Update NAGL in examples #12
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That did actually work it's just that the preproc action runs off this branch so the comments aren't on this branch yet - merging in |
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Hey @lilyminium - This seems to be working on main with nagl 0.2.2, but it doesn't like 0.2.3. Do you have any insight? The error in the two runs above is in openforcefield/openff-toolkit/QCArchive_interface/QCarchive_interface.ipynb, so it could be an intermittent error from QCA, but it was reliable for dozens of test runs while I was writing the PR so I wonder if its possible something has changed in the environment. When I run it locally the openforcefield/openff-toolkit/virtual_sites/vsite_showcase.ipynb The diff between the outputs of --- Last failed run Thu Jul 6 08:53:00 2023
+++ last successful run Thu Jul 6 08:53:00 2023
@@ -1,4 +1,4 @@
-Last failed run
+ last successful run
List of packages in environment: "/home/runner/micromamba/envs/openff-docs-examples"
Name Version Build Channel
@@ -226,7 +226,7 @@
openff-interchange 0.3.7 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.3.7 pyhd8ed1ab_0 conda-forge
openff-models 0.0.5 pyh1a96a4e_0 conda-forge
- openff-nagl 0.2.3 pyhd8ed1ab_0 conda-forge
+ openff-nagl 0.2.2 pyhd8ed1ab_0 conda-forge
openff-toolkit 0.14.0 pyhd8ed1ab_1 conda-forge
openff-toolkit-base 0.14.0 pyhd8ed1ab_1 conda-forge
openff-toolkit-examples 0.14.0 hd8ed1ab_1 conda-forge
@@ -251,7 +251,7 @@
pbr 5.11.1 pyhd8ed1ab_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
pdbfixer 1.9 pyh1a96a4e_0 conda-forge
- perl 5.32.1 3_hd590300_perl5 conda-forge
+ perl 5.32.1 2_h7f98852_perl5 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.0.0 py310h582fbeb_0 conda-forge
@@ -368,4 +368,3 @@
zipp 3.15.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
- zstd 1.5.2 h3eb15da_6 conda-forge I'll try adding zstd to the environment but I have no idea what it does |
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So the error is in other notebooks that don't use NAGL? That's surprising :/ there should be very little difference between v0.2.2 and v0.2.3 -- the only updates are in docs and metadata: |
Yep!
This feels like a huge understatement 😆 Jeff reckons the QCA time outs are spooky action at a distance from changes QCA serverside, so maybe its just my computer acting up. The timeout is extremely, worryingly reproducible - every time I recreate an environment with NAGL 0.2.2 it works, and with 0.2.3 it times out. Here's my latest conda environment diff: --- git checkout main Thu Jul 6 09:49:08 2023
+++ git checkout update-nagl Thu Jul 6 09:49:08 2023
@@ -1,4 +1,4 @@
-git checkout main
+git checkout update-nagl
List of packages in environment: "/home/joshmitchell/Documents/openff/openff-docs/.soap/examples"
Name Version Build Channel
@@ -232,7 +232,7 @@
openff-interchange 0.3.7 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.3.7 pyhd8ed1ab_0 conda-forge
openff-models 0.0.5 pyh1a96a4e_0 conda-forge
- openff-nagl 0.2.2 pyhd8ed1ab_0 conda-forge
+ openff-nagl 0.2.3 pyhd8ed1ab_0 conda-forge
openff-toolkit 0.14.0 pyhd8ed1ab_1 conda-forge
openff-toolkit-base 0.14.0 pyhd8ed1ab_1 conda-forge
openff-toolkit-examples 0.14.0 hd8ed1ab_1 conda-forge
@@ -374,4 +374,4 @@
zipp 3.15.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
- zstd 1.5.2 h3eb15da_6 conda-forge
+ zstd 1.5.2 h3eb15da_6 conda-forge I'll see what happens if I run the notebook in Jupyter Lab... |
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The vsites notebook works on Jupyter Lab. Jeff thinks its a thread safety thing (he's probably right). I don't understand why it happens so consistently but it's possible. I'm going to try running it a few more times in this PR and see what happens. |
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I think some of the failure may be due to failing to copy directories -- although this is a new addition in 0.3.x -- https://github.com/openforcefield/openff-docs/actions/runs/5851460527/job/15862259538#step:7:21 |
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Superseded by #42 |
I'm getting some very strange performance regressions locally but we'll see what happens here.