Release prep v1.6.1 (#1544)

* update partial charge tests now that a production NAGL model is available (#1506)

* update tests now that a production NAGL model is available

* fix mock

* clean up mocking

* add nagl test news item

* debug slow python 3.13 tests (#1468)

* Turn off minimization when we do a dry run
---------

Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>

* update quickrun execution docs and add MPS link (#1483)

* add jq cookbook (#1488)

* add jq code blocks

* use tutorial data

* news

* debug docs build (#1489)

* don't build openmm

* mambaforge->miniconda for rtd

* artifically small build for debugging

* dont build env

* just build python

* add channels

* add sphinx packages to env

* add all non-openfe-ecosystem deps

* remove shim channel

* add openfe package

* add everything except openmm and toolkit

* add openmm

* add openff-toolkit

* only openff-toolkit

* try openff-toolkit-base

* try latest openff

* everybody back in

* build without openmm

* build with openff-toolkit-base

* bump rtd

* add pip build

* remove any openff-toolkit

* build w/o openmm

* add pip install

* build everything without pip install

* try no deps

* try custom build

* only python and pip

* try openfe-toolkit-base

* add temp deps for build with openff-toolkit-base

* add temp deps for build with openff-toolkit-base

* mock imports

* dont mock with toolkit base

* bump toolkit version

* Revert "bump toolkit version"

This reverts commit 6e3108a836.

* add mocks

* try pinnint to toolkit-base 0.13.0, no mocks

* back to >= 0.13.0 toolkit to make sure it wasn't a fluke

* mock imports

* add pipe example for jq (#1505)

* add pipe example for jq

* pin to docutil 0.20

* try to avoid memory error

* debug rtd build memory error (#1510)

* try mambaforge build

* Revert "try mambaforge build"

This reverts commit 683e07f1ea.

* try explicit build

* try removing ambertools

* use the right env

* just add gufe pip install back

* add back openfe eco packages

* mock py3dmol

* add note for pip installs

* fix quote

* temporarily resort to SettingsBaseModel to get build

* specific imports

* dont use base settings placeholder

* temp pin numpy (#1542)

* Removing unnecessary limit on resids (#1539)

* Removing unnecessary limit on resids indices gathering

* Updated CHANGELOG for 1.6.1

* add summary

* update docs theme (#1545)

* adding new branding assets

* remove images

* update theme branch

* CantinaPurple accent

* lowercase convention

* updating text

* remove dark mode for now

* fix sidebars

* fix formatting

* capitalization

* don't break spaces

* bump ci

* favicon!

* whitespace :(

* pin to sphinx release

* pin to gufe 1.6.1

* move env info before test imports

* bump single file installer to 3.12.11 to match colab

---------

Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

.github/workflows/ci.yaml

@@ -87,17 +87,17 @@ jobs:
       - name: "Install"
         run: python -m pip install --no-deps -e .
 
-      - name: "Test imports"
-        run: |
-          # if we add more to this, consider changing to for + env vars
-          python -Ic "import openfe; print(openfe.__version__)"
-
       - name: "Environment Information"
         run: |
           micromamba info
           micromamba list
           pip list
 
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import openfe; print(openfe.__version__)"
+
       - name: "Run tests"
         env:
           # Set the OFE_SLOW_TESTS to True if running a Cron job

devtools/installer/construct.yaml

@@ -21,7 +21,7 @@ specs:
   - pytest-xdist
   # python needs to match https://github.com/googlecolab/backend-info/blob/main/os-info.txt
   # until colab pushes a fix
-  - python 3.11.12
+  - python 3.12.11
 
 # Not building an .exe for windows or a .pkg for macOS
 installer_type: sh

docs/CHANGELOG.rst

@@ -4,6 +4,25 @@ Changelog
 
 .. current developments
 
+v1.6.1
+====================
+This release includes minor fixes and updates to tests. 
+
+**Added:**
+
+* Added a cookbook for using ``jq`` to inspect JSON files.
+
+**Changed:**
+
+* Remove unnecessary limit on residues ids (``resids``) when getting mappings from topology in ``topology_helpers.py`` utility module.
+* The relative hybrid topology protocol no longer runs the FIRE minimizer when ``dry=True``.
+
+**Fixed:**
+
+* Updated tests to expect to find NAGL, now that it is supported.
+
+
+
 v1.6.0
 ====================
 This release adds support for OpenMM 8.3.0 and Python 3.13.