removing pickle and changing to json

CHANGELOG.md

@@ -10,7 +10,7 @@
 
 -   make_parcellation now uses templateflow and all atlases therein
 
--   save_tenetobids_snapshot to export current teneto settings. 
+-   save_tenetobids_snapshot to export current teneto settings. save_to_pickle (and corresponding load function) have been removed as they are not secure.
 
 ### Fixes
 

docs/tutorial/tenetobids/io.rst

@@ -3,14 +3,22 @@ Load/Save TenetoBIDS
 
 TenetoBIDS objects can be easily saved as a pickle file (.pkl). 
 
-You can save you progress by using *save_pickle*.
+You can save you progress by using *save_tenetobids_snapshot*.
 
 .. code-block:: python
 
-    tnet.save_aspickle('./tenetoobj.pkl')
+    path = './'
+    tnet.save_tenetobids_snapshot(path)
 
-Then to load it you just need to call *load_frompickle*:
+This creates a json file called, 
+Then to load it you just need to create a new TenetoBIDS object using these paramerers. 
+All the history (in tnet.history) is also perserved:
 
 .. code-block:: python
 
-    tnet = teneto.TenetoBIDS.load_frompickle('./tenetoobj.pkl')
+    import json
+    with open(path + 'TenetoBIDS_snapshot.json') as f
+        params = json.load(f)
+    tnet = teneto.TenetoBIDS(**params)
+
+Note that any loaded files need to be reloaded.

teneto/classes/bids.py

@@ -7,7 +7,6 @@
 import inspect
 import matplotlib.pyplot as plt
 import json
-import pickle
 import nilearn
 from concurrent.futures import ProcessPoolExecutor, as_completed
 from scipy.interpolate import interp1d
@@ -1531,38 +1530,6 @@ def print_dataset_summary(self):
             print('Numnber of selected files: ' + str(len(selected_files)))
             print('\n - '.join(selected_files))
 
-    def save_aspickle(self, fname):
-        if fname[-4:] != '.pkl':
-            fname += '.pkl'
-        with open(fname, 'wb') as f:
-            pickle.dump(self, f, pickle.HIGHEST_PROTOCOL)
-
-    @classmethod
-    def load_frompickle(cls, fname, reload_object=False):
-        """
-        Loaded saved instance of
-
-        fname : str
-            path to pickle object (output of TenetoBIDS.save_aspickle)
-        reload_object : bool (default False)
-            reloads object by calling teneto.TenetoBIDS (some information lost, for development)
-
-        Returns
-        -------
-            self :
-                TenetoBIDS instance
-        """
-        if fname[-4:] != '.pkl':
-            fname += '.pkl'
-        with open(fname, 'rb') as f:
-            tnet = pickle.load(f)
-        if reload_object:
-            reloadnet = teneto.TenetoBIDS(tnet.BIDS_dir, pipeline=tnet.pipeline, pipeline_subdir=tnet.pipeline_subdir, bids_tags=tnet.bids_tags,  bids_suffix=tnet.bids_suffix,
-                                          bad_subjects=tnet.bad_subjects, confound_pipeline=tnet.confound_pipeline, raw_data_exists=tnet.raw_data_exists, njobs=tnet.njobs)
-            reloadnet.histroy = tnet.history
-            tnet = reloadnet
-        return tnet
-
     # timelocked average
     # np.stack(a['timelocked-tvc'].values).mean(axis=0)
     # Remaked based on added meta data derived from events
@@ -1848,7 +1815,7 @@ def save_tenetobids_snapshot(self, path, filename='TenetoBIDS_snapshot'):
         Notes
         -----
 
-        To restart:
+        To load the snapshot:
 
         import json
         with open(path + 'TenetoBIDS_snapshot.json') as f

test/tenetobids/tnet_test.py

@@ -224,17 +224,6 @@ def test_tnet_checksidecar():
         raise AssertionError()
 
 
-def test_tnet_io():
-    tnet = teneto.TenetoBIDS(teneto.__path__[0] + '/data/testdata/dummybids/', pipeline='fmriprep',
-                             bids_suffix='preproc', bids_tags={'sub': '001', 'task': 'a', 'run': '01'}, raw_data_exists=False)
-    tnet.save_aspickle(teneto.__path__[0] +
-                       '/data/testdata/dummybids/teneosave.pkl')
-    tnet2 = teneto.TenetoBIDS.load_frompickle(
-        teneto.__path__[0] + '/data/testdata/dummybids/teneosave.pkl')
-    if not tnet2.get_selected_files() == tnet.get_selected_files():
-        raise AssertionError()
-
-
 def test_export_history():
     tnet = teneto.TenetoBIDS(teneto.__path__[0] + '/data/testdata/dummybids/', pipeline='fmriprep',
                              bids_suffix='preproc', bids_tags={'sub': '001', 'task': 'a', 'run': '01'}, raw_data_exists=False)