busclique integration testing

added integration tests for the busclique submodule
* fixed several bugs in busclique c++
* corrected issue where clear_all_caches wasn't removing directories
* addressed a -Werror=format-security issue for printing messages with no arguments

include/busclique/biclique_cache.hpp

@@ -43,7 +43,7 @@ class yieldcache {
 template<typename topo_spec>
 class biclique_cache {
   public:
-    biclique_cache(const biclique_cache&) = delete; 
+    biclique_cache(const biclique_cache&) = delete;
     biclique_cache(biclique_cache &&) = delete;
     const cell_cache<topo_spec> &cells;
   private:
@@ -101,7 +101,7 @@ class biclique_cache {
                     for(size_t x0 = 0; x0 <= cells.topo.dim[1]-w; x0++)
                         next.set(y0, x0, 0, bundles.get_line_score(0, x0, y0, y0+h-1));
             }
-            for(size_t w = 2; w < cells.topo.dim[1]; w++) {
+            for(size_t w = 2; w <= cells.topo.dim[1]; w++) {
                 yieldcache prev = get(h, w-1);
                 yieldcache next = get(h, w);
                 for(size_t y0 = 0; y0 <= cells.topo.dim[0]-h; y0++) {
@@ -124,7 +124,7 @@ class biclique_cache {
                     for(size_t x0 = 0; x0 <= cells.topo.dim[1]-w; x0++)
                         next.set(y0, x0, 1, bundles.get_line_score(1, y0, x0, x0+w-1));
             }
-            for(size_t h = 2; h < cells.topo.dim[0]; h++) {
+            for(size_t h = 2; h <= cells.topo.dim[0]; h++) {
                 yieldcache prev = get(h-1, w);
                 yieldcache next = get(h, w);
                 for(size_t x0 = 0; x0 <= cells.topo.dim[1]-w; x0++) {
@@ -177,13 +177,20 @@ class biclique_yield_cache {
     vector<vector<bound_t>> biclique_bounds;
 
   public:
+    biclique_yield_cache(const biclique_yield_cache&) = delete; 
+    biclique_yield_cache(biclique_yield_cache &&) = delete;
+
     biclique_yield_cache(const cell_cache<topo_spec> &c,
                          const bundle_cache<topo_spec> &b, 
                          const biclique_cache<topo_spec> &bicliques) :
         cells(c),
         bundles(b),
-        rows(cells.topo.dim[0]*cells.topo.shore),
-        cols(cells.topo.dim[1]*cells.topo.shore),
+
+        //note: the role of rows and columns is reversed, because the indices
+        //are chainlengths in a given direction (not the number of chains)
+        rows(cells.topo.dim[1]*cells.topo.shore),
+        cols(cells.topo.dim[0]*cells.topo.shore),
+
         chainlength(rows, vector<size_t>(cols, 0)),
         biclique_bounds(rows, vector<bound_t>(cols, bound_t(0,0,0,0))) {
         compute_cache(bicliques);
@@ -198,6 +205,8 @@ class biclique_yield_cache {
                         size_t s0 = cache.get(y, x, 0);
                         size_t s1 = cache.get(y, x, 1);
                         if (s0 == 0 || s1 == 0) continue;
+                        minorminer_assert(s0-1 < rows);
+                        minorminer_assert(s1-1 < cols);
                         size_t maxlen = cells.topo.biclique_length(y, y+h-1, x, x+w-1);
                         size_t prevlen = chainlength[s0-1][s1-1];
                         if(prevlen == 0 || prevlen > maxlen) {
@@ -227,7 +236,7 @@ class biclique_yield_cache {
             return true;
         }
       public:
-        iterator(size_t _s0, size_t _s1, const size_t r, const size_t c, 
+        iterator(size_t _s0, size_t _s1, const size_t &r, const size_t &c,
                  const vector<vector<size_t>> &cl,
                  const vector<vector<bound_t>> &_bounds,
                  const bundle_cache<topo_spec> &_bundles) :

include/busclique/clique_cache.hpp

@@ -102,6 +102,8 @@ class clique_cache {
             bundles(b),
             width(w),
             mem(new size_t[memsize()]{}) {
+        minorminer_assert(width <= cells.topo.dim[0]);
+        minorminer_assert(width <= cells.topo.dim[1]);
         mem[0] = width;
         for(size_t i = 1; i < width; i++)
             mem[i] = mem[i-1] + memsize(i-1);
@@ -399,7 +401,7 @@ class clique_yield_cache {
                 }
             stop_w1_scan:;
         }
-        for(size_t w = 2; w <= cells.topo.dim[0]; w++) {
+        for(size_t w = 2; w <= min(cells.topo.dim[0], cells.topo.dim[1]); w++) {
             size_t min_length, max_length;
             get_length_range(bundles, w, min_length, max_length);
             for(size_t len = min_length; len < max_length; len++) {

include/busclique/find_clique.hpp

@@ -98,7 +98,7 @@ bool find_clique_nice(const cell_cache<pegasus_spec> &cells,
         }
         if(minw > maxw) return false;
     } else {
-        maxw = (max_length)*6;
+        maxw = min(cells.topo.dim[0], (max_length)*6);
     }
     //we've already found an embedding; now try to find one with shorter chains
     for(size_t w = minw; w <= maxw; w++) {

include/find_embedding/util.hpp

@@ -184,11 +184,20 @@ class optional_parameters {
         localInteractionPtr->displayOutput(loglevel, buffer);
     }
 
+    void print_out(int loglevel, const char* format) const {
+        localInteractionPtr->displayOutput(loglevel, format);
+    }
+
+
     template <typename... Args>
     void print_err(int loglevel, const char* format, Args... args) const {
         char buffer[1024];
         snprintf(buffer, 1024, format, args...);
-        localInteractionPtr->displayError(loglevel, buffer);
+        localInteractionPtr->displayError(loglevel, buffer);\
+    }
+
+    void print_err(int loglevel, const char* format) const {
+        localInteractionPtr->displayError(loglevel, format);
     }
 
     template <typename... Args>

minorminer/busclique.pyx

@@ -23,7 +23,7 @@ import networkx as nx, dwave_networkx as dnx
 #increment this version any time there is a change made to the cache format,
 #when yield-improving changes are made to clique algorithms, or when bugs are
 #fixed in the same.
-cdef int __cache_version = 3
+cdef int __cache_version = 4
 
 cdef int __lru_size = 100
 cdef dict __global_locks = {'clique': threading.Lock(),
@@ -88,7 +88,7 @@ def find_clique_embedding(nodes, g, use_cache = True):
                     'chimera': _chimera_busgraph}[family]
     except (AttributeError, KeyError):
         raise ValueError("g must be either a dwave_networkx.chimera_graph or"
-                         "a dwave_networkx.pegasus_graph")
+                         " a dwave_networkx.pegasus_graph")
     if use_cache:
         return busgraph_cache(g).find_clique_embedding(nodes)
     else:
@@ -158,12 +158,18 @@ class busgraph_cache:
             if rootdir.exists():
                 dirstack.append(rootdir)
         while dirstack:
-            top = dirstack.pop()
+            top = dirstack[-1]
+            substack = []
             for item in top.iterdir():
                 if item.is_dir():
-                    dirstack.append(item)
+                    substack.append(item)
                 else:
                     item.unlink()
+            if substack:
+                dirstack.extend(substack)
+            else:
+                top.rmdir()
+                dirstack.pop()
 
     def _fetch_cache(self, dirname, compute):
         """