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 048:     cdef int int_i

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 092:         #peel[int_i, 0] = nodes_to_join[0].taxon

 093:         #peel[int_i, 1] = nodes_to_join[1].taxon

 094:         #node_pool.remove(nodes_to_join[0])

 095:         #node_pool.remove(nodes_to_join[1])

+096:         peel[int_i, 0] = node_to_join1.taxon

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    __pyx_t_9 = __pyx_v_node_to_join1->taxon;
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+097:         peel[int_i, 1] = node_to_join2.taxon

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    __pyx_t_9 = __pyx_v_node_to_join2->taxon;
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+098:         node_pool.remove(node_to_join1)

    if (unlikely(!__pyx_v_node_to_join1)) { __Pyx_RaiseUnboundLocalError("node_to_join1"); __PYX_ERR(0, 98, __pyx_L1_error) }
    __pyx_t_5 = __Pyx_CallUnboundCMethod1(&__pyx_umethod_PyList_Type_remove, __pyx_v_node_pool, ((PyObject *)__pyx_v_node_to_join1)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 98, __pyx_L1_error)
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+099:         node_pool.remove(node_to_join2)

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    __Pyx_GOTREF(__pyx_t_5);
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;

 100: 

 101:         # calculate the distances for the new node

+102:         for nd in node_pool:

    __pyx_t_5 = __pyx_v_node_pool; __Pyx_INCREF(__pyx_t_5); __pyx_t_12 = 0;
    for (;;) {
      if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_5)) break;
      #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS
      __pyx_t_7 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_12); __Pyx_INCREF(__pyx_t_7); __pyx_t_12++; if (unlikely(0 < 0)) __PYX_ERR(0, 102, __pyx_L1_error)
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      #endif
      if (!(likely(((__pyx_t_7) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_7, __pyx_ptype_6geophy_8tree_dec_2nj_Node))))) __PYX_ERR(0, 102, __pyx_L1_error)
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      __pyx_t_7 = 0;
/* … */
    }
    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;

 103:             # actual node-to-node distances

+104:             v1 = 0.0

      __pyx_v_v1 = 0.0;

 105:             #for node_to_join in nodes_to_join:

 106:             #    v1 += <np.double_t>nd._nj_distances[node_to_join]

 107:             #v3 = nodes_to_join[0]._nj_distances[nodes_to_join[1]]

+108:             v1 += <np.double_t>nd._nj_distances[node_to_join1]

      if (unlikely(__pyx_v_nd->_nj_distances == Py_None)) {
        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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      if (unlikely(!__pyx_v_node_to_join1)) { __Pyx_RaiseUnboundLocalError("node_to_join1"); __PYX_ERR(0, 108, __pyx_L1_error) }
      __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_nd->_nj_distances, ((PyObject *)__pyx_v_node_to_join1)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 108, __pyx_L1_error)
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+109:             v1 += <np.double_t>nd._nj_distances[node_to_join2]

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        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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+110:             v3 = node_to_join1._nj_distances[node_to_join2]

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+111:             dist = 0.5 * (v1 - v3)

      __pyx_v_dist = (0.5 * (__pyx_v_v1 - __pyx_v_v3));

+112:             new_node._nj_distances[nd] = dist

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+113:             nd._nj_distances[new_node] = dist

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 114: 

 115:             # Adjust/recalculate the values needed for the Q-matrix calculation

+116:             new_node._nj_xsub += dist

      __pyx_v_new_node->_nj_xsub = (__pyx_v_new_node->_nj_xsub + __pyx_v_dist);

+117:             nd._nj_xsub += dist

      __pyx_v_nd->_nj_xsub = (__pyx_v_nd->_nj_xsub + __pyx_v_dist);

 118:             #for node_to_join in nodes_to_join:

 119:             #    nd._nj_xsub -= <np.double_t>node_to_join._nj_distances[nd]

+120:             nd._nj_xsub -= <np.double_t>node_to_join1._nj_distances[nd]

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      if (unlikely(__pyx_v_node_to_join1->_nj_distances == Py_None)) {
        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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      __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_node_to_join1->_nj_distances, ((PyObject *)__pyx_v_nd)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 120, __pyx_L1_error)
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+121:             nd._nj_xsub -= <np.double_t>node_to_join2._nj_distances[nd]

      if (unlikely(!__pyx_v_node_to_join2)) { __Pyx_RaiseUnboundLocalError("node_to_join2"); __PYX_ERR(0, 121, __pyx_L1_error) }
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        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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      __pyx_t_7 = __Pyx_PyDict_GetItem(__pyx_v_node_to_join2->_nj_distances, ((PyObject *)__pyx_v_nd)); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 121, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_7);
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      __pyx_v_nd->_nj_xsub = (__pyx_v_nd->_nj_xsub - ((__pyx_t_5numpy_double_t)__pyx_t_19));

 122: 

 123:         # calculate the branch lengths

+124:         if n_pool > 2:

    __pyx_t_15 = ((__pyx_v_n_pool > 2) != 0);
    if (__pyx_t_15) {
/* … */
      goto __pyx_L19;
    }

 125:             #v1 = 0.5 * nodes_to_join[0]._nj_distances[nodes_to_join[1]]

+126:             v1 = 0.5 * node_to_join1._nj_distances[node_to_join2]

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      if (unlikely(__pyx_v_node_to_join1->_nj_distances == Py_None)) {
        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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      if (unlikely(!__pyx_v_node_to_join2)) { __Pyx_RaiseUnboundLocalError("node_to_join2"); __PYX_ERR(0, 126, __pyx_L1_error) }
      __pyx_t_5 = __Pyx_PyDict_GetItem(__pyx_v_node_to_join1->_nj_distances, ((PyObject *)__pyx_v_node_to_join2)); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 126, __pyx_L1_error)
      __Pyx_GOTREF(__pyx_t_5);
      __pyx_t_7 = PyNumber_Multiply(__pyx_float_0_5, __pyx_t_5); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 126, __pyx_L1_error)
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 127:             v4 = (

 128:                 1.0

+129:                 / (two * (<np.double_t>n_pool - two))

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        PyErr_SetString(PyExc_ZeroDivisionError, "float division");
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 130:                 #* (nodes_to_join[0]._nj_xsub - nodes_to_join[1]._nj_xsub)

+131:                 * (node_to_join1._nj_xsub - node_to_join2._nj_xsub)

      if (unlikely(!__pyx_v_node_to_join1)) { __Pyx_RaiseUnboundLocalError("node_to_join1"); __PYX_ERR(0, 131, __pyx_L1_error) }
      if (unlikely(!__pyx_v_node_to_join2)) { __Pyx_RaiseUnboundLocalError("node_to_join2"); __PYX_ERR(0, 131, __pyx_L1_error) }
      __pyx_v_v4 = ((((__pyx_t_5numpy_double_t)1.0) / __pyx_t_19) * (__pyx_v_node_to_join1->_nj_xsub - __pyx_v_node_to_join2->_nj_xsub));

 132:             )

+133:             delta_f = v1 + v4

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 134:             #delta_g = <np.double_t>nodes_to_join[0]._nj_distances[nodes_to_join[1]] - delta_f

 135:             #blens[nodes_to_join[0].taxon] = delta_f

 136:             #blens[nodes_to_join[1].taxon] = delta_g

+137:             delta_g = <np.double_t>node_to_join1._nj_distances[node_to_join2] - delta_f

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        PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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+138:             blens[node_to_join1.taxon] = delta_f

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      __pyx_t_16 = __pyx_v_node_to_join1->taxon;
      *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_double_t *, __pyx_pybuffernd_blens.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_blens.diminfo[0].strides) = __pyx_v_delta_f;

+139:             blens[node_to_join2.taxon] = delta_g

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      __pyx_t_16 = __pyx_v_node_to_join2->taxon;
      *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_double_t *, __pyx_pybuffernd_blens.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_blens.diminfo[0].strides) = __pyx_v_delta_g;

 140:         else:

 141:             #dist = nodes_to_join[0]._nj_distances[nodes_to_join[1]]

 142:             #blens[nodes_to_join[0].taxon] = dist / two

 143:             #blens[nodes_to_join[1].taxon] = dist / two

+144:             dist = node_to_join1._nj_distances[node_to_join2]

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+145:             blens[node_to_join1.taxon] = dist / two

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+146:             blens[node_to_join2.taxon] = dist / two

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    __pyx_L19:;

 147: 

 148:         # clean up

 149:         #for node_to_join in nodes_to_join:

 150:         #    node_to_join._nj_distances = {}

 151:         #    node_to_join._nj_xsub = 0.0

+152:         node_to_join1._nj_distances = {}

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