Update notebooks to work with latest version of the precompiled Colab…

… environment (#342) * Update precompiled env URL * Update Advanced Sampling Introduction notebook * Update HOOMD-blue Colab notebooks * Update OpenMM Colab notebooks
SSAGESLabs · Oct 31, 2024 · e059321 · e059321
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Showing 24 changed files with 2,770 additions and 3,289 deletions.
diff --git a/.trunk/trunk.yaml b/.trunk/trunk.yaml
@@ -41,30 +41,30 @@ lint:
       paths:
         - examples/Advanced_Sampling_Introduction.md
         - examples/Installing_a_PySAGES_Environment.md
-        - examples/openmm/Harmonic_Bias.md
         - examples/hoomd-blue/ann/Butane_ANN.md
-        - examples/hoomd-blue/harmonic_bias/Harmonic_Bias.md
-        - examples/openmm/metad/Metadynamics-ADP.md
         - examples/hoomd-blue/cff/Butane_CFF.md
+        - examples/hoomd-blue/harmonic_bias/Harmonic_Bias.md
         - examples/hoomd-blue/spectral_abf/Butane-SpectralABF.md
-        - examples/openmm/spectral_abf/ADP_SpectralABF.md
         - examples/hoomd-blue/funn/Butane_FUNN.md
         - examples/hoomd-blue/umbrella_integration/Umbrella_Integration.md
+        - examples/openmm/harmonic_bias/Harmonic_Bias.md
+        - examples/openmm/metad/Metadynamics-ADP.md
         - examples/openmm/metad/nacl/Metadynamics_NaCl.md
+        - examples/openmm/spectral_abf/ADP_SpectralABF.md
     - linters: [black]
       paths:
         - examples/Advanced_Sampling_Introduction.ipynb
         - examples/Installing_a_PySAGES_Environment.ipynb
-        - examples/openmm/Harmonic_Bias.ipynb
         - examples/hoomd-blue/ann/Butane_ANN.ipynb
         - examples/hoomd-blue/harmonic_bias/Harmonic_Bias.ipynb
-        - examples/openmm/metad/Metadynamics-ADP.ipynb
         - examples/hoomd-blue/cff/Butane_CFF.ipynb
         - examples/hoomd-blue/spectral_abf/Butane-SpectralABF.ipynb
-        - examples/openmm/spectral_abf/ADP_SpectralABF.ipynb
         - examples/hoomd-blue/funn/Butane_FUNN.ipynb
         - examples/hoomd-blue/umbrella_integration/Umbrella_Integration.ipynb
+        - examples/openmm/harmonic_bias/Harmonic_Bias.ipynb
+        - examples/openmm/metad/Metadynamics-ADP.ipynb
         - examples/openmm/metad/nacl/Metadynamics_NaCl.ipynb
+        - examples/openmm/spectral_abf/ADP_SpectralABF.ipynb
 
 merge:
   required_statuses:

diff --git a/examples/Advanced_Sampling_Introduction.ipynb b/examples/Advanced_Sampling_Introduction.ipynb