *** TODO Consider rewriting the work that perl does

binary_c_python.c

@@ -7,7 +7,7 @@
  * Remember: variables must be passed by references
  * (i.e. as pointers).
  *
- * See apitest.py for an expmple of how to use these functions.
+ * See apitest.py for an example of how to use these functions.
  *
  * See also
  * http://www-h.eng.cam.ac.uk/help/tpl/languages/mixinglanguages.html
@@ -230,4 +230,4 @@ static PyObject* binary_c_return_arglines(PyObject *self, PyObject *args)
     free(buffer);
     /* Return an object containing the arg list */
     return ret;
-}
+}
\ No newline at end of file

make_output.txt

-gcc -fPIC `/vol/ph/astro_code/dhendriks/binaryc/binary_c/binary_c-config --flags` -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src/ -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src/API    -c -o binary_c_python_api.o binary_c_python_api.c
-gcc -DBINARY_C=/vol/ph/astro_code/dhendriks/binaryc/binary_c -fPIC `/vol/ph/astro_code/dhendriks/binaryc/binary_c/binary_c-config --flags` -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src/ -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src/API   binary_c_python_api.c -c  -lbinary_c `/vol/ph/astro_code/dhendriks/binaryc/binary_c/binary_c-config --libs`  
-gcc -DBINARY_C=/vol/ph/astro_code/dhendriks/binaryc/binary_c -shared -o libbinary_c_api.so binary_c_python_api.o
+gcc -fPIC `/home/david/projects/binary_c_root/binary_c/binary_c-config --flags` -I/home/david/projects/binary_c_root/binary_c/src/ -I/home/david/projects/binary_c_root/binary_c/src/API    -c -o binary_c_python_api.o binary_c_python_api.c
+gcc -DBINARY_C=/home/david/projects/binary_c_root/binary_c -fPIC `/home/david/projects/binary_c_root/binary_c/binary_c-config --flags` -I/home/david/projects/binary_c_root/binary_c/src/ -I/home/david/projects/binary_c_root/binary_c/src/API   binary_c_python_api.c -c  -lbinary_c `/home/david/projects/binary_c_root/binary_c/binary_c-config --libs`  
+gcc -DBINARY_C=/home/david/projects/binary_c_root/binary_c -shared -o libbinary_c_api.so binary_c_python_api.o
 python3 setup.py build_ext --inplace 
 running build_ext
 building 'binary_c' extension
-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DALIGNSIZE=16 -DCPUFREQ=3600 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__HAVE_PERF_EVENTS__ -DGIT_REVISION=1:20190808:97d7029f -DGIT_URL=gitlab@gitlab.eps.surrey.ac.uk:ri0005/binary_c.git -DGIT_BRANCH=branch_david -D__HAVE_AVX__ -D__HAVE_DRAND48__ -D__HAVE_GSL__ -DUSE_GSL -D__HAVE_LIBBSD__ -D__HAVE_MALLOC_H__ -D__HAVE_PKG_CONFIG__ -D__HAVE_VALGRIND__ -D__SHOW_STARDATA__ -DBINARY_C_API_H=/vol/ph/astro_code/dhendriks/binaryc/binary_c/src/API/binary_c_API.h -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src -I/vol/ph/astro_code/dhendriks/binaryc/binary_c/src/API -I/vol/ph/astro_code/dhendriks/binaryc/binary_c -I/usr/include -I/user/HS128/dh00601/gsl/include -I/user/HS128/dh00601/.pyenv/versions/binaryc_py3.6.4/include -I/user/HS128/dh00601/.pyenv/versions/3.6.4/include/python3.6m -c binary_c_python.c -o build/temp.linux-x86_64-3.6/binary_c_python.o
-gcc -pthread -shared -L/user/HS128/dh00601/.pyenv/versions/3.6.4/lib -L/user/HS128/dh00601/.pyenv/versions/3.6.4/lib build/temp.linux-x86_64-3.6/binary_c_python.o -L/vol/ph/astro_code/dhendriks/binaryc/binary_c/src -L./ -L-L/vol/ph/astro_code/dhendriks/binaryc/binary_c -L-L/user/HS128/dh00601/gsl/lib -Wl,--enable-new-dtags,-R/vol/ph/astro_code/dhendriks/binaryc/binary_c/src -Wl,--enable-new-dtags,-R./ -Wl,--enable-new-dtags,-R-L/vol/ph/astro_code/dhendriks/binaryc/binary_c -Wl,--enable-new-dtags,-R-L/user/HS128/dh00601/gsl/lib -lbinary_c -lgsl -lgslcblas -lm -lbsd -lc -lm -ldl -lbinary_c_api -o /vol/ph/astro_code/dhendriks/binaryc/binary_c-python/binary_c.cpython-36m-x86_64-linux-gnu.so
+gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DALIGNSIZE=16 -DCPUFREQ=3900 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__DIFF_STARDATA__ -DGIT_REVISION=4519:20191029:e21f3501 -DGIT_URL=gitlab@gitlab.eps.surrey.ac.uk:ri0005/binary_c.git -DGIT_BRANCH=master -D__HAVE_AVX__ -D__HAVE_DRAND48__ -D__HAVE_GSL__ -DUSE_GSL -D__HAVE_MALLOC_H__ -D__HAVE_PKG_CONFIG__ -D__SHOW_STARDATA__ -DBINARY_C_API_H=/home/david/projects/binary_c_root/binary_c/src/API/binary_c_API.h -I/home/david/projects/binary_c_root/binary_c/src -I/home/david/projects/binary_c_root/binary_c/src/API -I/home/david/projects/binary_c_root/binary_c -I/usr/include -I/home/david/gsl/include -I/home/david/.pyenv/versions/3.6.4/include/python3.6m -c binary_c_python.c -o build/temp.linux-x86_64-3.6/binary_c_python.o
+gcc -pthread -shared -L/home/david/.pyenv/versions/3.6.4/lib -L/home/david/.pyenv/versions/3.6.4/lib build/temp.linux-x86_64-3.6/binary_c_python.o -L/home/david/projects/binary_c_root/binary_c/src -L./ -L-L/home/david/projects/binary_c_root/binary_c -L-L/home/david/gsl/lib -Wl,--enable-new-dtags,-R/home/david/projects/binary_c_root/binary_c/src -Wl,--enable-new-dtags,-R./ -Wl,--enable-new-dtags,-R-L/home/david/projects/binary_c_root/binary_c -Wl,--enable-new-dtags,-R-L/home/david/gsl/lib -lbinary_c -lgsl -lgslcblas -lm -lc -lm -ldl -lbinary_c_api -o /home/david/projects/binary_c_root/binary_c-python/binary_c.cpython-36m-x86_64-linux-gnu.so