Add test coverage report in documentation

Now tests are run through the coverage utility and a report is generated
and available in the FAQ of the html doc.

Makefile

@@ -61,7 +61,7 @@ clean:
 
 venv:
 	@virtualenv --python=python3 --system-site-packages ci_venv $(SUPPRESS_OUPUT)
-	@. "./ci_venv/bin/activate" && pip install --upgrade pip numpy ase h5py lxml pint terminaltables pycairo sphinx $(SUPPRESS_OUPUT)
+	@. "./ci_venv/bin/activate" && pip install --upgrade pip numpy ase h5py lxml pint terminaltables pycairo sphinx coverage $(SUPPRESS_OUPUT)
 
 doc:
 	@echo "Building pdf and html documentation..."

doc/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    = 
-SPHINXBUILD   = python -m sphinx
+SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build
 
@@ -83,9 +83,13 @@ html0: banner images
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-html: html0 ownership $(BUILDDIR)/html/sitemap.xml
+html: html0 ownership $(BUILDDIR)/html/sitemap.xml coverage_report
 	@echo
 
+coverage_report:
+	@echo "Generating coverage report..."
+	@mv source/htmlcov $(BUILDDIR)/html/_static
+
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo

doc/source/conf.py

@@ -20,6 +20,8 @@ import sys, os
 sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../src'))
 sys.path.insert(0, os.path.abspath('../src/msspec'))
+sys.path.insert(0, os.path.abspath('../../src'))
+sys.path.insert(0, os.path.abspath('../../src/msspec'))
 #sys.path.insert(0, os.path.abspath('../'))
 
 

doc/source/faq/coverage_report/coverage_report.rst

@@ -0,0 +1,8 @@
+.. _coverage_report_faq:
+
+Test coverage
+-------------
+
+.. raw:: html
+	
+	<iframe src="../../_static/htmlcov/index.html" height="600px" width="100%"></iframe>

doc/source/faq/index.rst

@@ -7,3 +7,4 @@ FAQ
 .. toctree::
 
     hemispherical_cluster/hemispherical_cluster
+    coverage_report/coverage_report

src/Makefile

@@ -27,7 +27,12 @@ results: pybinding
 
 tests: pybinding
 	@echo "Runing unittests"
-	@python -c "from msspec.tests import run_tests; run_tests()" 1>/dev/null
+#	@python -c "from msspec.tests import run_tests; run_tests()" 1>/dev/null
+	@coverage run --source=./ --omit=msspec/es/*,msspec/msspecgui/* msspec/tests.py 1>/dev/null
+#	create the html coverage report
+#	@mv .coverage ../doc/source
+	@coverage html -d ../doc/source/htmlcov
+	@rm .coverage
 
 clean:
 	@echo "Cleaning all..."

src/msspec/es/es_mod/es_apollonius.py

@@ -24,7 +24,7 @@ def Apollonius_CCC(circles_data) :
     rmin=min(circles_data[1])
     nbmin=circles_data[1].count(rmin)#So it is the number of circles with the smallest radius
     if nbmin==1 : #then we have 1 little circle, we go to Apollonius CCP
-
+        pass
     elif nbmin==2: #then we have 2 little circles, we go to Apollonius CPP
         if r1!=rmin :
             data=[[O1,r1],O2,O3]

src/msspec/es/es_mod/es_sym_analys.py

@@ -54,16 +54,16 @@ def compare_sym(Nsym,Osym):
     print("New number of sym :", N)
     if N>O :
         output=2
-        print "Symmetries gained. Symmetry-list updated"
+        print("Symmetries gained. Symmetry-list updated")
     elif O==1 :
         output=-1
-        print "No symmetry existing to help at decision"
+        print("No symmetry existing to help at decision")
     elif N == O:
         output=1
-        print "Symmetry has been conserved."
+        print("Symmetry has been conserved.")
     elif N<O :
         output=0
-        print "Symmetries Lost: Fusion-Operation on last empty-spheres advised"
+        print("Symmetries Lost: Fusion-Operation on last empty-spheres advised")
     return output
 # ===================================================================
 def read_sym_file(symfile) :
@@ -279,7 +279,7 @@ def Cluster_emptyness_informations(Structure) :
         raw_input("\nPress Enter to continue ...\n")
 
         Allproportions.append(proportion)
-    print "AllProportions : ",Allproportions
+    print("AllProportions : ",Allproportions)
 
     print("Hull volume = {}".format(set_volume))
     return spheres_volume / set_volume * 100
@@ -341,7 +341,7 @@ def Vertice_Sphere_Proportion(O,hull,Structure) :
                     V1 = tool.vector_def(Point_list[O], P1)
                     V2 = tool.vector_def(Point_list[O], P2)
                     V3 = tool.vector_def(Point_list[O], P3)
-                    print "Vectors from top of pyramid to base points" , [V1, V2, V3]
+                    print("Vectors from top of pyramid to base points" , [V1, V2, V3])
                     a = tool.angle_vector(V1, V2)
                     b = tool.angle_vector(V2, V3)
                     c = tool.angle_vector(V3, V1)
@@ -430,7 +430,7 @@ def convex_base(Neil,Simplices) :
             Last=ConvBase[-1]
             print(Last)
             Neighborsi=hull_search_neighbors(i,Simplices)
-            print ("The last elements :{}\nHis neighbors : {}".format(ConvBase[-1],Neighborsi))
+            print("The last elements :{}\nHis neighbors : {}".format(ConvBase[-1],Neighborsi))
             if ConvBase[-1] in Neighborsi :
                 ConvBase.append(i)
                 Rest.remove(i)
@@ -459,7 +459,7 @@ def Hull_Neighbors_List(O,Structure,hull)  :
     # Returns the list of all atom's indexes in hull wich are neighbors of Atom indexed numAtom (numAtom must be int, 0 included)
     Allfacets = np.ndarray.tolist(hull.simplices)
     Hull_Neilist = []
-    print Allfacets
+    print(Allfacets)
     for facet in Allfacets :
         if O in facet :
             for index in facet :

src/msspec/msspecgui/msspec/gui/clustereditor.py

@@ -179,9 +179,9 @@ class BulkGui(dataflow.IOperatorCreator.IAction):
         if result == wx.ID_OK:
             print("execute_on_operator : signaling operator %d as modified" % operator.id)
             operator.data_flow.on_modified_operator(operator)
-            print "OK"
+            print("OK")
         else:
-            print "Cancel"
+            print("Cancel")
         dialog.Destroy()
 
 

src/msspec/msspecgui/msspec/gui/clusterviewer3d/GLPanel.py

@@ -65,7 +65,7 @@ class GLPanel(wx.Panel):
         else:
             self.scale /= 1.1
         #self._gl_scale()
-        print self.scale
+        print(self.scale)
         w, h = self.canvas.GetClientSize()
         self._gl_init_view(w, h)
         self._gl_draw()
@@ -82,7 +82,7 @@ class GLPanel(wx.Panel):
         winz = glReadPixels(winx, winy, 1, 1, GL_DEPTH_COMPONENT, GL_FLOAT)[0][0]
         coords = gluUnProject(winx, winy, winz, mvmatrix, projmatrix, viewport)
         self.coords0 = coords
-        print "coords0 = ", coords
+        print("coords0 = ", coords)
 
 
     def onMotionEvent(self, event):
@@ -112,10 +112,10 @@ class GLPanel(wx.Panel):
             translation = [x - self.coords0[0], y - self.coords0[1], 0]
             #print x, y, z#translation
             if winx < w and winx > 0 and winy < h and winy > 0:
-                print 'here'
+                print('here')
                 glTranslatef(*translation)
                 #self.translation = translation
-            print translation
+            print(translation)
 
         self._gl_draw()
 

src/msspec/tests.py

@@ -151,3 +151,7 @@ def create_tests_results():
 
 def delete_results_file():
     os.remove(RESULTS_FILENAME)
+
+
+if __name__ == "__main__":
+    run_tests()