From 7f3f35d7148a1b868f7e02891fb82ee6a30e1a83 Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Tue, 23 Jul 2019 12:11:17 +0200 Subject: [PATCH 1/5] Fix for building/deploying docs for all versions --- devtools/ci/after_sucess.sh | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/devtools/ci/after_sucess.sh b/devtools/ci/after_sucess.sh index 5c9cb051b..c398e23c2 100755 --- a/devtools/ci/after_sucess.sh +++ b/devtools/ci/after_sucess.sh @@ -2,10 +2,19 @@ DEPLOY_PY="3.7" +echo "Running after success for:" +echo "* Python version: ${CONDA_PY}\n* Branch: ${TRAVIS_BRANCH}" +echo "* Pull request: $TRAVIS_PULL_REQUEST" + if [[ "$TRAVIS_PULL_REQUEST" != "false" ]]; then echo "This is a pull request. No deployment will be done."; exit 0 fi +if [[ "$CONDA_PY" != "$DEPLOY_PY" ]]; then + echo "Only deploy from Python ${DEPLOY_PY}. This is Python ${CONDA_PY}." + exit 0 +fi + #if [[ "$TRAVIS_BRANCH" != "master" ]]; then #echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0 #fi @@ -56,8 +65,8 @@ if [[ "$TRAVIS_BRANCH" == "master" ]]; then elif [[ "$TRAVIS_BRANCH" == "docs_deploy" ]]; then # change the behavior for the docs testing branch (docs_deploy branch in # the openpathsampling/openpathsampling GitHub repo) in this block - #echo "No docs deploy on branch $TRAVIS_BRANCH" - python devtools/ci/push-docs-to-s3.py --clobber + echo "No docs deploy on branch $TRAVIS_BRANCH" + #python devtools/ci/push-docs-to-s3.py --clobber else echo "No docs deploy on branch $TRAVIS_BRANCH" fi From 92965ed04f92b01fca3de397f955b96f0dc743b6 Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Tue, 23 Jul 2019 12:26:49 +0200 Subject: [PATCH 2/5] Update license; add acknowledgments --- docs/api_sections.rst | 2 ++ docs/index.rst | 10 ++++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/docs/api_sections.rst b/docs/api_sections.rst index 0db568c08..1d9bb4baa 100644 --- a/docs/api_sections.rst +++ b/docs/api_sections.rst @@ -1,3 +1,5 @@ +.. _api_main: + OpenPathSampling API ==================== diff --git a/docs/index.rst b/docs/index.rst index 6abd27e4f..e1a13b9ad 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,7 +17,7 @@ To learn more about what OPS can do, look at our :ref:`examples `. If you want to jump right in, take a look at how easy it is to :ref:`install `! -OPS is an open-source project, distributed under the LGPL. Join us in +OPS is an open-source project, distributed under the MIT license. Join us in the development process on GitHub_, and follow `@pathsampling `_ on Twitter for updates! @@ -72,9 +72,15 @@ For Developers developers/index api_sections +.. toctree:: + :hidden: + + acknowledgments + -------------------------------------------------------------------------------- License ------- -OpenPathSampling is licensed under the LGPL, v. 2.1 or later. +OpenPathSampling is licensed under the `MIT license +`_. From 29b75cbdf10bbe6a0c62e04b184acd80fa82172e Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Tue, 23 Jul 2019 12:30:19 +0200 Subject: [PATCH 3/5] update install instructions based on #846 --- docs/install.rst | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/docs/install.rst b/docs/install.rst index 37b1eb865..ebd64c1c6 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -4,9 +4,9 @@ Installation ************ -OpenPathSampling currently only works on Mac and Linux. It should work with -either Python 2.7 or Python 3.5+, although there may be some corners of the -code that aren't Python 3-compatible yet. +OpenPathSampling currently only works on Mac and Linux. It is tested against +Python 2.7, 3.6, and 3.7, although there may be some corners of the code +that aren't Python 3-compatible yet. .. _install-with-conda: @@ -75,9 +75,8 @@ Testing Your Installation .. _run-tests: Running the tests is a great way to verify that everything is working. The -test suite uses both `pytest `_ and, for the time being, -`nose `_. You can pick these up via -``conda`` if you don't already have them. :: +test suite uses `pytest `_ and, for legacy reasons, also +requires the `nose `_ package. You can pick these up via ``conda`` if you don't already have them. :: $ conda install pytest nose From dc57f2a244aab2ef017e11e33d245f35d72c2700 Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Tue, 23 Jul 2019 12:36:53 +0200 Subject: [PATCH 4/5] correct alphabetization of acknowledgments --- docs/acknowledgments.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/acknowledgments.rst b/docs/acknowledgments.rst index d9c8f500d..ce8c46dd8 100644 --- a/docs/acknowledgments.rst +++ b/docs/acknowledgments.rst @@ -16,15 +16,15 @@ those who developed new tools that build on OPS during their participation in E-CAM Extended Software Development Workshops (one held in Traunkirchen, Austria in 2016, and one in Leiden, Netherlands, in 2017): -* Jony Castagna (STFC, Sci-Tech Daresbury Laboratory) * Raffaella Cabriolu (Norwegian University of Science and Technology) +* Jony Castagna (STFC, Sci-Tech Daresbury Laboratory) * Nicole de Groot (University of Amsterdam) * Sonya Hanson (Memorial Sloan Kettering Cancer Center) * Colm Herbert (University College Dublin) * Hendrik Jung (Max Planck Institute for Biophysics) * Anders Lervik (Norwegian University of Science and Technology) -* Anastasiia Maslechko (Norwegian University of Science and Technology) * Donal MacKernan (University College Dublin) +* Anastasiia Maslechko (Norwegian University of Science and Technology) * Sarah McCartan (University College Dublin) * Clemens Moritz (University of Vienna) * Alberto Pérez de Alba Ortíz (University of Amsterdam) From 60df60840d87c3afc538e8c2032851990ec385c4 Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Tue, 23 Jul 2019 12:38:36 +0200 Subject: [PATCH 5/5] remove need for conda in dev install env --- devtools/install_recipe_requirements.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/devtools/install_recipe_requirements.py b/devtools/install_recipe_requirements.py index 72348114b..e61852bf9 100644 --- a/devtools/install_recipe_requirements.py +++ b/devtools/install_recipe_requirements.py @@ -6,7 +6,7 @@ import argparse # This requires that you have already installed conda and pyyaml -import conda.cli +# import conda.cli import yaml def parse_arguments(): @@ -45,6 +45,7 @@ def recipe_to_requirements(recipe_yaml): if args.dry: print(req_file_str) else: + raise RuntimeError("Only dry run works") for install in required_packages: channels = ['conda-forge', 'omnia'] channel_str = sum([['-c', channel] for channel in channels], [])