Merge branch 'improve_reproducib' into motif

Author: rzitomer

Snakefile

@@ -0,0 +1,21 @@
+rule run_analysis:
+    input:
+        data_path = "/Users/richiezitomer/Documents/RStudio-Data-Repository/clean_data/commits.feather"
+    output:
+        results_path = directory("results/")
+    params:
+        python_hash_seed = 0,
+        n_workers = 8,
+        n_projects = 1000,
+        min_commits = None,
+        min_count = 5,
+        n_personas = 5,
+        n_neurons = 128,
+        n_iter = 10,
+        random_state = 1
+    shell:
+        "PYTHONHASHSEED={params.python_hash_seed} python src/github_analysis/main.py -dp {input.data_path} -rp {output.results_path} -nw {params.n_workers} -np {params.n_projects} -mc {params.min_commits} -mcount {params.min_count} -nps {params.n_personas} -nn {params.n_neurons} -ni {params.n_iter} -rs {params.random_state}"
+
+# Commented out because repo is currently over bandwidth: https://help.github.com/en/articles/about-storage-and-bandwidth-usage
+#rule clone_data_repo:
+#    shell: "git clone https://github.com/UBC-MDS/RStudio-Data-Repository.git"

src/github_analysis/main.py

@@ -57,7 +57,7 @@ def main(args):
     projectClusterTime = time.time()
     logging.info("Projects Clustered: " + str(projectClusterTime - reduceTime) + " seconds")
 
-    cluster_personas = p.Personas(clusters, commits_dl, args.n_personas, 1, output_path=args.results_path + "cluster_personas.csv")
+    # cluster_personas = p.Personas(clusters, commits_dl, args.n_personas, 1, output_path=args.results_path + "cluster_personas.csv")
     personaGenerationTime = time.time()
     logging.info("Personas Generated: " + str(personaGenerationTime - projectClusterTime) + " seconds")
 
@@ -80,13 +80,19 @@ def main(args):
     print("Frequency Graph Time:\t" +   str(freqGraphTime - motifTime) +                    "\tseconds")
     print("Total Time:\t\t" +           str(freqGraphTime - startTime) +                    "\tseconds")
 
+
+def none_or_str(value):
+    if value == 'None':
+        return None
+    return value
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser.add_argument("-rp",      "--results_path",   help="The folder to output results of the analysis. e.g. embeddings and plots", default="./results/")
     parser.add_argument("-nw",      "--n_workers",      help="The number of workers to use when running the analysis.", default=8, type=int)
-    parser.add_argument("-dp",      "--data_path",      help="The path to the commits.feather file. e.g. /home/user/RStudio-Data-Repository/clean_data/commits.feather", default="./results/")
+    parser.add_argument("-dp",      "--data_path",      help="The path to the commits.feather file. e.g. /home/user/RStudio-Data-Repository/clean_data/commits_by_org.feather", default="/home/user/RStudio-Data-Repository/clean_data/commits_by_org.feather")
     parser.add_argument("-np",      "--n_projects",     help="The number of projects to sample from the dataset.", default=1000, type=int)
-    parser.add_argument("-mc",      "--min_commits",    help="The minimum number of commits for a project to be included in the sample.", default=None, type=int)
+    parser.add_argument("-mc",      "--min_commits",    help="The minimum number of commits for a project to be included in the sample.", default=None, type=none_or_str)
     parser.add_argument("-mcount",  "--min_count",      help="The min_count parameter for the graph2vec model.", default=5, type=int)
     parser.add_argument("-nps",     "--n_personas",     help="The number of personas to extract from each cluster.", default=5, type=int)
     parser.add_argument("-nn",      "--n_neurons",      help="The number of neurons to use for Graph2Vec (project level)", default=128, type=int)