fix multiple warnings

• Use the undeprecaded sympy objects and imports
• Avoid potentially creating an array of arrays with different shape
• Properly use pytest.warns
• Update dependencies to match upcoming Kwant
• Silence the unfixable warnings from old scipy and sympy in pytest.

.gitlab-ci.yml

@@ -5,7 +5,7 @@ variables:
     import kwant.tests.test_qsymm;
     print(os.path.abspath(kwant.tests.test_qsymm.__file__));
 
-image: continuumio/miniconda
+image: continuumio/miniconda3
 
 ## Documentation for the format of this file can be found here:
 ## https://docs.gitlab.com/ce/ci/yaml/README.html#configuration-of-your-builds-with-gitlab-ci-yml