From a8016fd010f8a39a2a8e010858f3a87dbaa873f3 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Jul 2018 01:21:17 -0700 Subject: [PATCH 1/5] switched from coverall to codecov fix ##1445 (and restores full coverage reporting) --- .travis.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index ec7592a6efc..24d19d8ca6c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -21,14 +21,14 @@ env: # Set default python version to avoid repetition later - PYTHON_VERSION=3.5 - BUILD_DOCS=false - - COVERALLS=false + - CODECOV=false - PYTEST_FLAGS="--disable-pytest-warnings --numprocesses 2 --durations=50" - PYTEST_LIST="testsuite/MDAnalysisTests" - MAIN_CMD="pytest ${PYTEST_LIST}" - SETUP_CMD="${PYTEST_FLAGS}" - BUILD_CMD="pip install -v package/ && pip install testsuite/" - - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython joblib matplotlib scipy griddataformats hypothesis gsd" - - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn coveralls" + - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython joblib matplotlib scipy griddataformats hypothesis gsd codecov" + - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn" - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - PIP_DEPENDENCIES="duecredit sphinx-sitemap" @@ -37,7 +37,7 @@ env: matrix: # Run a coverage test - - COVERALLS="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" + - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - PYTHON_VERSION=3.6 - PYTHON_VERSION=3.4 - PYTHON_VERSION=2.7 @@ -104,8 +104,8 @@ script: after_success: - | - if [[ $COVERALLS == 'true' ]]; then \ - coveralls; \ + if [[ $CODECOV == 'true' ]]; then \ + codecov; \ fi # can't use test here since this leads to travis fails even though the build passes - if [[ ${TRAVIS_PULL_REQUEST} == "false" ]] && [[ ${BUILD_DOCS} == "true" ]] && [[ ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} ]]; then From 0b02e16724f4dec1098907c62c51fc16c747c2ab Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Jul 2018 02:25:19 -0700 Subject: [PATCH 2/5] generate coverage for python 2.7 - merge coverage for 2.7 and 3.5 with codecov - only install sphinx-sitemap (and sphinx) for the doc building target --- .travis.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 24d19d8ca6c..414dfde220c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -31,16 +31,16 @@ env: - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn" - CONDA_CHANNELS='biobuilds conda-forge' - CONDA_CHANNEL_PRIORITY=True - - PIP_DEPENDENCIES="duecredit sphinx-sitemap" + - PIP_DEPENDENCIES="duecredit" - NUMPY_VERSION=stable - INSTALL_HOLE="true" matrix: - # Run a coverage test + # Run a coverage test for 3.5 and 2.7 - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - - PYTHON_VERSION=3.6 + - PYTHON_VERSION=3.6 - PYTHON_VERSION=3.4 - - PYTHON_VERSION=2.7 + - PYTHON_VERSION=2.7 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - NUMPY_VERSION=1.10.4 - NUMPY_VERSION=dev EVENT_TYPE="cron" @@ -53,6 +53,7 @@ matrix: BUILD_DOCS=true BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace" INSTALL_HOLE="false" + PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx-sitemap" - env: NAME="Lint" PYLINTRC="${TRAVIS_BUILD_DIR}/package/.pylintrc" From b1939326ef031fc80d26b816287744d005d9b6ee Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Jul 2018 02:37:39 -0700 Subject: [PATCH 3/5] replaced coveralls URL with codecov URL - badges - links to site - minor formatting of reST indentation --- README.rst | 18 +++++++++--------- package/SUMMARY.txt | 18 +++++++++--------- testsuite/README | 10 +++++----- testsuite/setup.py | 2 +- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/README.rst b/README.rst index 069ec44afc1..9aff2028aea 100644 --- a/README.rst +++ b/README.rst @@ -102,17 +102,17 @@ to find uncovered code. :target: https://www.mdanalysis.org/mdanalysis/ .. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop - :alt: Build Status - :target: https://travis-ci.org/MDAnalysis/mdanalysis + :alt: Build Status + :target: https://travis-ci.org/MDAnalysis/mdanalysis -.. |cov| image:: https://coveralls.io/repos/MDAnalysis/mdanalysis/badge.svg?branch=develop - :alt: Coverage Status - :target: https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop +.. |cov| image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg + :alt: Coverage Status + :target: https://codecov.io/gh/MDAnalysis/mdanalysis .. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg - :alt: Anaconda - :target: https://anaconda.org/conda-forge/mdanalysis + :alt: Anaconda + :target: https://anaconda.org/conda-forge/mdanalysis .. |mybinder| image:: https://mybinder.org/badge.svg - :alt: My Binder - :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master + :alt: My Binder + :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master diff --git a/package/SUMMARY.txt b/package/SUMMARY.txt index 9e7d893ed78..9e9a7c81b80 100644 --- a/package/SUMMARY.txt +++ b/package/SUMMARY.txt @@ -121,18 +121,18 @@ For citations of included algorithms and sub-modules please see the references_. :target: https://docs.mdanalysis.org .. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop - :alt: Build Status - :target: https://travis-ci.org/MDAnalysis/mdanalysis + :alt: Build Status + :target: https://travis-ci.org/MDAnalysis/mdanalysis -.. |cov| image:: https://coveralls.io/repos/MDAnalysis/mdanalysis/badge.svg?branch=develop - :alt: Coverage Status - :target: https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop +.. |cov| image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg + :alt: Coverage Status + :target: https://codecov.io/gh/MDAnalysis/mdanalysis .. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg - :alt: Anaconda - :target: https://anaconda.org/conda-forge/mdanalysis + :alt: Anaconda + :target: https://anaconda.org/conda-forge/mdanalysis .. |mybinder| image:: https://mybinder.org/badge.svg - :alt: My Binder - :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master + :alt: My Binder + :target: https://mybinder.org/v2/gh/MDAnalysis/binder-notebook/master diff --git a/testsuite/README b/testsuite/README index ebc78b15536..d1c116b7163 100644 --- a/testsuite/README +++ b/testsuite/README @@ -41,12 +41,12 @@ Help is also available through the mailing list at https://groups.google.com/gro .. badges .. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop - :alt: Build Status - :target: https://travis-ci.org/MDAnalysis/mdanalysis + :alt: Build Status + :target: https://travis-ci.org/MDAnalysis/mdanalysis -.. |cov| image:: https://coveralls.io/repos/MDAnalysis/mdanalysis/badge.svg?branch=develop - :alt: Coverage Status - :target: https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop +.. |cov| image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg + :alt: Coverage Status + :target: https://codecov.io/gh/MDAnalysis/mdanalysis .. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg :alt: Documentation (development version) diff --git a/testsuite/setup.py b/testsuite/setup.py index 8b73a641456..15912d67843 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -170,7 +170,7 @@ def dynamic_author_list(): download_url='https://github.com/MDAnalysis/mdanalysis/releases', project_urls={'Documentation': 'https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests', 'CI Tests': 'https://travis-ci.org/MDAnalysis/mdanalysis', - 'CI Coverage': 'https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop', + 'CI Coverage': 'https://codecov.io/gh/MDAnalysis/mdanalysis', 'Developer Group': 'https://groups.google.com/forum/#!forum/mdnalysis-devel', 'Issue Tracker': 'https://github.com/mdanalysis/mdanalysis/issues', 'Source': 'https://github.com/mdanalysis/mdanalysis', From aed747a6eb32206134641c02dc885a5413fd1bd9 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Jul 2018 03:02:27 -0700 Subject: [PATCH 4/5] try coverage merge for most Linux runs (2.7, 3.x, minimal) --- .travis.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 414dfde220c..5ebc7461165 100644 --- a/.travis.yml +++ b/.travis.yml @@ -36,10 +36,10 @@ env: - INSTALL_HOLE="true" matrix: - # Run a coverage test for 3.5 and 2.7 + # Run a coverage test for most versions - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - - PYTHON_VERSION=3.6 - - PYTHON_VERSION=3.4 + - PYTHON_VERSION=3.6 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" + - PYTHON_VERSION=3.4 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - PYTHON_VERSION=2.7 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - NUMPY_VERSION=1.10.4 - NUMPY_VERSION=dev EVENT_TYPE="cron" @@ -72,6 +72,8 @@ matrix: - env: NAME='minimal' CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES} INSTALL_HOLE="false" + CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" + allow_failures: - env: NUMPY_VERSION=dev EVENT_TYPE="cron" From 7c996654b8d791373f9f632a3b370a1aa4ef61eb Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Wed, 11 Jul 2018 10:42:11 -0500 Subject: [PATCH 5/5] tabs to spaces? --- .travis.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 5ebc7461165..957cbb219d0 100644 --- a/.travis.yml +++ b/.travis.yml @@ -53,7 +53,7 @@ matrix: BUILD_DOCS=true BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace" INSTALL_HOLE="false" - PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx-sitemap" + PIP_DEPENDENCIES="${PIP_DEPENDENCIES} sphinx-sitemap" - env: NAME="Lint" PYLINTRC="${TRAVIS_BUILD_DIR}/package/.pylintrc" @@ -72,8 +72,8 @@ matrix: - env: NAME='minimal' CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES} INSTALL_HOLE="false" - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" - + CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" + allow_failures: - env: NUMPY_VERSION=dev EVENT_TYPE="cron"