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[WIP] Add state/mappers to new workflow syntax #2648

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248d39a
Merge branch 'enh/workflow_syntax' of https://github.com/effigies/nip…
djarecka Jul 10, 2018
f568d78
Adding auxiliary and state from nipype2_tmp
djarecka Jul 12, 2018
682248a
updating exceptions and __init__; updating logger to the current vers…
djarecka Jul 13, 2018
7b3bba6
starting updating NewNode using mapper and state from nipype2_tmp; ch…
djarecka Jul 13, 2018
c944685
adding simple tests
djarecka Jul 14, 2018
4da8737
adding run_interface method for NewNode (still have to add run method)
djarecka Jul 15, 2018
7ff7722
copy submitter and workers from nipype2_tmp; adding SubmitterNode and…
djarecka Jul 15, 2018
502f617
fixing run method for node (previously it didn work for dask and cf):…
djarecka Jul 16, 2018
784ec22
adding reading results; changing node names (node name shouldn have _)
djarecka Jul 16, 2018
18a6176
adding dask to requirements
djarecka Jul 16, 2018
601c15b
adding distributed package
djarecka Jul 16, 2018
d5ceb24
skipping tests for py2; sorting results (not sure if the node should …
djarecka Jul 16, 2018
692bc1b
removing printing the bokeh address (doesnt work with travis)
djarecka Jul 17, 2018
ccf8926
adding tests for node mappers
djarecka Jul 17, 2018
8300a98
changing requirments to py>3.4 (fails with py3.4, not sure if we want…
djarecka Jul 17, 2018
46684a4
moving many attributes from NewNodeBase/NewNodeCore to NewNode, so I …
djarecka Jul 22, 2018
26496ae
starting NewWorkflow class that inherits from NewNode (for now only a…
djarecka Jul 24, 2018
40562a8
adding add and method methods to NewWorkflow
djarecka Jul 24, 2018
9fb54c3
fixing one test
djarecka Jul 24, 2018
39e6b50
adding add method to NewWOrkflow
djarecka Jul 24, 2018
e795961
adding comments to the tests
djarecka Jul 24, 2018
e6f445e
Merge remote-tracking branch 'upstream/enh/workflow_syntax' into effi…
effigies Jul 25, 2018
15b4ba8
[wip] rearranging classes - showing the problem with cf/dask when pas…
djarecka Jul 26, 2018
d0bdf1d
Revert "[wip] rearranging classes - showing the problem with cf/dask …
djarecka Jul 27, 2018
522f64c
rearranging classes, NewNode and NewWorkflow inherit from NewBase; fi…
djarecka Jul 30, 2018
2e02f69
allowing for kwarg arg in add method instead of connect method
djarecka Jul 31, 2018
730f371
allowing for using mapper from previous nodes, e.g. [_NA, b], addding…
djarecka Jul 31, 2018
1732b88
removing globals mapper2rpn
djarecka Aug 15, 2018
f1d603e
adding index_generator to the state class
djarecka Aug 15, 2018
25c501c
changing string representation of directories names and inputs names
djarecka Aug 29, 2018
1e4067c
adding comments
djarecka Aug 29, 2018
b93ef44
[wip] adding inner workflow if workflow has a mapper (doesnt work pro…
djarecka Aug 29, 2018
c7737d0
[wip] adding some asserts to the test with inner workflows [skip ci]
djarecka Aug 29, 2018
2214404
Adding comments
djarecka Aug 29, 2018
d0e8c76
fixing inner_workflows (had to add deepcopy to node), changing syntax…
djarecka Sep 4, 2018
dfe7bd5
[skip ci] fixing _check_all_results (bug introduced in f1d603e, but w…
djarecka Sep 4, 2018
409aa84
[skip ci] adding example from #2539 (not running yet); small changes …
djarecka Sep 5, 2018
1bc5350
small update to tests; adding DotDict to auxiliary (but dont use it r…
djarecka Sep 19, 2018
a2d33b9
adding tests for inner workflows
djarecka Sep 19, 2018
b87782c
small edits
djarecka Sep 24, 2018
fa8710b
removing the concept of inner workflow from workflow with mapper
djarecka Sep 24, 2018
2cec408
adding outputs_nm list for NewWorkflow, adding _reading_result for wo…
djarecka Sep 24, 2018
14ebc78
alloing for mapper in workflows (copying workflows in teh submitter);…
djarecka Sep 30, 2018
a9407b4
updating tests for mappers
djarecka Sep 30, 2018
63fe2f4
adding inputs and imports to newnode_nero
djarecka Oct 1, 2018
1c48416
introducing workflows that can be treated as a node: adding results, …
djarecka Oct 3, 2018
ef2b4cf
moving run node/wf to tests and removing run from Node/Workflow (at l…
djarecka Oct 4, 2018
935c8ea
merging all submitter classes
djarecka Oct 4, 2018
8c8aa29
adding comments; cleaning connect methods
djarecka Oct 4, 2018
970eb16
changing orders of the methods
djarecka Oct 4, 2018
89395f2
changing directory format for node without mapper (one layer less, si…
djarecka Oct 4, 2018
a0cdf31
wf has map the same as a node and map_node to change a mapper for the…
djarecka Oct 4, 2018
2f11ad6
adding fixture to change directory in the tests; changing nodedir to …
djarecka Oct 4, 2018
bf54454
adding wrapper to the current interfaces (with simple tests for bet);…
djarecka Oct 5, 2018
0becd3a
updating wf.add method to include nipype interfaces
djarecka Oct 6, 2018
d61519c
test_newnode_neuro works: fixing CurrentInterface and adding _reading…
djarecka Oct 8, 2018
2e3ea2a
[skip ci] small naming change
djarecka Oct 8, 2018
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[wip] rearranging classes - showing the problem with cf/dask when pas…
…sisng node=self to SumitterNode
  • Loading branch information
djarecka committed Jul 26, 2018
commit 15b4ba8552feda36f3ae718bc609d02802ddabef
6 changes: 3 additions & 3 deletions nipype/pipeline/engine/submitter.py
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ def run_workflow(self):
for (i_n, node) in enumerate(self.graph):
# submitting all the nodes who are self sufficient (self.graph is already sorted)
if node.sufficient:
self.submit_work(node.nodecore)
self.submit_work(node)
# if its not, its been added to a line
else:
break
Expand Down Expand Up @@ -103,8 +103,8 @@ def _nodes_check(self):
_to_remove = []
for (to_node, i, ind) in self.node_line:
print("NODE LINE", self.node_line)
if to_node.nodecore.checking_input_el(ind):
self._submit_work_el(to_node.nodecore, i, ind)
if to_node.checking_input_el(ind):
self._submit_work_el(to_node, i, ind)
_to_remove.append((to_node, i, ind))
else:
pass
Expand Down
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