Never use DH cipher and remove several warnings (#30)

morphapi/api/neuromorphorg.py

@@ -1,14 +1,12 @@
 import logging
 import os
-from functools import partial
 
 from morphapi.morphology.morphology import Neuron
 from morphapi.paths_manager import Paths
 from morphapi.utils.webqueries import connected_to_internet
 from morphapi.utils.webqueries import request
 
 logger = logging.getLogger(__name__)
-request_no_ssl = partial(request, verify=False)
 
 
 class NeuroMorpOrgAPI(Paths):
@@ -26,7 +24,7 @@ def __init__(self, *args, **kwargs):
 
         # Check that neuromorpho.org is not down
         try:
-            request_no_ssl("https://neuromorpho.org/api/health")
+            request("https://neuromorpho.org/api/health")
         except Exception as e:
             raise ConnectionError(
                 f"It seems that neuromorphos API is down: {e}"
@@ -40,7 +38,7 @@ def fields(self):
         Fields contains the types of fields that can be used to restrict queries
         """
         if self._fields is None:
-            self._fields = request_no_ssl(self._base_url + "/fields").json()[
+            self._fields = request(self._base_url + "/fields").json()[
                 "Neuron Fields"
             ]
         return self._fields
@@ -53,7 +51,7 @@ def get_fields_values(self, field):
         max_page = 1
         values = []
         while current_page < max_page:
-            req = request_no_ssl(
+            req = request(
                 self._base_url
                 + f"/fields/{field}?&size=1000&page={current_page}"
             ).json()
@@ -100,7 +98,7 @@ def get_neurons_metadata(self, size=100, page=0, **criteria):
         url += f"&size={int(size)}&page={int(page)}"
 
         try:
-            req = request_no_ssl(url)
+            req = request(url)
             neurons = req.json()
             valid_url = req.ok and "error" not in neurons
         except ValueError:
@@ -137,13 +135,13 @@ def get_neuron_by_id(self, nid):
         """
         Get a neuron's metadata given it's id number
         """
-        return request_no_ssl(self._base_url + f"/id/{nid}").json()
+        return request(self._base_url + f"/id/{nid}").json()
 
     def get_neuron_by_name(self, nname):
         """
         Get a neuron's metadata given it's name
         """
-        return request_no_ssl(self._base_url + f"/name/{nname}").json()
+        return request(self._base_url + f"/name/{nname}").json()
 
     def build_filepath(self, neuron_id):
         """
@@ -202,7 +200,7 @@ class is used to download neurons for other APIs
                     url = f"https://neuromorpho.org/dableFiles/{neuron['archive'].lower()}/{self._version}/{neuron['neuron_name']}.swc"
 
                 try:
-                    req = request_no_ssl(url)
+                    req = request(url)
                     with open(filepath, "w") as f:
                         f.write(req.content.decode("utf-8"))
                 except ValueError as exc:

morphapi/morphology/morphology.py

@@ -112,7 +112,7 @@ def load_from_swc(self):
 
         self.repair_swc_file()
 
-        nrn = nm.load_neuron(self.data_file)
+        nrn = nm.load_morphology(self.data_file)
 
         # Get position and radius of some
         soma_pos = nrn.soma.points[0, :3]
@@ -247,7 +247,7 @@ def create_mesh(
                 pos=coords,
                 r=self.points["soma"].radius * soma_radius,
                 c=soma_color,
-            ).computeNormals()
+            ).compute_normals()
             neurites["soma"] = soma.clone().c(soma_color)
 
             # Create neurites actors
@@ -273,15 +273,15 @@ def create_mesh(
                 if actors:
                     neurites[ntype] = merge(
                         actors
-                    ).computeNormals()  # .smoothMLS2D(f=0.1)
+                    ).compute_normals()  # .smoothMLS2D(f=0.1)
                 else:
                     neurites[ntype] = None
 
             # Merge actors to get the entire neuron
             actors = [
                 act.clone() for act in neurites.values() if act is not None
             ]
-            whole_neuron = merge(actors).clean().computeNormals()
+            whole_neuron = merge(actors).clean().compute_normals()
 
             # Write to cache
             to_write = neurites.copy()

morphapi/utils/webqueries.py

@@ -21,10 +21,9 @@ def request(url, verify=True):
 
     try:
         _DEFAULT_CIPHERS = requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS
-        if not verify:
-            requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS = (
-                _DEFAULT_CIPHERS + ":HIGH:!DH:!aNULL"
-            )
+        requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS = (
+            _DEFAULT_CIPHERS + ":HIGH:!DH:!aNULL"
+        )
         response = requests.get(url, verify=verify)
     finally:
         requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS = _DEFAULT_CIPHERS
@@ -48,9 +47,7 @@ def query_mouselight(query):
             "You need an internet connection for API queries, sorry."
         )
 
-    base_url = "https://ml-neuronbrowser.janelia.org/"
-
-    full_query = base_url + query
+    full_query = mouselight_base_url + query
 
     # send the query, package the return argument as a json tree
     response = requests.get(full_query)
@@ -108,8 +105,8 @@ def post_mouselight(url, query=None, clean=False, attempts=3):
         if request is None:
             raise ConnectionError(
                 "\n\nMouseLight API query failed with error message:\n{}.\
-                        \nPerhaps the server is down, visit 'https://ml-neuronbrowser.janelia.org' to find out.".format(
-                    exception
+                        \nPerhaps the server is down, visit '{}' to find out.".format(
+                    exception, mouselight_base_url
                 )
             )
     else:

pytest.ini

@@ -1,3 +1,6 @@
 [pytest]
 addopts = --cov=morphapi
 
+filterwarnings =
+    ignore:distutils Version classes are deprecated:DeprecationWarning
+    ignore:The hookimpl CovPlugin.pytest_.* uses old-style configuration options:pytest.PytestDeprecationWarning

setup.py

@@ -10,13 +10,13 @@
 requirements = [
     "bg_atlasapi",
     "imagecodecs; python_version>='3.9'",
-    "neurom<4",
+    "neurom>=3,<4",
     "numpy",
     "pandas",
     "pyyaml>=5.3",
     "retry",
     "rich",
-    "vedo>=2020.3.3",
+    "vedo>=2021.0.3",
     "vtk",
 ]