Merge pull request #897 from openpathsampling/release-1.2

Release 1.2
openpathsampling · Jan 31, 2020 · fcc5ef5 · fcc5ef5
2 parents f8d2949 + 36ca37d
commit fcc5ef5
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diff --git a/.coveragerc b/.coveragerc
@@ -5,6 +5,7 @@ omit =
     */openpathsampling/tests/*
     */mdtraj/*
     */setup.py
+    openpathsampling/version.py
 exclude_lines = 
     pragma: no cover
     def __repr__

diff --git a/.travis.yml b/.travis.yml
@@ -24,8 +24,8 @@ install:
   - export OPS_ENV="openpathsampling-py${CONDA_PY}"
   - if [ -z "$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@ops_fixes
-  #- pip install autorelease
+  #- pip install git+https://github.com/dwhswenson/autorelease.git@v0.1.2
+  - pip install autorelease
   - pip install --no-deps -e .
 
 before_script: 
@@ -50,6 +50,7 @@ addons:
 
 env:
   global:
+    - COVERALLS_PARALLEL=true
     - TWINE_USERNAME="dwhswenson"
     # TWINE_PASSWORD (set via web)
     #- secure: "zs/3PN46wXFzTDli8LE9jJmNov27xAy7REaTK4s3DV9Ocmf5grqIUbUfFfa7XyOvamr6C7TSHib1SqQvEbHv416AcOD9FWZm9iNj0MO2dBimyXrvR50TFKG/dcp0Qzlp54hYFM4bEzWJZUVN120xynIKgfy74YBOA8DQ6B7FlyY="
@@ -65,4 +66,4 @@ env:
     - CONDA_PY=3.7
 
 import:
-  - dwhswenson/autorelease:autorelease-travis.yml@ops_fixes
+  - dwhswenson/autorelease:autorelease-travis.yml@v0.1.2
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1,4 @@
 # include visualization .css files
+LICENSE
 graft openpathsampling
-include openpathsampling/resources/*.css
+include openpathsampling/resources/*.css
diff --git a/devtools/ci/after_sucess.sh b/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

diff --git a/devtools/ci/push-docs-to-s3.py b/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

diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
-  name: openpathsampling-dev
-  version: "1.1.0"
+  name: openpathsampling
+  version: "1.2.0"
 
 source:
   path: ../../

diff --git a/devtools/minimal_testing.txt b/devtools/minimal_testing.txt
@@ -1,4 +1,4 @@
 nose
-pytest
+pytest!=5.3.4
 pytest-cov
 coveralls
diff --git a/devtools/testing_requirements.txt b/devtools/testing_requirements.txt
@@ -1,5 +1,5 @@
 nose
-pytest
+pytest!=5.3.4
 pytest-cov
-python-coveralls
+coveralls
 ipynbtest
diff --git a/docs/analysis.rst b/docs/analysis.rst
@@ -0,0 +1,34 @@
+.. _analysis:
+
+.. currentmodule:: openpathsampling.analysis
+
+Analysis Tools
+==============
+
+Path histograms
+---------------
+
+.. autosummary::
+   :toctree: api/generated/
+
+   PathHistogram
+   PathDensityHistogram
+
+
+Replica network analysis
+------------------------
+
+.. autosummary::
+   :toctree: api/generated/
+
+   ReplicaNetwork
+   ReplicaNetworkGraph
+
+Other analysis tools
+--------------------
+
+.. autosummary::
+   :toctree: api/generated/
+
+   ChannelAnalysis
+   ShootingPointAnalysis
diff --git a/docs/api_sections.rst b/docs/api_sections.rst
@@ -10,17 +10,19 @@ OpenPathSampling API
     collectivevariable
     volume
     ensemble
+    pathmover
+    engines/index
+    storage
+    pathsimulator
     shooting
     snapshot_modifiers
-    pathmover
     movestrategy
-    pathsimulator
-    storage
-    treemixin
+    interface_set
     network
-    engines/index
     netcdfplus/index
     numerics
+    treemixin
+    analysis
     tis_analysis
 ..    snapshot_features
 

diff --git a/docs/collectivevariable.rst b/docs/collectivevariable.rst
@@ -6,11 +6,11 @@ CollectiveVariable Functions
 ============================
 :class:`openpathsampling.CollectiveVariable`
 
-    >>> import openpathsampling as paths
-    >>> mover = paths.CollectiveVariable()
+For an introduction on collective variables, read the user guide topic on
+:ref:`creating-cvs`.
 
-basic orderparamters
---------------------
+Basic CVs
+---------
 .. autosummary::
    :toctree: api/generated/
 
@@ -19,31 +19,13 @@ basic orderparamters
    CoordinateFunctionCV
    GeneratorCV
    CoordinateGeneratorCV
-
-simple collectivevariables
---------------------------
-.. autosummary::
-   :toctree: api/generated/
-
    InVolumeCV
 
-mdtraj orderparamters
----------------------
-.. autosummary::
-   :toctree: api/generated/
-
-   MDTrajFunctionCV
-
-msmbuilder3 collectivevariables
+Integrating with other packages
 -------------------------------
 .. autosummary::
    :toctree: api/generated/
 
-   MSMBFeaturizerCV
-
-PyEMMA collectivevariables
---------------------------
-.. autosummary::
-   :toctree: api/generated/
-
+   MDTrajFunctionCV
    PyEMMAFeaturizerCV
+   MSMBFeaturizerCV
diff --git a/docs/conf.py b/docs/conf.py
@@ -95,7 +95,7 @@
 
 # General information about the project.
 project = u'OpenPathSampling'
-copyright = u'2014-2019, David W.H. Swenson, Jan-Hendrik Prinz, John Chodera, Peter Bolhuis'
+copyright = u'2014-2020, David W.H. Swenson, Jan-Hendrik Prinz, John Chodera, Peter Bolhuis'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -104,7 +104,8 @@
 # The full version, including alpha/beta/rc tags.
 release = pkg_resources.get_distribution('openpathsampling').version
 # The short X.Y version.
-version = packaging.version.Version(release).base_version
+# version = packaging.version.Version(release).base_version
+version = release  # prefer to have the .dev0 label on 'latest'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/data_objects.rst b/docs/data_objects.rst
@@ -1,12 +1,15 @@
 .. _data-object-api:
 
-Data Objects API
-================
+Data Objects
+============
 
 This describes some of the objects used to describe data. Note that
 :class:`Trajectories <.Trajectory>` and :class:`Snapshots <.Snapshot>` are
 described in the :ref:`Engines <engine>` section.
 
+A less-technical overview is provided in the :ref:`data-objects` section of
+the user guide; we recommend that you read that first.
+
 .. currentmodule:: openpathsampling
 
 .. autosummary::

diff --git a/docs/ensemble.rst b/docs/ensemble.rst
@@ -2,8 +2,8 @@
 
 .. currentmodule:: openpathsampling.ensemble
 
-Ensembles API
-=============
+Ensembles
+=========
 
 The concept of the path ensemble, the (appropriately weighted) set of
 trajectories satisfying particular conditions, is at the heart of path

diff --git a/docs/examples/index.rst b/docs/examples/index.rst
@@ -4,15 +4,15 @@ Examples
 ========
 
 This page provides a series of examples, tutorials and recipes to help you
-get started with ``openpathsampling``.
+get started with OpenPathSampling.
 
 Each subsection of the pages linked below is a notebook.  To open these
 notebooks in a "live" session and execute the documentation interactively,
 open them using ``jupyter notebook NOTEBOOK_NAME.ipynb``. 
 
-If you installed `openpathsampling` from source, you can find these in the
-``examples`` directory within the root ``openpathsampling`` directory. You
-cn also find them in our `GitHub repository
+If you installed OPS from source, you can find these in the ``examples``
+directory within the root ``openpathsampling`` directory. You can also find
+them in our `GitHub repository
 <https://github.com/openpathsampling/openpathsampling/tree/master/examples>`_.
 
 .. note:: It's a *lot* more fun to run these examples live than to just read

diff --git a/docs/examples/mstis.rst b/docs/examples/mstis.rst
@@ -16,16 +16,29 @@ For more advanced techniques based on the same system, see the subsequent
 notebooks in the `directory containing these examples
 <https://github.com/openpathsampling/openpathsampling/tree/master/examples/toy_model_mstis>`_.
 
+* :ref:`Obtaining the first trajectories for a toy model
+  <toy-mstis-first-traj>`
+* :ref:`Running an MSTIS simulation <toy-mstis-running>`
+* :ref:`Analyzing the MSTIS simulations <toy-mstis-analysis>`
+
+.. _toy-mstis-first-traj:
+
 -----
 
+
 .. notebook:: examples/toy_model_mstis/toy_mstis_1_setup.ipynb
    :skip_exceptions:
 
+.. _toy-mstis-running:
+
 -----
 
+
 .. notebook:: examples/toy_model_mstis/toy_mstis_2_run.ipynb
    :skip_exceptions:
 
+.. _toy-mstis-analysis:
+
 -----
 
 .. notebook:: examples/toy_model_mstis/toy_mstis_3_analysis.ipynb

diff --git a/docs/index.rst b/docs/index.rst
@@ -10,8 +10,8 @@ flux calculations. In addition, it is a powerful library to build new path
 sampling methods.
 
 OPS is independent of the underlying molecular dynamics engine, and
-currently has support for OpenMM, as well as an internal engine suitable for
-2D toy models.
+currently has support for OpenMM and Gromacs, as well as an internal engine
+suitable for 2D toy models.
 
 To learn more about what OPS can do, look at our :ref:`examples <examples>`.
 If you want to jump right in, take a look at how easy it is to
@@ -24,6 +24,8 @@ the development process on GitHub_, and follow `@pathsampling
 .. _GitHub: http://github.com/openpathsampling/openpathsampling
 
 .. note:: Documentation is still in progress; if you have questions, please
+          `open an issue 
+          <https://github.com/openpathsampling/openpathsampling/issues>`_ or
           contact the development team.
 
 To see the most recent updates to the code, see the `release notes
@@ -60,6 +62,7 @@ For Users
     install
     examples/index
     topics/index
+    videos
     faq
 
 

diff --git a/docs/install.rst b/docs/install.rst
@@ -10,7 +10,7 @@ that aren't Python 3-compatible yet.
 
 .. note:: As of OpenPathSampling 1.1, OpenMM will no longer be automatically
           installed when you install OPS. However, the OpenMM engine will be
-          immediately available if you install OpenMM youself. See the
+          immediately available if you install OpenMM yourself. See the
           `OpenMM installation instructions
           <http://docs.openmm.org/latest/userguide/application.html#installing-openmm>`_
           for a detailed guide, but ``conda install -c conda-forge -c omnia
@@ -28,12 +28,13 @@ scientific Python, and which handles binary dependencies seamlessly.  If you
 don't want the full ``conda`` installation, the ``miniconda`` package
 provides much of the convenience of ``conda`` with a smaller footprint.
 
-OpenPathSampling is part of the ``omnia`` channel in ``conda``, although
-some requirements are best found in the ``conda-forge`` channel. To install
-the most recent release of OpenPathSampling with conda, use the following
-command ::
+OpenPathSampling is part of the ``conda-forge`` channel in ``conda``.  To
+install the most recent release of OpenPathSampling with conda, use the
+following command ::
 
-  $ conda install -c conda-forge -c omnia openpathsampling
+  $ conda install -c conda-forge openpathsampling
+
+With that, you should be ready to use OPS!
 
 .. _developer-install-conda:
 
@@ -67,9 +68,9 @@ If you don't want to use ``conda``, you will have to manually obtain the
 dependencies, which you can see listed under ``install_requires`` in
 ``setup.py``. Then you can install from our GitHub repository.
 
-Clone the source code repository from github::
+Clone the source code repository from GitHub::
 
-  $ git clone git://github.com/openpathsampling/openpathsampling.git
+  $ git clone https://github.com/openpathsampling/openpathsampling.git
 
 Then, in the directory containing the source code, you can install it with ::
 
@@ -79,9 +80,10 @@ Or, for a developer install ::
 
   $ python setup.py develop
 
+.. _run-tests:
+
 Testing Your Installation
 =========================
-.. _run-tests:
 
 Running the tests is a great way to verify that everything is working. The
 test suite uses `pytest <http://pytest.org>`_ and, for legacy reasons, also
@@ -90,7 +92,8 @@ requires the `nose <https://nose.readthedocs.org/en/latest/>`_ package. You can
   $ conda install pytest nose
 
 From the source directory ``openpathsampling/tests``, you can run the tests
-by typing ``py.test`` on the command line.
+by typing ``py.test`` on the command line. The test suite includes over 900
+individual tests, and runs in around 2-3 minutes.
 
 Beta testing experimental updates
 =================================