dwhswenson · Sep 26, 2020 · Jan 29, 2020 · Jan 30, 2020 · Feb 1, 2020 · Feb 3, 2020
diff --git a/.project b/.project
diff --git a/.pydevproject b/.pydevproject
diff --git a/.travis.yml b/.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
 
@@ -49,6 +49,11 @@ addons:
     - pandoc
 
 env:
+  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"
@@ -59,11 +64,6 @@ env:
     - 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
 
 import:
-  - dwhswenson/autorelease:autorelease-travis.yml@v0.1.2
+  - dwhswenson/autorelease:autorelease-travis.yml@v0.2.1
diff --git a/devtools/README.md b/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.
diff --git a/autorelease_check.py → devtools/autorelease_check.py b/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']

diff --git a/devtools/ci/miniconda_install.sh b/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"

diff --git a/devtools/conda-recipe/README.md b/devtools/conda-recipe/README.md
diff --git a/devtools/conda-recipe/build.sh b/devtools/conda-recipe/build.sh
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
diff --git a/devtools/conda-recipe/requirements.txt b/devtools/conda-recipe/requirements.txt
diff --git a/devtools/conda_install_reqs.sh b/devtools/conda_install_reqs.sh
@@ -21,26 +21,24 @@ 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 ${DEVTOOLS_DIR}/tested_integrations.txt | tr "\n" " "`
 PY_INSTALL="python=$CONDA_PY"
-PINS=`cat ${DEVTOOLS_DIR}/../pinned | tr -d " " | tr "\n" " "`
 
+echo "REQUIREMENTS=$REQUIREMENTS"
 echo "WORKAROUNDS=$WORKAROUNDS"
+echo "INTEGRATIONS=$INTEGRATIONS"
 echo "PY_INSTALL=$PY_INSTALL"
-echo "PACKAGES=$PACKAGES"
 echo "TESTING=$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 $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
diff --git a/devtools/install_recipe_requirements.py b/devtools/install_recipe_requirements.py
diff --git a/devtools/minimal_testing.txt b/devtools/minimal_testing.txt
@@ -1,4 +1,4 @@
 nose
-pytest!=5.3.4
+pytest
 pytest-cov
 coveralls
diff --git a/devtools/optional_packages.txt b/devtools/optional_packages.txt
diff --git a/devtools/setup_cfg_reqs.py b/devtools/setup_cfg_reqs.py
@@ -0,0 +1,36 @@
+try:
+    import configparser
+except ImportError:
+    import ConfigParser as configparser
+
+import argparse
+import os.path
+
+def make_parser():
+    default_setup = os.path.join(os.path.dirname(__file__), "..",
+                                 "setup.cfg")
+    parser = argparse.ArgumentParser()
+    parser.add_argument('setup_cfg', nargs='?', default=default_setup)
+    parser.add_argument('--extra', default=None)
+    return parser
+
+def clean(string):
+    return " ".join(string.split("\n"))
+
+def main(setup_cfg, extra):
+    config = configparser.ConfigParser()
+    config.read(setup_cfg)
+    # replace get with the __getitem__ syntax when we drop py27
+    if extra is None:
+        # reqs = config['options']['install_requires']
+        reqs = config.get('options', 'install_requires')
+    else:
+        # reqs = config['options.extras_require'][extra]
+        reqs = config.get('options.extras_require', extra)
+    return clean(reqs)
+
+if __name__ == "__main__":
+    argparser = make_parser()
+    args = argparser.parse_args()
+    print(main(args.setup_cfg, args.extra))
+
diff --git a/devtools/tested_integrations.txt b/devtools/tested_integrations.txt
@@ -0,0 +1,6 @@
+jupyter
+openmm
+openmmtools
+py-plumed
+pyemma
+
diff --git a/devtools/testing_requirements.txt b/devtools/testing_requirements.txt