Turn the calculation setup script into something that runs in pytest

tests/generate_strain_test.py

@@ -0,0 +1,64 @@
+# Test the setup code by comparing generated files
+# with files previously generated for jadeite. Do 
+# comparison on line by line and word by word basis
+# allowing for numerical errors in numerical values
+
+import os
+import shutil
+import subprocess
+import glob
+
+import numpy as np
+
+def compare_files(file1, file2):
+    """
+    Line by line, word by word diff with roundoff
+
+    Reads two files and does nothing if they match,
+    raises an exeption if they differ
+    """
+    with open(file1) as f1:
+        with open(file2) as f2:
+            for line1, line2 in zip(f1, f2):
+                words1 = line1.split()
+                words2 = line2.split()
+                assert len(words1) == len(words2), "line length:\n" + line1 + "\n" + line2
+                for word1, word2 in zip(words1, words2):
+                    try:
+                        num1 = float(word1)
+                        num2 = float(word2)
+                        np.testing.assert_allclose(num1, num2)
+                    except:
+                        assert word1 == word2, "words:\n" + line1 + "\n" + line2
+
+
+def test_jadeite_setup(tmpdir):
+    """
+    Run generate_strain.py with the jadeite input
+
+    In a tempdir run generate strain and check the files
+    that are made match (to high precission) reference 
+    files.
+    """
+    tmpdir = str(tmpdir) # We may run in python 2 with old os
+    input_path = os.path.dirname(os.path.realpath(__file__)) + "/generate_strain_files/Input"
+    reference_path = os.path.dirname(os.path.realpath(__file__)) + "/generate_strain_files/Output"
+    shutil.copytree(input_path, tmpdir + "/input")
+
+    # Run analysis and check results
+    olddir = os.getcwd()
+    try:
+        os.chdir(tmpdir + "/input")
+        return_code = subprocess.call([olddir + "/generate_strain.py", "-s 0.1", "jadeite_4_30_GPa"])
+
+        files = glob.glob("*")
+        for file in files:
+            compare_files(file, reference_path + "/" + file)
+
+    finally:
+        os.chdir(olddir)
+
+
+if __name__ == "__main__":
+    import sys
+    compare_files(sys.argv[1], sys.argv[2])