Merge pull request #212 from prjemian/188_check_L

merge continued lines in data file before parsing data

.travis.yml

@@ -13,6 +13,7 @@ python:
   - "3.5"
   - "3.6"
   - "3.7"
+  # - "3.8"  #   ERROR: Failed building wheel for h5py
 
 before_script:
   - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh

CHANGES.rst

@@ -15,6 +15,12 @@ Production
 
 :2021.1.7: expected *2020.01*
 
+    * `#213 <https://github.com/prjemian/spec2nexus/issues/213>`_
+       copy data file to gallery
+
+    * `#188 <https://github.com/prjemian/spec2nexus/issues/188>`_
+       catenate continued lines before parsing data
+
 :2021.1.6: released *2019.11.01*
 
     * `#210 <https://github.com/prjemian/spec2nexus/issues/210>`_

src/spec2nexus/spec.py

@@ -615,7 +615,7 @@ def interpret(self):
         if self.__interpreted__:    # do not do this twice
             return
         self.__lazy_interpret__ = False     # set now to avoid recursion
-        lines = self.raw.splitlines()
+        lines = self.raw.replace('\\\n', ' ').splitlines()
         for _i, line in enumerate(lines, start=1):
             if len(line) == 0:
                 continue            # ignore blank lines
@@ -681,8 +681,7 @@ def addH5writer(self, label, func):
     def _interpret_data_row(self, row_text):
         buf = {}
         for col, val in enumerate(row_text.split()):
-            label = self.L[col]
-            buf[label] = float(val)
+            buf[self.L[col]] = float(val)
         return buf
 
     def _unique_key(self, label, keylist):

src/spec2nexus/specplot_gallery.py

@@ -230,10 +230,18 @@ def sorter(d):
                 ]
 
             html = buildIndexHtml(specFile, plot_list, problem_scans)
-            f = open(htmlFile, "w")
-            f.write(html)
-            f.close()
+            with open(htmlFile, "w") as f:
+                f.write(html)
 
+        # copy specFile to the plot_path, if newer
+        target = os.path.join(plot_path, os.path.basename(specFile))
+        if (
+            not os.path.exists(target)
+            or
+            (os.path.getmtime(target) < os.path.getmtime(specFile))
+            ):
+            shutil.copyfile(specFile, target)
+
         # touch to update the mtime on the plot_path
         os.utime(plot_path, None)
 

tests/__init__.py

@@ -46,6 +46,7 @@ def suite(*args, **kw):
     from tests import issue119
     from tests import issue123
     from tests import issue161
+    from tests import issue188
 
     test_list = [
         data_03_06_JanTest,
@@ -70,6 +71,7 @@ def suite(*args, **kw):
         issue119,
         issue123,
         issue161,
+        issue188,
         ]
 
     test_suite = unittest.TestSuite()

tests/issue188.py

@@ -0,0 +1,90 @@
+
+'''
+test punx tests/common module (supports unit testing)
+'''
+
+#-----------------------------------------------------------------------------
+# :author:    Pete R. Jemian
+# :email:     prjemian@gmail.com
+# :copyright: (c) 2014-2019, Pete R. Jemian
+#
+# Distributed under the terms of the Creative Commons Attribution 4.0 International Public License.
+#
+# The full license is in the file LICENSE.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+import os
+import sys
+import unittest
+
+_test_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+_path = os.path.abspath(os.path.join(_test_path, 'src'))
+
+sys.path.insert(0, _path)
+sys.path.insert(0, _test_path)
+
+import spec2nexus.extractSpecScan
+import spec2nexus.spec
+
+import tests.common
+
+
+class Issue188(unittest.TestCase):
+
+    def setUp(self):
+        self.testfile = os.path.join(_path, 'spec2nexus', 'data', 'startup_1.spec')
+        self.sys_argv0 = sys.argv[0]
+
+    def tearDown(self):
+        sys.argv = [self.sys_argv0,]
+
+    def test_scan_unrecognized(self):
+        self.assertTrue(os.path.exists(self.testfile))
+
+        specData = spec2nexus.spec.SpecDataFile(self.testfile)
+        self.assertTrue(isinstance(specData, spec2nexus.spec.SpecDataFile))
+
+        scanNum = 16
+        scan = specData.getScan(scanNum)
+        scan.interpret()
+
+        self.assertTrue(hasattr(scan, "data"))
+        self.assertTrue(hasattr(scan, "_unrecognized"))
+        self.assertEqual(len(scan._unrecognized), 112)
+
+    def test_data_file(self):
+        self.assertTrue(os.path.exists(self.testfile))
+
+        specData = spec2nexus.spec.SpecDataFile(self.testfile)
+        self.assertTrue(isinstance(specData, spec2nexus.spec.SpecDataFile))
+
+        for scanNum in specData.getScanNumbers():
+            scan = specData.getScan(scanNum)
+            self.assertTrue(isinstance(scan, spec2nexus.spec.SpecDataFileScan))
+            self.assertTrue(hasattr(scan, "L"))
+            self.assertIsInstance(scan.L, list)
+            self.assertTrue(hasattr(scan, "N"))
+            self.assertIsInstance(scan.N, list)
+            self.assertGreaterEqual(len(scan.N), 1)
+            self.assertEqual(len(scan.L), scan.N[0], "scan %s #L line" % scanNum)
+
+            self.assertTrue(hasattr(scan, "data"))
+            self.assertIsInstance(scan.data, dict)
+            n = len(scan.data.keys())
+            if n > 0:   # if ==0, then no data present
+                self.assertEqual(len(scan.L), n, "scan %s #L line" % scanNum)
+
+
+def suite(*args, **kw):
+    test_suite = unittest.TestSuite()
+    test_list = [
+        Issue188,
+        ]
+    for test_case in test_list:
+        test_suite.addTest(unittest.makeSuite(test_case))
+    return test_suite
+
+
+if __name__ == '__main__':
+    runner=unittest.TextTestRunner()
+    runner.run(suite())