Update installation

Author: hkjeldsberg

docs/source/installation.rst

@@ -1,13 +1,13 @@
 .. title:: Installation
-.. highlight:: console
 
 ============
 Installation
 ============
+.. highlight:: console
 
 morphMan (morphological manipulation) is a collection of scripts to objectively manipulate
 morphological features of patient-specific vascular geometries. The project is accessible through
-`GitHub <https://github.com/KVSlab/morphMan/>`_ and `Anaconda.org <https://anaconda.org/morphman/morphman>`_.
+`GitHub <https://github.com/KVSlab/morphMan/>`_ and `Anaconda <https://anaconda.org/morphman/morphman>`_.
 
 
 Compatibility and Dependencies
@@ -31,7 +31,7 @@ Then execute the following command in a terminal window to create a Conda enviro
 .. note::
     Replace ``your_environment`` with the environment name.
 
-You can then activate your environment by running ``source activate your_environment``.
+You can then activate your environment by running ``conda activate your_environment`` or ``source activate your_environment``.
 Now you are all set, and can start using morphMan. morphMan can be accessed by opening a Python console
 and typing::
 

test/fixtures.py

@@ -13,13 +13,13 @@
 from morphman.common import get_inlet_and_outlet_centers, get_path_names, compute_centerlines, prepare_surface
 
 
-def download_testdata(test_path, outputfile):
+def download_testdata(test_path, output_file):
     if platform == "darwin":
-        system("curl -L {} --output {}".format(test_path, outputfile))
+        system("curl -L {} --output {}".format(test_path, output_file))
     elif platform == "linux" or platform == "linux2":
-        system("wget -O {} {}".format(outputfile, test_path))
+        system("wget -O {} {}".format(output_file, test_path))
     elif platform == "win32":
-        system("bitsadmin /transfer download_model /download /priority high {} {}".format(test_path, outputfile))
+        system("bitsadmin /transfer download_model /download /priority high {} {}".format(test_path, output_file))
 
 
 @pytest.fixture(scope="module")
@@ -29,15 +29,16 @@ def surface_paths():
     # Path to test data
     # TODO: Replace with official Aneurisk database when available
     test_path = "https://github.com/hkjeldsberg/AneuriskDatabase/raw/master/models/C0001/surface/model.vtp"
-    outputfile = path.join(abs_path, "C0001", "surface", "model.vtp")
+    output_file = path.join(abs_path, "C0001", "surface", "model.vtp")
 
-    # Download test data if necessary
+    # Create test data folders
     if not path.exists(path.join(abs_path, "C0001", "surface")):
         makedirs(path.join(abs_path, "C0001", "surface"))
 
+    # Download test data if necessary
     if not path.exists(path.join(abs_path, "C0001", "surface", "model.vtp")):
         try:
-            download_testdata(test_path, outputfile)
+            download_testdata(test_path, output_file)
         except Exception:
             raise Exception("Problem downloading the testdata, please do it manually from "
                             + test_path + " and extract the compressed tarball in the test folder")