Merge remote-tracking branch 'upstream/master' into spring_shooting

.coveragerc

@@ -4,7 +4,9 @@ omit =
     */site-packages/nose/*
     */openpathsampling/tests/*
     */mdtraj/*
+    */openpathsampling/experimental/*
     */setup.py
+    openpathsampling/version.py
 exclude_lines = 
     pragma: no cover
     def __repr__

.travis.yml

@@ -1,41 +1,69 @@
+version: ~> 1.0
+
 language: python
 filter_secrets: false   # https://github.com/travis-ci/travis-ci/issues/8934
 
+branches:
+  only:
+    - master
+    - stable
+    - docs_deploy  # used for experimenting with docs builds
+    - /^v\d+(\.\d+)+/
+
+
+notifications:
+  webhooks: https://coveralls.io/webhook
+
 before_install:
   - deactivate  # virtual envs don't play nice with conda
   - export PYTHONUNBUFFERED=true  # immediately flush stdout to terminal
   - source devtools/ci/miniconda_install.sh
+  #- conda install -y pyyaml  # I don't think this is needed now...
 
 install:
   - export OPS_ENV="openpathsampling-py${CONDA_PY}"
-  - source devtools/conda_install_reqs.sh
+  - if [ -z "$MINIMAL" ] ; then source devtools/conda_install_reqs.sh; else pip install -r devtools/minimal.txt -r devtools/minimal_testing.txt; fi
+  # for the first OPS install, we will run the ops_fixes autorelease branch
+  #- pip install git+https://github.com/dwhswenson/autorelease.git@v0.1.2
+  - pip install autorelease
   - pip install --no-deps -e .
 
-before_script:
+before_script: 
   - python --version
   - python -c "import openpathsampling"
   - source devtools/ci/git_hash.sh
   - conda info --envs
   - conda list
 
 script:
+  - python devtools/autorelease_check.py --branch ${TRAVIS_BRANCH} --event ${TRAVIS_EVENT_TYPE}
   - source devtools/ci/pytests.sh
-  - source devtools/ci/ipythontests.sh
+  - if [ -z "$MINIMAL" ] ; then source devtools/ci/ipythontests.sh; fi
 
   # Upload new docs
-  - bash -x devtools/ci/after_sucess.sh
+  - if [ -z "$MINIMAL" ] ; then bash -x devtools/ci/after_sucess.sh; fi
 
 addons:
   apt:
     packages:
     - pandoc
 
 env:
-  global:
-    - secure: "NJvoSrLNd2ZR3HluJjEqI36gD5lsucwIvgnYjNmM4cwnnA77aLV9FRYTwlLRZn3XY9FL8KOzL5l0amNzMD7sQrf7bWwWv7iCUBddH549q9RSgiuOugtodYJ6VaXi76hk1rOgcJpDoCj9wTCIlMtWibPUzr1QHmdihfdM2iA2kkE="
-    - secure: "l9NJkZDD0ALhkErUvhRrreLsrcWErd+CXpWv8dxHGtkjemNx6CwVtyL+a30jz/QwMANSZbKll/cPK5yJQvuwDaWxja6UPLLKVNGtma+CmwKcIC/wwTwbMoxcS62fyLJ3kS0qR8oCQz2nCPKiYyRGADtPLWVMZckY1SJfNYcKuCM="
-    - secure: "kb37xmsSV3pEnESnINzwlW2Cju/UFzA/G+m+NsihAwO8RMPZwKCrZK/rptgkUDACXJxom5M690WEukQkHnOt+OTrWhu7WKZgYeVuWUs2++RohYv/m5npaOHMMn+uYmF328v4PvPmXxbD02zzg5Tgdn82x8oa6J8BKX8ohOQ6Xpg="
   matrix:
+    - CONDA_PY=3.7 MINIMAL=true
     - CONDA_PY=2.7
     - CONDA_PY=3.6
     - CONDA_PY=3.7
+  global:
+    - COVERALLS_PARALLEL=true
+    - TWINE_USERNAME="dwhswenson"
+    # TWINE_PASSWORD (set via web)
+    #- secure: "zs/3PN46wXFzTDli8LE9jJmNov27xAy7REaTK4s3DV9Ocmf5grqIUbUfFfa7XyOvamr6C7TSHib1SqQvEbHv416AcOD9FWZm9iNj0MO2dBimyXrvR50TFKG/dcp0Qzlp54hYFM4bEzWJZUVN120xynIKgfy74YBOA8DQ6B7FlyY="
+    # AUTORELEASE_TOKEN (set via web)
+    #- secure: "r9u8xvXo3avaloOogrqIVF/oFDeMLSYvZbBYv3y3nBN17p3I9C2FhUbu/VpiRBA0kX6U2BsAHh5DF8ymRD254/f3s8L1BapanLfmoRjp9cXAJ95RZhZ8Cxw9W36VEGcIa+JG1G31oqabEBW4ozQmXsGPSYI3+wfFmhchJPpaDRE="
+    - secure: "NJvoSrLNd2ZR3HluJjEqI36gD5lsucwIvgnYjNmM4cwnnA77aLV9FRYTwlLRZn3XY9FL8KOzL5l0amNzMD7sQrf7bWwWv7iCUBddH549q9RSgiuOugtodYJ6VaXi76hk1rOgcJpDoCj9wTCIlMtWibPUzr1QHmdihfdM2iA2kkE="
+    - secure: "l9NJkZDD0ALhkErUvhRrreLsrcWErd+CXpWv8dxHGtkjemNx6CwVtyL+a30jz/QwMANSZbKll/cPK5yJQvuwDaWxja6UPLLKVNGtma+CmwKcIC/wwTwbMoxcS62fyLJ3kS0qR8oCQz2nCPKiYyRGADtPLWVMZckY1SJfNYcKuCM="
+    - secure: "kb37xmsSV3pEnESnINzwlW2Cju/UFzA/G+m+NsihAwO8RMPZwKCrZK/rptgkUDACXJxom5M690WEukQkHnOt+OTrWhu7WKZgYeVuWUs2++RohYv/m5npaOHMMn+uYmF328v4PvPmXxbD02zzg5Tgdn82x8oa6J8BKX8ohOQ6Xpg="
+
+import:
+  - dwhswenson/autorelease:autorelease-travis.yml@v0.2.1

MANIFEST.in

@@ -1,3 +1,4 @@
 # include visualization .css files
+LICENSE
 graft openpathsampling
-include openpathsampling/resources/*.css
+include openpathsampling/resources/*.css

devtools/README.md

@@ -5,47 +5,24 @@ Assorted notes for developers.
 
 How to do a release
 -------------------
-- Update the whatsnew.rst document. Use the github view that shows all the
-  commits to master since the last release to write it.
-- Update the version number in `setup.py`, change `ISRELEASED` to `True`
-- Commit to master, and [tag](https://github.com/SimTk/mdtraj/releases) the
-  release on github
-- To push the source to PyPI, use `python setup.py sdist --formats=gztar,zip upload`
-- Conda binaries need to built separately on each platform (`conda build mdtraj;
-  binstar upload <path to .tar.bz2>`)
-- Make an announcement on github / email
-- After tagging the release, make a NEW commit that changes `ISRELEASED` back
-  to `False` in `setup.py`
 
-
-It's important that the version which is tagged on github for the release be
-the one with the ISRELEASED flag in setup.py set to true.
+1. Make a branch in the upstream `openpathsampling/openpathsampling`
+   repository.
+2. In that branch, change the version in `setup.cfg` to be a release version
+   (not ending in `.dev0`, etc.)
+3. Push that branch and make a PR against the `stable` branch. It should test,
+   then perform a test deployment to `test.pypi`, then download the test
+   deployment and run tests again. The logic for this is in the Autorelease
+   repository. The text of the top post in this PR should be the release notes
+   (use the write-release-notes script included in Autorelease to do this).
+4. Merge the PR. This will create a GitHub release, and then take that release
+   and push it to pypi. All of this logic is in Autorelease.
 
 
 Docs Building & Hosting
 -----------------------
 
 After a travis build succeeds, the docs are built with sphinx and pushed to
-the mdtraj.org amazon s3 account. The credentials for that account are stored,
-encrypted, in the .travis.yml file.
+the openpathsampling.org amazon s3 account (owned by John Chodera). The
+credentials for that account are stored, encrypted, in the .travis.yml file.
 (http://docs.travis-ci.com/user/build-configuration/#Secure-environment-variables)
-
-As of version 0.7-dev (0.8 release) multiple versions of the docs are hosted
-online. When a build happens on a version with ISRELEASED==False, it's put into
-the "latest" folder on the S3 bucket. If ISRELEASED==True, it's put into a
-subfolder with the name of the short release. The relevant logic is in
-`tools/ci/push-docs-to-s3.py`.
-
-In order for the select bar at the bottom of the docs that toggles between
-versions to work, these folders MUST match up with the tag names on github.
-This is because the list of items to put in that little dropdown menu is
-dynamically determined from the github API in the browser. This is the only
-way I could think of to make sure the old docs have a link to the latest
-version. The logic that populates the version dropdown menu in the browser is in
-
-`docs/themes/sphinx_rtd_theme-0.1.5/sphinx_rtd_theme/versions.html`
-
-Specifically note that it goes to https://api.github.com/repos/rmcgibbo/mdtraj/releases,
-and uses the `tag_names` to build the links. So these much line up with the
-prefix of `mdtraj.version.short_version` used in `tools/ci/push-docs-to-s3.py`
-for the links not to break.

devtools/autorelease_check.py

@@ -0,0 +1,29 @@
+#/usr/bin/env python
+from __future__ import print_function
+import setup
+import openpathsampling
+from autorelease import DefaultCheckRunner, conda_recipe_version
+from autorelease.version import get_setup_version
+from packaging.version import Version
+
+repo_path = '.'
+SETUP_VERSION = get_setup_version(None, directory='.')
+versions = {
+    'package': openpathsampling.version.version,
+    'netcdfplus': openpathsampling.netcdfplus.version.version,
+    'setup.py': SETUP_VERSION,
+}
+
+RELEASE_BRANCHES = ['stable']
+RELEASE_TAG = "v" + Version(SETUP_VERSION).base_version
+
+if __name__ == "__main__":
+    checker = DefaultCheckRunner(
+        versions=versions,
+        setup=setup,
+        repo_path='.'
+    )
+    checker.release_branches = RELEASE_BRANCHES + [RELEASE_TAG]
+
+    tests = checker.select_tests_from_sysargs()
+    n_fails = checker.run_as_test(tests)

devtools/ci/after_sucess.sh

@@ -65,8 +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

devtools/ci/miniconda_install.sh

@@ -13,7 +13,7 @@ conda_version="latest"
 #conda_version="4.4.10"  # can pin a miniconda version like this, if needed
 
 MINICONDA=Miniconda${pyV}-${conda_version}-Linux-x86_64.sh
-MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
+MINICONDA_MD5=$(curl -sL https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
 wget https://repo.continuum.io/miniconda/$MINICONDA
 if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
     echo "Miniconda MD5 mismatch"
@@ -29,4 +29,8 @@ export PATH=$HOME/miniconda${pyV}/bin:$PATH
 conda config --add channels http://conda.anaconda.org/omnia
 conda config --add channels http://conda.anaconda.org/conda-forge
 
+# next two lines are workaround for conda/conda#9337
+pip uninstall -y setuptools
+conda install --yes setuptools
+
 conda update --yes conda

devtools/ci/push-docs-to-s3.py

@@ -16,10 +16,11 @@
 CLOBBER = opts.clobber
 
 BUCKET_NAME = 'openpathsampling.org'
-if not openpathsampling.version.release:
-    PREFIX = 'latest'
-else:
-    PREFIX = openpathsampling.version.short_version
+PREFIX = 'latest'
+# if not openpathsampling.version.release:
+    # PREFIX = 'latest'
+# else:
+    # PREFIX = openpathsampling.version.short_version
 
 def is_s3cmd_installed():
     dists = pkg_resources.working_set

devtools/ci/pytests.sh

@@ -6,9 +6,23 @@ echo Run pytest tests ...
 testfail=0
 pytest -vv -s --cov --cov-report xml:cov.xml || testfail=1
 #nosetests -v -s --with-coverage || testfail=1
-coveralls
+COVERALLS_PARALLEL=true coveralls
 echo travis_fold:end:pytests
 
+if [ $testfail -eq 1 ]
+then
+    exit 1
+fi
+
+if [ $CONDA_PY != "2.7" ] && [ -z "$MINIMAL" ]; then
+    # experimental does not need to support Python 2
+    echo travis_fold:start:experimental
+    echo Running tests on experimental features
+    pytest openpathsampling/experimental/ -vv -s || testfail=1
+    echo travis_fold:end:experimental
+fi
+
+
 if [ $testfail -eq 1 ]
 then
     exit 1