update for pip

Author: sapiris

grim/grim.py

@@ -23,18 +23,30 @@
 #
 
 
-from validation import runfile
-from imputation.graph_generation import generate_neo4j_multi_hpf
+from .validation import runfile
+from .imputation.graph_generation import generate_neo4j_multi_hpf
 
-from imputation.imputegl import Imputation
-from imputation.imputegl.networkx_graph import Graph
+from .imputation.imputegl import Imputation
+from .imputation.imputegl.networkx_graph import Graph
+import os
+
+def graph_freqs(conf_file = "", freq_file='default', path='default', for_em = False,  em_pop=None ):
+    if conf_file == "":
+        conf_file = os.path.dirname(os.path.realpath(__file__))  + '/conf/minimal-configuration.json'
+    if path == "default":
+        path = os.path.dirname(os.path.realpath(__file__)) +  '/imputation/graph_generation/'
+    if freq_file == "default":
+        freq_file = 'output/hpf.csv'
 
-def graph_freqs(conf_file = "./conf/minimal-configuration.json", for_em = False,  em_pop=None, freq_file='hpf.csv', path='imputation/graph_generation/' ):
     generate_neo4j_multi_hpf.generate_graph(freq_file=freq_file, path=path, config_file=conf_file, em_pop=em_pop,
                        em=for_em)
 
-def impute(conf_file = "./conf/minimal-configuration.json"):
-    runfile.run_impute(conf_file)
+def impute(conf_file = ""):
+    project_dir = ""
+    if conf_file == "":
+        conf_file = os.path.dirname(os.path.realpath(__file__)) + '/conf/minimal-configuration.json'
+        project_dir = os.path.dirname(os.path.realpath(__file__)) + '/'
+    runfile.run_impute(conf_file, project_dir)
 
 def impute_instance(config):
     graph = Graph(config)

grim/imputation/graph_generation/generate_neo4j_multi_hpf.py

@@ -192,7 +192,7 @@ def loci_order(loc_values):
 
     return FULL_LOCI, full_name_index_dict
 
-def generate_graph(freq_file = 'hpf.csv', path = '', config_file = "../../conf/minimal-configuration.json", em_pop = None, em= False):
+def generate_graph(freq_file = 'output/hpf.csv', path = '', config_file = "../../conf/minimal-configuration.json", em_pop = None, em= False):
     ##############################################################################
     # Configure
     ##############################################################################
@@ -201,7 +201,7 @@ def generate_graph(freq_file = 'hpf.csv', path = '', config_file = "../../conf/m
     pathlib.Path(csvdir).mkdir(parents=True, exist_ok=True)
 
     # Input file
-    freq_file = path + 'output/' + freq_file
+    freq_file = path  + freq_file
 
     parser = argparse.ArgumentParser()
     parser.add_argument("-c", "--config",

grim/validation/runfile.py

@@ -7,20 +7,21 @@
 
 sys.path.insert(0, os.path.join(".."))
 
-from imputation.imputegl import Imputation
-from imputation.imputegl.networkx_graph import Graph
+from ..imputation.imputegl import Imputation
+from ..imputation.imputegl.networkx_graph import Graph
 
 # Profiler start
 #pr = cProfile.Profile()
 #pr.enable()
 
-def run_impute(conf_file = "../conf/minimal-configuration.json"):
+def run_impute(conf_file = "../conf/minimal-configuration.json", project_dir = ""):
 
     configuration_file = conf_file
 
-    project_dir = ""# "../"
+    #project_dir = ""# "../"
     output_dir = "output/"
 
+
     # Read configuration file and load properties
     with open(configuration_file) as f:
         json_conf = json.load(f)

requirements.txt

@@ -1,2 +1,2 @@
-numpy==1.20.2
+numpy>=1.20.2
 networkx==2.5.1