Merge branch 'master' into upgrade_python_3

setup.sh

@@ -4,7 +4,9 @@
 # were 'realpath' is defined, but just in case...
 if [[ ( "$OSTYPE" == "darwin"* ) && ( -z "$(command -v realpath)" ) ]]; then
   echo "ERROR: realpath command not found!"
-  echo "Please, check that you are using the Docker container."
+  echo "Please," 
+  echo " - either use the Docker Container,"
+  echo " - or install the command using Homebrew (brew install coreutils)."
   return 1
 fi
 

tests/test_merge.py

@@ -0,0 +1,75 @@
+# make 2 HDF5 files
+
+import glob
+import subprocess
+
+import tables as tb
+import numpy as np
+
+def create_mock_file(tmpdir, filename):
+
+    filepath = tmpdir.join(filename)
+    outfile = tb.open_file(filepath.strpath, mode="w", title="Run_1")
+
+    cameras = ["NectarCam", "CHEC"]
+
+    output_variables = dict(
+        n=tb.Int16Col(dflt=-1, pos=0)
+    )
+
+    outdata = {}
+    out_table = {}
+    for cam_id in cameras:
+        if cam_id not in outdata:
+            out_table[cam_id] = outfile.create_table(
+                            "/", cam_id, output_variables,
+                        )
+            outdata[cam_id] = out_table[cam_id].row
+        for n_image in range(50):
+            outdata[cam_id]["n"] = 0
+            outdata[cam_id].append()
+
+    outfile.close()
+
+    return None
+
+def test_merge(tmpdir):
+
+    print(tmpdir.strpath)
+
+    # create 1st file
+    create_mock_file(tmpdir, "run1.h5")
+    # create 2nd file
+    create_mock_file(tmpdir, "run2.h5")
+    # define merged file
+    merged_file_path = tmpdir.join("merged_file.h5").strpath
+
+    # call script to merge
+    subprocess.check_call(["python",
+                           "merge_tables.py", 
+                           "--indir", tmpdir.strpath,
+                           "--template_file_name", "*run*",
+                           "--outfile", merged_file_path
+                          ])
+
+    cameras = ["NectarCam", "CHEC"]
+    n_images_from_runs = dict.fromkeys(cameras, 0)
+    n_tot_images = dict.fromkeys(cameras, 0)
+
+    single_files = glob.glob("{}/*run*.h5".format(tmpdir.strpath))
+
+    # Get total number of table rows cumulatively from each files per table
+    for file in single_files:
+        with tb.open_file(file, "r") as f:
+            table_name_list = [table.name for table in f.root]
+            assert sorted(table_name_list) == sorted(cameras)
+            for child in f.root:
+                n_images_from_runs[child._v_name] += len(child)
+
+    # Get total number of table rows from merged file
+    with tb.open_file(merged_file_path, "r") as f:
+        for child in f.root:
+            n_tot_images[child._v_name] = len(child)
+
+    for camera in cameras:
+        assert n_images_from_runs[camera] == n_tot_images[camera]