Sage 2.0 (#14)

* add script for generating new submissions

* add sage 2.0.0 submission

* reorder and align table

* bump yammbs to 0.1.1 for faster loading

* fix default dataset path

* Add benchmark results

* update readme with 2.0 DOI and fix redundant descriptions

---------

Co-authored-by: root <[email protected]>

README.md

@@ -48,11 +48,13 @@ See [datasets/README.md](datasets/README.md)
 
 ## Benchmark Results
 
-| Submission                    | Description                       | DOI                                                                |
-|-------------------------------|-----------------------------------|--------------------------------------------------------------------|
-| [Sage-2.1.0]                  | Constrained openff-2.1.0.offxml   | [10.5281/zenodo.14053221](https://doi.org/10.5281/zenodo.14053221) |
-| [Sage-2.1.0-unconstrained]    | Unconstrained openff-2.1.0.offxml | [10.5281/zenodo.14058464](https://doi.org/10.5281/zenodo.14058464) |
-| [Parsley-1.3.1-unconstrained] | Unconstrained openff-1.3.1.offxml | [10.5281/zenodo.14172472](https://doi.org/10.5281/zenodo.14172472) |
+| Submission                                      | Description                       | DOI                                                                |
+|-------------------------------------------------|-----------------------------------|--------------------------------------------------------------------|
+| [Parsley-1.3.1-unconstrained]                   | openff_unconstrained-1.3.1.offxml | [10.5281/zenodo.14172472](https://doi.org/10.5281/zenodo.14172472) |
+| [Sage-2.0.0](submissions/2024-11-19-Sage-2.0.0) | openff_unconstrained-2.0.0.offxml | [10.5281/zenodo.14188644](https://doi.org/10.5281/zenodo.14188644) |
+| [Sage-2.1.0]                                    | openff-2.1.0.offxml               | [10.5281/zenodo.14053221](https://doi.org/10.5281/zenodo.14053221) |
+| [Sage-2.1.0-unconstrained]                      | openff_unconstrained-2.1.0.offxml | [10.5281/zenodo.14058464](https://doi.org/10.5281/zenodo.14058464) |
+<!-- ENDOFTABLE -->
 
 [Sage-2.1.0]: submissions/2024-11-07-Sage-2.1.0
 [Sage-2.1.0-unconstrained]: submissions/2024-11-08-Sage-2.1.0-unconstrained

devtools/env.yaml

@@ -22,4 +22,4 @@ dependencies:
   - tqdm
 
   - pip:
-    - git+https://github.com/openforcefield/[email protected].0
+    - git+https://github.com/openforcefield/[email protected].1

scripts/new_submission.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+sub_name=${1?no submission name given}
+sub_dir=submissions/$(date +%F)-${sub_name}
+
+mkdir -p ${sub_dir}
+
+cat > ${sub_dir}/input.yaml <<INP
+forcefield: openff_unconstrained-2.1.0.offxml
+datasets:
+    - datasets/OpenFF-Industry-Benchmark-Season-1-v1.1/cache.json
+INP
+
+sed -i "/ENDOFTABLE/i | [$sub_name]($sub_dir) | TODO | [TODO](https://doi.org/TODO) |" README.md

submissions/2024-11-19-Sage-2.0.0/input.yaml

@@ -0,0 +1,3 @@
+forcefield: openff_unconstrained-2.0.0.offxml
+datasets:
+    - datasets/OpenFF-Industry-Benchmark-Season-1-v1.1/cache.json