Merge pull request #200 from BlueBrain/apical_and_yaml

new option for no apical + str for yaml

Author: wvangeit

bluepymm/prepare_combos/parse_files.py

@@ -128,10 +128,10 @@ def read_mm_recipe_yaml(recipe_filename):
     mecombos = pandas.DataFrame(columns=["layer", "fullmtype", "etype"])
     for region in recipe['neurons']:
         for etype in region['traits']['etype'].keys():
-            n_combos = len(mecombos)
-            mecombos.loc[n_combos, 'layer'] = region['traits']['layer']
-            mecombos.loc[n_combos, 'fullmtype'] = region['traits']['mtype']
-            mecombos.loc[n_combos, 'etype'] = etype
+            end = len(mecombos)
+            mecombos.loc[end, 'layer'] = str(region['traits']['layer'])
+            mecombos.loc[end, 'fullmtype'] = str(region['traits']['mtype'])
+            mecombos.loc[end, 'etype'] = str(etype)
     return mecombos
 
 

bluepymm/prepare_combos/prepare_emodel_dirs.py

@@ -305,5 +305,4 @@ def prepare_emodel_dirs(
     for emodel_dir_dict in pool.map(prepare_emodel_dir, arg_list, chunksize=1):
         for emodel, emodel_dir in emodel_dir_dict.items():
             emodel_dirs[emodel] = emodel_dir
-
     return emodel_dirs

bluepymm/run_combos/calculate_scores.py

@@ -139,7 +139,6 @@ def run_emodel_morph(
             if hasattr(setup, 'multieval'):
 
                 prefix = 'mm'
-
                 altmorph = [[prefix, morph_path, apical_point_isec]]
                 evaluator = setup.evaluator.create(etype='%s' % emodel,
                                                    altmorph=altmorph)
@@ -193,7 +192,7 @@ def run_emodel_morph(
 
 
 def create_arg_list(scores_db_filename, emodel_dirs, final_dict,
-                    extra_values_error=False):
+                    extra_values_error=False, use_apical_points=True):
     """Create list of argument tuples to be used as an input for
     run_emodel_morph.
 
@@ -203,6 +202,7 @@ def create_arg_list(scores_db_filename, emodel_dirs, final_dict,
             input files
         final_dict: a dict mapping e-models to dicts with e-model parameters
         extra_values_error: boolean to raise an exception upon a missing key
+        use_apical_points: boolean to use apical points or not
 
     Raises:
         ValueError, if one of the database entries contains has value None for
@@ -217,7 +217,7 @@ def create_arg_list(scores_db_filename, emodel_dirs, final_dict,
 
         apical_points_isec = {}
         setup = tools.load_module('setup', emodel_dirs[one_row['emodel']])
-        if hasattr(setup, 'multieval'):
+        if hasattr(setup, 'multieval') and use_apical_points:
             apical_points_isec = tools.load_json(
                 os.path.join(one_row['morph_dir'], "apical_points_isec.json")
             )
@@ -320,7 +320,8 @@ def expand_scores_to_score_values_table(scores_sqlite_filename):
 
 
 def calculate_scores(final_dict, emodel_dirs, scores_db_filename,
-                     use_ipyp=False, ipyp_profile=None, timeout=10):
+                     use_ipyp=False, ipyp_profile=None, timeout=10,
+                     use_apical_points=True):
     """Calculate scores of e-model morphology combinations and update the
     database accordingly.
 
@@ -333,10 +334,14 @@ def calculate_scores(final_dict, emodel_dirs, scores_db_filename,
         use_ipyp: bool indicating whether ipyparallel is used. Default is
             False.
         ipyp_profile: path to ipyparallel profile. Default is None.
+        use_apical_points: boolean to use apical points or not
     """
 
     print('Creating argument list for parallelisation')
-    arg_list = create_arg_list(scores_db_filename, emodel_dirs, final_dict)
+    arg_list = create_arg_list(scores_db_filename,
+                               emodel_dirs,
+                               final_dict,
+                               use_apical_points=use_apical_points)
 
     print('Parallelising score evaluation of %d me-combos' % len(arg_list))
 

bluepymm/run_combos/main.py

@@ -56,14 +56,20 @@ def run_combos_from_conf(conf_dict, ipyp=None, ipyp_profile=None, timeout=10):
             'emodel_dirs.json'))
     scores_db_path = os.path.abspath(conf_dict['scores_db'])
 
+    if 'use_apical_points' in conf_dict:
+        use_apical_points = conf_dict['use_apical_points']
+    else:
+        use_apical_points = True
+
     print('Calculating scores')
     calculate_scores.calculate_scores(
         final_dict,
         emodel_dirs,
         scores_db_path,
         use_ipyp=ipyp,
         ipyp_profile=ipyp_profile,
-        timeout=timeout)
+        timeout=timeout,
+        use_apical_points=use_apical_points)
 
 
 def run_combos(conf_filename, ipyp=None, ipyp_profile=None):

bluepymm/tests/test_calculate_scores.py

@@ -379,11 +379,12 @@ def test_calculate_scores():
             time.sleep(10)
 
         with tools.cd(TEST_DIR):
-            run_combos.calculate_scores.calculate_scores(final_dict,
-                                                         emodel_dirs,
-                                                         test_db_filename,
-                                                         use_ipyp=use_ipyp
-                                                         )
+            run_combos.calculate_scores.calculate_scores(
+                final_dict,
+                emodel_dirs,
+                test_db_filename,
+                use_ipyp=use_ipyp
+            )
 
         if use_ipyp:
             ip_proc.terminate()

bluepymm/tests/test_parse_files.py

@@ -158,10 +158,10 @@ def test_read_mm_recipe_yaml():
     recipe_filename = os.path.join(
         BASE_DIR,
         'examples/simple1/data/simple1_recipe.yaml')
-    expected_records = [(1, "mtype1", "etype1"),
-                        (1, "mtype1", "etype2"),
-                        (1, "mtype2", "etype1"),
-                        (2, "mtype1", "etype2"), ]
+    expected_records = [("1", "mtype1", "etype1"),
+                        ("1", "mtype1", "etype2"),
+                        ("1", "mtype2", "etype1"),
+                        ("2", "mtype1", "etype2"), ]
     expected_df = pandas.DataFrame(expected_records,
                                    columns=["layer", "fullmtype", "etype"],
                                    )

bluepymm/tests/test_run_combos.py

@@ -54,3 +54,8 @@ def test_run_combos():
 
         # verify output
         _verify_run_combos_output(config['scores_db'])
+
+        # with use_apical_points
+        config['use_apical_points'] = False
+        run_combos.main.run_combos_from_conf(config)
+        _verify_run_combos_output(config['scores_db'])

setup.py

@@ -27,7 +27,7 @@
     name="bluepymm",
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    install_requires=['sh', 'bluepyopt', 'matplotlib', 'pandas', 'numpy',
+    install_requires=['sh', 'bluepyopt', 'matplotlib', 'pandas', 'numpy', 'NEURON',
                       'ipyparallel', 'lxml', 'h5py', 'pyyaml'],
     packages=setuptools.find_packages(exclude=('notebook',)),
     author="BlueBrain Project, EPFL",

tox.ini

@@ -21,9 +21,9 @@ setenv =
     PYTHONPATH={env:TOX_NRNDIR}/local/lib/python:{env:TOX_NRNDIR}/local/lib64/python
 commands =
     make clean
-    ./.install_neuron.sh {env:TOX_NRNDIR}/src {env:TOX_NRNDIR}/local {basepython} 
+    ; ./.install_neuron.sh {env:TOX_NRNDIR}/src {env:TOX_NRNDIR}/local {basepython} 
 
-    make toxbinlinks
+    ; make toxbinlinks
 
     make simple1_git
     style: pycodestyle --ignore=E402,W503,W504 bluepymm