From f304bfd7eabd8a3d7cd6ab3b9660401d05d67888 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Tue, 30 Jul 2019 13:33:57 -0700 Subject: [PATCH 1/7] BLD: Remove dependency cap on sphinx --- .travis.yml | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index c537af4d..45f26bf6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -39,7 +39,7 @@ install: - source activate travis - conda install -c conda-forge phantomjs --yes # scikit-learn has to be pinned down due to a bug: https://github.com/scikit-learn/scikit-learn/issues/12671 - - pip install https://github.com/google/closure-linter/archive/master.zip 'sphinx<1.6' sphinx-bootstrap-theme coveralls 'scikit-learn==0.19.2' --no-binary scikit-learn + - pip install https://github.com/google/closure-linter/archive/master.zip sphinx sphinx-bootstrap-theme coveralls 'scikit-learn==0.19.2' --no-binary scikit-learn - pip install -e '.[all]' --verbose - npm install -g jsdoc diff --git a/setup.py b/setup.py index 2c9272ae..de39325e 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ skbio_3 = "scikit-bio >= 0.4.1" base = ["numpy >= 1.7", "scipy >= 0.17.0", "click", "pandas", skbio_2, "jinja2 >= 2.9", "future"] -doc = ["Sphinx < 1.6", "sphinx-bootstrap-theme"] +doc = ["Sphinx", "sphinx-bootstrap-theme"] test = ["pep8", "flake8"] all_deps = base + doc + test From ecb7d5409652f11d6147a9181fa9c4f5af260a85 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Tue, 30 Jul 2019 13:49:59 -0700 Subject: [PATCH 2/7] Remove scikit-learn install --- .travis.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 45f26bf6..b36f69b5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -35,11 +35,10 @@ before_install: - conda update --yes conda install: - - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython + - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn - source activate travis - conda install -c conda-forge phantomjs --yes - # scikit-learn has to be pinned down due to a bug: https://github.com/scikit-learn/scikit-learn/issues/12671 - - pip install https://github.com/google/closure-linter/archive/master.zip sphinx sphinx-bootstrap-theme coveralls 'scikit-learn==0.19.2' --no-binary scikit-learn + - pip install https://github.com/google/closure-linter/archive/master.zip sphinx sphinx-bootstrap-theme coveralls - pip install -e '.[all]' --verbose - npm install -g jsdoc From 666d528be99e55e8e2f5ca60fc9da1b49a7133b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Tue, 30 Jul 2019 14:21:40 -0700 Subject: [PATCH 3/7] Install certifi from conda --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index b36f69b5..5c6621fc 100644 --- a/.travis.yml +++ b/.travis.yml @@ -35,10 +35,10 @@ before_install: - conda update --yes conda install: - - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn + - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn requests certifi - source activate travis - conda install -c conda-forge phantomjs --yes - - pip install https://github.com/google/closure-linter/archive/master.zip sphinx sphinx-bootstrap-theme coveralls + - pip install https://github.com/google/closure-linter/archive/master.zip 'sphinx<1.6' sphinx-bootstrap-theme coveralls - pip install -e '.[all]' --verbose - npm install -g jsdoc From 9875c6052cca3835dc2159d1387be4b33900bb7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Tue, 30 Jul 2019 14:52:18 -0700 Subject: [PATCH 4/7] Add a comment and remove requests installation --- .travis.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 5c6621fc..0326959b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -35,7 +35,8 @@ before_install: - conda update --yes conda install: - - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn requests certifi + # install certifi using conda to avoid a distutils error + - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn certifi - source activate travis - conda install -c conda-forge phantomjs --yes - pip install https://github.com/google/closure-linter/archive/master.zip 'sphinx<1.6' sphinx-bootstrap-theme coveralls From 022af0f03c62da1934afdb4ea97ddfbbce62f884 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Tue, 30 Jul 2019 15:00:46 -0700 Subject: [PATCH 5/7] Install requests using conda --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 0326959b..ff3d6e2f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -35,8 +35,8 @@ before_install: - conda update --yes conda install: - # install certifi using conda to avoid a distutils error - - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn certifi + # install requests using conda to avoid a distutils error in certifi + - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn requests - source activate travis - conda install -c conda-forge phantomjs --yes - pip install https://github.com/google/closure-linter/archive/master.zip 'sphinx<1.6' sphinx-bootstrap-theme coveralls From 66df41f5edd39371718fdf3ff86f75b4ff6f0738 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Tue, 30 Jul 2019 15:29:11 -0700 Subject: [PATCH 6/7] Update .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index ff3d6e2f..86e223ff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -39,7 +39,7 @@ install: - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn requests - source activate travis - conda install -c conda-forge phantomjs --yes - - pip install https://github.com/google/closure-linter/archive/master.zip 'sphinx<1.6' sphinx-bootstrap-theme coveralls + - pip install https://github.com/google/closure-linter/archive/master.zip sphinx sphinx-bootstrap-theme coveralls - pip install -e '.[all]' --verbose - npm install -g jsdoc From c2a6fbfcaf40cb8a3f19228cffbd5fe95c0c116f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Tue, 30 Jul 2019 15:47:10 -0700 Subject: [PATCH 7/7] Re-add sphinx cap --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 86e223ff..ff3d6e2f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -39,7 +39,7 @@ install: - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython scikit-learn requests - source activate travis - conda install -c conda-forge phantomjs --yes - - pip install https://github.com/google/closure-linter/archive/master.zip sphinx sphinx-bootstrap-theme coveralls + - pip install https://github.com/google/closure-linter/archive/master.zip 'sphinx<1.6' sphinx-bootstrap-theme coveralls - pip install -e '.[all]' --verbose - npm install -g jsdoc