feat(huge): huge refactor (in progress).

Commented out libc includes to uncover all explicit dependencies.
A large fraction has now been ported over (no testing).
I did not port over the command line tools, such as the rc shell.
These will be done independently - as of now I just want the library to
stand independent.

Compilation currently fails due to the lack of math functions.

1 files changed, 7 insertions, 7 deletions

diff --git a/src/libbio/phylo.c b/src/libbio/phylo.c
index 41b0f04..1b0ae59 100644
--- a/src/libbio/phylo.c
+++ b/src/libbio/phylo.c
@@ -328,11 +328,11 @@ phylo·diameter(bio·Tree tree, int *len, bio·Node **path)
     sort·nodedists(n, fbuf, nbuf);
 
     path[0] = nbuf[n-1];
-    printf("first end '%s'\n", path[0]->name);
+    fmt·print("first end '%s'\n", path[0]->name);
 
     n = phylo·getdistsfrom(path[0], n, fbuf, nbuf);
     sort·nodedists(n, fbuf, nbuf);
-    printf("second end '%s'\n", nbuf[n-1]->name);
+    fmt·print("second end '%s'\n", nbuf[n-1]->name);
 
     *len = 0;
 
@@ -393,17 +393,17 @@ phylo·reroot(bio·Tree *tree, bio·Node *node, double d)
     // TODO: should check that node is part of this tree?
     // TODO: should we check if node->parent != nil?
 
-    if (fabs(d) < PREC) {
+    if(fabs(d) < PREC){
         new = node;
         rotateparent(node->parent, node);
-    } else if (fabs(d-node->dist) < PREC) {
+    }else if(fabs(d-node->dist) < PREC){
         new = node->parent;
         if (new->parent->parent) {
             rotateparent(new->parent->parent, new->parent);
         }
-    } else {
+    }else{
         new = tree->mem.alloc(tree->heap, 1, sizeof(*new));
-        memset(new, 0, sizeof(*new));
+        mem·set(new, sizeof(*new), 0);
 
         phylo·addchild(new, node);
         node->parent = new;
@@ -415,7 +415,7 @@ phylo·reroot(bio·Tree *tree, bio·Node *node, double d)
         node->parent->parent = new;
     }
 
-    printf("number of children on old root: %d\n", tree->root->nchild);
+    fmt·print("number of children on old root: %d\n", tree->root->nchild);
     tree->root  = new;
     tree->nleaf = 0;