Move to codecov (#60)

brainglobe · Jul 27, 2022 · 9fb775d · 9fb775d
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diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: tests
 
 on: [push, pull_request]
@@ -12,20 +9,14 @@ jobs:
       - uses: brainglobe/actions/lint@v1
 
   test:
-    needs: linting
+    needs: [linting]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # Run all supported Python versions on linux
-        python-version: ["3.8", "3.9"]
-        os: [ubuntu-latest]
-        # Include one windows and macos run
-        include:
-        - os: macos-latest
-          python-version: "3.9"
-        - os: windows-latest
-          python-version: "3.9"
+        # Run all supported Python versions on linux and windows
+        python-version: ["3.8", "3.9", "3.10"]
+        os: [ubuntu-latest, windows-latest]
 
     steps:
       # Setup pyqt libraries

diff --git a/README.md b/README.md
@@ -4,8 +4,7 @@
 [![Development Status](https://img.shields.io/pypi/status/brainreg-segment.svg)](https://github.com/brainglobe/brainreg-segment)
 [![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainreg-segment/tests)](
     https://github.com/brainglobe/brainreg-segment/actions)
-[![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainreg-segment/badge.svg?branch=master)](https://coveralls.io/github/brainglobe/brainreg-segment?branch=master)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+[![codecov](https://codecov.io/gh/brainglobe/brainreg-segment/branch/master/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainreg-segment)[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
 
 # brainreg-segment

diff --git a/brainreg_segment/segment.py b/brainreg_segment/segment.py
@@ -2,11 +2,11 @@
 
 import napari
 import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
 from napari.qt.threading import thread_worker
 from qtpy import QtCore
 from qtpy.QtWidgets import QFileDialog, QGridLayout, QGroupBox, QLabel, QWidget
 
+from bg_atlasapi import BrainGlobeAtlas
 from brainreg_segment.atlas.utils import (
     get_available_atlases,
     structure_from_viewer,

diff --git a/pyproject.toml b/pyproject.toml
@@ -23,3 +23,5 @@ exclude = '''
 [tool.isort]
 profile = "black"
 line_length = 79
+sections=["FUTURE","STDLIB","THIRDPARTY","BRAINGLOBE","FIRSTPARTY","LOCALFOLDER"]
+known_brainglobe=["brainreg", "brainreg_segment", "brainglobe_napari_io", "bg_space", "bg_atlasapi"]
diff --git a/pytest.ini b/pytest.ini
diff --git a/setup.py b/setup.py
@@ -35,8 +35,8 @@
             "black",
             "pytest-cov",
             "pytest",
-            "pytest-qt",
-            "coverage",
+            "gitpython",
+            "coverage>=5.0.3",
             "bump2version",
             "pre-commit",
             "flake8",

diff --git a/tests/__init__.py b/tests/__init__.py
diff --git a/tests/tests/test_integration/test_tracks/test_track_analysis.py b/tests/tests/test_integration/test_tracks/test_track_analysis.py
@@ -2,8 +2,8 @@
 
 import numpy as np
 import pandas as pd
-from bg_atlasapi import BrainGlobeAtlas
 
+from bg_atlasapi import BrainGlobeAtlas
 from brainreg_segment.tracks.analysis import run_track_analysis
 
 atlas_name = "allen_mouse_50um"

diff --git a/tests/tests/test_unit/test_atlas/test_atlas_utils.py b/tests/tests/test_unit/test_atlas/test_atlas_utils.py
@@ -1,6 +1,6 @@
 import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
 
+from bg_atlasapi import BrainGlobeAtlas
 from brainreg_segment.atlas import utils as atlas_utils
 
 atlas_name = "allen_mouse_50um"

diff --git a/tox.ini b/tox.ini
@@ -1,26 +1,37 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{38,39}
+envlist = py{38,39,310}-{linux,windows}
 
 [gh-actions]
 python =
     3.8: py38
     3.9: py39
+    3.10: py310
+
+[gh-actions:env]
+PLATFORM =
+    ubuntu-latest: linux
+    windows-latest: windows
 
 [testenv]
+platform =
+    macos: darwin
+    linux: linux
+    windows: win32
 passenv =
     CI
     GITHUB_ACTIONS
     DISPLAY XAUTHORITY
     NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
     PYVISTA_OFF_SCREEN
 deps =
-    # Even though napari is a requirement for cellfinder-napari, we have to
-    # ensure it is installed with the default Qt backend here.
-    napari[pyqt]
     pytest  # https://docs.pytest.org/en/latest/contents.html
     pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
-    pytest-qt
     pytest-xvfb ; sys_platform == 'linux'
-commands =
-    pytest -v --color=yes --cov=brainreg_segment --cov-report=xml
+    # you can remove these if you don't use them
+    napari
+    magicgui
+    pytest-qt
+    qtpy
+    pyqt5
+commands = pytest -v --color=yes --cov=brainreg_segment --cov-report=xml