Merge branch 'main' into spookynet

choderalab · Nov 10, 2024 · b28d660 · b28d660
2 parents 57e7b49 + 426171a
commit b28d660
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diff --git a/.codecov.yml b/.codecov.yml
@@ -4,7 +4,8 @@ coverage:
     patch: false
     project:
       default:
-        threshold: 50%
+        target: 90%
+        threshold: 5%
 comment:
   layout: "header"
   require_changes: false

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,12 +1,19 @@
-## Description
+## Pull Request Summary
 Provide a brief description of the PR's purpose here.
 
-## Todos
+### Key changes
 Notable points that this PR has either accomplished or will accomplish.
-  - [ ] TODO 1
+ - [ ] Change 1
 
-## Questions
-- [ ] Question1
+### Questions
+ - [ ] Question 1
 
-## Status
-- [ ] Ready to go
+### Associated Issue(s)
+ - [ ] Issue 1
+
+## Pull Request Checklist
+ - [ ] Issue(s) raised/addressed and linked
+ - [ ] Includes appropriate unit test(s)
+ - [ ] Appropriate docstring(s) added/updated
+ - [ ] Appropriate .rst doc file(s) added/updated
+ - [ ] PR is ready for review
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -35,6 +35,11 @@ jobs:
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: ["3.10", "3.11"]
+        include:
+          - os: ubuntu-latest
+            n_procs: auto
+          - os: macOS-latest
+            n_procs: 0
 
     steps:
       - uses: actions/checkout@v3
@@ -73,12 +78,15 @@ jobs:
       - name: Run tests
         # conda setup requires this special shell
         run: |
-          pytest -v --cov=modelforge --cov-report=xml --color=yes --durations=10 modelforge/tests/
+          pytest -n ${{matrix.n_procs}} --dist loadgroup -v --cov=modelforge --cov-report=xml --color=yes --durations=50 modelforge/tests/
 
       - name: CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ github.event != 'schedule' }}  # Don't upload results on scheduled runs
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           flags: unittests
           name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -0,0 +1,19 @@
+name: Lint
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+        with:
+          options: "--check --verbose --line-length 88"
+          src: "./modelforge"
diff --git a/.gitignore b/.gitignore
@@ -182,61 +182,15 @@ $RECYCLE.BIN/
 *.lnk
 
 # End of https://www.toptal.com/developers/gitignore/api/osx,windows,linux
-qm9tut/
 lightning_logs/
 
 
 *.gz
 *.npz
 *.hdf5
-scripts/tb_logs/*
-notebooks/tb_logs/training/version_0/events.out.tfevents.1712567395.fedora.24017.0
-notebooks/tb_logs/training/version_0/hparams.yaml
-notebooks/tb_logs/training/version_0/checkpoints/epoch=0-step=210.ckpt
-notebooks/tb_logs/training/version_1/events.out.tfevents.1712567945.fedora.24017.1
-notebooks/tb_logs/training/version_1/hparams.yaml
-notebooks/tb_logs/training/version_1/checkpoints/epoch=4-step=1050.ckpt
-notebooks/tb_logs/training/version_10/events.out.tfevents.1713300058.fedora.156712.0
-notebooks/tb_logs/training/version_10/hparams.yaml
-notebooks/tb_logs/training/version_10/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_11/events.out.tfevents.1713300137.fedora.157775.0
-notebooks/tb_logs/training/version_11/hparams.yaml
-notebooks/tb_logs/training/version_11/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_12/events.out.tfevents.1713300163.fedora.158807.0
-notebooks/tb_logs/training/version_12/hparams.yaml
-notebooks/tb_logs/training/version_12/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_13/events.out.tfevents.1713300213.fedora.159869.0
-notebooks/tb_logs/training/version_13/hparams.yaml
-notebooks/tb_logs/training/version_13/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_14/events.out.tfevents.1713300437.fedora.161554.0
-notebooks/tb_logs/training/version_14/hparams.yaml
-notebooks/tb_logs/training/version_14/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_15/events.out.tfevents.1713301163.fedora.166274.0
-notebooks/tb_logs/training/version_15/hparams.yaml
-notebooks/tb_logs/training/version_15/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_16/events.out.tfevents.1715177168.fedora.59344.0
-notebooks/tb_logs/training/version_16/events.out.tfevents.1715177661.fedora.59344.1
-notebooks/tb_logs/training/version_16/events.out.tfevents.1715177672.fedora.59344.2
-notebooks/tb_logs/training/version_16/events.out.tfevents.1715177678.fedora.59344.3
-notebooks/tb_logs/training/version_16/hparams.yaml
-notebooks/tb_logs/training/version_2/events.out.tfevents.1712569996.fedora.33244.0
-notebooks/tb_logs/training/version_3/events.out.tfevents.1712570094.fedora.33244.1
-notebooks/tb_logs/training/version_3/hparams.yaml
-notebooks/tb_logs/training/version_4/events.out.tfevents.1712570244.fedora.33244.2
-notebooks/tb_logs/training/version_4/hparams.yaml
-notebooks/tb_logs/training/version_4/checkpoints/epoch=4-step=1050.ckpt
-notebooks/tb_logs/training/version_5/events.out.tfevents.1713272484.fedora.65117.0
-notebooks/tb_logs/training/version_5/hparams.yaml
-notebooks/tb_logs/training/version_5/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_6/events.out.tfevents.1713273578.fedora.65117.1
-notebooks/tb_logs/training/version_6/hparams.yaml
-notebooks/tb_logs/training/version_6/checkpoints/epoch=99-step=100.ckpt
-notebooks/tb_logs/training/version_7/events.out.tfevents.1713273988.fedora.65117.2
-notebooks/tb_logs/training/version_7/hparams.yaml
-notebooks/tb_logs/training/version_7/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_8/events.out.tfevents.1713274608.fedora.85750.0
-notebooks/tb_logs/training/version_8/hparams.yaml
-notebooks/tb_logs/training/version_8/checkpoints/epoch=4-step=5.ckpt
-notebooks/tb_logs/training/version_9/events.out.tfevents.1713299697.fedora.154578.0
-notebooks/tb_logs/training/version_9/hparams.yaml
-notebooks/tb_logs/training/version_9/checkpoints/epoch=4-step=5.ckpt
+*/tb_logs/*
+.vscode/settings.json
+logs/*
+cache/*
+*/logs/*
+*/cache/*
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -10,7 +10,7 @@ sphinx:
   fail_on_warning: true
 
 conda:
-  environment: devtools/conda-envs/doc_env.yaml
+  environment: devtools/conda-envs/docs_env.yaml
 
 python:
   # Install our python package before building the docs

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1,8 @@
 include CODE_OF_CONDUCT.md
 
+include modelforge/dataset/yaml_files/*.yaml
+include modelforge/curation/yaml_files/*.yaml
+include modelforge/tests/data/potential_defaults/*.toml
+include modelforge/tests/data/training_defaults/*.toml
+
 global-exclude *.py[cod] __pycache__ *.so
diff --git a/README.md b/README.md
@@ -3,6 +3,7 @@ modelforge
 [//]: # (Badges)
 [![CI](https://github.com/choderalab/modelforge/actions/workflows/CI.yaml/badge.svg)](https://github.com/choderalab/modelforge/actions/workflows/CI.yaml)
 [![codecov](https://codecov.io/gh/choderalab/modelforge/branch/main/graph/badge.svg)](https://codecov.io/gh/choderalab/modelforge/branch/main)
+[![Documentation Status](https://readthedocs.org/projects/modelforge/badge/?version=latest)](https://modelforge.readthedocs.io/en/latest/?badge=latest)
 [![Github release](https://badgen.net/github/release/choderalab/modelforge)](https://github.com/choderalab/modelforge/)
 [![GitHub license](https://img.shields.io/github/license/choderalab/modelforge?color=green)](https://github.com/choderalab/modelforge/blob/main/LICENSE)
 [![GitHub issues](https://img.shields.io/github/issues/choderalab/modelforge?style=flat)](https://github.com/choderalab/modelforge/issues)

diff --git a/devtools/conda-envs/doc_env.yaml → devtools/conda-envs/docs_env.yaml b/devtools/conda-envs/doc_env.yaml → devtools/conda-envs/docs_env.yaml
@@ -8,7 +8,7 @@ dependencies:
   - pip
   - h5py
   - tqdm
-  - qcelemental=0.25.1
+  - qcelemental
   - qcportal>=0.50
   - pytorch>=2.1
   - loguru
@@ -21,6 +21,8 @@ dependencies:
   - rdkit
   - retry
   - sqlitedict
+  - pydantic>=2
+  - ray-all
 
   # Testing
   - pytest>=2.1
@@ -36,5 +38,6 @@ dependencies:
       - jax
       - flax
       - pytorch2jax
+      #- "ray[data,train,tune,serve]"
       - git+https://github.com/ArnNag/sake.git@nanometer
-      - "ray[data,train,tune,serve]"
+      - torchviz2
diff --git a/devtools/conda-envs/env.yaml b/devtools/conda-envs/env.yaml
@@ -0,0 +1,27 @@
+name: modelforge_env
+channels:
+  - conda-forge
+  - pytorch
+dependencies:
+  # Base depends
+  - python
+  - pip
+  - h5py
+  - tqdm
+  - toml
+  - qcportal>=0.50
+  - qcelemental
+  - pytorch>=2.1
+  - loguru
+  - lightning>=2.0.8
+  - tensorboard
+  - torchvision
+  - openff-units
+  - torchmetrics>=1.4
+  - pint=0.23
+  - rdkit
+  - retry
+  - sqlitedict
+  - pydantic>=2
+  - ray-all
+  - jax
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -8,19 +8,23 @@ dependencies:
   - pip
   - h5py
   - tqdm
-  - qcelemental=0.25.1
+  - toml
   - qcportal>=0.50
+  - qcelemental
   - pytorch>=2.1
   - loguru
   - lightning>=2.0.8
   - tensorboard
   - torchvision
   - openff-units
   - torchmetrics>=1.4
-  - pint
+  - pint=0.23
   - rdkit
   - retry
   - sqlitedict
+  - pydantic>=2
+  - ray-all
+  - graphviz
 
   # Testing
   - pytest>=2.1
@@ -29,11 +33,12 @@ dependencies:
   - requests
   - versioneer
 
-  # Docs
-  - sphinx_rtd_theme
-
   - pip:
+      - jax
+      - flax
       - pytorch2jax
       - git+https://github.com/ArnNag/sake.git@nanometer
-      - "ray[data,train,tune,serve]"
       - flax
+      - torch
+      - pytest-xdist
+
diff --git a/devtools/conda-envs/test_env_mac.yaml b/devtools/conda-envs/test_env_mac.yaml
@@ -9,8 +9,8 @@ dependencies:
   - pip
   - h5py
   - tqdm
-  - qcelemental=0.25.1
   - qcportal>=0.50
+  - qcelemental
   - pytorch>=2.1
   - loguru
   - lightning>=2.0.8
@@ -23,6 +23,9 @@ dependencies:
   - sqlitedict
   - jax
   - flax
+  - pydantic>=2.0
+  - graphviz
+  -
 
   # Testing
   - pytest>=2.1
@@ -31,12 +34,10 @@ dependencies:
   - requests
   - versioneer
 
-  # Docs
-  - sphinx_rtd_theme
-
   # pip installs
   - pip:
       - pytorch2jax
       - git+https://github.com/ArnNag/sake.git@nanometer
       - jax
       - flax
+      - pytest-xdist
diff --git a/docs/_static/README.md b/docs/_static/README.md
diff --git a/docs/_static/test.txt b/docs/_static/test.txt
@@ -0,0 +1 @@
+test
diff --git a/docs/_templates/README.md b/docs/_templates/README.md
diff --git a/docs/api.rst b/docs/api.rst
@@ -2,6 +2,11 @@ API Documentation
 =================
 
 .. autosummary::
-   :toctree: autosummary
+    :toctree: autosummary
+    :recursive:
+
+    modelforge.potential
+    modelforge.dataset
+    modelforge.utils
+    modelforge.curation
 
-   modelforge.canvas