Do not use AmberTools in examples

[mattwthompson]

• Tag issue being addressed
• Add tests
• Update docstrings/documentation, if applicable
• Lint codebase
• Update changelog

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[mattwthompson]

Outstanding issues:

1. QCArchive is rejecting our requests (probably a rate-limit)
2. sander is also needed for one of the tests, arguably could be skipped
   a. A vastly better solution is Make releases less monolithic conda-forge/ambertools-feedstock#138
3. openmmforcefields use as discussed elsewhere Examples workflow broken #2182 (comment)

[mattwthompson]

Maybe not so intermittent:

=================================== FAILURES ===================================
_______ examples/QCArchive_interface/QCarchive_interface.ipynb::Cell 10 ________
[gw0] darwin -- Python 3.12.13 /Users/runner/micromamba/envs/base-examples/bin/python
Notebook cell execution failed
Cell 10: Cell execution caused an exception

Input:
# note the result is in QC units of hartrees
print(result.return_result)

Traceback:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[1], line 2
      1 # note the result is in QC units of hartrees
----> 2 print(result.return_result)

AttributeError: 'FailedOperation' object has no attribute 'return_result'

============================= slowest 10 durations =============================
222.31s call     examples/visualization/visualization.ipynb::Cell 12
171.04s call     examples/toolkit_showcase/toolkit_showcase.ipynb::Cell 4
131.00s call     examples/toolkit_showcase/toolkit_showcase.ipynb::Cell 11
60.06s call     examples/toolkit_showcase/toolkit_showcase.ipynb::Cell 12
39.15s call     examples/toolkit_showcase/toolkit_showcase.ipynb::Cell 9
12.38s call     examples/toolkit_showcase/toolkit_showcase.ipynb::Cell 10
7.80s call     examples/visualization/visualization.ipynb::Cell 13
6.34s call     examples/toolkit_showcase/toolkit_showcase.ipynb::Cell 7
6.30s call     examples/virtual_sites/vsite_showcase.ipynb::Cell 0
5.74s call     examples/QCArchive_interface/QCarchive_interface.ipynb::Cell 0
=========================== short test summary info ============================
FAILED examples/QCArchive_interface/QCarchive_interface.ipynb::Cell 10
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!! xdist.dsession.Interrupted: stopping after 1 failures !!!!!!!!!!!!!
============= 1 failed, 74 passed, 2 skipped in 437.17s (0:07:17) ==============
Error: Process completed with exit code 2.

[mattwthompson]

Here's all of the nudges I used to help the solver out; some of them are inconsequential but others might be worth adding in:

diff --git a/devtools/conda-envs/base-examples.yaml b/devtools/conda-envs/base-examples.yaml
index ff04213f..e4289bbe 100644
--- a/devtools/conda-envs/base-examples.yaml
+++ b/devtools/conda-envs/base-examples.yaml
@@ -3,31 +3,31 @@ channels:
   - conda-forge
 dependencies:
     # Base depends
-  - python
+  - python =3.12
   - versioningit
   - packaging
-  - numpy <2.3
+  - numpy >=2
   - networkx
   - cachetools
   # https://github.com/openforcefield/openff-toolkit/issues/2150
   - xmltodict <=1.0.2
   - python-constraint
-  - openmm >=7.6
-  - openff-forcefields >=2023.11
+  - openmm >=8.4
+  - openff-forcefields >=2025.12
   - openff-amber-ff-ports >=0.0.3
   - openff-units
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
-  - nomkl
-  - openff-nagl-base >=0.4.0
-  - openff-nagl-models >=0.3.0
+  # nomkl
+  - openff-nagl-base >=0.5.2
+  - openff-nagl-models >=2025
   - typing_extensions
   - nglview
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
   - rdkit >=2024
     # Test-only/optional/dev/typing/examples
-  - pytest =8
+  - pytest
   - pytest-xdist
   - pytest-rerunfailures
   - pyyaml