clang-format after moving to c++ (#96)

- previous PR from Jeremy didn't update source style
- disable indentation of namespaces

.clang-format

@@ -63,7 +63,7 @@ KeepEmptyLinesAtTheStartOfBlocks: false
 MacroBlockBegin: ''
 MacroBlockEnd:   ''
 MaxEmptyLinesToKeep: 1
-NamespaceIndentation: All
+NamespaceIndentation: None
 ObjCBlockIndentWidth: 2
 ObjCSpaceAfterProperty: false
 ObjCSpaceBeforeProtocolList: false

CMakeLists.txt

@@ -185,7 +185,17 @@ if(CLANG_FORMAT_FOUND)
 
     # exclude ezoption header file
     list(REMOVE_ITEM SRC_FILES_FOR_CLANG_FORMAT
-        "${PROJECT_SOURCE_DIR}/coreneuron/utils/ezoption/ezOptionParser.hpp")
+        ${PROJECT_SOURCE_DIR}/coreneuron/utils/ezoption/ezOptionParser.hpp
+        ${PROJECT_SOURCE_DIR}/coreneuron/utils/endianness.h
+        ${PROJECT_SOURCE_DIR}/coreneuron/utils/swap_endian.h)
+
+    # exclude random123 files
+    file (GLOB_RECURSE RANDOM123_FILES
+        ${PROJECT_SOURCE_DIR}/coreneuron/utils/randoms/Random123/*.cpp
+        ${PROJECT_SOURCE_DIR}/coreneuron/utils/randoms/Random123/*.h)
+    foreach (R123_PATH ${RANDOM123_FILES})
+        list (REMOVE_ITEM SRC_FILES_FOR_CLANG_FORMAT ${R123_PATH})
+    endforeach(R123_PATH)
 
     add_custom_target(formatsource COMMAND ${CMAKE_COMMAND}
         -DSOURCE_FILES:STRING="${SRC_FILES_FOR_CLANG_FORMAT}"

README.md

@@ -239,7 +239,7 @@ If you have installed `clang-format`, you can reformat/reindent generated .c fil
 make formatbuild
 ```
 
-The `.clang-format` file in the source repository is compatible with version 3.9 and 4.0.
+The `.clang-format` file in the source repository is compatible with version 5.0.
 
 ## License
 * See LICENSE.txt

coreneuron/coreneuron.h

@@ -67,6 +67,6 @@ extern void nrn_cur_ion(NrnThread* _nt, Memb_list* ml, int type);
 extern void nrn_alloc_ion(double* data, Datum* pdata, int type);
 extern void second_order_cur(NrnThread* _nt, int secondorder);
 
-} //namespace coreneuron
+}  // namespace coreneuron
 
 #endif

coreneuron/engine.h

@@ -4,9 +4,9 @@
 #ifdef __cplusplus
 extern "C" {
 #endif
-    extern int solve_core (int argc, char** argv);
+extern int solve_core(int argc, char** argv);
 #ifdef __cplusplus
-    } 
+}
 #endif
 
 #endif

coreneuron/mech/cfile/cabvars.h

@@ -26,7 +26,6 @@ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 THE POSSIBILITY OF SUCH DAMAGE.
 */
 
-
 namespace coreneuron {
 
 extern void capacitance_reg(void), _passive_reg(void),
@@ -43,4 +42,4 @@ static void (*mechanism[])(void) = {/* type will start at 3 */
 #endif
                                     _stim_reg, _hh_reg, _expsyn_reg, _netstim_reg, _exp2syn_reg, 0};
 
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/mech/mod2c_core_thread.h

@@ -139,6 +139,6 @@ extern void _modl_set_dt_thread(double, NrnThread*);
 
 void nrn_sparseobj_copyto_device(SparseObj* so);
 
-} // namespace coreneuron
+}  // namespace coreneuron
 
 #endif

coreneuron/nrnconf.h

@@ -35,7 +35,6 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <errno.h>
 #include <stdint.h>
 
-
 namespace coreneuron {
 
 #define NRNBBCORE 1
@@ -57,7 +56,6 @@ typedef char Symbol;
 #define VEC_AREA(i) (_nt->_actual_area[(i)])
 #define VECTORIZE 1
 
-
 extern double celsius;
 
 extern double t, dt;
@@ -93,6 +91,6 @@ typedef struct Point_process {
 
 extern char* pnt_name(Point_process* pnt);
 
-} //namespace coreneuron
+}  // namespace coreneuron
 
 #endif

coreneuron/nrniv/balance.cpp

@@ -103,4 +103,4 @@ size_t warp_balance(size_t ncell, VecTNode& nodevec) {
 
     return nwarp;
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/cellorder.cpp

@@ -683,5 +683,5 @@ void solve_interleaved(int ith) {
         solve_interleaved1(ith);
     }
 }
-} //namespace coreneuron 
+}  // namespace coreneuron
 #endif

coreneuron/nrniv/cellorder.h

@@ -57,5 +57,5 @@ void copy_array(T*& dest, T* src, size_t n) {
 #if INTERLEAVE_DEBUG
 void mk_cell_indices();
 #endif
-} //namespace coreneuron
+}  // namespace coreneuron
 #endif

coreneuron/nrniv/cellorder1.cpp

@@ -669,4 +669,4 @@ for (int i = 0; i <= nwarp; ++i){
 }
 #endif
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/cellorder2.cpp

@@ -530,4 +530,4 @@ void group_order2(VecTNode& nodevec, size_t groupsize, size_t ncell) {
     std::sort(nodevec.begin() + ncell, nodevec.end(), final_nodevec_cmp);
     set_nodeindex(nodevec);
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/cvodestb.cpp

@@ -35,7 +35,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 
 #include "coreneuron/nrniv/nrn_acc_manager.h"
 
-namespace coreneuron{
+namespace coreneuron {
 
 // for fixed step thread
 // check thresholds and deliver all (including binqueue) events
@@ -112,4 +112,4 @@ int at_time(NrnThread* nt, double te) {
     }
     return 0;
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/global_vars.cpp

@@ -106,4 +106,4 @@ void set_globals(const char* path) {
     delete n2v;
     n2v = NULL;
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/have2want.h

@@ -260,4 +260,4 @@ static void have_to_want(HAVEWANT_t* have,
     recv_from_have_cnt = want_s_cnt;
     recv_from_have_displ = want_s_displ;
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/ivocvect.cpp

@@ -42,7 +42,7 @@ double* vector_vec(IvocVect* v) {
  * Retro-compatibility implementations
  */
 void* vector_new1(int n) {
-    return (void*) (new IvocVect(n));
+    return (void*)(new IvocVect(n));
 }
 
 int vector_capacity(void* v) {
@@ -52,4 +52,4 @@ double* vector_vec(void* v) {
     return ((IvocVect*)v)->data();
 }
 
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/ivocvect.h

@@ -29,7 +29,6 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #ifndef ivoc_vector_h
 #define ivoc_vector_h
 
-
 #include <stdio.h>
 #include "coreneuron/nrniv/nrnmutdec.h"
 namespace coreneuron {
@@ -93,6 +92,6 @@ extern void* vector_new1(int n);
 extern int vector_capacity(void* v);
 extern double* vector_vec(void* v);
 
-} //namespace coreneuron
+}  // namespace coreneuron
 
 #endif

coreneuron/nrniv/main1.cpp

@@ -57,7 +57,6 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <string.h>
 #include <climits>
 
-
 #if 0
 #include <fenv.h>
 #define NRN_FEEXCEPT (FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW)
@@ -242,7 +241,6 @@ void call_prcellstate_for_prcellgid(int prcellgid, int compute_gpu, int is_init)
     }
 }
 
-
 /* perform forwardskip and call prcellstate for prcellgid */
 void handle_forward_skip(double forwardskip, int prcellgid) {
     double savedt = dt;
@@ -267,11 +265,10 @@ void handle_forward_skip(double forwardskip, int prcellgid) {
 const char* nrn_version(int) {
     return "version id unimplemented";
 }
-} //namespace coreneuron
+}  // namespace coreneuron
 
 using namespace coreneuron;
 extern "C" int solve_core(int argc, char** argv) {
-
 #if NRNMPI
     nrnmpi_init(1, &argc, &argv);
 #endif
@@ -393,4 +390,3 @@ extern "C" int solve_core(int argc, char** argv) {
 
     return 0;
 }
-

coreneuron/nrniv/memory.h

@@ -34,48 +34,48 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/nrniv/nrn_assert.h"
 
 namespace coreneuron {
-    /** Independent function to compute the needed chunkding,
-        the chunk argument is the number of doubles the chunk is chunkded upon.
-    */
-    template <int chunk>
-    inline int soa_padded_size(int cnt, int layout) {
-        int imod = cnt % chunk;
-        if (layout == 1)
-            return cnt;
-        if (imod) {
-            int idiv = cnt / chunk;
-            return (idiv + 1) * chunk;
-        }
+/** Independent function to compute the needed chunkding,
+    the chunk argument is the number of doubles the chunk is chunkded upon.
+*/
+template <int chunk>
+inline int soa_padded_size(int cnt, int layout) {
+    int imod = cnt % chunk;
+    if (layout == 1)
         return cnt;
+    if (imod) {
+        int idiv = cnt / chunk;
+        return (idiv + 1) * chunk;
     }
+    return cnt;
+}
 
-    /** Check for the pointer alignment.
-     */
-    inline bool is_aligned(void* pointer, size_t alignment) {
-        return (((uintptr_t)(const void*)(pointer)) % (alignment) == 0);
-    }
+/** Check for the pointer alignment.
+ */
+inline bool is_aligned(void* pointer, size_t alignment) {
+    return (((uintptr_t)(const void*)(pointer)) % (alignment) == 0);
+}
 
-    /** Allocate the aligned memory.
-     */
-    inline void* emalloc_align(size_t size, size_t alignment) {
-        void* memptr;
-        nrn_assert(posix_memalign(&memptr, alignment, size) == 0);
-        nrn_assert(is_aligned(memptr, alignment));
-        return memptr;
-    }
+/** Allocate the aligned memory.
+ */
+inline void* emalloc_align(size_t size, size_t alignment) {
+    void* memptr;
+    nrn_assert(posix_memalign(&memptr, alignment, size) == 0);
+    nrn_assert(is_aligned(memptr, alignment));
+    return memptr;
+}
 
-    /** Allocate the aligned memory and set it to 1.
-     */
-    inline void* ecalloc_align(size_t n, size_t alignment, size_t size) {
-        void* p;
-        if (n == 0) {
-            return (void*)0;
-        }
-        nrn_assert(posix_memalign(&p, alignment, n * size) == 0);
-        nrn_assert(is_aligned(p, alignment));
-        memset(p, 1, n * size);  // Avoid native division by zero (cyme...)
-        return p;
+/** Allocate the aligned memory and set it to 1.
+ */
+inline void* ecalloc_align(size_t n, size_t alignment, size_t size) {
+    void* p;
+    if (n == 0) {
+        return (void*)0;
     }
+    nrn_assert(posix_memalign(&p, alignment, n * size) == 0);
+    nrn_assert(is_aligned(p, alignment));
+    memset(p, 1, n * size);  // Avoid native division by zero (cyme...)
+    return p;
+}
 }  // namespace coreneuron
 
 #endif

coreneuron/nrniv/mk_mech.cpp

@@ -172,4 +172,4 @@ const char* nrn_get_mechname(int type) {
     }
     return NULL;
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/multisend.cpp

@@ -466,4 +466,4 @@ void nrn_multisend_setup() {
 #endif
 }
 #endif  // NRN_MULTISEND
-} // namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/multisend.h

@@ -19,5 +19,5 @@ void nrn_multisend_cleanup();
 void nrn_multisend_setup();
 
 void nrn_multisend_setup_targets(int use_phase2, int*& targets_phase1, int*& targets_phase2);
-} //namespace coreneuron
+}  // namespace coreneuron
 #endif  // nrnmultisend_h

coreneuron/nrniv/multisend_setup.cpp

@@ -702,5 +702,5 @@ static int setup_target_lists(int use_phase2, int** r_return) {
     *r_return = r;
     return sz;
 }
-} //namespace coreneuron
+}  // namespace coreneuron
 #endif  // NRN_MULTISEND

coreneuron/nrniv/netcon.h

@@ -183,5 +183,5 @@ class NetParEvent : public DiscreteEvent {
 
     virtual void pr(const char*, double t, NetCvode*);
 };
-} //namespace coreneuron
+}  // namespace coreneuron
 #endif

coreneuron/nrniv/netcvode.cpp

@@ -810,4 +810,4 @@ void NetCvode::deliver_net_events(NrnThread* nt) {  // for default method
         (*net_buf_receive_[i])(nt);
     }
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/netcvode.h

@@ -92,5 +92,5 @@ class NetCvode {
     void init_events();
     void point_receive(int, Point_process*, double*, double);
 };
-} //namespace coreneuron
+}  // namespace coreneuron
 #endif

coreneuron/nrniv/netpar.cpp

@@ -914,4 +914,4 @@ int nrnmpi_spike_compress(int nspike, bool gid_compress, int xchng_meth) {
     return 0;
 #endif
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/node_permute.cpp

@@ -329,4 +329,4 @@ void permute_nodeindices(Memb_list* ml, int* p) {
     invert_permute(ml->_permute, ml->nodecount);
     permute_ptr(ml->nodeindices, ml->nodecount, ml->_permute);
 }
-} //namespace coreneuron
+}  // namespace coreneuron

coreneuron/nrniv/node_permute.h

@@ -18,5 +18,5 @@ void permute_ml(Memb_list* ml, int type, NrnThread& nt);
 int nrn_index_permute(int, int type, Memb_list* ml);
 
 int* inverse_permute(int* p, int n);
-} //namespace coreneuron
+}  // namespace coreneuron
 #endif

coreneuron/nrniv/nrn_acc_manager.cpp

@@ -991,5 +991,4 @@ void nrn_sparseobj_copyto_device(SparseObj* so) {
     }
 #endif
 }
-} //namespace coreneuron
-
+}  // namespace coreneuron

coreneuron/nrniv/nrn_acc_manager.h

@@ -20,5 +20,5 @@ void update_net_receive_buffer(NrnThread* _nt);
 void realloc_net_receive_buffer(NrnThread* nt, Memb_list* ml);
 void update_net_send_buffer_on_host(NrnThread* nt, NetSendBuffer_t* nsb);
 
-} //namespace coreneuron
+}  // namespace coreneuron
 #endif  // _nrn_device_manager_