update for imporvement to git metadata collection

KarrLab · Jul 5, 2019 · 51cebe8 · 51cebe8
1 parent 6400a35
commit 51cebe8
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Showing 6 changed files with 12 additions and 12 deletions.
diff --git a/rand_wc_model_gen/__main__.py b/rand_wc_model_gen/__main__.py
@@ -66,12 +66,12 @@ def _default(self):
             os.makedirs(os.path.dirname(config['kb']['path']['seq']))
         wc_kb.io.Writer().run(config['kb']['path']['core'], kb,
                               seq_path=config['kb']['path']['seq'],
-                              set_repo_metadata_from_path=config['kb_gen']['set_repo_metadata_from_path'])
+                              data_repo_metadata=config['kb_gen']['data_repo_metadata'])
 
         if not os.path.isdir(os.path.dirname(config['model']['path'])):
             os.makedirs(os.path.dirname(config['model']['path']))
         wc_lang.io.Writer().run(config['model']['path'], model,
-                                set_repo_metadata_from_path=config['model_gen']['set_repo_metadata_from_path'])
+                                data_repo_metadata=config['model_gen']['data_repo_metadata'])
 
 
 class SimulateController(cement.Controller):

diff --git a/rand_wc_model_gen/config/core.default.cfg b/rand_wc_model_gen/config/core.default.cfg
@@ -4,7 +4,7 @@
         id = rand_wc_model
         name = Random whole-cell model
         version = ${version}
-        set_repo_metadata_from_path = true
+        data_repo_metadata = true
 
         [[[component]]]
             [[[[PropertiesGenerator]]]]
@@ -39,7 +39,7 @@
         id = rand_wc_model
         name = Random whole-cell model
         version = ${version}
-        set_repo_metadata_from_path = true
+        data_repo_metadata = true
 
         [[[component]]]
             [[[[TranscriptionSubmodelGenerator]]]]

diff --git a/rand_wc_model_gen/config/core.schema.cfg b/rand_wc_model_gen/config/core.schema.cfg
@@ -4,7 +4,7 @@
         id = string()
         name = string()
         version = string()
-        set_repo_metadata_from_path = boolean()
+        data_repo_metadata = boolean()
 
         [[[component]]]
             [[[[PropertiesGenerator]]]]
@@ -39,7 +39,7 @@
         id = string()
         name = string()
         version = string()
-        set_repo_metadata_from_path = boolean()
+        data_repo_metadata = boolean()
 
         [[[component]]]
             [[[[TranscriptionSubmodelGenerator]]]]

diff --git a/rand_wc_model_gen/config/rand_wc_model_gen.cfg b/rand_wc_model_gen/config/rand_wc_model_gen.cfg
@@ -1,11 +1,11 @@
 [rand_wc_model_gen]
     [[kb_gen]]
-        # set_repo_metadata_from_path = false
+        # data_repo_metadata = false
         [[[component]]]
             [[[[GenomeGenerator]]]]
                 num_chromosomes = 1
                 mean_num_genes = 100.
                 mean_gene_len = 10.
                 seq_path = ${package_path}/kb/seq.fna
     [[model_gen]]
-        # set_repo_metadata_from_path = false
+        # data_repo_metadata = false
diff --git a/rand_wc_model_gen/config/rand_wc_model_gen_without_git.cfg b/rand_wc_model_gen/config/rand_wc_model_gen_without_git.cfg
@@ -1,11 +1,11 @@
 [rand_wc_model_gen]
     [[kb_gen]]
-        set_repo_metadata_from_path = false
+        data_repo_metadata = false
         [[[component]]]
             [[[[GenomeGenerator]]]]
                 num_chromosomes = 1
                 mean_num_genes = 100.
                 mean_gene_len = 10.
                 seq_path = ${package_path}/kb/seq.fna
     [[model_gen]]
-        set_repo_metadata_from_path = false
+        data_repo_metadata = false
diff --git a/tests/test_main.py b/tests/test_main.py
@@ -37,7 +37,7 @@ def setUp(self):
         with open(self.config_path, 'w') as file:
             file.write('[rand_wc_model_gen]\n')
             file.write('    [[kb_gen]]\n')
-            file.write('        set_repo_metadata_from_path = false\n')
+            file.write('        data_repo_metadata = false\n')
             file.write('        [[[component]]]\n')
             file.write('            [[[[GenomeGenerator]]]]\n')
             file.write('                num_chromosomes = 1\n')
@@ -49,7 +49,7 @@ def setUp(self):
             file.write('            core = {}\n'.format(self.kb_core_path))
             file.write('            seq = {}\n'.format(self.kb_seq_path))
             file.write('    [[model_gen]]\n')
-            file.write('        set_repo_metadata_from_path = false\n')
+            file.write('        data_repo_metadata = false\n')
             file.write('    [[model]]\n')
             file.write('        path = {}\n'.format(self.model_path))
             file.write('    [[sim]]\n')