Updated CHANGELOG for 2.0 (#156)

* Updated CHANGELOG for 2.0

* fix links

* fix links

* fix formatting

* add missing URL

Author: mikemhenry

docs/CHANGELOG.rst

@@ -4,6 +4,35 @@ Kartograf Change Log
 
 .. current developments
 
+v2.0
+====================
+
+**Added:**
+
+* Added documentation for molecule alignment algorithms, including guidance on choosing between skeleton-based MCS alignment and shape-based Open3DAlign alignment (`PR #141 <https://github.com/OpenFreeEnergy/kartograf/issues/141>`_).
+* Added a ``kartograf.__version__`` version attribute (`PR #132 <https://github.com/OpenFreeEnergy/kartograf/pull/132>`_)
+
+**Changed:**
+
+* We now use https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.cdist.html#scipy.spatial.distance.cdist internally to calculate the distance matrix which improves performance.
+* **BREAKING CHANGE** The default for ``KartografAtomMapper``'s ``map_hydrogens_on_hydrogens_only`` option is now ``True``.
+  Previously it was ``False``.
+* **BREAKING CHANGE** We moved the visualization widget to ``gufe``.
+  Instead of ``from kartograf.utils.mapping_visualization_widget import display_mappings_3d`` use ``from gufe.visualization.mapping_visualization import display_mappings_3d``
+
+**Deprecated:**
+
+* We no longer distribute the package on PyPI.
+  Since all of the dependences of the package do not exist on PyPI, users would have to install the dependences manually.
+  We have decided that all new kartograf releases will be solely distributed via conda-forge.
+  We have uploaded a placeholder version of the package that when imported, directs users to install the package from conda-forge instead of PyPI.
+
+**Fixed:**
+
+* Clarified atom-mapping warnings when configured filters remove all geometrically found candidate atom pairs (`issue #51 <https://github.com/OpenFreeEnergy/kartograf/issues/51>`_).
+
+
+
 v1.2.0
 ====================