update CI/dockers

* drop tox
* install py27

.github/workflows/ci-testing.yml

@@ -41,6 +41,8 @@ jobs:
       if: matrix.python-version == 2.7
       run: |
         cp -r requirements-py27.txt requirements.txt
+        # required for matplotlib @py2
+        pip install -U backports.functools_lru_cache
 
     - name: Set min. dependencies
       if: matrix.requires == 'minimal'
@@ -66,8 +68,6 @@ jobs:
     - name: Install dependencies
       run: |
         pip install $(grep "numpy" requirements.txt)
-        # required for matplotlib @py2
-        pip install -U backports.functools_lru_cache
         # v46 crashes openslide-python install
         pip install "setuptools<46" -U
         pip install --requirement requirements.txt --quiet --upgrade
@@ -77,15 +77,18 @@ jobs:
         pip list
       shell: bash
 
-    - name: Tests
-      env:
-        DISPLAY: ""
+    - name: Pkg install
       run: |
-        check-manifest --ignore tox.ini
+        check-manifest
         python setup.py check --metadata --strict
         python setup.py install --dry-run --user
-        coverage run --source birl -m py.test birl tests bm_dataset bm_experiments bm_ANHIR -v --doctest-modules --durations=25 --junitxml=junit/test-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}.xml
-        flake8 .
+
+    - name: Tests and coverage
+      env:
+        DISPLAY: ""
+      run: |
+        coverage run --source birl -m pytest birl tests bm_dataset bm_experiments bm_ANHIR -v --durations=25 --junitxml=junit/test-results-${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.requires }}.xml
+        # flake8 .
 
     - name: Upload pytest test results
       uses: actions/upload-artifact@master
@@ -107,8 +110,6 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.xml
-        flags: cpu,pytest
-        name: CPU-coverage
         fail_ci_if_error: false
 
     - name: Run sample experiment

.travis.yml

@@ -20,7 +20,6 @@ matrix:
       language: python
       python: 2.7
       dist: xenial  # Ubuntu 16.04
-      env: TOXENV=py27
       #- os: linux
       #  language: python
       #  python: 3.5
@@ -30,21 +29,17 @@ matrix:
       language: python
       python: 3.6
       dist: bionic  # Ubuntu 18.04
-      env: TOXENV=py36
     - os: linux
       language: python
       python: 3.7
       dist: bionic  # Ubuntu 18.04
-      env: TOXENV=py37
     - os: linux
       language: python
       python: 3.8
       dist: bionic  # Ubuntu 18.04
-      env: TOXENV=py38
     - os: osx
       osx_image: xcode10.3
       language: generic
-      env: TOXENV=py37
       addons:
         homebrew:
           # update: true
@@ -69,7 +64,6 @@ matrix:
         - python -m pip install --upgrade pip
         - choco install -y opencv
       env:
-        - TOXENV=py37
         - PATH=/c/Python37:/c/Python37/Scripts:%OPENCV_DIR%/bin:$PATH
   # https://towardsdatascience.com/extensive-python-testing-on-travis-ci-4c24db9bf961
   allow_failures:
@@ -97,7 +91,10 @@ install:
 
 script:
   # integration
-  - tox -v
+  - check-manifest
+  - python setup.py check --metadata --strict
+  - python setup.py install --dry-run
+  - coverage run --source birl -m pytest birl tests bm_dataset bm_experiments bm_ANHIR -v
   # sample run
   - mkdir results && touch configs/sample_config.yaml
   - python bm_experiments/bm_comp_perform.py -o ./results -n 1

README.md

@@ -1,6 +1,6 @@
 # BIRL: Benchmark on Image Registration methods with Landmark validation
 
-[![Build Status](https://travis-ci.org/Borda/BIRL.svg?branch=master)](https://travis-ci.org/Borda/BIRL)
+[![Build Status](https://travis-ci.com/Borda/BIRL.svg?branch=master)](https://travis-ci.com/Borda/BIRL)
 [![CircleCI](https://circleci.com/gh/Borda/BIRL.svg?style=svg&circle-token=e58b9845aab1b02d749df60060afbac54138ea28)](https://circleci.com/gh/Borda/BIRL)
 [![Build status](https://ci.appveyor.com/api/projects/status/rmfvuxix379eu6fh/branch/master?svg=true)](https://ci.appveyor.com/project/Borda/birl/branch/master)
 [![codecov](https://codecov.io/gh/Borda/BIRL/branch/master/graph/badge.svg?token=JZwA1rlUGA)](https://codecov.io/gh/Borda/BIRL)

appveyor.yml

@@ -14,22 +14,18 @@ environment:
     #- PYTHON: "C:\\Python27"
     #  PYTHON_VERSION: "2.7.x"
     #  PYTHON_ARCH: "32"
-    #  TOXENV: "py27"
 
     #- PYTHON: "C:\\Python27-x64"
     #  PYTHON_VERSION: "2.7.x"
     #  PYTHON_ARCH: "64"
-    #  TOXENV: "py27"
 
     #- PYTHON: "C:\\Python36-x64"
     #  PYTHON_VERSION: "3.6.x"
     #  PYTHON_ARCH: "64"
-    #  TOXENV: "py36"
 
     - PYTHON: "C:\\Python37-x64"
       PYTHON_VERSION: "3.7.x"
       PYTHON_ARCH: "64"
-      TOXENV: "py37"
 
 build: off
 
@@ -55,7 +51,6 @@ install:
   - pip install "setuptools<46" -U  # v46 crashes openslide-python install
   - pip install -r requirements.txt
   - pip install -r ./tests/requirements.txt
-  - pip install tox
 
 # scripts to run before tests (working directory and environment changes are persisted from the previous steps such as "before_build")
 before_test:
@@ -66,7 +61,7 @@ before_test:
 
 # to run your custom scripts instead of automatic tests
 test_script:
-  - tox -v --sitepackages --parallel auto
+  - coverage run --source birl -m pytest birl tests bm_dataset bm_experiments bm_ANHIR -v
   - mkdir results && touch configs/sample_config.yaml
   - python bm_experiments/bm_comp_perform.py -o ./results -n 1
   - python birl/bm_template.py -n anhir -t ./data-images/pairs-imgs-lnds_mix.csv -o ./results --preprocessing matching-rgb gray --unique --visual -cfg configs/sample_config.yaml

birl/utilities/drawing.py

@@ -32,21 +32,21 @@ def draw_image_points(image, points, color='green', marker_size=5, shape='o'):
     :return: np.ndarray
 
     >>> image = np.zeros((10, 10, 3))
-    >>> points = np.array([[7, 9], [2, 2], [5, 5]])
-    >>> img = draw_image_points(image, points, marker_size=1)
+    >>> points = np.array([[9, 1], [2, 2], [5, 5]])
+    >>> img = draw_image_points(image, points, marker_size=1, shape='s')
     >>> img.shape == (10, 10, 3)  # Windows x64 returns (10L, 10L, 3L)
     True
     >>> np.round(img[:, :, 1], 2)
-    array([[ 0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ],
-           [ 0. ,  0.5,  0.5,  0.5,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ],
-           [ 0. ,  0.5,  0. ,  0.5,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ],
+    array([[ 0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0.5,  0.5],
+           [ 0. ,  0.5,  0.5,  0.5,  0. ,  0. ,  0. ,  0. ,  0.5,  0. ],
+           [ 0. ,  0.5,  0. ,  0.5,  0. ,  0. ,  0. ,  0. ,  0.5,  0.5],
            [ 0. ,  0.5,  0.5,  0.5,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ],
            [ 0. ,  0. ,  0. ,  0. ,  0.5,  0.5,  0.5,  0. ,  0. ,  0. ],
            [ 0. ,  0. ,  0. ,  0. ,  0.5,  0. ,  0.5,  0. ,  0. ,  0. ],
            [ 0. ,  0. ,  0. ,  0. ,  0.5,  0.5,  0.5,  0. ,  0. ,  0. ],
            [ 0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ],
            [ 0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ],
-           [ 0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0.5,  0. ]])
+           [ 0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ,  0. ]])
     >>> img = draw_image_points(None, points, marker_size=1)
     """
     assert list(points), 'missing points'
@@ -64,6 +64,8 @@ def draw_image_points(image, points, color='green', marker_size=5, shape='o'):
             draw.ellipse(pos_marker, outline=color)
         elif shape == '.':
             draw.ellipse(pos_marker, fill=color)
+        elif shape == 's':
+            draw.rectangle(pos_marker, outline=color)
         else:
             draw.ellipse(pos_marker, fill=color, outline=color)
         draw.text(pos_text, str(i + 1), fill=(0, 0, 0))

bm_ANHIR/Dockerfile

@@ -2,6 +2,8 @@
 FROM python:3.7-slim-stretch
 #FROM borda/docker_python-opencv-ffmpeg:py3
 
+LABEL maintainer="[email protected]"
+
 # Install packages
 RUN apt-get update -qq && apt-get install -y --no-install-recommends \
         git>=2.0 \

bm_experiments/Dockerfile

@@ -1,9 +1,10 @@
 #FROM ubuntu:bionic
 FROM ubuntu:20.04
 
-
 ARG PYTHON_VERSION=3.7
 
+LABEL maintainer="[email protected]"
+
 SHELL ["/bin/bash", "-c"]
 
 # for installing tzdata see: https://stackoverflow.com/a/58264927/4521646

circle.yml

@@ -41,7 +41,7 @@ references:
         unset DISPLAY
         pip install -r ./tests/requirements.txt
         mkdir test-reports && mkdir results
-        coverage run --source birl -m py.test birl tests bm_dataset bm_experiments bm_ANHIR -v --doctest-modules --junitxml=test-reports/pytest_junit.xml
+        coverage run --source birl -m pytest birl tests bm_dataset bm_experiments bm_ANHIR -v --junitxml=test-reports/pytest_junit.xml
         coverage report
         codecov
         rm -rf results

docs/source/conf.py

@@ -21,8 +21,9 @@
 
 import m2r
 
-PATH_ROOT = os.path.join('..', '..')
+PATH_UP = os.path.join('..', '..')
 PATH_HERE = os.path.abspath(os.path.dirname(__file__))
+PATH_ROOT = os.path.abspath(os.path.join(PATH_HERE, PATH_UP))
 sys.path.insert(0, os.path.abspath(PATH_ROOT))
 
 import birl  # noqa: E402
@@ -65,7 +66,7 @@
 readme = re.sub(r'(!\[.*.gif\))', '', readme)
 for dir_name in (os.path.basename(p) for p in glob.glob(os.path.join(PATH_ROOT, '*'))
                  if os.path.isdir(p)):
-    readme = readme.replace('](%s/' % dir_name, '](%s/%s/' % (PATH_ROOT, dir_name))
+    readme = readme.replace('](%s/' % dir_name, '](%s/%s/' % (PATH_UP, dir_name))
 with open('readme.md', 'w') as fp:
     fp.write(readme)
 

requirements-py27.txt

@@ -1,15 +1,15 @@
-numpy>=1.8.2
+numpy>=1.9
 scipy>=0.10.0
 pandas>=0.17.1
 six>=1.7.3
-pillow>=2.1.0, !=7.1  # 7.x fails to load PNG via skimage
+pillow>=4.0, <7  # 7.x fails to load PNG via skimage
 matplotlib>=2.0.2, <3.0.0  # new version does not support py2
 tqdm>=4.7.4, <=4.30  # higher fails ascii for py2
 pyyaml
 scikit-image
 opencv-python-headless<4.3
 openslide-python<=1.1.1
-nibabel
+nibabel<3.0
 SimpleITK
 psutil
 pathos

requirements.txt

@@ -2,7 +2,7 @@ numpy>=1.13.3
 scipy>=1.0
 pandas>=0.21
 six>=1.10
-pillow>=4.0, !=7.1 # 7.x fails to load PNG via skimage
+pillow>=4.0, !=7  # 7.x fails to load PNG via skimage
 matplotlib>=2.0.2
 tqdm>=4.7.4
 pyyaml>=3.12

setup.cfg

@@ -8,16 +8,22 @@ requirements-file = requirements.txt
 
 [flake8]
 # http://flake8.pycqa.org/en/latest/user/configuration.html
-ignore = E402,E731
-max-line-length = 100
 exclude = .tox,*.egg,build,temp
 select = E,W,F
 doctests = True
 verbose = 2
-# max-complexity = 10
+# https://pep8.readthedocs.io/en/latest/intro.html#error-codes
+ignore =
+    E402
+    E501
+format = pylint
+max-line-length = 100
 
 [tool:pytest]
-log_cli = 1
+addopts =
+    --doctest-modules
+    --color=yes
+log_cli = 0
 log_cli_level = CRITICAL
 #log_cli_format = %(message)s
 log_file = pytest.log

setup.py

@@ -9,6 +9,7 @@
 """
 
 # Always prefer setuptools over distutils
+import sys
 from os import path
 from setuptools import setup
 # io.open is needed for projects that support Python 2.7
@@ -21,10 +22,20 @@
 
 PATH_HERE = path.abspath(path.dirname(__file__))
 
-with open(path.join(PATH_HERE, 'requirements.txt'), encoding='utf-8') as fp:
-    reqs = [rq.rstrip() for rq in fp.readlines()]
+
+def load_requirements(fname='requirements.txt'):
+    with open(path.join(PATH_HERE, fname), encoding='utf-8') as fp:
+        reqs = [rq.rstrip() for rq in fp.readlines()]
     reqs = [ln[:ln.index('#')] if '#' in ln else ln for ln in reqs]
-    requirements = [ln for ln in reqs if ln]
+    reqs = [ln for ln in reqs if ln]
+    return reqs
+
+
+if sys.version_info.major == 2:
+    requirements = load_requirements('requirements-py27.txt')
+else:
+    requirements = load_requirements('requirements.txt')
+
 
 # Get the long description from the README file
 # with open(path.join(PATH_HERE, 'README.md'), encoding='utf-8') as fp:

tests/requirements.txt

@@ -7,5 +7,4 @@ flake8
 check-manifest
 codacy-coverage
 parameterized
-tox
 mock