Merge pull request #13311 from mantidproject/feature/13310_Doctests_for_Python_Introduction

Doctests for training courses

Code/Mantid/Testing/Data/DocTest/EQSANS_6071_event.nxs.md5

+ac963bf816b36ca7353f6922ce856604

Code/Mantid/Testing/Data/DocTest/GEM38370_Focussed.nxs.md5

+01acf5f7645c9901efece0ed8dd00ced

Code/Mantid/Testing/Data/DocTest/GEM40979.raw.md5

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Code/Mantid/Testing/Data/DocTest/HRP39182.RAW.md5

+b6f6a905288dd986b5340673d08f93cb

Code/Mantid/Testing/Data/DocTest/LOQ48097.raw.md5

+435f4d573bfe6e64b014223d793e02a2

Code/Mantid/Testing/Data/DocTest/LogWS.nxs.md5

+602cbf8646a81b25e221bba3fe691a93

Code/Mantid/Testing/Data/DocTest/MAR11015.raw.md5

+22402246b0d14072b1fd9e6d920c3bb6

Code/Mantid/Testing/Data/DocTest/MAR11060.raw.md5

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Code/Mantid/Testing/Data/DocTest/PG3_4871_event.nxs.md5

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Code/Mantid/Testing/Data/DocTest/SXD23767.raw.md5

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Code/Mantid/Testing/Data/DocTest/Training_Exercise3a_SNS.nxs.md5

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Code/Mantid/Testing/Data/DocTest/Training_Exercise3b_SNS.nxs.md5

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Code/Mantid/Testing/Data/DocTest/peaks_qLab.nxs.md5

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Code/Mantid/docs/source/concepts/PropertiesFile.rst

@@ -126,6 +126,7 @@ to alter and those properties are detailed below.
 +-------------------------------------------+---------------------------------------------------+-----------------------+
 |logging.channels.fileChannel.path          | The Path to the log file.                         |../logs/mantid.log     |
 +-------------------------------------------+---------------------------------------------------+-----------------------+
+
 The logging priority levels for the file logging and console logging can also be adjusted in python using the commands:
 
 .. testcode:: LoggingConfigExample
@@ -135,8 +136,6 @@ The logging priority levels for the file logging and console logging can also be
   #Set the file to only log at critical level (2=critical)
   ConfigService.setConsoleLogLevel(2)
   
-.. testoutput:: AddSampleLogExample 
-
 
 
 MantidPlot Properties

Code/Mantid/docs/sphinxext/mantiddoc/doctest.py

@@ -42,7 +42,7 @@
     Document: bar/FooDoc
     --------------------
     **********************************************************************
-    File "bar/FooDoc.rst", line 127, in Ex2
+    File "bar/FooDoc.rst", line 127, in Ex2[31]
     Failed example:
         print "Multi-line failed"
         print "test"
@@ -62,13 +62,13 @@
     **********************************************************************
     2 items had failures:
        1 of   1 in Ex1
-       1 of   1 in Ex2
+       1 of   1 in Ex2[31]
     2 tests in 2 items.
     0 passed and 2 failed.
     ***Test Failed*** 2 failures.
     2 items passed all tests:
        1 tests in Ex1 (cleanup code)
-       1 tests in Ex2 (cleanup code)
+       1 tests in Ex2[31] (cleanup code)
     2 tests in 2 items.
     2 passed and 0 failed.
     Test passed.
@@ -152,7 +152,7 @@ NUMBER_PASSED_RE = re.compile(r"^(\d+) items passed all tests:$")
 
 TEST_PASSED_END_RE = re.compile(r"Test passed.")
 TEST_FAILED_END_RE = re.compile(r"\*\*\*Test Failed\*\*\* (\d+) failures.")
-FAILURE_LOC_RE = re.compile(r"^File \"(.+)\",\s+line\s+(\d+),\s+in\s+(\w+)(\s\((setup|cleanup) code\))?$")
+FAILURE_LOC_RE = re.compile(r"^File \"(.+)\",\s+line\s+(\d+),\s+in\s+(\S+)(\s\((setup|cleanup) code\))?$")
 MIX_FAIL_RE = re.compile(r'^\s+(\d+)\s+of\s+(\d+)\s+in\s+(\w+)$')
 
 #-------------------------------------------------------------------------------

Code/Mantid/docs/sphinxext/mantiddoc/tests/test_doctest.py

@@ -149,7 +149,7 @@ ALL_FAIL_EX = \
 """Document: algorithms/AllFailed
 ------------------------------
 **********************************************************************
-File "algorithms/AllFailed.rst", line 127, in Ex2
+File "algorithms/AllFailed.rst", line 127, in Ex2[31]
 Failed example:
     print "Multi-line failed"
     print "test"
@@ -169,13 +169,13 @@ Got:
 **********************************************************************
 2 items had failures:
    1 of   1 in Ex1
-   1 of   1 in Ex2
+   1 of   1 in Ex2[31]
 2 tests in 2 items.
 0 passed and 2 failed.
 ***Test Failed*** 2 failures.
 2 items passed all tests:
    1 tests in Ex1 (cleanup code)
-   1 tests in Ex2 (cleanup code)
+   1 tests in Ex2[31] (cleanup code)
 2 tests in 2 items.
 2 passed and 0 failed.
 Test passed.
@@ -275,9 +275,9 @@ class DocTestOutputParserTest(unittest.TestCase):
         self.assertEquals(2, suite.ntests)
 
         cases = suite.testcases
-        expected_names = ["Ex2", "Ex1"]
+        expected_names = ["Ex2[31]", "Ex1"]
         expected_errors = [
-"""File "algorithms/AllFailed.rst", line 127, in Ex2
+"""File "algorithms/AllFailed.rst", line 127, in Ex2[31]
 Failed example:
     print "Multi-line failed"
     print "test"

Code/Tools/scripts/TestWikiPython.py

+###########################################################################################
+# Extracts code blocks marked as python from mediawiki pages and checks they run
+# run with -h for command line arguments
+#
+##########################################################################################
+import os
+import re
+import sys
+import urllib2
+import urlparse
+import argparse
+import json
+
+def readWebPage(url):
+    # set your environment HTTP_PROXY to be your proxy
+    # for ral HTTP_PROXY=http://wwwcache.rl.ac.uk:8080
+    aResp = urllib2.urlopen(url)
+    web_pg = aResp.read()
+    return web_pg
+
+
+def getTestablePages(url):
+    retList = []
+    print "Reading Testable pages from " + url
+    output = readWebPage(url)
+    jsonObj = json.loads(output)
+    for member in jsonObj['query']['categorymembers']:
+        retList.append(member['title'])
+    return retList
+
+
+def convertURLToRaw(url):
+    return url.replace(" ","%20") + "?action=raw"
+def writeTestRst(filepath,mediawikiText,pageName):
+    '''
+    for a block of wiki text, writes out all tests found to an rst page
+    :param mediawikiText: mediawiki text
+    :param filepath: the filepath to write out the rst file to, if None then print to stdout
+    :return: None
+    '''
+    try:
+        if filepath is not None:
+            sys.stdout = open(filepath, 'w')
+        print ":orphan:\n"
+        findCodeSections(mediawikiText,pageName)
+    finally:
+        sys.stdout = sys.__stdout__
+
+def findCodeSections(mediawikiText,pageName):
+    '''
+    Finds code sections that look like this:
+
+    #<div style="border:1pt dashed blue; background:#f9f9f9;padding: 1em 0;">
+    # <!--skip-->
+    # <!-- setup
+    # x=1
+    # y=2
+    # file.open()
+    # -->
+    # <source lang="python">
+    # x = 'The meaning of life is ... '
+    # answer = 42
+    # y = x + str(answer)  # This converts the number 5 to a string and joins
+    #                      # it with the first string and then assigns y to a
+    #                      # new string containing the concatenated string
+    # </source>
+    # <!-- teardown
+    # print y # print statements can be in the teardown if you do not want them visible
+    # file.close()
+    # -->
+    # <!-- result
+    # the lazy dog
+    # -->
+    # </div>
+    '''
+
+    wikiTestPattern = re.compile(
+        r'''(<!--\s*skip\s*-->)?\s*                             # optional skip section (group 1)
+            (<!--\s*testsetup\s*(.*?)\s*-->)?\s*                    # optional setup section (group 2), just setup code (group 3)
+            <source.*?lang="python".*?>\s*(.*?)\s*<\/source>\s* # mandatory source section, code (group 4)
+            (<!--\s*testcleanup\s*(.*?)\s*-->)?\s*                 # optional teardown section (group 5), code (group 6)
+            (<!--\s+testoutput\s*(.*?)\s*-->)?                      # optional result section (group 7), text group (8)
+            ''', re.IGNORECASE + re.DOTALL + re.VERBOSE)
+
+    for m in re.finditer(wikiTestPattern, mediawikiText):
+        (line,col) = coords_of_str_index(mediawikiText, m.start(0))
+        testName = pageName + "[" + str(line) + "]"
+        #print the test
+        if m.group(1) is not None:
+            print ".. Skipping Test ", testName
+            print
+        else:
+            printDirective("testsetup",testName,m.group(3),True)
+            printDirective("testcode",testName,m.group(4),False)
+            printDirective("testcleanup",testName,m.group(6),True)
+            printDirective("testoutput",testName,m.group(8),True, "+ELLIPSIS, +NORMALIZE_WHITESPACE")
+        print
+
+def printDirective (directive, name, contents, hideIfNone = False,options = None):
+    if not(hideIfNone and contents is None):
+        print ".. {}:: {}".format(directive,name)
+        if options is not None:
+            print "   :options: {}".format(options)
+        print
+        if contents is not None:
+            for line in contents.split("\n"):
+                print "   " + line
+        print
+
+def coords_of_str_index(string, index):
+    """Get (line_number, col) of `index` in `string`."""
+    lines = string.splitlines(True)
+    curr_pos = 0
+    for linenum, line in enumerate(lines):
+        if curr_pos + len(line) > index:
+            return linenum + 1, index-curr_pos
+        curr_pos += len(line)
+
+def ensureDirectoriesExist(path):
+    try:
+        os.makedirs(path)
+    except OSError:
+        pass
+
+################################################################################################################
+
+parser = argparse.ArgumentParser(description='Extracts code blocks marked as python from mediawiki pages and tests they run.')
+parser.add_argument('-i', '--i',
+                    help='The title of a mediawiki page, if not specified it will search the Tested Examples category')
+parser.add_argument('-s', '--s',
+                    help='The url of a mantid mediawiki site')
+parser.add_argument('-o', '--o',
+                    help='Provide a path to output to an output directory')
+
+args = parser.parse_args()
+urlList = [];
+baseUrl = "http://www.mantidproject.org/"
+if args.s is not None:
+    baseUrl = args.s
+if args.i is None:
+    urlList = getTestablePages(baseUrl +
+                               "api.php?action=query&list=categorymembers&format=json&cmlimit=500&cmtitle=Category:Tested%20Examples")
+else:
+    urlList.append(args.i)
+
+outputDir = None
+if args.o is not None:
+    ensureDirectoriesExist(args.o)
+    if not os.path.isdir(args.o):
+        print "Output directory not found", args.o
+        print "Output will be to stdout"
+    else:
+        outputDir = args.o
+
+for url in urlList:
+    pageName = "mwTest_" + url.replace(" ","_").replace(":","")
+    print "Parsing ", pageName,
+
+    outputFile = None
+    if outputDir is not None:
+        outputFile = os.path.join(outputDir, pageName+".rst")
+    print "->", outputFile
+
+    #run pandoc and get the output in rst
+    mediawikiText = readWebPage(convertURLToRaw(baseUrl + url))
+    writeTestRst(outputFile,mediawikiText,pageName)
+
+
+