Merge pull request #596 from choderalab/PreRelease0141

Cut 0.14.1: "Early Access of 1.0" Release

devtools/README.md

@@ -31,7 +31,7 @@ Checklist for Major Revisions (YANK X.Y+1.0)
 - [ ] Update `docs/changelog.rst`
 - [ ] Update `setup.py` with version number and `ISRELEASED` to `True`
 - [ ] Do the steps for All Upates
-- [ ] Create a new release on GitHub, reference the tag and copy the changes in `docs/changelog.rst`
+- [ ] Create a new release on GitHub, reference the tag and copy the changes in `docs/whatsnew.rst`
 - [ ] Update the `omnia-md/conda-recipies` repo by creating a new PR with updated versions
   * Be sure to pin dependencies to fixed version
 
@@ -41,6 +41,6 @@ Checklist for Minor Revisions (YANK X.Y.Z+1)
 - [ ] In `setup.py`, set `ISRELEASED` to `False`
 - [ ] Do all the steps for All Updates
   * If this is a critical bugfix (i.e. YANK X.Y.0 is broken and/or flat out wrong without the fix):
-- [ ] Update `docs/changelog.rst`
+- [ ] Update `docs/whatsnew.rst`
 - [ ] Update the released version on the site to this version, adjusting the tag and note that this is a critical bugfix which corrects the X.Y release
 - [ ] Update the `omnia-md/conda-recipies` repo to point at the corrected version

devtools/conda-recipe/meta.yaml

@@ -63,4 +63,4 @@ test:
 
 about:
   home: https://github.com/choderalab/yank
-  license: GNU Lesser General Public License v2 or later (LGPLv2+)
+  license: MIT License

docs/whatsnew.rst

@@ -6,6 +6,61 @@ This section features and improvements of note in each release.
 
 The full release history can be viewed `at the github yank releases page <https://github.com/choderalab/yank/releases>`_.
 
+0.14.1 Early Access of 1.0 Release
+----------------------------------
+- YAML Syntax Structure Frozen. YANK YAML Version 1.0. All YAML scripts from this version will be compatible with future versions until YAML 2.0
+  New features may appear in the time meantime, but scripts will be forwards compatible.
+- Initial support for OpenMM XML systems and PDB files
+- Support for separate solvent configurations for the two phases when defined from amber/gromacs/openmm files
+- `clearance` in YAML no mandatory parameter of explicit solvent, but only when molecule setup goes through pipeline
+- Boresch Orientational Restraints fully implemented and documented.
+- Long range anisotropic dispersion correction improved to work on both ends of thermodynamic cycle leg
+- Documentation updated with better algorithms and theory sections.
+- Full walkthroughs of ``yank-examples`` added to online documentation
+- Various other documentation improvements
+- Support for upcoming OpenMM 7.1 Release and features (still works with 7.0.1)
+- YANK now on MIT License
+- Many bugfixes
+
+0.12.0 (development)
+--------------------
+- Examples split into their own repository
+- Old CLI commands staring depreciation
+
+0.11.2 (development)
+--------------------
+- Better long range dispersion and electrostatics corrections
+- Best practices and guidelines for the YAML documentation published
+
+0.11.0 (development)
+--------------------
+- Full YAML documentation available online with all possible options specified
+- Developer documentation
+
+0.10.0 (development)
+--------------------
+- Python 3.X support
+- Online documentation has been updated to include the YAML input files
+- Selftests now provide more helpful output
+
+
+0.9.0 (development)
+-------------------
+- Changed YAML Syntax
+- New Command `yank analyze extrat-trajectory` to extract data from NetCDF4 file in a common trajectory format.
+- Support for solvation free energy calculations.
+- Automatic detection of MPI.
+- Various bug fixes.
+
+0.8.0 (development)
+-------------------
+- `alchemy` split to a standalone repository
+- YAML based input files for setting up and running simulations. Uses an AmberTools-based pipeline
+
+0.7.0 (development)
+-------------------
+- Convert to single `Context` Hamiltonian Replica Exchange
+
 v0.6.1 (development)
 --------------------
 - mpi4py automatically installed via conda

setup.py

@@ -17,7 +17,7 @@
 
 ########################
 VERSION = "0.14.1"
-ISRELEASED = False
+ISRELEASED = True
 __version__ = VERSION
 ########################
 CLASSIFIERS = """\