fixed min requirements (NeuralEnsemble#235)

* fixed min requirements

* travis install libopenmpi-dev

* added .coveragerc omit=elephant/test* rule not to count test files as source code

.coveragerc

@@ -0,0 +1,3 @@
+# .coveragerc to control coverage.py
+[report]
+omit = elephant/test/*

.travis.yml

@@ -41,14 +41,14 @@ matrix:
       python: 3.7
       env: DISTRIB="conda"
 
-  exclude:
-    - name: "pip 3.6 requirements min version"
-      # excluded due to unmet dependencies in neo, quantities, and scipy
+    - name: "pip 3.6 requirements-extras min version"
       python: 3.6
       env: DISTRIB="pip"
       before_install:
-        - sudo apt install libblas-dev liblapack-dev libatlas-base-dev gfortran
-        - sed -i 's/>=/==/g' requirements.txt
+        - sudo apt install -y libopenmpi-dev openmpi-bin
+        - sudo apt install -y libblas-dev liblapack-dev libatlas-base-dev gfortran
+        - sed -i 's/>=/==/g' requirements*.txt
+      before_script: pip install -r requirements-extras.txt
 
 
 install:

elephant/current_source_density_src/KCSD.py

@@ -48,7 +48,7 @@ def validate(self, ele_pos, pots):
         if ele_pos.shape[0] < 1+ele_pos.shape[1]: #Dim+1
             raise Exception("Number of electrodes must be at least :",
                             1+ele_pos.shape[1])
-        if utils.check_for_duplicated_electrodes(ele_pos) is False:
+        if utils.contains_duplicated_electrodes(ele_pos):
             raise Exception("Error! Duplicated electrode!")
 
     def sanity(self, true_csd, pos_csd):

elephant/current_source_density_src/utility_functions.py

@@ -35,17 +35,19 @@ def patch_quantities():
         lastdefinition = definition
     return
 
-def check_for_duplicated_electrodes(elec_pos):
+
+def contains_duplicated_electrodes(elec_pos):
     """Checks for duplicate electrodes
     Parameters
     ----------
     elec_pos : np.array
+
     Returns
     -------
     has_duplicated_elec : Boolean
     """
-    unique_elec_pos = np.unique(elec_pos, axis=0)
-    has_duplicated_elec = unique_elec_pos.shape == elec_pos.shape
+    unique_elec_pos = set(map(tuple, elec_pos))
+    has_duplicated_elec = len(unique_elec_pos) < len(elec_pos)
     return has_duplicated_elec
 
 

requirements-extras.txt

@@ -1,4 +1,4 @@
-pandas>=0.14.1
-scikit-learn
+pandas>=0.18.0
+scikit-learn>=0.19.0
 mpi4py>=3.0.1
 tqdm

requirements.txt

@@ -1,5 +1,5 @@
 neo>=0.7.1,<0.8.0
-numpy>=1.8.2
-quantities>=0.10.1
-scipy>=0.14.0
+numpy>=1.10.1
+quantities>=0.12.1
+scipy>=0.17.0
 six>=1.10.0