Fix failures in CI ahead of first release, drop Python 3.5

README.rst

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

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
@@ -212,8 +200,6 @@ jobs:
     vmImage: 'macOS-10.14'
   strategy:
     matrix:
-      Python35:
-        python.version: '3.5'
       Python36:
         python.version: '3.6'
       Python37:
@@ -327,9 +313,6 @@ jobs:
     vmImage: 'vs2017-win2016'
   strategy:
     matrix:
-      Python35:
-        python_ver: '35'
-        python.version: '3.5'
       Python36:
         python_ver: '36'
         python.version: '3.6'

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/tests/test_flagio.py

@@ -1,23 +1,43 @@
 """Testing for the python bindings of the C++ flagser library."""
 
+import os
+import shutil
+from tempfile import mkdtemp
+from urllib.request import urlopen
+
 import numpy as np
-import scipy.sparse as sp
 import pytest
-import os
+import scipy.sparse as sp
 from numpy.testing import assert_almost_equal
 
 from pyflagser import loadflag, saveflag
 
-flag_files = []
-
-dirname = os.path.join(os.path.dirname(__file__), "../../flagser/test")
-for file in os.listdir(dirname):
-    if file.endswith(".flag"):
-        flag_files.append(os.path.join(dirname, file))
+try:
+    dirname = os.path.join(os.path.dirname(__file__), "../../flagser/test")
+    list_dir = os.listdir(dirname)
+    flag_files = [os.path.join(dirname, fname)
+                  for fname in os.listdir(dirname)
+                  if fname.endswith(".flag")]
+    download_files = False
+except FileNotFoundError:
+    # Download from remote bucket
+    temp_dir = mkdtemp()
+    bucket_url = 'https://storage.googleapis.com/l2f-open-models/giotto-tda' \
+                 '/flagser/test/'
+    flag_files_list = bucket_url + 'flag_files_list.txt'
+    with urlopen(flag_files_list) as f:
+        flag_file_names = f.read().decode('utf8').splitlines()
+        flag_files = []
+        for fname in flag_file_names:
+            url = bucket_url + fname
+            fpath = os.path.join(temp_dir, fname)
+            with urlopen(url) as response, open(fpath, 'wb') as out_file:
+                shutil.copyfile(response, out_file)
+            flag_files.append(fpath)
+    download_files = True
 
 
-@pytest.mark.parametrize("flag_file",
-                         [(flag_file) for flag_file in flag_files])
+@pytest.mark.parametrize("flag_file", flag_files)
 def test_flagio(flag_file):
     flag_matrix = loadflag(flag_file)
     _, fname_temp = os.path.split(flag_file)
@@ -29,3 +49,7 @@ def test_flagio(flag_file):
                         flag_matrix_temp.diagonal())
     assert_almost_equal(np.sort(np.hstack([sp.find(flag_matrix)])),
                         np.sort(np.hstack([sp.find(flag_matrix_temp)])))
+
+
+if download_files:
+    shutil.rmtree(temp_dir)

pyflagser/tests/test_flagser.py

@@ -1,17 +1,15 @@
 """Testing for the python bindings of the C++ flagser library."""
 
-import pytest
 import os
+import shutil
+from tempfile import mkdtemp
+from urllib.request import urlopen
+
+import pytest
 from numpy.testing import assert_almost_equal
 
 from pyflagser import loadflag, flagser
 
-flag_files = []
-
-dirname = os.path.join(os.path.dirname(__file__), "../../flagser/test")
-for file in os.listdir(dirname):
-    if file.endswith(".flag"):
-        flag_files.append(os.path.join(dirname, file))
 
 betti = {
     'a.flag': [1, 2, 0],
@@ -33,6 +31,27 @@
     'd10.flag': [1, 0, 0, 0, 0, 0, 0, 0, 0, 1334961],
 }
 
+try:
+    dirname = os.path.join(os.path.dirname(__file__), "../../flagser/test")
+    list_dir = os.listdir(dirname)
+    flag_files = [os.path.join(dirname, fname)
+                  for fname in os.listdir(dirname)
+                  if fname.endswith(".flag")]
+    download_files = False
+except FileNotFoundError:
+    # Download from remote bucket
+    temp_dir = mkdtemp()
+    bucket_url = 'https://storage.googleapis.com/l2f-open-models/giotto-tda' \
+                 '/flagser/test/'
+    flag_files = []
+    for fname in betti.keys():
+        url = bucket_url + fname
+        fpath = os.path.join(temp_dir, fname)
+        with urlopen(url) as response, open(fpath, 'wb') as out_file:
+            shutil.copyfile(response, out_file)
+        flag_files.append(fpath)
+    download_files = True
+
 
 @pytest.mark.parametrize("flag_file, betti",
                          [(flag_file, betti[os.path.split(flag_file)[1]])
@@ -43,3 +62,7 @@ def test_flagser(flag_file, betti):
 
     ret = flagser(flag_matrix)
     assert_almost_equal(ret['betti'], betti)
+
+
+if download_files:
+    shutil.rmtree(temp_dir)

setup.cfg

@@ -2,6 +2,8 @@
 description-file = README.rst
 
 [tool:pytest]
+junit_family=xunit1
+
 addopts =
     --ignore flagser
     --ignore pybind11

setup.py

@@ -27,7 +27,7 @@
 MAINTAINER = 'Guillaume Tauzin'
 MAINTAINER_EMAIL = '[email protected]'
 URL = 'https://github.com/giotto-ai/pyflagser'
-LICENSE = 'AGPLv3'
+LICENSE = 'GNU AGPLv3'
 DOWNLOAD_URL = 'https://github.com/giotto-ai/pyflagser/tarball/v0.1.0'
 VERSION = __version__ # noqa
 CLASSIFIERS = ['Intended Audience :: Science/Research',
@@ -41,9 +41,9 @@
                'Operating System :: POSIX',
                'Operating System :: Unix',
                'Operating System :: MacOS',
-               'Programming Language :: Python :: 3.5',
                'Programming Language :: Python :: 3.6',
-               'Programming Language :: Python :: 3.7']
+               'Programming Language :: Python :: 3.7',
+               'Programming Language :: Python :: 3.8']
 KEYWORDS = 'topological data analysis, persistent ' + \
     'homology, directed flags complex, persistence diagrams'
 INSTALL_REQUIRES = requirements