From e729283ac9dd26b45440f84f858ad0245bbdb60b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Thu, 5 Oct 2023 10:24:24 +0200
Subject: [PATCH 01/10] remove compute_responses from export_emodels_hoc

Change-Id: I963423ad4eaabac29e14d95eace5cb7c0be87b71
---
 bluepyemodel/export_emodel/export_emodel.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/bluepyemodel/export_emodel/export_emodel.py b/bluepyemodel/export_emodel/export_emodel.py
index 26c14f7b..a54e6a5e 100644
--- a/bluepyemodel/export_emodel/export_emodel.py
+++ b/bluepyemodel/export_emodel/export_emodel.py
@@ -238,7 +238,6 @@ def export_emodels_hoc(
     only_validated=False,
     only_best=True,
     seeds=None,
-    map_function=map,
     new_emodel_name=None,
 ):
     """Export a set of emodels to a set of folder named after them. Each folder will contain a hoc
@@ -250,14 +249,13 @@ def export_emodels_hoc(
         access_point, include_validation_protocols=True
     )
 
-    emodels = compute_responses(
-        access_point,
-        cell_evaluator,
-        map_function,
-        seeds=seeds,
-        preselect_for_validation=False,
-        store_responses=False,
-    )
+    emodels = access_point.get_emodels()
+    if access_point.emodel_metadata.iteration:
+        emodels = [
+            model
+            for model in emodels
+            if model.emodel_metadata.iteration == access_point.emodel_metadata.iteration
+        ]
 
     emodels = select_emodels(
         access_point.emodel_metadata.emodel,

From baa855697ba0f287a1d827f47e514430db25679b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Thu, 5 Oct 2023 10:47:27 +0200
Subject: [PATCH 02/10] Put hoc path of export in a function

Change-Id: I2546447aa68148e1a5800e03bd1a7c14ee0f9d7d
---
 bluepyemodel/export_emodel/export_emodel.py | 41 ++++++++++++++-------
 1 file changed, 27 insertions(+), 14 deletions(-)

diff --git a/bluepyemodel/export_emodel/export_emodel.py b/bluepyemodel/export_emodel/export_emodel.py
index a54e6a5e..a655f266 100644
--- a/bluepyemodel/export_emodel/export_emodel.py
+++ b/bluepyemodel/export_emodel/export_emodel.py
@@ -29,6 +29,29 @@
 logger = logging.getLogger(__name__)
 
 
+def get_hoc_file_path(output_path):
+    """Get the hoc file path."""
+    output_path = pathlib.Path(output_path)
+    return str(output_path / "model.hoc")
+
+
+def get_output_path(emodel, output_dir=None, output_base_dir="export_emodels_hoc"):
+    """Get the output path.
+    
+    Args:
+        emodel (EModel): emodel
+        output_dir (str): output directory
+        output_base_dir (str): if output_dir is None, export to this directory instead,
+            using also emodel metadata in the path
+    """
+    if output_dir is None:
+        output_dir = f"./{output_base_dir}/{emodel.emodel_metadata.as_string(seed=emodel.seed)}/"
+    output_path = pathlib.Path(output_dir)
+    output_path.mkdir(parents=True, exist_ok=True)
+
+    return output_path
+
+
 def _write_node_file(emodel, model_template_path, node_file_path, morphology_path=None):
     """Creates a nodes.h5 file in the SONATA format. It contains the information
     needed to run the model. See https://bbpteam.epfl.ch/documentation/projects/
@@ -102,14 +125,8 @@ def _export_model_sonata(cell_model, emodel, output_dir=None, new_emodel_name=No
     if new_emodel_name is not None:
         emodel.emodel_metadata.emodel = new_emodel_name
 
-    if output_dir is None:
-        output_dir = (
-            f"./export_emodels_sonata/{emodel.emodel_metadata.as_string(seed=emodel.seed)}/"
-        )
-    output_path = pathlib.Path(output_dir)
-    output_path.mkdir(parents=True, exist_ok=True)
-
-    hoc_file_path = str(output_path / "model.hoc")
+    output_path = get_output_path(emodel, output_dir, output_base_dir="export_emodels_sonata")
+    hoc_file_path = get_hoc_file_path(output_path)
     node_file_path = str(output_path / "nodes.h5")
     morphology_path = str(output_path / pathlib.Path(cell_model.morphology.morphology_path).name)
 
@@ -212,12 +229,8 @@ def _export_emodel_hoc(cell_model, mo, output_dir=None, new_emodel_name=None):
     if new_emodel_name is not None:
         mo.emodel_metadata.emodel = new_emodel_name
 
-    if output_dir is None:
-        output_dir = f"./export_emodels_hoc/{mo.emodel_metadata.as_string(seed=mo.seed)}/"
-    output_path = pathlib.Path(output_dir)
-    output_path.mkdir(parents=True, exist_ok=True)
-
-    hoc_file_path = str(output_path / "model.hoc")
+    output_path = get_output_path(mo, output_dir, output_base_dir="export_emodels_hoc")
+    hoc_file_path = get_hoc_file_path(output_path)
     morphology_path = str(output_path / pathlib.Path(cell_model.morphology.morphology_path).name)
 
     # Copy the morphology

From 7bdc310080b6a3696f80ff535e63e38508e949b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Thu, 5 Oct 2023 11:08:04 +0200
Subject: [PATCH 03/10] add store function for hocs

Change-Id: I2600bf4bf2726a1f902d0c451d41ee66bc0be157
---
 bluepyemodel/access_point/local.py          | 19 +++++++++++++++++++
 bluepyemodel/export_emodel/export_emodel.py |  4 +---
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/bluepyemodel/access_point/local.py b/bluepyemodel/access_point/local.py
index 378c762c..58947c75 100644
--- a/bluepyemodel/access_point/local.py
+++ b/bluepyemodel/access_point/local.py
@@ -31,6 +31,8 @@
 from bluepyemodel.emodel_pipeline.emodel_metadata import EModelMetadata
 from bluepyemodel.emodel_pipeline.emodel_settings import EModelPipelineSettings
 from bluepyemodel.emodel_pipeline.emodel_workflow import EModelWorkflow
+from bluepyemodel.export_emodel.export_emodel import export_emodels_hoc
+from bluepyemodel.export_emodel.export_emodel import export_emodels_sonata
 from bluepyemodel.evaluation.evaluator import LEGACY_PRE_PROTOCOLS
 from bluepyemodel.evaluation.evaluator import PRE_PROTOCOLS
 from bluepyemodel.evaluation.fitness_calculator_configuration import FitnessCalculatorConfiguration
@@ -789,3 +791,20 @@ def add_entry_recipes(
 
         with recipes_path.open("w") as f:
             json.dump(recipes, f, indent=2)
+
+    def store_emodels_hoc(
+        self, only_validated=False, only_best=True, seeds=None, new_emodel_name=None
+    ):
+        export_emodels_hoc(self, only_validated, only_best, seeds, new_emodel_name)
+
+    def store_emodels_sonata(
+        self,
+        only_validated=False,
+        only_best=True,
+        seeds=None,
+        map_function=map,
+        new_emodel_name=None,
+    ):
+        export_emodels_sonata(
+            self, only_validated, only_best, seeds, map_function, new_emodel_name
+        )
diff --git a/bluepyemodel/export_emodel/export_emodel.py b/bluepyemodel/export_emodel/export_emodel.py
index a655f266..33f3175a 100644
--- a/bluepyemodel/export_emodel/export_emodel.py
+++ b/bluepyemodel/export_emodel/export_emodel.py
@@ -254,9 +254,7 @@ def export_emodels_hoc(
     new_emodel_name=None,
 ):
     """Export a set of emodels to a set of folder named after them. Each folder will contain a hoc
-    version of the model.
-
-    WARNING: this function is not compatible with multiprocessing."""
+    version of the model."""
 
     cell_evaluator = get_evaluator_from_access_point(
         access_point, include_validation_protocols=True

From ace00c7b8f7a706914e1302a8d0669de5b0522a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Thu, 5 Oct 2023 17:44:43 +0200
Subject: [PATCH 04/10] add emodelscript

Change-Id: I59ed7c5a43557ee9175e32ba6c276f45f6bd1c75
---
 bluepyemodel/access_point/local.py            | 20 +++--
 bluepyemodel/emodel_pipeline/emodel_script.py | 56 +++++++++++++
 bluepyemodel/export_emodel/export_emodel.py   | 64 ++-------------
 bluepyemodel/export_emodel/utils.py           | 79 +++++++++++++++++++
 4 files changed, 157 insertions(+), 62 deletions(-)
 create mode 100644 bluepyemodel/emodel_pipeline/emodel_script.py
 create mode 100644 bluepyemodel/export_emodel/utils.py

diff --git a/bluepyemodel/access_point/local.py b/bluepyemodel/access_point/local.py
index 58947c75..ca95d322 100644
--- a/bluepyemodel/access_point/local.py
+++ b/bluepyemodel/access_point/local.py
@@ -31,8 +31,6 @@
 from bluepyemodel.emodel_pipeline.emodel_metadata import EModelMetadata
 from bluepyemodel.emodel_pipeline.emodel_settings import EModelPipelineSettings
 from bluepyemodel.emodel_pipeline.emodel_workflow import EModelWorkflow
-from bluepyemodel.export_emodel.export_emodel import export_emodels_hoc
-from bluepyemodel.export_emodel.export_emodel import export_emodels_sonata
 from bluepyemodel.evaluation.evaluator import LEGACY_PRE_PROTOCOLS
 from bluepyemodel.evaluation.evaluator import PRE_PROTOCOLS
 from bluepyemodel.evaluation.fitness_calculator_configuration import FitnessCalculatorConfiguration
@@ -792,10 +790,22 @@ def add_entry_recipes(
         with recipes_path.open("w") as f:
             json.dump(recipes, f, indent=2)
 
+    def store_hocs(
+        self,
+        only_validated=False,
+        only_best=True,
+        seeds=None,
+        map_function=map,
+        new_emodel_name=None,
+        description=None,
+        output_base_dir="export_emodels_hoc"
+    ):
+        pass
+
     def store_emodels_hoc(
         self, only_validated=False, only_best=True, seeds=None, new_emodel_name=None
     ):
-        export_emodels_hoc(self, only_validated, only_best, seeds, new_emodel_name)
+        pass
 
     def store_emodels_sonata(
         self,
@@ -805,6 +815,4 @@ def store_emodels_sonata(
         map_function=map,
         new_emodel_name=None,
     ):
-        export_emodels_sonata(
-            self, only_validated, only_best, seeds, map_function, new_emodel_name
-        )
+        pass
diff --git a/bluepyemodel/emodel_pipeline/emodel_script.py b/bluepyemodel/emodel_pipeline/emodel_script.py
new file mode 100644
index 00000000..9db9b088
--- /dev/null
+++ b/bluepyemodel/emodel_pipeline/emodel_script.py
@@ -0,0 +1,56 @@
+"""EModelScript class"""
+
+"""
+Copyright 2023, EPFL/Blue Brain Project
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+"""
+
+
+class EModelScript:
+
+    """Contains an emodel hoc file path."""
+
+    def __init__(
+        self,
+        hoc_file_path=None,
+        seed=None,
+        workflow_id=None
+    ):
+        """Init
+
+        Args:
+            hoc_file_path (str): path to the hoc file of the emodel
+            seed (str): seed used during optimisation for this emodel.
+            workflow_id (str): id of the emodel workflow resource
+        """
+        self.hoc_file_path = hoc_file_path
+        self.seed = seed
+        self.workflow_id = workflow_id
+
+    def get_related_nexus_ids(self):
+        return {
+            "generation": {
+                "type": "Generation",
+                "activity": {
+                    "type": "Activity",
+                    "followedWorkflow": {"type": "EModelWorkflow", "id": self.workflow_id},
+                },
+            }
+        }
+
+    def as_dict(self):
+        return {
+            "nexus_distributions": [self.hoc_file_path],
+            "seed": self.seed,
+        }
diff --git a/bluepyemodel/export_emodel/export_emodel.py b/bluepyemodel/export_emodel/export_emodel.py
index 33f3175a..6be2a107 100644
--- a/bluepyemodel/export_emodel/export_emodel.py
+++ b/bluepyemodel/export_emodel/export_emodel.py
@@ -25,33 +25,13 @@
 
 from bluepyemodel.evaluation.evaluation import compute_responses
 from bluepyemodel.evaluation.evaluation import get_evaluator_from_access_point
+from bluepyemodel.export_emodel.utils import get_hoc_file_path
+from bluepyemodel.export_emodel.utils import get_output_path
+from bluepyemodel.export_emodel.utils import select_emodels
 
 logger = logging.getLogger(__name__)
 
 
-def get_hoc_file_path(output_path):
-    """Get the hoc file path."""
-    output_path = pathlib.Path(output_path)
-    return str(output_path / "model.hoc")
-
-
-def get_output_path(emodel, output_dir=None, output_base_dir="export_emodels_hoc"):
-    """Get the output path.
-    
-    Args:
-        emodel (EModel): emodel
-        output_dir (str): output directory
-        output_base_dir (str): if output_dir is None, export to this directory instead,
-            using also emodel metadata in the path
-    """
-    if output_dir is None:
-        output_dir = f"./{output_base_dir}/{emodel.emodel_metadata.as_string(seed=emodel.seed)}/"
-    output_path = pathlib.Path(output_dir)
-    output_path.mkdir(parents=True, exist_ok=True)
-
-    return output_path
-
-
 def _write_node_file(emodel, model_template_path, node_file_path, morphology_path=None):
     """Creates a nodes.h5 file in the SONATA format. It contains the information
     needed to run the model. See https://bbpteam.epfl.ch/documentation/projects/
@@ -151,33 +131,6 @@ def _export_model_sonata(cell_model, emodel, output_dir=None, new_emodel_name=No
     )
 
 
-def select_emodels(emodel_name, emodels, only_validated=False, only_best=True, seeds=None):
-    if not emodels:
-        logger.warning("In export_emodels_nexus, no emodel for %s", emodel_name)
-        return []
-
-    if only_best:
-        emodels = [sorted(emodels, key=lambda x: x.fitness)[0]]
-
-    if seeds:
-        emodels = [e for e in emodels if e.seed in seeds]
-        if not emodels:
-            logger.warning(
-                "In export_emodels_nexus, no emodel for %s and seeds %s", emodel_name, seeds
-            )
-            return []
-
-    if only_validated:
-        emodels = [e for e in emodels if e.passed_validation]
-        if not emodels:
-            logger.warning(
-                "In export_emodels_nexus, no emodel for %s that passed validation", emodel_name
-            )
-            return []
-
-    return emodels
-
-
 def export_emodels_sonata(
     access_point,
     only_validated=False,
@@ -212,6 +165,8 @@ def export_emodels_sonata(
         seeds=seeds,
     )
     if not emodels:
+        logger.warning("No emodels were selected in export_emodels_sonata. "
+                       "Stopping sonata export here.")
         return
 
     cell_model = cell_evaluator.cell_model
@@ -251,6 +206,7 @@ def export_emodels_hoc(
     only_validated=False,
     only_best=True,
     seeds=None,
+    map_function=map,
     new_emodel_name=None,
 ):
     """Export a set of emodels to a set of folder named after them. Each folder will contain a hoc
@@ -261,12 +217,6 @@ def export_emodels_hoc(
     )
 
     emodels = access_point.get_emodels()
-    if access_point.emodel_metadata.iteration:
-        emodels = [
-            model
-            for model in emodels
-            if model.emodel_metadata.iteration == access_point.emodel_metadata.iteration
-        ]
 
     emodels = select_emodels(
         access_point.emodel_metadata.emodel,
@@ -274,8 +224,10 @@ def export_emodels_hoc(
         only_validated=only_validated,
         only_best=only_best,
         seeds=seeds,
+        iteration=access_point.emodel_metadata.iteration,
     )
     if not emodels:
+        logger.warning("No emodels were selected in export_emodels_hoc. Stopping hoc export here.")
         return
 
     cell_model = cell_evaluator.cell_model
diff --git a/bluepyemodel/export_emodel/utils.py b/bluepyemodel/export_emodel/utils.py
new file mode 100644
index 00000000..b659003e
--- /dev/null
+++ b/bluepyemodel/export_emodel/utils.py
@@ -0,0 +1,79 @@
+"""Export the emodels in the SONATA format"""
+
+"""
+Copyright 2023, EPFL/Blue Brain Project
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+"""
+
+import logging
+import pathlib
+
+logger = logging.getLogger(__name__)
+
+
+def get_output_path(emodel, output_dir=None, output_base_dir="export_emodels_hoc"):
+    """Get the output path.
+    
+    Args:
+        emodel (EModel): emodel
+        output_dir (str): output directory
+        output_base_dir (str): if output_dir is None, export to this directory instead,
+            using also emodel metadata in the path
+    """
+    if output_dir is None:
+        output_dir = f"./{output_base_dir}/{emodel.emodel_metadata.as_string(seed=emodel.seed)}/"
+    output_path = pathlib.Path(output_dir)
+    output_path.mkdir(parents=True, exist_ok=True)
+
+    return output_path
+
+
+def get_hoc_file_path(output_path):
+    """Get the hoc file path."""
+    output_path = pathlib.Path(output_path)
+    return str(output_path / "model.hoc")
+
+
+def select_emodels(emodel_name, emodels, only_validated=False, only_best=True, seeds=None, iteration=None):
+    if not emodels:
+        logger.warning("In export_emodels_nexus, no emodel for %s", emodel_name)
+        return []
+    
+    if iteration:
+        emodels = [
+            model
+            for model in emodels
+            if model.emodel_metadata.iteration == iteration
+        ]
+
+    if only_best:
+        emodels = [sorted(emodels, key=lambda x: x.fitness)[0]]
+
+    if seeds:
+        emodels = [e for e in emodels if e.seed in seeds]
+        if not emodels:
+            logger.warning(
+                "In export_emodels_nexus, no emodel for %s and seeds %s", emodel_name, seeds
+            )
+            return []
+
+    if only_validated:
+        emodels = [e for e in emodels if e.passed_validation]
+        if not emodels:
+            logger.warning(
+                "In export_emodels_nexus, no emodel for %s that passed validation", emodel_name
+            )
+            return []
+
+    return emodels

From 6c8bdc0db38eb5dc3d677542b1b8612b769172ab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Fri, 6 Oct 2023 11:21:59 +0200
Subject: [PATCH 05/10] add store hoc function to DataAccessPoint

Change-Id: Ie3418546ab6c193b3c76756aa9ab4be359124918
---
 bluepyemodel/access_point/access_point.py | 27 +++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/bluepyemodel/access_point/access_point.py b/bluepyemodel/access_point/access_point.py
index 875144cb..776ded2f 100644
--- a/bluepyemodel/access_point/access_point.py
+++ b/bluepyemodel/access_point/access_point.py
@@ -167,6 +167,33 @@ def get_emodel_names(self):
         Returns:
             dict: keys are emodel names with seed, values are names without seed.
         """
+    
+    def store_hocs(
+        self,
+        only_validated=False,
+        only_best=True,
+        seeds=None,
+        map_function=map,
+        new_emodel_name=None,
+        description=None,
+        output_base_dir="export_emodels_hoc"
+    ):
+        """Store the hoc files"""
+
+    def store_emodels_hoc(
+        self, only_validated=False, only_best=True, seeds=None, new_emodel_name=None
+    ):
+        """Store hoc file produced by export_hoc"""
+
+    def store_emodels_sonata(
+        self,
+        only_validated=False,
+        only_best=True,
+        seeds=None,
+        map_function=map,
+        new_emodel_name=None,
+    ):
+        """Store hoc file produced by export_sonata"""
 
     def optimisation_state(self, seed=None, continue_opt=False):
         """Return the state of the optimisation.

From a082c05c70bb6d982b419d0682b08c05cbc38367 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Fri, 6 Oct 2023 13:47:26 +0200
Subject: [PATCH 06/10] lint fix

Change-Id: Ic0f73aa7a8b830ebad4dd7876c6be30f0316137e
---
 bluepyemodel/access_point/access_point.py | 2 +-
 bluepyemodel/export_emodel/utils.py       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bluepyemodel/access_point/access_point.py b/bluepyemodel/access_point/access_point.py
index 776ded2f..afb29a95 100644
--- a/bluepyemodel/access_point/access_point.py
+++ b/bluepyemodel/access_point/access_point.py
@@ -167,7 +167,7 @@ def get_emodel_names(self):
         Returns:
             dict: keys are emodel names with seed, values are names without seed.
         """
-    
+
     def store_hocs(
         self,
         only_validated=False,
diff --git a/bluepyemodel/export_emodel/utils.py b/bluepyemodel/export_emodel/utils.py
index b659003e..e0ff4fd9 100644
--- a/bluepyemodel/export_emodel/utils.py
+++ b/bluepyemodel/export_emodel/utils.py
@@ -24,7 +24,7 @@
 
 def get_output_path(emodel, output_dir=None, output_base_dir="export_emodels_hoc"):
     """Get the output path.
-    
+
     Args:
         emodel (EModel): emodel
         output_dir (str): output directory
@@ -49,7 +49,7 @@ def select_emodels(emodel_name, emodels, only_validated=False, only_best=True, s
     if not emodels:
         logger.warning("In export_emodels_nexus, no emodel for %s", emodel_name)
         return []
-    
+
     if iteration:
         emodels = [
             model

From 064390cfe5a848488cb7a3535b196d38145f9e3b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Fri, 6 Oct 2023 13:55:46 +0200
Subject: [PATCH 07/10] lint fix

Change-Id: I218c9613eb157bd8cab92af55a133d8b36ede9a1
---
 bluepyemodel/export_emodel/export_emodel.py | 1 -
 bluepyemodel/export_emodel/utils.py         | 4 +++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/bluepyemodel/export_emodel/export_emodel.py b/bluepyemodel/export_emodel/export_emodel.py
index 6be2a107..32c9a8a6 100644
--- a/bluepyemodel/export_emodel/export_emodel.py
+++ b/bluepyemodel/export_emodel/export_emodel.py
@@ -206,7 +206,6 @@ def export_emodels_hoc(
     only_validated=False,
     only_best=True,
     seeds=None,
-    map_function=map,
     new_emodel_name=None,
 ):
     """Export a set of emodels to a set of folder named after them. Each folder will contain a hoc
diff --git a/bluepyemodel/export_emodel/utils.py b/bluepyemodel/export_emodel/utils.py
index e0ff4fd9..4d79afcc 100644
--- a/bluepyemodel/export_emodel/utils.py
+++ b/bluepyemodel/export_emodel/utils.py
@@ -45,7 +45,9 @@ def get_hoc_file_path(output_path):
     return str(output_path / "model.hoc")
 
 
-def select_emodels(emodel_name, emodels, only_validated=False, only_best=True, seeds=None, iteration=None):
+def select_emodels(
+    emodel_name, emodels, only_validated=False, only_best=True, seeds=None, iteration=None
+):
     if not emodels:
         logger.warning("In export_emodels_nexus, no emodel for %s", emodel_name)
         return []

From 533e6e056f0c51e9ad781d5739a01bf684f3e6e6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Fri, 6 Oct 2023 14:03:38 +0200
Subject: [PATCH 08/10] black fix

Change-Id: I9fea93747a79928882b4ddcb5473803faf225061
---
 bluepyemodel/access_point/access_point.py     | 2 +-
 bluepyemodel/access_point/local.py            | 2 +-
 bluepyemodel/emodel_pipeline/emodel_script.py | 7 +------
 bluepyemodel/export_emodel/export_emodel.py   | 5 +++--
 bluepyemodel/export_emodel/utils.py           | 6 +-----
 5 files changed, 7 insertions(+), 15 deletions(-)

diff --git a/bluepyemodel/access_point/access_point.py b/bluepyemodel/access_point/access_point.py
index afb29a95..69e31f07 100644
--- a/bluepyemodel/access_point/access_point.py
+++ b/bluepyemodel/access_point/access_point.py
@@ -176,7 +176,7 @@ def store_hocs(
         map_function=map,
         new_emodel_name=None,
         description=None,
-        output_base_dir="export_emodels_hoc"
+        output_base_dir="export_emodels_hoc",
     ):
         """Store the hoc files"""
 
diff --git a/bluepyemodel/access_point/local.py b/bluepyemodel/access_point/local.py
index ca95d322..d10b9ed9 100644
--- a/bluepyemodel/access_point/local.py
+++ b/bluepyemodel/access_point/local.py
@@ -798,7 +798,7 @@ def store_hocs(
         map_function=map,
         new_emodel_name=None,
         description=None,
-        output_base_dir="export_emodels_hoc"
+        output_base_dir="export_emodels_hoc",
     ):
         pass
 
diff --git a/bluepyemodel/emodel_pipeline/emodel_script.py b/bluepyemodel/emodel_pipeline/emodel_script.py
index 9db9b088..baedd317 100644
--- a/bluepyemodel/emodel_pipeline/emodel_script.py
+++ b/bluepyemodel/emodel_pipeline/emodel_script.py
@@ -21,12 +21,7 @@ class EModelScript:
 
     """Contains an emodel hoc file path."""
 
-    def __init__(
-        self,
-        hoc_file_path=None,
-        seed=None,
-        workflow_id=None
-    ):
+    def __init__(self, hoc_file_path=None, seed=None, workflow_id=None):
         """Init
 
         Args:
diff --git a/bluepyemodel/export_emodel/export_emodel.py b/bluepyemodel/export_emodel/export_emodel.py
index 32c9a8a6..940111bb 100644
--- a/bluepyemodel/export_emodel/export_emodel.py
+++ b/bluepyemodel/export_emodel/export_emodel.py
@@ -165,8 +165,9 @@ def export_emodels_sonata(
         seeds=seeds,
     )
     if not emodels:
-        logger.warning("No emodels were selected in export_emodels_sonata. "
-                       "Stopping sonata export here.")
+        logger.warning(
+            "No emodels were selected in export_emodels_sonata. " "Stopping sonata export here."
+        )
         return
 
     cell_model = cell_evaluator.cell_model
diff --git a/bluepyemodel/export_emodel/utils.py b/bluepyemodel/export_emodel/utils.py
index 4d79afcc..d9d5550a 100644
--- a/bluepyemodel/export_emodel/utils.py
+++ b/bluepyemodel/export_emodel/utils.py
@@ -53,11 +53,7 @@ def select_emodels(
         return []
 
     if iteration:
-        emodels = [
-            model
-            for model in emodels
-            if model.emodel_metadata.iteration == iteration
-        ]
+        emodels = [model for model in emodels if model.emodel_metadata.iteration == iteration]
 
     if only_best:
         emodels = [sorted(emodels, key=lambda x: x.fitness)[0]]

From a6c5d6444c0af9bcdc613497f1d59c4661fc6748 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Fri, 6 Oct 2023 14:07:50 +0200
Subject: [PATCH 09/10] lint fix

Change-Id: I58c42b4223b453acf8105c6cd9fcc21be6196afc
---
 bluepyemodel/export_emodel/export_emodel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bluepyemodel/export_emodel/export_emodel.py b/bluepyemodel/export_emodel/export_emodel.py
index 940111bb..2f058ae4 100644
--- a/bluepyemodel/export_emodel/export_emodel.py
+++ b/bluepyemodel/export_emodel/export_emodel.py
@@ -166,7 +166,7 @@ def export_emodels_sonata(
     )
     if not emodels:
         logger.warning(
-            "No emodels were selected in export_emodels_sonata. " "Stopping sonata export here."
+            "No emodels were selected in export_emodels_sonata. Stopping sonata export here."
         )
         return
 

From f16d510602fd1443b287649c9079545ee5a993ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaquier=20Aur=C3=A9lien=20Tristan?=
 <aurelien.jaquier@epfl.ch>
Date: Fri, 6 Oct 2023 15:13:15 +0200
Subject: [PATCH 10/10] raise NotImplementedError instead of passing in hoc
 storing function of LocalAccesssPoint

Change-Id: I77a89de35e361a116b97befd3db1b9cb2b1e75c2
---
 bluepyemodel/access_point/local.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bluepyemodel/access_point/local.py b/bluepyemodel/access_point/local.py
index d10b9ed9..5e89698b 100644
--- a/bluepyemodel/access_point/local.py
+++ b/bluepyemodel/access_point/local.py
@@ -800,12 +800,12 @@ def store_hocs(
         description=None,
         output_base_dir="export_emodels_hoc",
     ):
-        pass
+        raise NotImplementedError
 
     def store_emodels_hoc(
         self, only_validated=False, only_best=True, seeds=None, new_emodel_name=None
     ):
-        pass
+        raise NotImplementedError
 
     def store_emodels_sonata(
         self,
@@ -815,4 +815,4 @@ def store_emodels_sonata(
         map_function=map,
         new_emodel_name=None,
     ):
-        pass
+        raise NotImplementedError