Release 1.4.1

conda_build.sh

@@ -57,7 +57,7 @@ do
     # Converting to the different platforms
     for platform in $platforms
     do
-        conda convert -p $platform $filename -o ../conda_dist
+        conda convert -p $platform $filename -o ../conda_dist &> build_log.txt
 
         # Checking the conversion was completed
         if [ $? -ne 0 ]
@@ -67,6 +67,19 @@ do
             exit 1
         fi
 
+        # Checking if a conversion was skipped due to same platform
+        if egrep --quiet Skipping build_log.txt; then
+            # Finding which platform was skipped
+            missing=$(
+                egrep Skipping build_log.txt |
+                egrep -o "'([[:alnum:]]+-[[:digit:]]+)'" |
+                uniq |
+                sed -e "s/'//g"
+            )
+            mkdir -p ../conda_dist/$missing
+            cp $filename ../conda_dist/$missing
+        fi
+
     done
 
     # Purging

genipe/task/launcher.py

@@ -10,10 +10,12 @@
 import os
 import re
 import sys
+import time
 import shlex
 import logging
 import traceback
 from os.path import isfile
+from datetime import datetime
 from multiprocessing import Pool
 from subprocess import Popen, PIPE
 from tempfile import NamedTemporaryFile
@@ -602,10 +604,18 @@ def _execute_command_drmaa(command_info):
         logging.debug("'{}' exit status problem".format(task_id))
         return False, name, "problem", None
 
-    # Getting the time
+    # Getting the launch time (should always been present)
     launch_time = float(ret_val.resourceUsage["submission_time"])
-    start_time = float(ret_val.resourceUsage["start_time"])
-    end_time = float(ret_val.resourceUsage["end_time"])
+
+    # Getting the start time. If 'start_time' is missing from the dictionary
+    # (e.g. using Slurm), we use the launch time as the start time
+    start_time = float(ret_val.resourceUsage.get("start_time", launch_time))
+
+    # Getting the end time. If 'end_time' is missing from the dictionary
+    # (e.g. using Slurm), we use the current time as the end time
+    end_time = float(ret_val.resourceUsage.get(
+        "end_time", time.mktime(datetime.now().timetuple()),
+    ))
 
     # The task was performed correctly, so we update to completed
     db.mark_drmaa_task_completed(task_id, launch_time, start_time, end_time,

genipe/tests/test_imputed_stats.py

@@ -550,8 +550,10 @@ def test_read_samples(self):
         # Checking
         with self.assertRaises(ValueError) as cm:
             imputed_stats.read_samples(sample_filename)
-        self.assertEqual("Index has duplicate keys: ['sample_2']",
-                         str(cm.exception))
+        self.assertTrue(str(cm.exception).startswith(
+            "Index has duplicate keys"
+        ))
+        self.assertTrue("sample_2" in str(cm.exception))
 
     def test_read_sites_to_extract(self):
         """Tests the 'test_read_sites_to_extract' function."""

genipe/tools/imputed_stats.py

@@ -733,7 +733,9 @@ def _extract_mixedlm_random_effect(fitted):
 
     # If it's a dictionary, we need to create a DataFrame
     if isinstance(random_effects, dict):
-        return pd.DataFrame(random_effects).T.rename(columns={"groups": "RE"})
+        return pd.DataFrame(random_effects).T.rename(
+            columns={"groups": "RE", "Group": "RE"},
+        )
 
     return random_effects.rename(columns={"Intercept": "RE"})
 

setup.py

@@ -17,7 +17,7 @@
 
 MAJOR = 1
 MINOR = 4
-MICRO = 0
+MICRO = 1
 VERSION = "{0}.{1}.{2}".format(MAJOR, MINOR, MICRO)