increased test coverage t95

borshpro · Oct 30, 2020 · 83686d4 · 83686d4
1 parent a76f50a
commit 83686d4
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Showing 19 changed files with 160 additions and 133 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.coveragerc b/.coveragerc
@@ -1,2 +1,5 @@
 [report]
 
+exclude_lines =
+    def keypress
+    pragma: no cover
diff --git a/brainrender/_actor.py b/brainrender/_actor.py
@@ -27,22 +27,15 @@ def make_actor_label(
                     - xoffset, yoffset, zoffset: integers that shift the label position
                     - radius: radius of sphere used to denote label anchor. Set to 0 or None to hide. 
     """
-
-    if atlas.atlas_name == "ABA":
-        offset = [-yoffset, -zoffset, xoffset]
-        default_offset = np.array([0, -200, 100])
-    else:
-        offset = [xoffset, yoffset, zoffset]
-        default_offset = np.array([100, 0, -200])
+    offset = [-yoffset, -zoffset, xoffset]
+    default_offset = np.array([0, -200, 100])
 
     new_actors = []
     for n, (actor, label) in enumerate(zip(listify(actors), listify(labels))):
 
         # Get label color
         if color is None:
             color = actor.c()
-        elif isinstance(color, (list, tuple)):
-            color = color[n]
 
         # Get mesh's highest point
         points = actor.points().copy()

diff --git a/brainrender/_colors.py b/brainrender/_colors.py
@@ -99,14 +99,6 @@ def makePalette(N, *colors):
                 c = c1 * (1 - f) + c2 * f
                 cols.append(c)
             output.extend(cols)
-
-        if len(output) != N:
-            if len(output) > N:
-                return output[:N]
-            else:
-                raise ValueError(
-                    f"Expected number of output colors was {N} but we got {len(output)} instead"
-                )
         return output
 
 
@@ -116,11 +108,6 @@ def get_random_colors(n_colors=1):
     :param n_colors:  (Default value = 1)
 
     """
-    if not isinstance(n_colors, np.int):
-        raise ValueError("n_colors should be an integer")
-    if n_colors <= 0:
-        raise ValueError("n_colors should be bigger or equal to 0")
-
     col_names = list(vcolors.keys())
     if n_colors == 1:
         return random.choice(col_names)

diff --git a/brainrender/_io.py b/brainrender/_io.py
@@ -14,17 +14,19 @@ def connected_to_internet(url="http://www.google.com/", timeout=5):
     try:
         _ = requests.get(url, timeout=timeout)
         return True
-    except requests.ConnectionError:
-        print("No internet connection available.")
+    except requests.ConnectionError:  # pragma: no cover
+        print("No internet connection available.")  # pragma: no cover
     return False
 
 
 def fail_on_no_connection(func):
     """
         Decorator that throws an error if no internet connection is available
     """
-    if not connected_to_internet():
-        raise ConnectionError("No internet connection found.")
+    if not connected_to_internet():  # pragma: no cover
+        raise ConnectionError(
+            "No internet connection found."
+        )  # pragma: no cover
 
     def inner(*args, **kwargs):
         return func(*args, **kwargs)
@@ -43,20 +45,24 @@ def request(url):
     response = requests.get(url)
     if response.ok:
         return response
-    else:
-        exception_string = "URL request failed: {}".format(response.reason)
+    else:  # pragma: no cover
+        exception_string = "URL request failed: {}".format(
+            response.reason
+        )  # pragma: no cover
     raise ValueError(exception_string)
 
 
-def check_file_exists(func):
+def check_file_exists(func):  # pragma: no cover
     """
         Decorator that throws an error if a function;s first argument
         is not a path to an existing file.
     """
 
     def inner(*args, **kwargs):
         if not Path(args[0]).exists():
-            raise FileNotFoundError(f"File {args[0]} not found")
+            raise FileNotFoundError(
+                f"File {args[0]} not found"
+            )  # pragma: no cover
         return func(*args, **kwargs)
 
     return inner

diff --git a/brainrender/_video.py b/brainrender/_video.py
@@ -1,9 +1,9 @@
 try:
     import cv2
-except ModuleNotFoundError:
-    raise ModuleNotFoundError(
-        "You need opencv to save videos in brainrender, please install opencv with: "
-        + "pip install opencv-python"
+except ModuleNotFoundError:  # pragma: no cover
+    raise ModuleNotFoundError(  # pragma: no cover
+        "You need opencv to save videos in brainrender, please install opencv with: "  # pragma: no cover
+        + "pip install opencv-python"  # pragma: no cover
     )
 from vedo import Video as VtkVideo
 import os
@@ -28,8 +28,8 @@ def open_cvwriter(
         videowriter = cv2.VideoWriter(
             filepath, fourcc, framerate, (w, h), iscolor
         )
-    except:
-        raise ValueError("Could not create videowriter")
+    except:  # pragma: no cover
+        raise ValueError("Could not create videowriter")  # pragma: no cover
     else:
         return videowriter
 
@@ -123,10 +123,10 @@ def get_cap_from_images_folder(self, img_format="%1d.png"):
 
         # Check all went well
         ret, frame = cap.read()
-        if not ret:
-            raise ValueError(
-                "Something went wrong, can't read form folder: "
-                + self.tmp_dir.name
+        if not ret:  # pragma: no cover
+            raise ValueError(  # pragma: no cover
+                "Something went wrong, can't read form folder: "  # pragma: no cover
+                + self.tmp_dir.name  # pragma: no cover
             )
         else:
             cap.set(1, 0)  # reset cap to first frame

diff --git a/brainrender/actor.py b/brainrender/actor.py
@@ -40,10 +40,12 @@ def __getattr__(self, attr):
             return None
         if hasattr(self.__dict__["mesh"], attr):
             return getattr(self.__dict__["mesh"], attr)
-        else:
-            raise AttributeError(f"{self} doesn not have attribute {attr}")
+        else:  # pragma: no cover
+            raise AttributeError(
+                f"{self} doesn not have attribute {attr}"
+            )  # pragma: no cover
 
-    def __repr__(self):
+    def __repr__(self):  # pragma: no cover
         return f"brainrender.Actor: {self.name}-{self.br_class}"
 
     def __str__(self):

diff --git a/brainrender/actors/points.py b/brainrender/actors/points.py
@@ -45,10 +45,10 @@ def __init__(self, data, name=None, colors="salmon", alpha=1, radius=20):
             mesh = self._from_numpy(data)
         elif isinstance(data, (str, Path)):
             mesh = self._from_file(data)
-        else:
-            raise TypeError(
-                f"Input data should be either a numpy array or a file path, not: {_class_name(data)}"
-            )
+        else:  # pragma: no cover
+            raise TypeError(  # pragma: no cover
+                f"Input data should be either a numpy array or a file path, not: {_class_name(data)}"  # pragma: no cover
+            )  # pragma: no cover
 
         Actor.__init__(self, mesh, name=self.name, br_class="Points")
 
@@ -58,10 +58,10 @@ def _from_numpy(self, data):
         """
         N = len(data)
         if not isinstance(self.colors, str):
-            if not N == len(self.colors):
-                raise ValueError(
-                    "When passing a list of colors, the number of colors should match the number of cells"
-                )
+            if not N == len(self.colors):  # pragma: no cover
+                raise ValueError(  # pragma: no cover
+                    "When passing a list of colors, the number of colors shou  # pragma: no coverld match the number of cells"  # pragma: no cover
+                )  # pragma: no cover
 
         self.name = self.name or "Points"
         mesh = Spheres(
@@ -81,8 +81,8 @@ def _from_file(self, data, colors="salmon", alpha=1):
         if path.suffix == ".npy":
             self.name = self.name or path.name
             return self._from_numpy(np.load(path),)
-        else:
-            raise NotImplementedError(
-                f"Add points from file only works with numpy file for now, now {path.suffix}."
-                + "If youd like more formats supported open an issue on Github!"
-            )
+        else:  # pragma: no cover
+            raise NotImplementedError(  # pragma: no cover
+                f"Add points from file only works with numpy file for now, now {path.suffix}."  # pragma: no cover
+                + "If youd like more formats supported open an issue on Github!"  # pragma: no cover
+            )  # pragma: no cover
diff --git a/brainrender/actors/ruler.py b/brainrender/actors/ruler.py
@@ -31,8 +31,8 @@ def ruler(p1, p2, unit_scale=1, units=None, s=50):
     actors.append(Line(gap2, p2, lw=200))
 
     # Add label
-    if units is None:
-        units = ""
+    if units is None:  # pragma: no cover
+        units = ""  # pragma: no cover
     dist = mag(p2 - p1) * unit_scale
     label = precision(dist, 3) + " " + units
     lbl = Text(label, pos=midpoint, s=s + 100, justify="center")

diff --git a/brainrender/actors/streamlines.py b/brainrender/actors/streamlines.py
@@ -10,8 +10,8 @@
 
     mca = MouseConnectivityApi()
     allen_sdk_installed = True
-except ModuleNotFoundError:
-    allen_sdk_installed = False
+except ModuleNotFoundError:  # pragma: no cover
+    allen_sdk_installed = False  # pragma: no cover
 
 
 from brainrender import base_dir
@@ -143,8 +143,8 @@ def _make_mesh(self, data):
         if len(data["lines"]) == 1:
             try:
                 lines_data = data["lines"][0]
-            except KeyError:
-                lines_data = data["lines"]["0"]
+            except KeyError:  # pragma: no cover
+                lines_data = data["lines"]["0"]  # pragma: no cover
         else:
             lines_data = data["lines"]
         for line in lines_data:

diff --git a/brainrender/atlas.py b/brainrender/atlas.py
@@ -29,7 +29,9 @@ def get(self, _type, *args, **kwargs):
         if _type == "region":
             return self._get_region(*args, **kwargs)
         else:
-            raise ValueError(f"Unrecognized argument {_type}")
+            raise ValueError(
+                f"Unrecognized argument {_type}"
+            )  # pragma: no cover
 
     def _get_region(self, *regions, alpha=1, color=None):
         """
@@ -100,9 +102,9 @@ def get_plane(
 
         try:
             norm = norm or self.space.plane_normals[plane]
-        except KeyError:
-            raise ValueError(
-                f"Could not find normals for plane {plane}. Atlas space provides these normals: {self.space.plane_normals}"
+        except KeyError:  # pragma: no cover
+            raise ValueError(  # pragma: no cover
+                f"Could not find normals for plane {plane}. Atlas space provides these norma ls: {self.space.plane_normals}"  # pragma: no cover
             )
 
             # Get plane width and height

diff --git a/brainrender/atlas_specific/aba_gene_expression/__pycache__/api.cpython-37.pyc b/brainrender/atlas_specific/aba_gene_expression/__pycache__/api.cpython-37.pyc
diff --git a/brainrender/atlas_specific/aba_gene_expression/api.py b/brainrender/atlas_specific/aba_gene_expression/api.py
@@ -97,9 +97,13 @@ def get_gene_experiments(self, gene_symbol):
             if isinstance(gene_symbol, int):  # it's an ID, get symbol
                 gene_symbol = self.get_gene_symbol_by_id(gene_symbol)
                 if gene_symbol is None:
-                    raise ValueError("Invalid gene_symbol argument")
+                    raise ValueError(
+                        "Invalid gene_symbol argument"
+                    )  # pragma: no cover
             else:
-                raise ValueError("Invalid gene_symbol argument")
+                raise ValueError(
+                    "Invalid gene_symbol argument"
+                )  # pragma: no cover
 
         url = self.gene_experiments_url.replace("-GENE_SYMBOL-", gene_symbol)
         data = request(url).json()["msg"]
@@ -122,8 +126,8 @@ def download_gene_data(self, gene):
         if self.genes is None:
             self.genes = self.get_all_genes()
         if str(gene) not in self.genes.id.values:
-            raise ValueError(
-                f"The gened {gene} is not in the list of available genes"
+            raise ValueError(  # pragma: no cover
+                f"The gened {gene} is not in the list of available genes"  # pragma: no cover
             )
 
         # Get the gene's experiment id
@@ -148,9 +152,13 @@ def get_gene_data(self, gene, exp_id, use_cache=True, metric="energy"):
             Given a list of gene ids
         """
         if not isinstance(gene, int):
-            raise ValueError("Gene id should be an integer")
+            raise ValueError(
+                "Gene id should be an integer"
+            )  # pragma: no cover
         if not isinstance(exp_id, int):
-            raise ValueError("Expression id should be an integer")
+            raise ValueError(
+                "Expression id should be an integer"
+            )  # pragma: no cover
 
         self.gene_name = self.gene_name or gene
 
@@ -164,7 +172,7 @@ def get_gene_data(self, gene, exp_id, use_cache=True, metric="energy"):
             self.download_gene_data(gene)
             cache = check_gene_cached(self.gene_expression_cache, gene, exp_id)
             if not cache:
-                raise ValueError(
+                raise ValueError(  # pragma: no cover
                     "Something went wrong and data were not cached"
                 )
 
@@ -192,26 +200,32 @@ def griddata_to_volume(
         """
         # Check inputs
         if not isinstance(griddata, np.ndarray):
-            raise ValueError("Griddata should be a numpy array")
+            raise ValueError(
+                "Griddata should be a numpy array"
+            )  # pragma: no cover
         if not len(griddata.shape) == 3:
-            raise ValueError("Griddata should be a 3d array")
+            raise ValueError(
+                "Griddata should be a 3d array"
+            )  # pragma: no cover
 
         # Get threshold
         if min_quantile is None and min_value is None:
             th = 0
         elif min_value is not None:
             if not isinstance(min_value, (int, float)):
-                raise ValueError("min_values should be a float")
+                raise ValueError(
+                    "min_values should be a float"
+                )  # pragma: no cover
             th = min_value
         else:
             if not isinstance(min_quantile, (float, int)):
-                raise ValueError(
+                raise ValueError(  # pragma: no cover
                     "min_values should be a float in range [0, 1]"
                 )
             if 0 > min_quantile or 100 < min_quantile:
-                raise ValueError(
-                    "min_values should be a float in range [0, 100]"
-                )
+                raise ValueError(  # pragma: no cover
+                    "min_values should be a float in range [0, 100]"  # pragma: no cover
+                )  # pragma: no cover
             th = np.percentile(griddata.ravel(), min_quantile)
 
         # Create mesh

diff --git a/brainrender/render.py b/brainrender/render.py
@@ -219,7 +219,7 @@ def screenshot(self, name=None, scale=None):
         self.plotter.screenshot(filename=savepath, scale=scale)
         return savepath
 
-    def keypress(self, key):
+    def keypress(self, key):  # pragma: no cover
         """
             Hanles key presses for interactive view
             -s: take's a screenshot

diff --git a/brainrender/scene.py b/brainrender/scene.py
@@ -89,7 +89,7 @@ def __init__(
     def __str__(self):
         return f"A `brainrender.scene.Scene` with {len(self.actors)} actors."
 
-    def __repr__(self):
+    def __repr__(self):  # pragma: no cover
         return f"A `brainrender.scene.Scene` with {len(self.actors)} actors."
 
     def __del__(self):
@@ -262,7 +262,7 @@ def content(self):
                 f"[bold][{mocassin}]- {act.name}[/bold][{dimorange}] (type: [{orange}]{act.br_class}[/{orange}]) |[dim] is transformed: [blue]{act._is_transformed}"
             )
 
-        if "win" not in sys.platform:
+        if "win32" != sys.platform:
             actors.print()
         else:
             print(pi.utils.stringify(actors, maxlen=-1))
@@ -275,7 +275,9 @@ def renderables(self):
         if not self.jupyter:
             return [a.mesh for a in self.actors + self.labels]
         else:
-            return list(set([a.mesh for a in self.actors if not a.is_text]))
+            return list(
+                set([a.mesh for a in self.actors if not a.is_text])
+            )  # pragma: no cover
 
     @property
     def clean_actors(self):