Merge branch 'master' into get_data

.travis.yml

@@ -2,9 +2,9 @@ language: python
 sudo: required
 python:
   - "2.7"
-  - "3.4"
   - "3.5"
   - "3.6"
+  - "3.7"
 env:
   global:
     - PATH=/home/travis/miniconda/bin:$PATH
@@ -26,7 +26,7 @@ install:
   # Useful for debugging any issues with conda
   - conda info -a
 
-  - conda create -n testenv --yes python=$TRAVIS_PYTHON_VERSION numpy scipy libgfortran matplotlib nose pillow
+  - conda create -n testenv --yes python=$TRAVIS_PYTHON_VERSION numpy scipy libgfortran-ng matplotlib nose pillow
   - source activate testenv
   - pip install -r ci/requirements.txt
   - pip install -r ci/requirements-test.txt

ci/requirements-3.7.txt

@@ -0,0 +1,2 @@
+# Additional requirements for Python 3.5
+pyyaml  # this is already in requirements.txt, but pip doesn't allow empty requirements files

test/system/test_ircr.py

@@ -22,6 +22,7 @@
                    assert_config, assert_label_equal, assert_records, assert_return_code,
                    edit_parameters, expected_short_list, substitute_labels)
 from functools import partial
+import re
 
 repository = "https://bitbucket.org/apdavison/ircr2013"
 #repository = "/Volumes/USERS/andrew/dev/ircr2013"  # during development
@@ -48,15 +49,15 @@ def wrapped():
      assert_in_output, "updating to branch default"),
     ("Run the computation without Sumatra",
      "python glass_sem_analysis.py default_parameters MV_HFV_012.jpg",
-     assert_in_output, "2416.86315789 60.0",
+     assert_in_output, re.compile(r"2416\.863[0-9]* 60\.0"),
      assert_file_exists, os.path.join("Data", datetime.now().strftime("%Y%m%d")),  # Data subdirectory contains another subdirectory labelled with today's date)
      ),  # assert(subdirectory contains three image files).
     ("Set up a Sumatra project",
      "smt init -d Data -i . ProjectGlass",
      assert_in_output, "Sumatra project successfully set up"),
     ("Run the ``glass_sem_analysis.py`` script with Sumatra",
      "smt run -e python -m glass_sem_analysis.py -r 'initial run' default_parameters MV_HFV_012.jpg",
-     assert_in_output, ("2416.86315789 60.0", "histogram.png")),
+     assert_in_output, (re.compile(r"2416\.863[0-9]* 60\.0"), "histogram.png")),
     ("Comment on the outcome",
      "smt comment 'works fine'"),
     ("Set defaults",

test/system/utils.py

@@ -23,7 +23,7 @@
 label_pattern = re.compile("Record label for this run: '(?P<label>[\w\-_]+)'")
 
 info_pattern = r"""Project name        : (?P<project_name>\w+)
-Default executable  : (?P<executable>\w+) \(version: \d+.\d+.\d+\) at /[\w\/_-]+/bin/python
+Default executable  : (?P<executable>\w+) \(version: \d+.\d+.\d+\) at /[\w\/_.-]+/bin/python
 Default repository  : MercurialRepository at \S+/sumatra_exercise \(upstream: \S+/ircr2013\)
 Default main file   : (?P<main>\w+.\w+)
 Default launch mode : serial
@@ -83,10 +83,13 @@ def get_label(p):
 
 def assert_in_output(p, texts):
     """Assert that the stdout from process 'p' contains all of the provided text."""
-    if isinstance(texts, str):
+    if isinstance(texts, (str, type(re.compile("")))):
         texts = [texts]
     for text in texts:
-        assert text in p.stdout.text, "'{0}' is not in '{1}'".format(text, p.stdout.text)
+        if isinstance(text, type(re.compile(""))):
+            assert text.search(p.stdout.text), "regular expression '{0}' has no match in '{1}'".format(text, p.stdout.text)
+        else:
+            assert text in p.stdout.text, "'{0}' is not in '{1}'".format(text, p.stdout.text)
 
 
 def assert_config(p, expected_config):