Fix failures in CI ahead of first release, drop Python 3.5 (#11)

* Silence junit_family warnings

* Remove Python 3.5 support

* Silence deprecation warnings for autodoc_default_flags

* Download flag files from cloud in tests when testing from generic dirs

* Bump Python version in README.rst

* Extend cloud download approach to test_flagser, fix incorrect url

* Correct dir path to file path

* Linting

* Use copyfile instead of copyfileobj

* Use urlretrieve instead of urlopen

* Add sudo permissions to pytest line in manylinux

* Remove sudo, add conftest file defining --webdl, implement on flagio

- Comment tests in test_flagser to silence failures

* Try new approach to avoid issues with --pyargs and command line arguments

* Add forgotten import dot and linting

* Remove nightlies from Azure CI

* Uninstall dev environment after testing it

* Change flagser docstring formatting to avoid sphinx errors

* Uninstall dev after testing dev in docker_scripts.sh

Also replace dot in pytest with pyflagser

* Avoid unnecessary coverage report generations and uploads

* Wording changes in comments

* Change bash to script in windows jobs

* Remove contradictory passed options

* Reintroduce coverage reports for all systems

* Try with sudo in manylinux, pass /D in windows

* Refactor tests

* Update CODE_AUTHORS

* UPDATE LICENSE

* Update RELEASE

* Update MAINTAINER variable in setup.py

* Update GOVERNANCE

* Better docstring formatting in flagser.py

* Add sudo to pytest steps in linux systems

* Remove sudo, create temp dir for pytests on wheels

* Add sudo only in one place

* Do not delete folders/files

* Minor improvements in docs and variable names

* Correct mistake in GOVERNANCE

.azure-ci/docker_scripts.sh

@@ -2,23 +2,25 @@
 
 set -x
 
-# upgrading pip and setuptools
+# Upgrade pip and setuptools. TODO: Monitor status of pip versions
 PYTHON_PATH=$(eval find "/opt/python/*${python_ver}*" -print)
 export PATH=${PYTHON_PATH}/bin:${PATH}
 pip install --upgrade pip==19.3.1 setuptools
 
-# installing cmake
+# Install CMake
 pip install cmake
 
-# installing and uninstalling pyflagser
+# Install dev environment
 cd /io
 pip install -e ".[doc, tests]"
-pip uninstall -y pyflagser
 
-# testing, linting
+# Test dev install with pytest and flake8
 pytest --cov . --cov-report xml
 flake8 --exit-zero /io/
 
-# building wheels
-pip install wheel twine
+# Uninstal pyflagser dev
+pip uninstall -y pyflagser
+
+# Build wheels
+pip install wheel
 python setup.py sdist bdist_wheel

CODE_AUTHORS

@@ -3,3 +3,4 @@
 
 Guillaume Tauzin, [email protected]
 Julian Burella Pérez, [email protected]
+Umberto Lupo, [email protected]

GOVERNANCE.rst

@@ -1,4 +1,4 @@
-This file describe the governance of the Giotto project.
+This file describe the governance of the pyflagser project.
 
 Project owner:
 --------------
@@ -10,12 +10,10 @@ Authors:
 
 - Please refer to the `authors <https://github.com/giotto-ai/pyflagser/blob/master/CODE_AUTHORS>`_ file
 
-Giotto Project Team:
---------------------
+Pyflagser Project Team:
+-----------------------
 
-- Umberto Lupo [email protected] (Maintainer & Developer)
+- Guillaume Tauzin [email protected] (Maintainer)
+- Umberto Lupo [email protected] (Maintainer)
+- Julian Burella Pérez [email protected] (Developer)
 - Matteo Caorsi [email protected] (Project Leader)
-- Philippe Nguyen [email protected] (Developer)
-
-Former Project Team Members:
-----------------------------

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2019 L2F SA.
+Copyright 2020 L2F SA.
 Licensed under the GNU Affero General Public License (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License below or at https://www.gnu.org/licenses/agpl-3.0.html

README.rst

@@ -43,7 +43,7 @@ Dependencies
 
 pyflagser requires:
 
-- Python (>= 3.5)
+- Python (>= 3.6)
 - numpy (>= 1.17.0)
 - scipy (>= 0.17.0)
 

RELEASE.rst

@@ -25,7 +25,7 @@ Thanks to our Contributors
 
 This release contains contributions from many people:
 
-Guillaume Tauzin and Julian Burella Pérez.
+Guillaume Tauzin, Julian Burella Pérez and Umberto Lupo.
 
 We are also grateful to all who filed issues or helped resolve them, asked and
 answered questions, and were part of inspiring discussions.

azure-pipelines.yml

@@ -7,8 +7,6 @@ jobs:
     vmImage: 'ubuntu-16.04'
   strategy:
     matrix:
-      Python35:
-        python.version: '3.5'
       Python36:
         python.version: '3.6'
       Python37:
@@ -43,8 +41,6 @@ jobs:
     vmImage: 'macOS-10.14'
   strategy:
     matrix:
-      Python35:
-        python.version: '3.5'
       Python36:
         python.version: '3.6'
       Python37:
@@ -85,9 +81,6 @@ jobs:
     vmImage: 'vs2017-win2016'
   strategy:
     matrix:
-      Python35:
-        python_ver: '35'
-        python.version: '3.5'
       Python36:
         python_ver: '36'
         python.version: '3.6'
@@ -128,11 +121,6 @@ jobs:
     vmImage: 'ubuntu-16.04'
   strategy:
     matrix:
-      Python35:
-        arch: x86_64
-        plat: manylinux2010_x86_64
-        python_ver: '35'
-        python.version: '3.5'
       Python36:
         arch: x86_64
         plat: manylinux2010_x86_64
@@ -154,14 +142,6 @@ jobs:
     inputs:
       versionSpec: '$(python.version)'
 
-  - bash: |
-      sed -i "s/'pyflagser'/'pyflagser-nightly'/1" setup.py
-      sed -i "s/__version__.*/__version__ = '$(Build.BuildNumber)'/1" pyflagser/_version.py
-      cat pyflagser/_version.py
-    failOnStderr: true
-    condition: eq(variables['nightly_check'], 'true')
-    displayName: 'Change name to pyflagser-nightly'
-
   - task: Bash@3
     inputs:
       filePath: .azure-ci/build_manylinux2010.sh
@@ -182,7 +162,7 @@ jobs:
       pip install pytest pytest-cov pytest-azurepipelines pytest-benchmark flake8 hypothesis
       mkdir tmp_test_cov
       cd tmp_test_cov
-      pytest --pyargs pyflagser --ignore-glob='flagser*' --no-cov --no-coverage-upload
+      python -m pyflagser.tests --webdl --no-cov --no-coverage-upload
     failOnStderr: true
     displayName: 'Test the wheels with pytest'
 
@@ -198,22 +178,13 @@ jobs:
       pathToPublish: '$(Build.ArtifactStagingDirectory)'
       artifactName: 'wheel_and_doc'
 
-  - bash: |
-      pip install twine
-      for f in dist/*linux* ; do sudo mv "$f" "${f/linux/manylinux2010}"; done
-      twine upload -u giotto-learn -p $(pypi_psw) --skip-existing dist/*
-    condition: eq(variables['nightly_check'], 'true')
-    displayName: 'Upload nightly wheels to PyPI'
-
 
 - job: 'macOS1014'
   condition: eq(variables['build_check'], 'true')
   pool:
     vmImage: 'macOS-10.14'
   strategy:
     matrix:
-      Python35:
-        python.version: '3.5'
       Python36:
         python.version: '3.6'
       Python37:
@@ -226,16 +197,6 @@ jobs:
     inputs:
       versionSpec: '$(python.version)'
 
-  - bash: |
-      sed -i.bak "s/'pyflagser'/'pyflagser-nightly'/1" setup.py
-      rm setup.py.bak
-      sed -i.bak "s/__version__.*/__version__ = '$(Build.BuildNumber)'/1" pyflagser/_version.py
-      cat pyflagser/_version.py
-      rm pyflagser/_version.py.bak
-    failOnStderr: true
-    condition: eq(variables['nightly_check'], 'true')
-    displayName: 'Change name to pyflagser-nightly'
-
   - script: |
       brew update
       brew install gcc
@@ -251,24 +212,17 @@ jobs:
     failOnStderr: true
     displayName: 'Install dev environment'
 
-  - script: |
-      pip uninstall -y pyflagser
-    condition: eq(variables['nightly_check'], 'false')
-    failOnStderr: true
-    displayName: 'Uninstall pyflagser dev'
-
-  - script: |
-      pip uninstall -y pyflagser-nightly
-    condition: eq(variables['nightly_check'], 'true')
-    failOnStderr: true
-    displayName: 'Uninstall pyflagser-nightly dev'
-
   - script: |
       pytest --cov pyflagser --cov-report xml
       flake8
     failOnStderr: true
     displayName: 'Test with pytest and flake8'
 
+  - script: |
+      pip uninstall -y pyflagser
+    failOnStderr: true
+    displayName: 'Uninstall pyflagser dev'
+
   - script: |
       pip install wheel
       python setup.py sdist bdist_wheel
@@ -282,7 +236,7 @@ jobs:
   - script: |
       mkdir tmp_test_cov
       cd tmp_test_cov
-      pytest --pyargs pyflagser --ignore-glob='flagser*' --no-cov --no-coverage-upload
+      python -m pyflagser.tests --webdl --no-cov --no-coverage-upload
     failOnStderr: true
     displayName: 'Test the wheels with pytest'
 
@@ -314,22 +268,13 @@ jobs:
       pathToPublish: '$(Build.ArtifactStagingDirectory)'
       artifactName: 'wheel_and_doc'
 
-  - bash: |
-      pip install twine
-      twine upload -u giotto-learn -p $(pypi_psw) --skip-existing dist/*
-    condition: eq(variables['nightly_check'], 'true')
-    displayName: 'Upload nightly wheels to PyPI'
-
 
 - job: 'win2016'
   condition: eq(variables['build_check'], 'true')
   pool:
     vmImage: 'vs2017-win2016'
   strategy:
     matrix:
-      Python35:
-        python_ver: '35'
-        python.version: '3.5'
       Python36:
         python_ver: '36'
         python.version: '3.6'
@@ -345,14 +290,6 @@ jobs:
     inputs:
       versionSpec: '$(python.version)'
 
-  - bash: |
-      sed -i "s/'pyflagser'/'pyflagser-nightly'/1" setup.py
-      sed -i "s/__version__.*/__version__ = '$(Build.BuildNumber)'/1" pyflagser/_version.py
-      cat pyflagser/_version.py
-    failOnStderr: true
-    condition: eq(variables['nightly_check'], 'true')
-    displayName: 'Change name to pyflagser-nightly'
-
   - script: |
       python -m pip install --upgrade pip setuptools
     failOnStderr: true
@@ -363,24 +300,17 @@ jobs:
     failOnStderr: true
     displayName: 'Install dev environment'
 
-  - script: |
-      pip uninstall -y pyflagser
-    condition: eq(variables['nightly_check'], 'false')
-    failOnStderr: true
-    displayName: 'Uninstall pyflagser dev'
-
-  - script: |
-      pip uninstall -y pyflagser-nightly
-    condition: eq(variables['nightly_check'], 'true')
-    failOnStderr: true
-    displayName: 'Uninstall pyflagser-nightly dev'
-
   - script: |
       pytest --cov pyflagser --cov-report xml
       flake8
     failOnStderr: true
     displayName: 'Test with pytest and flake8'
 
+  - script: |
+      pip uninstall -y pyflagser
+    failOnStderr: true
+    displayName: 'Uninstall pyflagser dev'
+
   - bash: |
       sed -i $'s/\r$//' README.rst
       pip install wheel
@@ -392,10 +322,10 @@ jobs:
     failOnStderr: true
     displayName: 'Install the wheels'
 
-  - bash: |
+  - script: |
       mkdir tmp_test_cov
       cd tmp_test_cov
-      pytest --pyargs pyflagser --ignore-glob='flagser*' --no-cov --no-coverage-upload
+      python -m pyflagser.tests --webdl --no-cov --no-coverage-upload
     failOnStderr: true
     displayName: 'Test the wheels with pytest'
 
@@ -410,10 +340,3 @@ jobs:
     inputs:
       pathToPublish: '$(Build.ArtifactStagingDirectory)'
       artifactName: 'wheel_and_doc'
-
-  - bash: |
-      pip install twine
-      twine upload -u giotto-learn -p $(pypi_psw) --skip-existing dist/*
-    failOnStderr: true
-    condition: eq(variables['nightly_check'], 'true')
-    displayName: 'Upload nightly wheels to PyPI'

doc/conf.py

@@ -58,7 +58,7 @@
     mathjax_path = ('https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/'
                     'MathJax.js?config=TeX-AMS_SVG')
 
-autodoc_default_flags = ['members', 'inherited-members']
+autodoc_default_options = {'members': True, 'inherited-members': True}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['templates']

pyflagser/_version.py

@@ -1,6 +1,4 @@
-"""
-``pyflagser`` is a python API for the C++ flagser library.
-"""
+"""``pyflagser`` is a python API for the C++ flagser library."""
 
 # PEP0440 compatible formatted version, see:
 # https://www.python.org/dev/peps/pep-0440/

pyflagser/flagio.py

@@ -5,12 +5,13 @@
 
 
 def loadflag(fname, fmt='csr', dtype=None):
-    """Load a flag matrix from a ``.flag`` file.
+    """Load a ``.flag`` file, and return a matrix representation.
 
     Parameters
     ----------
     fname : file, str, or pathlib.Path, required
-        Filename of extension ``.flag``.
+        Filename of extension ``.flag`` containing the information of a flag
+        matrix.
 
     fmt : {'dense', 'dia', 'csr', 'csc', 'lil', ...}, optional, default: 'csr'
         Matrix format of the result. By default, a CSR sparse matrix is