Closed aschluter closed 1 year ago
This issue sometimes comes up when some of the python 3.6 dependencies aren't up to date. I haven't fully narrowed down which packages it is yet, but if you update python it usually resolves it. I'll get back to you after I do a little more testing and isolate the solution.
This turns out to be an issue with an incompatibility with pickling particular objects within the DictList cobrapy data structure. This becomes problematic when trying to parallelize growth simulations. The latest version of ritpide should fix this issue.
Hi,
when I try the last Human-GEM model I got an error in the deepcopy process. Thanks in advance.
Initializing model and integrating transcriptomic data... Traceback (most recent call last): File "", line 1, in
File "/home/agatha/python-virtual-environments/env/lib/python3.6/site-packages/riptide/riptide.py", line 612, in contextualize
riptide_model = copy.deepcopy(model)
File "/usr/lib/python3.6/copy.py", line 180, in deepcopy
y = _reconstruct(x, memo, rv)
File "/usr/lib/python3.6/copy.py", line 280, in _reconstruct
state = deepcopy(state, memo)
File "/usr/lib/python3.6/copy.py", line 150, in deepcopy
y = copier(x, memo)
File "/usr/lib/python3.6/copy.py", line 240, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
File "/usr/lib/python3.6/copy.py", line 150, in deepcopy
y = copier(x, memo)
File "/usr/lib/python3.6/copy.py", line 240, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
File "/usr/lib/python3.6/copy.py", line 180, in deepcopy
y = _reconstruct(x, memo, rv)
File "/usr/lib/python3.6/copy.py", line 280, in _reconstruct
state = deepcopy(state, memo)
File "/usr/lib/python3.6/copy.py", line 150, in deepcopy
y = copier(x, memo)
File "/usr/lib/python3.6/copy.py", line 240, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
File "/usr/lib/python3.6/copy.py", line 169, in deepcopy
rv = reductor(4)
TypeError: can't pickle SwigPyObject objects