Merge pull request #15 from bmatern/master

Logging and Python 3 updates

AlleleSubInstallerOptions_Windows.spec

@@ -22,27 +22,26 @@
 
 block_cipher = None
 
-
-a = Analysis(['saddlebags\AlleleSubMain.py'],
-             binaries=None,
-             datas=[('images\horse_image_icon.ico', 'images')] ,
-             hiddenimports=['six', 'packaging', 'packaging.requirements', 'packaging.version', 'packaging.specifiers', 'Tkinter', 'tkFileDialog', 'Tkconstants', 'saddlebags.AlleleSubMainGui'],
-             hookspath=[],
-             runtime_hooks=[],
-             excludes=['tkinter'],
-             win_no_prefer_redirects=False,
-             win_private_assemblies=False,
-             cipher=block_cipher)
+a = Analysis(['AlleleSubMain.py'],
+    binaries=None,
+    datas=[('images\horse_image_icon.ico', 'images')] ,
+    hiddenimports=[],
+    hookspath=[],
+    runtime_hooks=[],
+    excludes=[],
+    win_no_prefer_redirects=False,
+    win_private_assemblies=False,
+    cipher=block_cipher)
 pyz = PYZ(a.pure, a.zipped_data,
-             cipher=block_cipher)
+    cipher=block_cipher)
 exe = EXE(pyz,
-          a.scripts,
-          a.binaries,
-          a.zipfiles,
-          a.datas,
-          name='SaddlebagsWindows',
-          debug=False,
-          strip=False,
-          upx=True,
-          console=False,
-          icon='images\horse_image_icon.ico' )
+    a.scripts,
+    a.binaries,
+    a.zipfiles,
+    a.datas,
+    name='SaddlebagsWindows',
+    debug=False,
+    strip=False,
+    upx=True,
+    console=False,
+    icon='images\horse_image_icon.ico' )

saddlebags/AlleleSubMain.py → AlleleSubMain.py

@@ -13,43 +13,48 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
-import Tkinter
-import sys
+#import Tkinter
+#import sys
+from sys import argv, exc_info
+from tkinter import Tk
 
+from saddlebags.AlleleSubCommon import loadConfigurationFile
+from saddlebags.AlleleSubMainGui import AlleleSubMainGui
 # This exception handling is necessary for packaging the modules in pyinstaller.
 # The namespace(?) is required to find the modules in pyinstaller.  
-try:
-    from AlleleSubMainGui import AlleleSubMainGui
-    from AlleleSubCommon import loadConfigurationFile
-except:
-    from saddlebags.AlleleSubMainGui import AlleleSubMainGui
-    from saddlebags.AlleleSubCommon import loadConfigurationFile
+
+#try:
+#    from AlleleSubMainGui import AlleleSubMainGui
+#    from AlleleSubCommon import loadConfigurationFile
+#except:
+#    from saddlebags.AlleleSubMainGui import AlleleSubMainGui
+#    from saddlebags.AlleleSubCommon import loadConfigurationFile
 
-SoftwareVersion = 'saddlebags Version 1.1'
+SoftwareVersion = 'saddlebags Version 1.2'
 
 if __name__=='__main__':
     try:
         # This is a really simple way to read commandline args, 
         # because there really shouldn't be any.
         # TODO: Be more graceful with this, there are better ways to read args.
         # No parameters are expected at all.  sys.argv[0] doesn't count.
-        if (len(sys.argv) == 1):
+        if (len(argv) == 1):
 
             loadConfigurationFile()
 
             print('\n\n\n\n\n***Starting the HLA Allele Submission Tool***\n')
 
-            root = Tkinter.Tk()
+            root = Tk()
             AlleleSubMainGui(root).pack()
             root.mainloop()
 
             print('Done.  Hooray.')
 
         # Print the Software Version
-        elif (len(sys.argv) == 2 and (
-            sys.argv[1].lower() == '-v' or 
-            sys.argv[1].lower() == '--version' or 
-            sys.argv[1].lower() == '-version')        
+        elif (len(argv) == 2 and (
+            argv[1].lower() == '-v' or 
+            argv[1].lower() == '--version' or 
+            argv[1].lower() == '-version')        
         ):
             print (SoftwareVersion)
             pass
@@ -61,13 +66,13 @@
                 "\tRun this program using standard python call:\n" + 
                 "\t$python AlleleSubmissionMain.py\n" + 
                 "\tbiopython must be accessible in your python environment.  To run using Anaconda,\n"
-                "\tCheck readme at https://github.com/transplantation-immunology/saddle-bags\n"
+                "\tCheck readme at https://github.com/transplantation-immunology-maastricht/saddle-bags\n"
             )
 
 
     except Exception:
         # Top Level exception handling like a pro.
         # This is not really doing anything.
-        print 'Unexpected problem during execution:'
-        print sys.exc_info()[1]
+        print ('Unexpected problem during execution:')
+        print (exc_info()[1])
         raise

MakeExecutables.bat

@@ -23,8 +23,8 @@
 SET CodePath=saddlebags
 SET BinPath=bin
 SET SpecFile=AlleleSubInstallerOptions_Windows.spec
-SET CondaEnvironment=minionvironment
+SET VirtualEnvironmentLocation=C:\Users\ben\Envs\minionvenv\Scripts
 
 :: Run Pyinstaller to create executables
 :: cd %CodePath%
-activate %CondaEnvironment% && pyinstaller %SpecFile% --distpath %BinPath% --clean && deactivate
+activate %VirtualEnvironmentLocation%\activate && pyinstaller %SpecFile% --distpath %BinPath% --clean && deactivate

README.md

@@ -6,31 +6,49 @@ Download an executable for Windows from the Release page.
 [Download Saddlebags for Windows Here](https://github.com/transplantation-immunology-maastricht/saddle-bags/releases)
 
 ## Run using Python
-Alternatively, you can run this program using Python 2.7. This works for Mac and Linux users (or Windows). There are prerequesites, I recommend you install them inside an Anaconda environment. See Run_allele_submission.sh and Run_allele_submission.bat for an example of this in Linux and Windows environments, respectively.
+Alternatively, you can run this program using Python 3.6. The required packages can be installed within a python virtual environment. This works for Mac and Linux users, or Windows. See Run_allele_submission.bat and Run_allele_submission.sh for an example of launching Saddlebags in Windows, or Linux/Mac, respectively..
+
+## To configure Virtual Environment.
+The general installation instructions are similar for Windows and Linux/Mac environments.
+
+Install the Git commandline. In Windows, there is an option to include the git bash console, I recommend doing this, as it is very useful.
+
+Install Python 3.6, 64 or 32 bit.
+[Download Python](https://www.python.org/downloads/release/python-363/)
+
+The python installer includes pip, which is necessary for the next steps.
+
+Install Virtual Environment. This requires a couple steps, because there is a windows wrapper to get virtual environment working with powershell. 
 
 ```
-python AlleleSubmissionMain.py
+pip install virtualenv
+pip install virtualenvwrapper-win
 ```
+[More info](http://timmyreilly.azurewebsites.net/python-pip-virtualenv-installation-on-windows/)
 
-## To configure Anaconda
-Anaconda uses separate environments to run your programs in.  
-Install Anaconda for python 2.7.  
-https://www.continuum.io/downloads  
-To set up the environment in anaconda:  
+Create the virtual environment. I typically use an environment called "minionvenv":
+```
+mkvirtualenv minionvenv
+```
+The mkvirtualenv command should automatically activate the new environment. If not, activate the environment.
+```
+C:\Users\ben\Envs\minionvenv\Scripts\activate
+```
 
-Linux/Mac:  
+Is your environment activated? Then use pip to install the packages that saddlebags needs:
 ```
-conda create --name minionvironment biopython six pycurl
-source activate minionvironment  
-pip install pyinstaller packaging  
-source deactivate  
-```  
-Windows:  
-```  
-conda create --name minionvironment biopython six pywin32 pycurl
-call activate minionvironment && pip install pyinstaller packaging && call deactivate  
+pip install biopython six pycurl pyinstaller packaging 
 ```
 
+In Ubuntu, Installing pycurl was a bit difficult inside of virtualenv.
+
+https://stackoverflow.com/questions/37669428/error-in-installation-pycurl-7-19-0
+sudo apt-get install libgnutls-dev
+
+In linux, i needed Needed the "dev" verson of python 3.6
+sudo apt-get install python3.6-dev
+
+
 ## Run using a bash or .bat script using anaconda
 You can execute the following scripts to run the tool inside of Anaconda:  
 Linux/Mac:  

Run_allele_submission.bat

@@ -13,9 +13,7 @@
 :: You should have received a copy of the GNU Lesser General Public License
 :: along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
-:: Version 1.0
+:: See the file README.MD for how to set up your virtual environment.
 
-:: See the file README.MD for how to set up your anaconda environment.
-
-activate minionvironment && cd saddlebags && python AlleleSubMain.py && deactivate
+C:\Users\ben\Envs\minionvenv\Scripts\activate &&  python AlleleSubMain.py 
 

Run_allele_submission.sh

@@ -13,12 +13,8 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
-# See the file README.MD for how to set up your anaconda environment.
-
-cd saddlebags
-
-source activate minionvironment
-python AlleleSubMain.py
-source deactivate
-
+# Activate the virtual environment.
+source /home/ben/minionvenv/bin/activate
 
+# Launch the Python.
+python AlleleSubMain.py