Merge pull request #57 from MJOLNIRPackage/develop

Test suite update

.gitignore

@@ -44,3 +44,5 @@ Report/
 */.coverage*
 
 coverage_html_report
+samlpedata/*
+docs/Commissioning/*

.travis.yml

@@ -4,35 +4,113 @@ services:
   - xvfb
 
 language: python
+# ===== Linux ======
 
 python:
-  - "3.5"
-  - "3.6"
-  - "3.7"
-  - "3.8"
-
-
-#before_install:
-#- sudo apt-get -qq update && sudo apt-get install -y --no-install-recommends texlive-fonts-recommended texlive-latex-extra texlive-fonts-extra dvipng texlive-latex-recommended
-
-
-before_script: # configure a headless display to test plot generation
-#  - xvfb-run --server-args="-screen 0 1024x768x24"
-  - sleep 3 # give xvfb some time to start
-#  - "/sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -ac -screen 0 1280x1024x24"
-
-
-install:
+  - 3.5
+  - 3.6
+  - 3.7
+  - 3.8
+matrix:
+  include:      
+    - name: "Python 3.7.5 on macOS 10.14"
+      os: osx
+      osx_image: xcode10.2  # Python 3.7.5 running on macOS 10.14.3
+      language: shell       # 'language: python' is an error on Travis CI macOS
+      before_install:
+        - python3 --version
+        - sleep 3 # give xvfb some time to start
+        - pip3 install -U pip
+        - pip install pytest>=3.6 pycodestyle python-coveralls pytest-cov>=2.5 coveralls
+        - pip install .
+        - wget -UseBasicParsing 'https://www.psi.ch/en/media/60041/download'
+        - unzip download
+      script: py.test test/ -vv
+    - name: "Python 3.8.0 on macOS 10.14"
+      os: osx
+      osx_image: xcode11.3  # Python 3.8.0 running on macOS 10.14.6
+      language: shell       # 'language: python' is an error on Travis CI macOS
+      before_install:
+        - python3 --version
+        - sleep 3 # give xvfb some time to start
+        - pip3 install -U pip
+        - pip install pytest>=3.6 pycodestyle python-coveralls pytest-cov>=2.5 coveralls
+        - pip install .
+        - wget -UseBasicParsing 'https://www.psi.ch/en/media/60041/download'
+        - unzip download
+      script: py.test test/ -vv
+    - name: "Python 3.5.4 on Windows"
+      os: windows           # Windows 10.0.17134 N/A Build 17134
+      language: shell       # 'language: python' is an error on Travis CI Windows
+      before_install:
+        - choco install python --version 3.5.4
+        - python --version
+        - sleep 3 # give xvfb some time to start
+        - python -m pip install --upgrade pip
+        - pip3 install pytest>=3.6 pycodestyle python-coveralls pytest-cov>=2.5 coveralls
+        - python setup.py sdist
+        - pip3 install .
+        - curl -o download.zip https://www.psi.ch/en/media/60041/download
+        - 7z e download.zip "-osamlpedata"
+      script: py.test test/ -vv
+      env: PATH=/c/Python35:/c/Python35/Scripts:$PATH
+    - name: "Python 3.6.8 on Windows"
+      os: windows           # Windows 10.0.17134 N/A Build 17134
+      language: shell       # 'language: python' is an error on Travis CI Windows
+      before_install:
+        - choco install python --version 3.6.8
+        - python --version
+        - sleep 3 # give xvfb some time to start
+        - python -m pip install --upgrade pip
+        - pip3 install pytest>=3.6 pycodestyle python-coveralls pytest-cov>=2.5 coveralls
+        - python setup.py sdist
+        - pip3 install .
+        - curl -o download.zip https://www.psi.ch/en/media/60041/download
+        - 7z e download.zip "-osamlpedata"
+      env: PATH=/c/Python36:/c/Python36/Scripts:$PATH
+    - name: "Python 3.7.9 on Windows"
+      os: windows           # Windows 10.0.17134 N/A Build 17134
+      language: shell       # 'language: python' is an error on Travis CI Windows
+      before_install:
+        - choco install python --version 3.7.9
+        - python --version
+        - sleep 3 # give xvfb some time to start
+        - python -m pip install --upgrade pip
+        - pip3 install pytest>=3.6 pycodestyle python-coveralls pytest-cov>=2.5 coveralls
+        - python setup.py sdist
+        - pip3 install .
+        - curl -o download.zip https://www.psi.ch/en/media/60041/download
+        - 7z e download.zip "-osamlpedata"
+      env: PATH=/c/Python37:/c/Python37/Scripts:$PATH
+    - name: "Python 3.8.5 on Windows"
+      os: windows           # Windows 10.0.17134 N/A Build 17134
+      language: shell       # 'language: python' is an error on Travis CI Windows
+      before_install:
+        - choco install python --version 3.8.5
+        - python --version
+        - sleep 3 # give xvfb some time to start
+        - python -m pip install --upgrade pip
+        - pip3 install pytest>=3.6 pycodestyle python-coveralls pytest-cov>=2.5 coveralls
+        - python setup.py sdist
+        - pip3 install .
+        - curl -o download.zip https://www.psi.ch/en/media/60041/download
+        - 7z e download.zip "-osamlpedata"
+      env: PATH=/c/Python38:/c/Python38/Scripts:$PATH
+before_install:
   - pip install pytest>=3.6 pycodestyle python-coveralls pytest-cov>=2.5 coveralls
   - pip install --upgrade pip
   - pip install .
-#  - pip install -r requirements.txt
+  - wget 'https://www.psi.ch/en/media/60041/download' 
+  - unzip download
+
+#before_script:
+#  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then export DISPLAY=:99.0; sh -e /etc/init.d/xvfb start; sleep 3; fi
 
 script: 
-  - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then py.test MJOLNIR/ -vv --cov=MJOLNIR/; fi
-  - if [[ $TRAVIS_PYTHON_VERSION == 3.5 ]]; then py.test MJOLNIR/ -vv --ignore=MJOLNIR/CommandLineScripts/MJOLNIRHistory.py --ignore=MJOLNIR/CommandLineScripts/MJOLNIRCalibrationInspector.py --ignore=MJOLNIR/CommandLineScripts/MJOLNIR3DView.py --ignore=MJOLNIR/CommandLineScripts/MJOLNIRConvert.py; fi
-  - if [[ $TRAVIS_PYTHON_VERSION > 3.6 ]]; then py.test MJOLNIR/ -vv; fi
-  - if [[ $TRAVIS_PYTHON_VERSION < 3.5 ]]; then py.test MJOLNIR/ -vv; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then py.test test/ -vv --cov=test/; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == 3.5 ]]; then py.test test/ -vv --ignore=test/CommandLineScripts/MJOLNIRHistory.py --ignore=test/CommandLineScripts/MJOLNIRCalibrationInspector.py --ignore=test/CommandLineScripts/MJOLNIR3DView.py --ignore=test/CommandLineScripts/MJOLNIRConvert.py; fi
+  - if [[ $TRAVIS_PYTHON_VERSION > 3.6 ]]; then py.test test/ -vv; fi
+  - if [[ $TRAVIS_PYTHON_VERSION < 3.5 ]]; then py.test test/ -vv; fi
 
 after_success:
   - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]];

MJOLNIR/CommandLineScripts/MJOLNIR3DView.py

@@ -12,7 +12,7 @@
 import argparse
 import numpy as np
 import matplotlib.pyplot as plt
-plt.ion()
+
 import os
 import sys
 from MJOLNIR.CommandLineScripts import _tools
@@ -62,7 +62,6 @@
 
 V.caxis = [VMin,VMax]
 
-plt.show()
 
 def main():
-    pass
+    plt.show()

MJOLNIR/CommandLineScripts/MJOLNIRCalibrationInspector.py

@@ -14,8 +14,6 @@
 import matplotlib.pyplot as plt
 import matplotlib._pylab_helpers
 
-plt.ion()
-
 from MJOLNIR.CommandLineScripts import _tools
 import sys,os
 settingsName = 'CalibrationInspectorDir'
@@ -47,9 +45,20 @@ def switch(argument):
 
 args = parser.parse_args()
 
-file = _tools.extractDataFiles(args,settingsName,oneFile=True)
+if not args.save is '':
+    saveFile = True
+    saveLocation = os.path.realpath(args.save.strip())
+    if not os.path.exists(saveLocation):
+        os.mkdir(saveLocation)
+    else:
+        if not os.path.isdir(saveLocation):
+            raise FileNotFoundError("[Errno 2] No such file or directory: '{}'".format(saveLocation))
+else:
+    saveFile = False
+
+file = _tools.extractDataFiles(args,settingsName,oneFile=True)[0]
 
-directory = os.path.split(file)[0]
+directory = os.path.split(file)
 
 _tools.updateSetting(settingsName,directory)
 
@@ -68,12 +77,6 @@ def switch(argument):
 
 
 
-if not args.save is '':
-    saveFile = True
-    saveLocation = os.path.realpath(args.save.strip())
-else:
-    saveFile = False
-
 File = DataFile.DataFile(file)
 
 for id in argsIdx:
@@ -115,7 +118,7 @@ def switch(argument):
             f.savefig(os.path.join(saveLocation,title+'.png'))
 
 
-plt.show()
+
 
 def main():
-    pass
+    plt.show()

MJOLNIR/CommandLineScripts/test_commandline.py

@@ -1,47 +1,32 @@
 from MJOLNIR.Data import DataFile
 import subprocess
-import os
+import os,sys
 import pytest
 
-dataFiles = ['Data/camea2018n000136.hdf','Data/camea2018n000136.nxs',
-'Data/camea2018n000137.nxs',
-'Data/camea2018n000178.hdf']
-
-multiFLEXXDataFiles = ['/home/lass/Dropbox/PhD/Software/MJOLNIR/Data/065059']
+dataFiles = [os.path.join('Data',f) for f in ['camea2018n000136.hdf','camea2018n000136.nxs',
+'camea2018n000137.nxs',
+'camea2018n000178.hdf']]
 
 returnText = [b'camea2018n000136.hdf: sc a3 0 da3 0.5 np 121 mn 150000	A3 scan around 1 0 0 YMnO3 T=10, 2T= -20\n',
 b'camea2018n000136.nxs: sc a3 0 da3 0.5 np 121 mn 150000	A3 scan around 1 0 0 YMnO3 T=10, 2T= -20\n',
 b'camea2018n000137.nxs: sc a3 0 da3 0.5 np 121 mn 150000	A3 scan around 1 0 0 YMnO3 T=10, 2T= -24\n',
 b'camea2018n000178.hdf: sc a3 0 da3 1 np 181 mn 100000	PbTi T=1.5K Ei=5.5 2t=-10 HHL plane around 1 1 0\n'
 ]
 
-
+if sys.platform == 'win32':
+    returnText = [t[:-1] + b'\r\n' for t in returnText]
 
 
 ## Calibration inspector
 
 def test_CalibrationInspector_Help_Text():
     result = subprocess.check_output(['MJOLNIRCalibrationInspector','-h'])
-    helpText = b"""usage: MJOLNIRCalibrationInspector [-h] [-s SAVE]
-                                   [-p [PLOTLIST [PLOTLIST ...]]] [-b BINNING]
-                                   [DataFile]
-
-Inspection tool to visualize calibration tables in a data file.
+    if sys.platform == 'win32':
+        print(result)
+        helpText = b'usage: MJOLNIRCalibrationInspector [-h] [-s SAVE]\r\n                                   [-p [PLOTLIST [PLOTLIST ...]]] [-b BINNING]\r\n                                   [DataFile]\r\n\r\nInspection tool to visualize calibration tables in a data file.\r\n\r\npositional arguments:\r\n  DataFile              Data file from which calibration table is to be\r\n                        plotted. If none provided file dialogue will appear.\r\n\r\noptional arguments:\r\n  -h, --help            show this help message and exit\r\n  -s SAVE, --save SAVE  Location to which the generated file will be saved.\r\n  -p [PLOTLIST [PLOTLIST ...]], --plot [PLOTLIST [PLOTLIST ...]]\r\n                        List of wanted plots to be generated. Should be\r\n                        "A4","Normalization","Ef","EfOverview". Default all of\r\n                        them.\r\n  -b BINNING, --binning BINNING\r\n                        Binning to be inspected. Default \'8\'\r\n'
+    else:
+        helpText = b'usage: MJOLNIRCalibrationInspector [-h] [-s SAVE]\n                                   [-p [PLOTLIST [PLOTLIST ...]]] [-b BINNING]\n                                   [DataFile]\n\nInspection tool to visualize calibration tables in a data file.\n\npositional arguments:\n  DataFile              Data file from which calibration table is to be\n                        plotted. If none provided file dialogue will appear.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -s SAVE, --save SAVE  Location to which the generated file will be saved.\n  -p [PLOTLIST [PLOTLIST ...]], --plot [PLOTLIST [PLOTLIST ...]]\n                        List of wanted plots to be generated. Should be\n                        "A4","Normalization","Ef","EfOverview". Default all of\n                        them.\n  -b BINNING, --binning BINNING\n                        Binning to be inspected. Default \'8\'\n'
 
-positional arguments:
-  DataFile              Data file from which calibration table is to be
-                        plotted. If none provided file dialogue will appear.
-
-optional arguments:
-  -h, --help            show this help message and exit
-  -s SAVE, --save SAVE  Location to which the generated file will be saved.
-  -p [PLOTLIST [PLOTLIST ...]], --plot [PLOTLIST [PLOTLIST ...]]
-                        List of wanted plots to be generated. Should be
-                        "A4","Normalization","Ef","EfOverview". Default all of
-                        them.
-  -b BINNING, --binning BINNING
-                        Binning to be inspected. Default '8'
-"""
     assert(result == helpText)
 
 @pytest.mark.skip(reason="Fails on the headless Travis-ci")
@@ -67,7 +52,11 @@ def test_CalibrationInsepctor_Run():
 
 def test_History_Help_Text():
     result = subprocess.check_output(['MJOLNIRHistory', '-h'])
-    helpText = b"""usage: MJOLNIRHistory [-h] [-s SAVE] [-r] [DataFile [DataFile ...]]
+    if sys.platform == 'win32':
+        print(result)
+        helpText = b'usage: MJOLNIRHistory [-h] [-s SAVE] [-r] [DataFile [DataFile ...]]\r\n\r\nHistory tool for displaying files and command for selected data files.\r\n\r\npositional arguments:\r\n  DataFile              Data file(s) to be used. If none provided file\r\n                        dialogue will appear. Using string format, directory\r\n                        and year is also possible. See documentation.\r\n\r\noptional arguments:\r\n  -h, --help            show this help message and exit\r\n  -s SAVE, --save SAVE  Location to which the generated history will be saved.\r\n  -r, --reuse           Set flag to reuse files from previous usage. Default\r\n                        false.\r\n'
+    else:
+        helpText = b"""usage: MJOLNIRHistory [-h] [-s SAVE] [-r] [DataFile [DataFile ...]]
 
 History tool for displaying files and command for selected data files.
 
@@ -113,7 +102,11 @@ def test_History_MultipleFiles_repeat():
 
 def test_Convert_Help_Text():
     result = subprocess.check_output(['MJOLNIRConvert', '-h'])
-    helpText = b"""usage: MJOLNIRConvert [-h] [-s SAVE] [-b BINNING] [-r]
+    if sys.platform == 'win32':
+        print(result)
+        helpText = b"usage: MJOLNIRConvert [-h] [-s SAVE] [-b BINNING] [-r]\r\n                      [DataFile [DataFile ...]]\r\n\r\nConversion tool for converting output h5 files to nxs files.\r\n\r\npositional arguments:\r\n  DataFile              Data file(s) to be used. If none provided file\r\n                        dialogue will appear. Using string format, directory\r\n                        and year is also possible. See documentation.\r\n\r\noptional arguments:\r\n  -h, --help            show this help message and exit\r\n  -s SAVE, --save SAVE  Location to which the generated file will be saved.\r\n  -b BINNING, --binning BINNING\r\n                        Binning performed. Default '8'\r\n  -r, --reuse           Set flag to reuse files from previous usage. Default\r\n                        false.\r\n"
+    else:
+        helpText = b"""usage: MJOLNIRConvert [-h] [-s SAVE] [-b BINNING] [-r]
                       [DataFile [DataFile ...]]
 
 Conversion tool for converting output h5 files to nxs files.
@@ -140,15 +133,15 @@ def test_Convert_binning():
     assert(f.binning == 8)
     subprocess.check_output(['MJOLNIRConvert',dataFiles[0],'-b 1'])
     f = DataFile.DataFile(dataFiles[0].replace('hdf','nxs'))
-    assert(f.name == dataFiles[0].split('/')[1].replace('hdf','nxs'))
+    assert(f.name == dataFiles[0].split(os.path.sep)[1].replace('hdf','nxs'))
     assert(f.binning == 1)
 
 def test_Convert_SaveLocation():
-    if not os.path.isdir('Data/Data'):
-          os.makedirs('Data/Data')
-    subprocess.check_output(['MJOLNIRConvert',dataFiles[0],'-s Data/'])
-    fileName = dataFiles[0].split('/')[1].replace('hdf','nxs')
-    f = DataFile.DataFile('Data/'+fileName)
+    if not os.path.isdir(os.path.join('Data','Data')):
+          os.makedirs(os.path.join('Data','Data'))
+    subprocess.check_output(['MJOLNIRConvert',dataFiles[0],'-s Data'+os.path.sep])
+    fileName = dataFiles[0].split(os.path.sep)[1].replace('hdf','nxs')
+    f = DataFile.DataFile('Data'+os.path.sep+fileName)
 
     assert(f.binning == 8)
     print(fileName)
@@ -171,7 +164,11 @@ def test_Convert_Reuse():
 ### 3DView
 def test_3DView_Help_Text():
     result = subprocess.check_output(['MJOLNIR3DView','-h'])
-    helpText = b"""usage: MJOLNIR3DView [-h] [-r] [-b BINNING] [-d DQXDQYDE DQXDQYDE DQXDQYDE]
+    print(result)
+    if sys.platform == 'win32':
+        helpText = b"usage: MJOLNIR3DView [-h] [-r] [-b BINNING] [-d DQXDQYDE DQXDQYDE DQXDQYDE]\r\n                     [-M VMAX] [-m VMIN]\r\n                     [DataFile [DataFile ...]]\r\n\r\nConversion tool for quick visualization using the viewer3D.\r\n\r\npositional arguments:\r\n  DataFile              Data file(s) to be used. If none provided file\r\n                        dialogue will appear. Using string format, directory\r\n                        and year is also possible. See documentation.\r\n\r\noptional arguments:\r\n  -h, --help            show this help message and exit\r\n  -r, --reuse           Set flag to reuse files from previous usage. Default\r\n                        false.\r\n  -b BINNING, --binning BINNING\r\n                        Binning performed. Default '8'\r\n  -d DQXDQYDE DQXDQYDE DQXDQYDE, --dQxdQydE DQXDQYDE DQXDQYDE DQXDQYDE\r\n                        Binning used to plot in 3D, Default [0.03,0.03,0.08]\r\n  -M VMAX, --VMax VMAX  Maximal value for plotting, default max of data\r\n  -m VMIN, --VMin VMIN  Minimal value for plotting, default min of data\r\n"
+    else:
+        helpText = b"""usage: MJOLNIR3DView [-h] [-r] [-b BINNING] [-d DQXDQYDE DQXDQYDE DQXDQYDE]
                      [-M VMAX] [-m VMIN]
                      [DataFile [DataFile ...]]