Merge pull request #13 from openforcefield/run-torsions

Begin setting up torsion automation

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/run.yaml → .github/workflows/opt.yaml

@@ -1,6 +1,6 @@
 # this is adapted from openff-docs/cookbook_preproc.yaml
 
-name: Run benchmarks and commit the results
+name: Run optimization benchmarks
 
 on:
   workflow_dispatch:
@@ -90,7 +90,7 @@ jobs:
                 status: 'in_progress',
                 started_at: new Date().toISOString(),
                 output: {
-                  title: 'Run benchmarks',
+                  title: 'Run optimization benchmarks',
                   summary: 'Results and progress: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}',
                   text: ''
                 },
@@ -116,7 +116,7 @@ jobs:
         with:
           environment-file: ${{ inputs.env }}
 
-      - name: Run benchmarks
+      - name: Run optimization benchmarks
         env:
             LICENSE: ${{ secrets.OE_LICENSE }}
         shell: bash -l {0}
@@ -190,7 +190,7 @@ jobs:
         with:
           pr_number: ${{ inputs.pr_number }}
           message: >
-            A workflow dispatched to run benchmarks for this PR has just finished.
+            A workflow dispatched to run optimization benchmarks for this PR has just finished.
 
 
             - Run ID: [${{ github.run_id }}]
@@ -210,7 +210,7 @@ jobs:
         with:
           pr_number: ${{ inputs.pr_number }}
           message: >
-            A workflow dispatched to run benchmarks for this PR has just failed.
+            A workflow dispatched to run optimization benchmarks for this PR has just failed.
 
 
             - Run ID: [${{ github.run_id }}]

.github/workflows/run_trigger.yaml

@@ -1,6 +1,8 @@
 # this is adapted from openff-docs/cookbook_pr_trigger.yaml
 
-name: Trigger benchmark run on comment with "/run-benchmark"
+name: Trigger benchmark run
+
+# comment on a PR with "/run-optimization-benchmark" or "/run-torsion-benchmark"
 
 on:
   issue_comment:
@@ -27,9 +29,9 @@ jobs:
             // Return early if comment is not one of the trigger phrases. Otherwise
             // set the type of workflow to dispatch
             let benchmark_workflow;
-            if (comment.body.startsWith('/run-benchmark')) {
-               benchmark_workflow = "run.yaml"
-            } else if (comment.body.startsWith('/run-torsions')) {
+            if (comment.body.startsWith('/run-optimization-benchmarks')) {
+               benchmark_workflow = "opt.yaml"
+            } else if (comment.body.startsWith('/run-torsion-benchmarks')) {
                benchmark_workflow = "torsions.yaml"
             } else {
               console.log("Comment is not trigger phrase")

.github/workflows/torsions.yaml

@@ -1,6 +1,6 @@
 # this is adapted from openff-docs/cookbook_preproc.yaml
 
-name: Run benchmarks and commit the results
+name: Run torsion benchmarks
 
 on:
   workflow_dispatch:
@@ -90,7 +90,7 @@ jobs:
                 status: 'in_progress',
                 started_at: new Date().toISOString(),
                 output: {
-                  title: 'Run benchmarks',
+                  title: 'Run torsion benchmarks',
                   summary: 'Results and progress: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}',
                   text: ''
                 },
@@ -104,6 +104,7 @@ jobs:
 
       - name: Install git-lfs
         run: |
+          sudo apt update
           sudo apt install -y git-lfs
 
       - uses: actions/checkout@v3
@@ -115,7 +116,7 @@ jobs:
         with:
           environment-file: ${{ inputs.env }}
 
-      - name: Run benchmarks
+      - name: Run torsion benchmarks
         env:
             LICENSE: ${{ secrets.OE_LICENSE }}
         shell: bash -l {0}
@@ -145,8 +146,10 @@ jobs:
 
           input_file=${{ inputs.path }}                        # path to the input YAML file
           input_dir=$(dirname $input_file)                     # parent directory of input YAML file
-          git add $input_dir/output/{log_sse}.csv
-          git add $input_dir/output/{log_sse}.csv
+          git add $input_dir/output/rmsd.csv
+          git add $input_dir/output/een.csv
+          git add $input_dir/output/minimized.json
+          git add $input_dir/output/metrics.json
           git commit -m "Add benchmark results"
           git push
 
@@ -155,14 +158,16 @@ jobs:
       - name: Upload to zenodo
         env:
             ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }}
+            ZENODO_URL:  "https://zenodo.org"
         shell: bash -l {0}
         run: |
           # TODO: make and bundle plot(s)
-          bzip2 tmp.sqlite
+          bzip2 torsions-dev.sqlite
           micromamba env export > env.yaml
           input_files=$(python get_files.py ${{ inputs.path }})
           python zenodo_upload.py --title "YDS Upload ${{ inputs.pr_number }}" \
-            tmp.sqlite.bz2 $input_dir/output/{log_sse}.csv \
+            torsions-dev.sqlite.bz2 $input_dir/output/rmsd.csv \
+            torsions-dev.sqlite.bz2 $input_dir/output/een.csv \
             env.yaml torsions.py $input_files
 
       - name: Report status to PR
@@ -172,7 +177,7 @@ jobs:
         with:
           pr_number: ${{ inputs.pr_number }}
           message: >
-            A workflow dispatched to run benchmarks for this PR has just finished.
+            A workflow dispatched to run torsion benchmarks for this PR has just finished.
 
 
             - Run ID: [${{ github.run_id }}]
@@ -192,7 +197,7 @@ jobs:
         with:
           pr_number: ${{ inputs.pr_number }}
           message: >
-            A workflow dispatched to run benchmarks for this PR has just failed.
+            A workflow dispatched to run torsion benchmarks for this PR has just failed.
 
 
             - Run ID: [${{ github.run_id }}]

.gitignore

@@ -1,2 +1,5 @@
 oe_license.txt
 /__pycache__/
+
+# macOS
+.DS_Store

datasets/torsion-dev/larger.py

@@ -0,0 +1,10 @@
+from openff.qcsubmit.results import TorsionDriveResultCollection
+from yammbs.torsion.inputs import QCArchiveTorsionDataset
+
+dspath = "/home/brent/omsf/projects/valence-fitting/02_curate-data/datasets/combined-td.json"
+td = TorsionDriveResultCollection.parse_file(dspath)
+
+ytd = QCArchiveTorsionDataset.from_qcsubmit_collection(td)
+
+with open("larger.json", "w") as out:
+    out.write(ytd.model_dump_json())

devtools/env.yaml

@@ -22,4 +22,4 @@ dependencies:
   - tqdm
 
   - pip:
-    - git+https://github.com/openforcefield/yammbs.git@0.1.1
+    - git+https://github.com/openforcefield/yammbs.git@add-torsion-models

devtools/torsions.yaml

@@ -0,0 +1,25 @@
+name: yammbs-dataset-submission
+
+channels:
+  - conda-forge
+  - openeye
+
+dependencies:
+  - python
+  - pip
+
+  - qcportal ~=0.55
+  - openff-qcsubmit >=0.52
+  - openff-toolkit
+  - openeye-toolkits
+  - geometric =1
+
+  - click
+  - matplotlib
+  - numpy
+  - pandas
+  - seaborn
+  - tqdm
+
+  - pip:
+    - git+https://github.com/openforcefield/yammbs.git@add-torsion-models