Merge branch 'main' into dependabot/github_actions/actions/checkout-5

Author: lbluque

.github/release-drafter-data-omol.yml

@@ -0,0 +1,37 @@
+include-paths:
+  - src/fairchem/data/omol
+  - packages/fairchem-data-omol
+tag-prefix: fairchem_data_omol
+tag-template: 'fairchem_data_omol-$RESOLVED_VERSION'
+name-template: 'fairchem_data_omol-$RESOLVED_VERSION'
+exclude-contributors: [github-actions]
+categories:
+  - title: New Features / Enhancements
+    labels: [enhancement]
+  - title: Bug Fixes
+    labels: [bug]
+  - title: Documentation
+    labels: [documentation]
+  - title: Tests
+    labels: [test]
+  - title: Deprecations
+    labels: [deprecation]
+  - title: Dependencies
+    labels: [dependencies]
+  - title: Other Changes
+    labels: ["*"]
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+template: |
+  ## What’s Changed
+
+  $CHANGES

.github/workflows/build.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Build
         run: |
           # add packages that are supposed to be built to this list
-          for package in fairchem-core fairchem-data-oc fairchem-demo-ocpapi fairchem-applications-cattsunami
+          for package in fairchem-core fairchem-data-oc fairchem-demo-ocpapi fairchem-applications-cattsunami fairchem-data-omol
           do
             pushd packages/$package
             hatch build
@@ -58,3 +58,9 @@ jobs:
         with:
           name: dist-applications-cattsunami
           path: dist-applications-cattsunami/*
+
+      - name: Upload data-omol artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist-data-omol
+          path: dist-data-omol/*

.github/workflows/perf-test.yml

@@ -4,8 +4,8 @@ on:
   workflow_call:
   workflow_dispatch:
   schedule:
-    # Run every night at midnight
-    - cron: "0 0 * * *"
+    # Run everyday at 8am UTC (midight or 1am pacific time)
+    - cron: "0 8 * * *"
 
 jobs:
   perf-test:

.github/workflows/release-drafter-data-omol.yml

@@ -0,0 +1,28 @@
+name: Release Drafter - fairchem-data-omol
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'src/fairchem/data/omol/**'
+      - 'packages/fairchem-data-omol/**'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+        # write permission is required to create a github release
+        contents: write
+        pull-requests: read
+    runs-on: ubuntu-latest
+    steps:
+      - uses: release-drafter/release-drafter@v6
+        with:
+          disable-autolabeler: true
+          config-name: release-drafter-data-omol.yml
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
   test:
     uses: ./.github/workflows/test.yml
     secrets: inherit
-  
+
   perf-test:
     uses: ./.github/workflows/perf-test.yml
     secrets: inherit
@@ -128,3 +128,28 @@ jobs:
           verbose: true
           packages-dir: dist-applications-cattsunami/
           skip-existing: true
+
+  release-data-omol:
+    needs: [ build ]
+    runs-on: ubuntu-latest
+    if: |
+      ( github.event.inputs.release-pypi == 'true' && startsWith(github.ref_name, 'fairchem_data_omol-') ) || startsWith(github.event.release.tag_name, 'fairchem_data_omol-')
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fairchem-data-omol/
+
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          name: dist-data-omol
+          path: dist-data-omol
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          packages-dir: dist-data-omol/
+          skip-existing: true

.github/workflows/test-release.yml

@@ -125,3 +125,29 @@ jobs:
           verbose: true
           packages-dir: dist-applications-cattsunami/
           skip-existing: true
+
+  release-data-omol:
+    needs: [ build ]
+    runs-on: ubuntu-latest
+    if: |
+      github.event.inputs.release-pypi == 'true' && startsWith(github.ref_name, 'fairchem_data_omol-')
+
+    environment:
+      name: test-pypi
+      url: https://test.pypi.org/p/fairchem-data-omol/
+
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          name: dist-data-omol
+          path: dist-data-omol
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+          packages-dir: dist-data-omol/
+          skip-existing: true

configs/uma/benchmark/omol-geom.yaml

@@ -0,0 +1,43 @@
+defaults:
+  - cluster: v100
+  - checkpoint: uma_sm
+  - _self_
+
+benchmark_name: geom_conformers
+
+job:
+  run_name: ${checkpoint.model_name}
+  run_dir: ${cluster.run_dir}
+  device_type: ${cluster.device}
+  debug: ${cluster.debug}
+  scheduler:
+    mode: ${cluster.mode}
+    distributed_init_method: FILE
+    num_array_jobs: 400
+    slurm:
+      partition: ${cluster.partition}
+      mem_gb: ${cluster.mem_gb}
+      timeout_hr: 72
+  logger:
+    _target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
+    _partial_: true
+    entity: fairchem
+    project: uma-benchmarks
+    group: ${checkpoint.model_name}
+    job_type: ${benchmark_name}
+
+runner:
+  _target_: fairchem.core.components.calculate.omol_runner.OMolRunner
+  calculator:
+    _target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
+    name_or_path: ${checkpoint.ckpt_path}
+    task_name: omol
+  input_data: ${cluster.data_root_dir}/conformer_inputs.pkl
+  benchmark_name: ${benchmark_name}
+  benchmark:
+    _target_: fairchem.core.components.calculate.recipes.omol.conformers
+    _partial_: True
+
+reducer:
+  _target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
+  benchmark_name: ${benchmark_name}

configs/uma/benchmark/omol-ieea.yaml

@@ -0,0 +1,43 @@
+defaults:
+  - cluster: v100
+  - checkpoint: uma_sm
+  - _self_
+
+benchmark_name: ie_ea
+
+job:
+  run_name: ${checkpoint.model_name}
+  run_dir: ${cluster.run_dir}
+  device_type: ${cluster.device}
+  debug: ${cluster.debug}
+  scheduler:
+    mode: ${cluster.mode}
+    distributed_init_method: FILE
+    num_array_jobs: 10
+    slurm:
+      partition: ${cluster.partition}
+      mem_gb: ${cluster.mem_gb}
+      timeout_hr: 72
+  logger:
+    _target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
+    _partial_: true
+    entity: fairchem
+    project: uma-benchmarks
+    group: ${checkpoint.model_name}
+    job_type: ${benchmark_name}
+
+runner:
+  _target_: fairchem.core.components.calculate.omol_runner.OMolRunner
+  calculator:
+    _target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
+    name_or_path: ${checkpoint.ckpt_path}
+    task_name: omol
+  input_data: ${cluster.data_root_dir}/ieea_inputs.pkl
+  benchmark_name: ${benchmark_name}
+  benchmark:
+    _target_: fairchem.core.components.calculate.recipes.omol.ieea
+    _partial_: True
+
+reducer:
+  _target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
+  benchmark_name: ${benchmark_name}

configs/uma/benchmark/omol-pocket.yaml

@@ -0,0 +1,43 @@
+defaults:
+  - cluster: v100
+  - checkpoint: uma_sm
+  - _self_
+
+benchmark_name: ligand_pocket
+
+job:
+  run_name: ${checkpoint.model_name}
+  run_dir: ${cluster.run_dir}
+  device_type: ${cluster.device}
+  debug: ${cluster.debug}
+  scheduler:
+    mode: ${cluster.mode}
+    distributed_init_method: FILE
+    num_array_jobs: 1
+    slurm:
+      partition: ${cluster.partition}
+      mem_gb: ${cluster.mem_gb}
+      timeout_hr: 72
+  logger:
+    _target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
+    _partial_: true
+    entity: fairchem
+    project: uma-benchmarks
+    group: ${checkpoint.model_name}
+    job_type: ${benchmark_name}
+
+runner:
+  _target_: fairchem.core.components.calculate.omol_runner.OMolRunner
+  calculator:
+    _target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
+    name_or_path: ${checkpoint.ckpt_path}
+    task_name: omol
+  input_data: ${cluster.data_root_dir}/ligand_pocket_inputs.pkl
+  benchmark_name: ${benchmark_name}
+  benchmark:
+    _target_: fairchem.core.components.calculate.recipes.omol.ligand_pocket
+    _partial_: True
+
+reducer:
+  _target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
+  benchmark_name: ${benchmark_name}

configs/uma/benchmark/omol-prot.yaml

@@ -0,0 +1,43 @@
+defaults:
+  - cluster: v100
+  - checkpoint: uma_sm
+  - _self_
+
+benchmark_name: protonation_energies
+
+job:
+  run_name: ${checkpoint.model_name}
+  run_dir: ${cluster.run_dir}
+  device_type: ${cluster.device}
+  debug: ${cluster.debug}
+  scheduler:
+    mode: ${cluster.mode}
+    distributed_init_method: FILE
+    num_array_jobs: 400
+    slurm:
+      partition: ${cluster.partition}
+      mem_gb: ${cluster.mem_gb}
+      timeout_hr: 72
+  logger:
+    _target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
+    _partial_: true
+    entity: fairchem
+    project: uma-benchmarks
+    group: ${checkpoint.model_name}
+    job_type: ${benchmark_name}
+
+runner:
+  _target_: fairchem.core.components.calculate.omol_runner.OMolRunner
+  calculator:
+    _target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
+    name_or_path: ${checkpoint.ckpt_path}
+    task_name: omol
+  input_data: ${cluster.data_root_dir}/protonation_inputs.pkl
+  benchmark_name: ${benchmark_name}
+  benchmark:
+    _target_: fairchem.core.components.calculate.recipes.omol.protonation
+    _partial_: True
+
+reducer:
+  _target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
+  benchmark_name: ${benchmark_name}