code stringlengths 3 6.57k |
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xp.max() |
ax2.invert_xaxis() |
ax3.yaxis_inverted() |
ax2.invert_yaxis() |
ax2.axis('off') |
sca(ax3) |
axes.remove(None) |
colorbar(mappable=im, ax=axes, anchor=(0, 0) |
colorbar(mappable=im, extend=cb_extend) |
sca(ax3) |
sci(im) |
ImageCursor(ax3, im) |
connect('button_press_event', cursor.onClick) |
ax3.tick_params(axis='x', rotation=xtickrotation) |
reorderMatrix(names, matrix, tree, axis=None) |
ValueError('matrix should be a 2D matrix.') |
TypeError('matrix should be a numpy array.') |
np.shape(matrix) |
np.shape(matrix) |
ValueError('matrix should be a square matrix') |
np.asarray(names) |
np.isscalar(names) |
TypeError('names should be list-like') |
len(names) |
TypeError('names is empty') |
isinstance(tree, Phylo.BaseTree.Tree) |
TypeError('tree should be a BioPython Tree') |
len(names) |
len(matrix) |
ValueError('names should have entries for each matrix row/column') |
tree.get_terminals() |
len(names) |
len(terminals) |
ValueError('names should have entries for each tree terminal') |
len(terminals) |
len(matrix) |
ValueError('matrix should have a row for each tree terminal') |
np.where(names == name) |
len(locs) |
ValueError('inconsistent names and tree: %s not in names'%name) |
len(locs) |
ValueError('inconsistent names and tree: duplicate name %s in names'%name) |
indices.append(locs[0]) |
np.arange(s) |
np.isscalar(axis) |
np.ix_(*I) |
findSubgroups(tree, c, method='naive', **kwargs) |
method.lower() |
strip() |
tree.get_terminals() |
getLinkage(names, tree) |
print('Failed to build linkage; fall back to naive criterion') |
range(len(terminals) |
tree.distance(curr_clade, next_clade) |
subgroups.append([]) |
append(next_clade.name) |
fcluster(Z, c, criterion=method, **kwargs) |
np.unique(T) |
range(len(labels) |
enumerate(T) |
append(names[i]) |
py.log.setconsumer("rtyper", py.log.STDOUT) |
not_really_random() |
random.random() |
range(12000) |
BaseTestRDict(BaseRtypingTest) |
test_dict_creation(self) |
createdict(i) |
self.newdict() |
self.interpret(createdict, [42]) |
test_dict_getitem_setitem(self) |
func(i) |
self.newdict() |
self.interpret(func, [6]) |
test_dict_getitem_keyerror(self) |
func(i) |
self.newdict() |
self.interpret(func, [6]) |
test_dict_del_simple(self) |
func(i) |
self.newdict() |
len(d) |
self.interpret(func, [6]) |
test_dict_clear(self) |
func(i) |
self.newdict() |
d.clear() |
len(d) |
self.interpret(func, [7]) |
test_empty_strings(self) |
func(i) |
self.newdict() |
self.interpret(func, [6]) |
func(i) |
self.newdict() |
len(d) |
self.interpret(func, [6]) |
test_dict_bool(self) |
func(i) |
self.newdict() |
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