Upgrade HOOMD-blue and OpenMM in Colab (SSAGESLabs#341)

Since we've been supporting HOOMD-blue `v4.x` series for a while now, it makes sense to try to modernize our example notebooks. I'll start just with the Installation Notebook, and will update the examples separately. This would in principle break our HOOMD-blue notebooks, but all notebooks are broken for other reasons, like SSAGESLabs#339. We will updated the notebooks in a separate PR.
yihengwuKP · Oct 14, 2024 · 791bbfa · 791bbfa
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diff --git a/.trunk/trunk.yaml b/.trunk/trunk.yaml
@@ -40,7 +40,7 @@ lint:
     - linters: [prettier]
       paths:
         - examples/Advanced_Sampling_Introduction.md
-        - examples/Install_PySAGES_Environment.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
@@ -54,7 +54,7 @@ lint:
     - linters: [black]
       paths:
         - examples/Advanced_Sampling_Introduction.ipynb
-        - examples/Install_PySAGES_Environment.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

diff --git a/README.md b/README.md
@@ -81,4 +81,4 @@ page](https://docs.trunk.io/docs).
 <!-- References -->
 
 [Colab Badge]: https://colab.research.google.com/assets/colab-badge.svg
-[Install Notebook]: https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/Install_PySAGES_Environment.ipynb
+[Install Notebook]: https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/Installing_a_PySAGES_Environment.ipynb
diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -42,4 +42,4 @@ and OpenMM can be built and installed in such an environment: [Install Notebook]
 
 <!-- References -->
 
-[Install Notebook]: https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/Install_PySAGES_Environment.ipynb
+[Install Notebook]: https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/Installing_a_PySAGES_Environment.ipynb
diff --git a/examples/Install_PySAGES_Environment.md b/examples/Install_PySAGES_Environment.md
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Expand Up		@@ -42,4 +42,4 @@ and OpenMM can be built and installed in such an environment: [Install Notebook]

		<!-- References -->

		[Install Notebook]: https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/Install_PySAGES_Environment.ipynb
		[Install Notebook]: https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/Installing_a_PySAGES_Environment.ipynb