Merge 2129b92 into dbea039

.flake8

@@ -16,8 +16,6 @@
 # Raymond Hettinger’s “Beyond PEP 8” talk and highway patrol not stopping you
 # if you drive < 5mph too fast. Disable E501 to avoid duplicate warnings.
 
-exclude = src/histolab/filter.py # remove this line when filter is ok
-
 max-line-length = 80
 max-complexity = 12
 select = E,F,W,C,B,B9

.travis.yml

@@ -1,18 +1,53 @@
 # Wire up travis
 language: python
-sudo: false
 
-python:
-  - "3.6"
-  - "3.7"
-
-before_install:
-  - sudo apt-get install openslide-tools
+language: python            # this works for Linux but is an error on macOS or Windows
+jobs:
+  include:
+    - name: "Python 3.6 on Xenial Linux"
+      python: 3.6           # this works for Linux but is ignored on macOS or Windows
+    - name: "Python 3.7 on Xenial Linux"
+      python: 3.7          # this works for Linux but is ignored on macOS or Windows
+    - name: "Python 3.6.5 on macOS"
+      os: osx
+      osx_image: xcode9.4  # Python 3.7.4 running on macOS 10.14.4
+      language: shell       # 'language: python' is an error on Travis CI macOS
+      before_install:
+        - brew update
+        - brew install openslide
+        - echo 'export PATH="/usr/local/Frameworks/Python.framework/Versions/Current/bin:$PATH"' >> /Users/travis/.bash_profile
+        - echo $PATH
+    - name: "Python 3.7.4 on macOS"
+      os: osx
+      osx_image: xcode11.2  # Python 3.7.4 running on macOS 10.14.4
+      language: shell       # 'language: python' is an error on Travis CI macOS
+      before_install:
+        - brew install openslide
+        - echo 'export PATH="/usr/local/Frameworks/Python.framework/Versions/Current/bin:$PATH"' >> /Users/travis/.bash_profile
+        - echo $PATH
+    - name: "Python 3.6.8 on Windows"
+      os: windows           # Windows 10.0.17134 N/A Build 17134
+      language: shell       # 'language: python' is an error on Travis CI Windows
+      before_install:
+        - choco install python --version 3.6.8
+        - python -m pip install --upgrade pip
+        - wget https://github.com/openslide/openslide-winbuild/releases/download/v20171122/openslide-win64-20171122.zip -P /c/downloads
+        - 7z e /c/downloads/openslide-win64-20171122.zip -aoa
+      env: PATH=/c/Python36:/c/Python36/Scripts:/c/downloads/openslide-win64-20171122/bin:$PATH
+    - name: "Python 3.7 on Windows"
+      os: windows           # Windows 10.0.17134 N/A Build 17134
+      language: shell       # 'language: python' is an error on Travis CI Windows
+      before_install:
+        - choco install python --version 3.7
+        - python -m pip install --upgrade pip
+        - wget https://github.com/openslide/openslide-winbuild/releases/download/v20171122/openslide-win64-20171122.zip -P /c/downloads
+        - 7z e /c/downloads/openslide-win64-20171122.zip -aoa
+      env: PATH=/c/Python37:/c/Python37/Scripts:/c/downloads/openslide-win64-20171122/bin:$PATH
 
 # command to install dependencies
 install:
-  - pip install -e .[testing]
-  - pip install flake8
+  - pip3 install -e .[testing]
+  - pip3 install flake8
 
 services:
   - xvfb
@@ -30,4 +65,8 @@ after_success:
   - coveralls
 
 notifications:
-  slack: mpba:fBrjUWlUSa3XKeCA8zFsTFu2
+  slack: mpba:fBrjUWlUSa3XKeCA8zFsTFu2
+
+addons:
+  apt:
+    packages: openslide-tools

src/histolab/tiler.py

@@ -387,8 +387,8 @@ def max_iter(self) -> int:
     def max_iter(self, max_iter_: int = 1e4):
         if max_iter_ < self.n_tiles:
             raise ValueError(
-                f"The maximum number of iterations ({max_iter_}) must be grater than or "
-                f"equal to the maximum number of tiles ({self.n_tiles})."
+                f"The maximum number of iterations ({max_iter_}) must be grater than or"
+                f" equal to the maximum number of tiles ({self.n_tiles})."
             )
         self._valid_max_iter = max_iter_
 

tests/integration/test_morphological_filters.py

@@ -1,5 +1,5 @@
-import pytest
 import numpy as np
+import pytest
 
 import histolab.filters.morphological_filters_functional as mof
 
@@ -15,28 +15,32 @@
             3000,
             True,
             95,
-            "mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-remove-small-objects-mask",
+            "mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-remove-small-"
+            "objects-mask",
         ),
         (
             NPY.DIAGNOSTIC_SLIDE_THUMB_HSV_OTSU_THRESHOLD_MASK,
             3000,
             True,
             95,
-            "mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-remove-small-objects-mask",
+            "mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-remove-small-objects"
+            "-mask",
         ),
         (
             NPY.DIAGNOSTIC_SLIDE_THUMB_HSV_OTSU_THRESHOLD_MASK,
             3000,
             False,
             95,
-            "mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-remove-small-objects2-mask",
+            "mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-remove-small-objects"
+            "2-mask",
         ),
         (
             NPY.DIAGNOSTIC_SLIDE_THUMB_RGB1_HYSTERESIS_THRESHOLD_MASK,
             1200,
             True,
             25,
-            "mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-remove-small-objects2-mask",
+            "mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-remove-small-"
+            "objects2-mask",
         ),
     ),
 )

tests/unit/test_slide.py

@@ -1,5 +1,6 @@
 # encoding: utf-8
 
+import errno
 import math
 import os
 from collections import namedtuple
@@ -108,7 +109,7 @@ def it_knows_its_thumbnails_path(self, resampled_dims_):
             "/foo/bar/myslide.svs",
             "/foo/bar/myslide/processed",
             (345, 111, 333, 444),
-            "/foo/bar/myslide/processed/thumbnails/myslide.png",
+            os.path.join("/foo/bar/myslide/processed", "thumbnails", "myslide.png"),
         )
         resampled_dims_.return_value = slide_dims
         slide = Slide(slide_path, proc_path)
@@ -216,7 +217,8 @@ def or_it_raises_an_PIL_exception(self, tmpdir):
 
         assert isinstance(err.value, PIL.UnidentifiedImageError)
         assert (
-            str(err.value) == f"cannot identify image file '{os.path.join(slide_path)}'"
+            str(err.value) == "cannot identify image file "
+            f"{repr(os.path.join(slide_path))}"
         )
 
     def it_can_resample_itself(self, tmpdir, resampled_dims_):
@@ -444,7 +446,7 @@ def but_it_raises_error_when_it_doesnt_exist(self):
         assert (
             str(err.value)
             == "Cannot display the slide thumbnail:[Errno 2] No such file or "
-            "directory: 'processed/thumbnails/b.png'"
+            f"directory: {repr(os.path.join('processed', 'thumbnails', 'b.png'))}"
         )
 
     def it_knows_its_level_dimensions(self, tmpdir):
@@ -508,25 +510,31 @@ def slide_ext_fixture(self, request):
                 "/foo/bar/myslide.svs",
                 "/foo/bar/myslide/processed",
                 (345, 111, 333, 444),
-                "/foo/bar/myslide/processed/myslide-22x-345x111-333x444.png",
+                os.path.join(
+                    "/foo/bar/myslide/processed", "myslide-22x-345x111-333x444.png"
+                ),
             ),
             (
                 "/foo/bar/myslide2.svs",
                 "/foo/bar/myslide/processed",
                 (345, 111, None, None),
-                "/foo/bar/myslide/processed/myslide2-22x-345x111-NonexNone.png",
+                os.path.join(
+                    "/foo/bar/myslide/processed", "myslide2-22x-345x111-NonexNone.png"
+                ),
             ),
             (
                 "/foo/bar/myslide2.svs",
                 "/foo/bar/myslide/processed",
                 (345, 111, 123, 123),
-                "/foo/bar/myslide/processed/myslide2-22x-345x111-123x123.png",
+                os.path.join(
+                    "/foo/bar/myslide/processed", "myslide2-22x-345x111-123x123.png"
+                ),
             ),
             (
                 "/foo/bar/myslide2.svs",
                 "/foo/bar/myslide/processed",
                 (None, None, None, None),
-                "/foo/bar/myslide/processed/myslide2*.png",
+                os.path.join("/foo/bar/myslide/processed", "myslide2*.png"),
             ),
         ]
     )
@@ -542,47 +550,47 @@ def scaled_img_path_fixture(self, request):
                 "/foo/bar/myslide.svs",
                 "processed",
                 64,
-                "/foo/bar/b/0/9/myslide-64x-245x123-145x99.png",
+                os.path.join("/foo/bar/b/0/9", "myslide-64x-245x123-145x99.png"),
             ),
             (
                 (245, 123, 145, 99),
                 "/foo/bar/b/0/9",
                 "/foo/bar/myslide.svs",
                 "processed",
                 32,
-                "/foo/bar/b/0/9/myslide-32x-245x123-145x99.png",
+                os.path.join("/foo/bar/b/0/9", "myslide-32x-245x123-145x99.png"),
             ),
             (
                 (None, None, None, None),
                 "/foo/bar/b/0/9",
                 "/foo/bar/myslide.svs",
                 "processed",
                 64,
-                "/foo/bar/b/0/9/myslide*.png",
+                os.path.join("/foo/bar/b/0/9", "myslide*.png"),
             ),
             (
                 (None, 234, 192, None),
                 "/foo/bar/b/0/9",
                 "/foo/bar/myslide.svs",
                 "processed",
                 64,
-                "/foo/bar/b/0/9/myslide-64x-Nonex234-192xNone.png",
+                os.path.join("/foo/bar/b/0/9", "myslide-64x-Nonex234-192xNone.png"),
             ),
             (
                 (123, 234, 192, None),
                 "/foo/bar/b/0/9",
                 "/foo/bar/myslide.svs",
                 "processed",
                 64,
-                "/foo/bar/b/0/9/myslide-64x-123x234-192xNone.png",
+                os.path.join("/foo/bar/b/0/9", "myslide-64x-123x234-192xNone.png"),
             ),
             (
                 (None, None, 192, None),
                 "/foo/bar/b/0/9",
                 "/foo/bar/myslide.svs",
                 "processed",
                 64,
-                "/foo/bar/b/0/9/myslide-64x-NonexNone-192xNone.png",
+                os.path.join("/foo/bar/b/0/9", "myslide-64x-NonexNone-192xNone.png"),
             ),
         ]
     )
@@ -706,7 +714,7 @@ def it_knows_its_slides(self, tmpdir):
             slides = slideset.slides
 
         assert isinstance(err.value, FileNotFoundError)
-        assert str(err.value) == "[Errno 2] No such file or directory: 'fake/path'"
+        assert err.value.errno == errno.ENOENT
 
     def it_constructs_its_sequence_of_slides_to_help(self, request, Slide_, tmpdir):
         slides_path = tmpdir.mkdir("mypath")

tests/unit/test_tiler.py

@@ -1,3 +1,4 @@
+import csv
 import os
 from unittest.mock import call
 
@@ -68,7 +69,8 @@ def or_it_has_wrong_max_iter(self, request):
         assert isinstance(err.value, ValueError)
         assert (
             str(err.value)
-            == "The maximum number of iterations (3) must be grater than or equal to the maximum number of tiles (10)."
+            == "The maximum number of iterations (3) must be grater than or equal to "
+            "the maximum number of tiles (10)."
         )
 
     def or_it_has_wrong_seed(self, request, tmpdir):
@@ -850,15 +852,16 @@ def it_can_save_report(self, request, tmpdir):
         filenames = ["tile0.png", "tile1.png"]
         random_scorer_ = instance_mock(request, RandomScorer)
         score_tiler = ScoreTiler(random_scorer_, (10, 10), 2, 2)
-        report_ = ["filename,score\n", "tile0.png,0.8\n", "tile1.png,0.7\n"]
+        report_ = ["filename,score", "tile0.png,0.8", "tile1.png,0.7"]
 
         score_tiler._save_report(
             os.path.join(tmp_path_, "report.csv"), highest_score_tiles, filenames
         )
 
         assert os.path.exists(os.path.join(tmp_path_, "report.csv"))
-        with open(os.path.join(tmp_path_, "report.csv")) as f:
-            report = f.readlines()
+        with open(os.path.join(tmp_path_, "report.csv"), newline="") as f:
+            reader = csv.reader(f)
+            report = [",".join(row) for row in reader]
             assert report == report_
 
     def it_can_extract_score_tiles_and_save_report(self, request, tmpdir):