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

.coveragerc

@@ -4,6 +4,7 @@ omit =
     */site-packages/nose/*
     */openpathsampling/tests/*
     */mdtraj/*
+    */openpathsampling/experimental/*
     */setup.py
     openpathsampling/version.py
 exclude_lines = 

.travis.yml

@@ -36,7 +36,7 @@ before_script:
   - conda list
 
 script:
-  - python autorelease_check.py --branch ${TRAVIS_BRANCH} --event ${TRAVIS_EVENT_TYPE}
+  - python devtools/autorelease_check.py --branch ${TRAVIS_BRANCH} --event ${TRAVIS_EVENT_TYPE}
   - source devtools/ci/pytests.sh
   - if [ -z "$MINIMAL" ] ; then source devtools/ci/ipythontests.sh; fi
 
@@ -66,4 +66,4 @@ env:
     - secure: "kb37xmsSV3pEnESnINzwlW2Cju/UFzA/G+m+NsihAwO8RMPZwKCrZK/rptgkUDACXJxom5M690WEukQkHnOt+OTrWhu7WKZgYeVuWUs2++RohYv/m5npaOHMMn+uYmF328v4PvPmXxbD02zzg5Tgdn82x8oa6J8BKX8ohOQ6Xpg="
 
 import:
-  - dwhswenson/autorelease:autorelease-travis.yml@v0.1.2
+  - dwhswenson/autorelease:autorelease-travis.yml@v0.2.1

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.

autorelease_check.py → devtools/autorelease_check.py

@@ -12,7 +12,6 @@
     'package': openpathsampling.version.version,
     'netcdfplus': openpathsampling.netcdfplus.version.version,
     'setup.py': SETUP_VERSION,
-    'conda-recipe': conda_recipe_version('devtools/conda-recipe/meta.yaml'),
 }
 
 RELEASE_BRANCHES = ['stable']

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"

devtools/ci/pytests.sh

@@ -9,6 +9,20 @@ pytest -vv -s --cov --cov-report xml:cov.xml || testfail=1
 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

devtools/conda_install_reqs.sh

@@ -21,26 +21,26 @@ fi
 # always obeys if you explicitly request a pinned version)
 #conda config --env --add pinned_packages python=$CONDA_PY
 #cp $DEVTOOLS_DIR/../pinned $CONDA_PREFIX/
-PACKAGES=`python ${DEVTOOLS_DIR}/install_recipe_requirements.py --dry ${DEVTOOLS_DIR}/conda-recipe/meta.yaml | tr "\n" " "`
 
 # WORKAROUNDS is normally empty; needed if other pkgs don't list all deps
-WORKAROUNDS="pymbar"
-TESTING=`cat ${DEVTOOLS_DIR}/testing_requirements.txt | tr "\n" " "`
-EXTRA=`cat ${DEVTOOLS_DIR}/optional_packages.txt | tr "\n" " "`
+WORKAROUNDS=""
+REQUIREMENTS=`python ${DEVTOOLS_DIR}/setup_cfg_reqs.py`
+TESTING=`python ${DEVTOOLS_DIR}/setup_cfg_reqs.py --extra test`
+INTEGRATIONS=`cat ${DEVTOOLS_DIR}/tested_integrations.txt | tr "\n" " "`
+EXPERIMENTAL=`cat ${DEVTOOLS_DIR}/experimental_reqs.txt | tr "\n" " "`
 PY_INSTALL="python=$CONDA_PY"
-PINS=`cat ${DEVTOOLS_DIR}/../pinned | tr -d " " | tr "\n" " "`
 
-echo "WORKAROUNDS=$WORKAROUNDS"
 echo "PY_INSTALL=$PY_INSTALL"
-echo "PACKAGES=$PACKAGES"
+echo "REQUIREMENTS=$REQUIREMENTS"
+echo "INTEGRATIONS=$INTEGRATIONS"
+echo "EXPERIMENTAL=$EXPERIMENTAL"
+echo "WORKAROUNDS=$WORKAROUNDS"
 echo "TESTING=$TESTING"
-echo "PINS=$PINS"
 
-if [ "$CONDA_PY" != "3.7" ]; then
-    ALL_PACKAGES="$WORKAROUNDS $PACKAGES $TESTING $EXTRA"
-else
-    ALL_PACKAGES="$WORKAROUNDS $PACKAGES $TESTING"  # no msmbuilder for py3.7?
-fi
+# TODO: allow different installs for different versions
+# (needed this when msmbuilder was only available on older pythons; similar
+# situations may come up in the future)
+ALL_PACKAGES="$WORKAROUNDS $REQUIREMENTS $INTEGRATIONS $EXPERIMENTAL $TESTING"
 
-echo "conda install -y -q -c conda-forge -c omnia $PY_INSTALL $ALL_PACKAGES $PINS"
-conda install -y -q -c conda-forge -c omnia $PY_INSTALL $ALL_PACKAGES $PINS
+echo "conda install -y -q -c conda-forge -c omnia $PY_INSTALL $ALL_PACKAGES"
+conda install -y -q -c conda-forge -c omnia $PY_INSTALL $ALL_PACKAGES

devtools/experimental_reqs.txt

@@ -0,0 +1 @@
+sqlalchemy