CI Tests

.github/workflows/test.yml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
      - master
+     - develop
 
 jobs:
 
@@ -34,3 +35,4 @@ jobs:
         run: |
           conda activate shapepipe
           python setup.py test
+          shapepipe_run -c example/config.ini

example/config.ini

@@ -42,7 +42,7 @@ NUMBERING_SCHEME = _0
 ## ShapePipe job handling options
 [JOB]
 # BATCH_SIZE (optional) default is 1, i.e. run all jobs in serial
-SMP_BATCH_SIZE = 3
+SMP_BATCH_SIZE = 2
 # SMP_BACKEND (opional) options are loky, multiprocessing or threading, default is loky
 ; SMP_BACKEND = multiprocessing
 # TIMEOUT (optional) default is None, i.e. no timeout limit applied

shapepipe/modules/galsim_shapes_v2_runner.py

@@ -712,8 +712,10 @@ def process(tile_cat_path, tile_weight_path, gal_vignet_path, bkg_vignet_path,
 
         if skip_col:
             # Skip this object if marked, also if mark is nan
-            if tile_skip[i_tile] == skip_val \
-                or (np.isnan(tile_skip[i_tile]) and np.isnan(skip_val)):
+            if (
+                tile_skip[i_tile] == skip_val
+                or (np.isnan(tile_skip[i_tile]) and np.isnan(skip_val))
+            ):
                 continue
 
         count = count + 1

shapepipe/modules/python_example.py

@@ -12,6 +12,20 @@
 from numpy.random import randint
 from shapepipe.modules.module_decorator import module_runner
 
+# Test import of key dependencies
+import astropy
+import galsim
+import joblib
+import mccd
+import ngmix
+import pandas
+import pysap
+import scipy
+import sf_tools
+import sip_tpv
+import sqlitedict
+import treecorr
+
 
 class Dummy(object):
 

shapepipe/utilities/canfar.py

@@ -9,7 +9,7 @@
 """
 
 import os
-import sys  
+import sys
 
 try:
     import vos.commands as vosc
@@ -92,6 +92,7 @@ def __call__(self, *args, **kwargs):
             raise vosError('Error in VOs command: {}'
                            ''.format(self._command.__name__))
 
+
 def download(source, target, verbose=False):
     """Download file from vos.