Pin versions before moving to region-grower >= 0.2

Change-Id: If9b5778cf125e7816868943d219773a33c4ae9b0

requirements/base.pip

@@ -1,26 +1,25 @@
 atlas_analysis>0.0.1
 brainbuilder>=0.14
-bluepyefe
-bluepyopt
+bluepy>=2.3,<3
 bluepymm
-diameter_synthesis>=0.1.8
+diameter_synthesis<=0.2
 gitpython
 jinja2
 joblib
 luigi
 luigi-tools>=0.0.10
 matplotlib
 morph_tool>=2.3.1
-morphio>=2.7
+morphio>=3,<4
 neuroc
-neurom>=2.0.1
+neurom>=2.0.1,<2.1
 pandas
 placement_algorithm>=2.1.3
 PyYAML
-region_grower
+region_grower<0.2
 scipy
 seaborn
-tns>=2.3.3
+tns>=2.3.3,<2.4
 tmd
 tqdm
-voxcell>=3
+voxcell>=3,<4

src/morphval/common.py

@@ -5,8 +5,9 @@
 from copy import deepcopy
 
 from neurom import viewer, geom, NeuriteType
-from neurom.core import Population, iter_neurites
+from neurom.core import iter_neurites
 from neurom.core.dataformat import COLS
+from neurom.core.population import Population
 from neurom.core.types import tree_type_checker as is_type
 from region_grower.utils import NumpyEncoder
 

src/synthesis_workflow/tasks/circuit.py

@@ -51,7 +51,7 @@ class CreateAtlasLayerAnnotations(WorkflowTask):
     )
 
     def run(self):
-        """"""
+        """ """
         annotation, layer_mapping = get_layer_tags(CircuitConfig().atlas_path)
 
         if self.use_half:
@@ -70,7 +70,7 @@ def run(self):
         )
 
     def output(self):
-        """"""
+        """ """
         annotation_path = Path(self.layer_annotations_path)
         annotation_base_name = annotation_path.with_suffix("").name
         layer_mapping_path = annotation_path.with_name(
@@ -124,11 +124,11 @@ class CreateAtlasPlanes(WorkflowTask):
     )
 
     def requires(self):
-        """"""
+        """ """
         return CreateAtlasLayerAnnotations()
 
     def run(self):
-        """"""
+        """ """
         layer_annotation = VoxelData.load_nrrd(self.input()["annotations"].path)
         planes, centerline = create_planes(
             layer_annotation,
@@ -143,7 +143,7 @@ def run(self):
         save_planes_centerline(self.output().path, planes, centerline)
 
     def output(self):
-        """"""
+        """ """
         return AtlasLocalTarget(self.atlas_planes_path + ".npz")
 
 
@@ -172,11 +172,11 @@ class BuildCircuit(WorkflowTask):
     seed = luigi.IntParameter(default=None, description=":int: Pseudo-random generator seed.")
 
     def requires(self):
-        """"""
+        """ """
         return GetSynthesisInputs()
 
     def run(self):
-        """"""
+        """ """
         cell_composition_path = self.input().pathlib_path / self.cell_composition_path
         mtype_taxonomy_path = self.input().pathlib_path / self.mtype_taxonomy_path
 
@@ -197,7 +197,7 @@ def run(self):
         cells.save(self.output().path)
 
     def output(self):
-        """"""
+        """ """
         return CircuitLocalTarget(CircuitConfig().circuit_somata_path)
 
 
@@ -225,14 +225,14 @@ class SliceCircuit(WorkflowTask):
     )
 
     def requires(self):
-        """"""
+        """ """
         return {
             "atlas_planes": CreateAtlasPlanes(),
             "circuit": BuildCircuit(),
         }
 
     def run(self):
-        """"""
+        """ """
         planes = load_planes_centerline(self.input()["atlas_planes"].path)["planes"]
 
         _slicer = partial(
@@ -249,5 +249,5 @@ def run(self):
             raise Exception("No cells will be synthtesized, better stop here.")
 
     def output(self):
-        """"""
+        """ """
         return CircuitLocalTarget(self.sliced_circuit_path)

src/synthesis_workflow/tasks/diametrizer.py

@@ -81,7 +81,7 @@ class BuildDiameterModels(WorkflowTask):
     plot_models = BoolParameter()
 
     def run(self):
-        """"""
+        """ """
         raise DeprecationWarning("This task must be updated to be used")
         # pylint: disable=unreachable
 
@@ -117,7 +117,7 @@ def run(self):
             _plot_models(models_params, models_data, fig_folder="figures", ext=".png")
 
     def output(self):
-        """"""
+        """ """
         return OutputLocalTarget(self.diameter_models_path)
 
 
@@ -160,11 +160,11 @@ class Diametrize(WorkflowTask):
     new_morphs_df_path = luigi.Parameter(default="diametrized_morphs_df.csv")
 
     def requires(self):
-        """"""
+        """ """
         return BuildDiameterModels()
 
     def run(self):
-        """"""
+        """ """
         raise DeprecationWarning("This task must be updated to be used")
         # pylint: disable=unreachable
 
@@ -197,5 +197,5 @@ def run(self):
         update_morphs_df(self.morphs_df_path, morphs_df).to_csv(self.output().path, index=False)
 
     def output(self):
-        """"""
+        """ """
         return OutputLocalTarget(self.new_morphs_df_path)

src/synthesis_workflow/tasks/synthesis.py

@@ -65,11 +65,11 @@ class BuildMorphsDF(WorkflowTask):
     )
 
     def requires(self):
-        """"""
+        """ """
         return GetSynthesisInputs()
 
     def run(self):
-        """"""
+        """ """
 
         neurondb_path = find_case_insensitive_file(self.neurondb_path)
 
@@ -89,7 +89,7 @@ def run(self):
         morphs_df.to_csv(self.output().path)
 
     def output(self):
-        """"""
+        """ """
         return MorphsDfLocalTarget(PathConfig().morphs_df_path)
 
 
@@ -105,14 +105,14 @@ class ApplySubstitutionRules(WorkflowTask):
     )
 
     def requires(self):
-        """"""
+        """ """
         return {
             "synthesis_input": GetSynthesisInputs(),
             "morphs_df": BuildMorphsDF(),
         }
 
     def run(self):
-        """"""
+        """ """
         substitution_rules_path = (
             self.input()["synthesis_input"].pathlib_path / self.substitution_rules_path
         )
@@ -125,7 +125,7 @@ def run(self):
         substituted_morphs_df.to_csv(self.output().path, index=False)
 
     def output(self):
-        """"""
+        """ """
         return MorphsDfLocalTarget(PathConfig().substituted_morphs_df_path)
 
 
@@ -148,14 +148,14 @@ class BuildSynthesisParameters(WorkflowTask):
     )
 
     def requires(self):
-        """"""
+        """ """
         return {
             "synthesis_input": GetSynthesisInputs(),
             "morphologies": ApplySubstitutionRules(),
         }
 
     def run(self):
-        """"""
+        """ """
         morphs_df = pd.read_csv(self.input()["morphologies"].path)
         mtypes = sorted(morphs_df.mtype.unique())
         neurite_types = get_neurite_types(morphs_df, mtypes)
@@ -188,7 +188,7 @@ def run(self):
             json.dump(tmd_parameters, f, cls=NumpyEncoder, indent=4, sort_keys=True)
 
     def output(self):
-        """"""
+        """ """
         return SynthesisLocalTarget(self.tmd_parameters_path)
 
 
@@ -205,11 +205,11 @@ class BuildSynthesisDistributions(WorkflowTask):
     """
 
     def requires(self):
-        """"""
+        """ """
         return ApplySubstitutionRules()
 
     def run(self):
-        """"""
+        """ """
         L.debug("reading morphs df from: %s", self.input().path)
         morphs_df = pd.read_csv(self.input().path)
 
@@ -237,7 +237,7 @@ def run(self):
             json.dump(tmd_distributions, f, cls=NumpyEncoder, indent=4, sort_keys=True)
 
     def output(self):
-        """"""
+        """ """
         return SynthesisLocalTarget(SynthesisConfig().tmd_distributions_path)
 
 
@@ -250,7 +250,7 @@ class BuildAxonMorphsDF(BuildMorphsDF):
     )
 
     def output(self):
-        """"""
+        """ """
         return MorphsDfLocalTarget(self.axon_morphs_df_path)
 
 
@@ -319,7 +319,7 @@ def get_neuron_db_path(self, ext):
         return (Path(self.axon_cells_path) / self.neurondb_basename).with_suffix("." + ext)
 
     def requires(self):
-        """"""
+        """ """
         tasks = {"circuit": SliceCircuit()}
 
         neurondb_path = self.get_neuron_db_path("xml")
@@ -331,7 +331,7 @@ def requires(self):
         return tasks
 
     def run(self):
-        """"""
+        """ """
         if self.annotations_path is None:
             annotations_file = None
             neurondb_path = None
@@ -394,7 +394,7 @@ def run(self):
         )
 
     def output(self):
-        """"""
+        """ """
         targets = {
             "morphs": MorphsDfLocalTarget(self.axon_morphs_path),
         }
@@ -447,7 +447,7 @@ class Synthesize(WorkflowTask):
     seed = luigi.IntParameter(default=0, description=":int: Pseudo-random generator seed.")
 
     def requires(self):
-        """"""
+        """ """
 
         return {
             "substituted_cells": ApplySubstitutionRules(),
@@ -458,7 +458,7 @@ def requires(self):
         }
 
     def run(self):
-        """"""
+        """ """
 
         axon_morphs_path = self.input()["axons"]["morphs"].path
         out_mvd3 = self.output()["out_mvd3"]
@@ -506,7 +506,7 @@ def run(self):
         )
 
     def output(self):
-        """"""
+        """ """
         outputs = {
             "out_mvd3": SynthesisLocalTarget(self.out_circuit_path),
             "out_morphologies": SynthesisLocalTarget(PathConfig().synth_output_path),
@@ -540,15 +540,15 @@ class AddScalingRulesToParameters(WorkflowTask):
     )
 
     def requires(self):
-        """"""
+        """ """
         return {
             "synthesis_input": GetSynthesisInputs(),
             "morphologies": ApplySubstitutionRules(),
             "tmd_parameters": BuildSynthesisParameters(),
         }
 
     def run(self):
-        """"""
+        """ """
         tmd_parameters = json.load(self.input()["tmd_parameters"].open("r"))
 
         if self.scaling_rules_path is not None:
@@ -572,7 +572,7 @@ def run(self):
             json.dump(tmd_parameters, f, cls=NumpyEncoder, indent=4, sort_keys=True)
 
     def output(self):
-        """"""
+        """ """
         return SynthesisLocalTarget(self.tmd_parameters_path)
 
 
@@ -619,11 +619,11 @@ class RescaleMorphologies(WorkflowTask):
     )
 
     def requires(self):
-        """"""
+        """ """
         return ApplySubstitutionRules()
 
     def run(self):
-        """"""
+        """ """
         morphs_df = pd.read_csv(self.input().path)
         scaling_rules = yaml.full_load(open(self.scaling_rules_path, "r"))
         rescaled_morphs_df = rescale_morphologies(
@@ -640,5 +640,5 @@ def run(self):
         rescaled_morphs_df.to_csv(self.output().path, index=False)
 
     def output(self):
-        """"""
+        """ """
         return MorphsDfLocalTarget(self.rescaled_morphs_df_path)