merge

.travis.yml

@@ -7,6 +7,6 @@ python:
 before_script:
  - chmod +x binaries
 # command to install dependencies
-install: "pip install grapetree"
+install: "pip install -r requirements.txt"
 # command to run tests
 script: pytest

build_win.bat

@@ -1,6 +1,7 @@
 pyinstaller -n GrapeTree_win  --icon=GT_icon.ico ^
     --add-binary binaries/edmonds.exe;binaries/ ^
     --add-binary binaries/fastme.exe;binaries/ ^
-    --add-data MSTree_holder.html;grapetree/MSTree_holder.html ^
-    --add-data static/;grapetree/static/ ^
+    --add-data MSTree_holder.html;. ^
+    --add-data static/;static/ ^
+    --hidden-import psutil ^
     grapetree.py 

grapetree.py

@@ -34,6 +34,8 @@
 import os
 import sys
 from module.MSTrees import backend, add_args
+import psutil
+
 
 __licence__ = 'GPLv3'
 __author__ = 'EnteroBase development team'
@@ -73,4 +75,6 @@ def main() :
             os._exit(1)
 
 if __name__ == "__main__":
+    import multiprocessing
+    multiprocessing.freeze_support()
     main()

module/MSTrees.py

@@ -623,7 +623,7 @@ def estimate_Consumption(platform, method, matrix, n_proc, n_loci, n_profile) :
 
     return max(time, 5), max(memory, 50*1024*1024)
 
-if __name__ == '__main__' :
-    tre = backend(**add_args())
-    print tre
+#if __name__ == '__main__' :
+    #tre = backend(**add_args())
+    #print tre
 

module/__init__.py

@@ -4,7 +4,7 @@
 import os
 
 if getattr(sys, 'frozen', False):
-    template_folder = os.path.join(sys._MEIPASS, 'grapetree','templates')
+    template_folder = sys._MEIPASS #os.path.join(sys._MEIPASS, 'templates')
     static_folder = os.path.join(sys._MEIPASS, 'static')
     app = Flask(__name__, template_folder=template_folder, static_folder=static_folder)
 else:

module/views.py

@@ -20,7 +20,7 @@ def generate_tree():
         for param in params:
             if isinstance(params[param], list):
                 params[param] = params[param][0]
-        tree = backend (profile= params['profile'],
+        tree = backend(profile= params['profile'],
                         method=params['method'],
                         checkEnv = params['checkEnv'],
                         )

requirements.txt

@@ -1,19 +1,12 @@
-appdirs==1.4.3
 click==6.7
-colorama==0.3.9
-decorator==4.0.11
-DendroPy==4.2.0
+decorator==4.3.0
+DendroPy==4.3.0
 Flask==0.12.2
-future==0.16.0
+grapetree==1.3.2
 itsdangerous==0.24
-Jinja2==2.9.6
+Jinja2==2.10
 MarkupSafe==1.0
-networkx==1.11
-numpy==1.12.1
-packaging==16.8
-py==1.4.33
-pyparsing==2.2.0
-pytest==3.0.7
-psutil==5.4.3
-six==1.10.0
-Werkzeug==0.12.2
+networkx==2.1
+numpy==1.14.2
+psutil==5.4.5
+Werkzeug==0.14.1