Use luigi-tools package

Change-Id: I385315a95e57bed8162d04a2aa9075453a62bd21

.pylintrc

@@ -2,7 +2,16 @@
 ignore=version.py
 
 [MESSAGES CONTROL]
-disable=bad-continuation,fixme,invalid-name,len-as-condition,no-else-return,empty-docstring,too-many-lines
+disable=
+	bad-continuation,
+	empty-docstring,
+	fixme,
+	invalid-name,
+	len-as-condition,
+	no-else-return,
+	no-member,
+	too-many-ancestors,
+	too-many-lines,
 
 [FORMAT]
 # Maximum number of characters on a single line.

setup.py

@@ -24,6 +24,7 @@
     "jinja2",
     "joblib",
     "luigi",
+    "luigi-tools>=0.0.2",
     "matplotlib",
     "morph_tool>=2.2.21",
     "morph_validator",

src/synthesis_workflow/tasks/circuit.py

@@ -23,7 +23,7 @@
 from synthesis_workflow.tasks.luigi_tools import BoolParameter
 from synthesis_workflow.tasks.luigi_tools import copy_params
 from synthesis_workflow.tasks.luigi_tools import OptionalChoiceParameter
-from synthesis_workflow.tasks.luigi_tools import ParamLink
+from synthesis_workflow.tasks.luigi_tools import ParamRef
 from synthesis_workflow.tasks.luigi_tools import RatioParameter
 from synthesis_workflow.tasks.luigi_tools import WorkflowTask
 from synthesis_workflow.tasks.utils import GetSynthesisInputs
@@ -153,7 +153,7 @@ def output(self):
 
 
 @copy_params(
-    mtype_taxonomy_path=ParamLink(PathConfig),
+    mtype_taxonomy_path=ParamRef(PathConfig),
 )
 class BuildCircuit(WorkflowTask):
     """Generate cell positions and me-types from atlas, compositions and taxonomy.
@@ -184,8 +184,8 @@ def requires(self):
 
     def run(self):
         """"""
-        cell_composition_path = self.input().ppath / self.cell_composition_path
-        mtype_taxonomy_path = self.input().ppath / self.mtype_taxonomy_path
+        cell_composition_path = self.input().pathlib_path / self.cell_composition_path
+        mtype_taxonomy_path = self.input().pathlib_path / self.mtype_taxonomy_path
 
         thickness_mask_path = None
         if self.mask_path is not None:
@@ -210,7 +210,7 @@ def output(self):
 
 
 @copy_params(
-    mtypes=ParamLink(SynthesisConfig),
+    mtypes=ParamRef(SynthesisConfig),
 )
 class SliceCircuit(WorkflowTask):
     """Create a smaller circuit .mvd3 file for subsampling.

src/synthesis_workflow/tasks/cli.py

@@ -8,10 +8,10 @@
 from pathlib import Path
 
 import luigi
+from luigi_tools.utils import get_dependency_graph
 
 import synthesis_workflow
 from synthesis_workflow.tasks import workflows
-from synthesis_workflow.tasks.luigi_tools import get_dependency_graph
 from synthesis_workflow.utils import setup_logging
 
 

src/synthesis_workflow/tasks/diametrizer.py

@@ -24,7 +24,7 @@
 from synthesis_workflow.tasks.config import RunnerConfig
 from synthesis_workflow.tasks.luigi_tools import BoolParameter
 from synthesis_workflow.tasks.luigi_tools import copy_params
-from synthesis_workflow.tasks.luigi_tools import ParamLink
+from synthesis_workflow.tasks.luigi_tools import ParamRef
 from synthesis_workflow.tasks.luigi_tools import WorkflowTask
 from synthesis_workflow.tools import update_morphs_df
 
@@ -67,7 +67,7 @@ def _plot_models(models_params, models_data, fig_folder="figures", ext=".png"):
 
 
 @copy_params(
-    nb_jobs=ParamLink(RunnerConfig),
+    nb_jobs=ParamRef(RunnerConfig),
 )
 class BuildDiameterModels(WorkflowTask):
     """Task to build diameter models from set of cells.