update dev branch with new CI

.pre-commit-config.yaml

@@ -4,25 +4,25 @@ fail_fast: true
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 24.1.1
     hooks:
       - id: black
 
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.10.1
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
 
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 5.0.1
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
     hooks:
       - id: flake8
         additional_dependencies: [ flake8-isort ]

.readthedocs.yaml

@@ -17,4 +17,4 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/source/conf.py
+   configuration: docs/source/conf.py

apax/cli/templates/train_config_full.yaml

@@ -11,7 +11,7 @@ data:
   #train_data_path: <PATH>
   #val_data_path: <PATH>
   #test_data_path: <PATH>
-  
+
   n_train: 1000
   n_valid: 100
 

apax/data/input_pipeline.py

@@ -134,14 +134,12 @@ def dataset_from_dicts(
     for key, val in labels["fixed"].items():
         labels["fixed"][key] = tf.constant(val)
 
-    ds = tf.data.Dataset.from_tensor_slices(
-        (
-            inputs["ragged"],
-            inputs["fixed"],
-            labels["ragged"],
-            labels["fixed"],
-        )
-    )
+    ds = tf.data.Dataset.from_tensor_slices((
+        inputs["ragged"],
+        inputs["fixed"],
+        labels["ragged"],
+        labels["fixed"],
+    ))
     return ds
 
 

apax/train/checkpoints.py

@@ -40,10 +40,7 @@ def create_single_train_state(params):
         return state
 
     if n_models > 1:
-        train_state_fn = jax.vmap(
-            create_single_train_state,
-            axis_name="ensemble"
-        )
+        train_state_fn = jax.vmap(create_single_train_state, axis_name="ensemble")
     else:
         train_state_fn = create_single_train_state
 
@@ -129,9 +126,7 @@ def load_params(model_version_path: Path, best=True) -> FrozenDict:
     try:
         # keep try except block for zntrack load from rev
         raw_restored = checkpoints.restore_checkpoint(
-            model_version_path,
-            target=None,
-            step=None
+            model_version_path, target=None, step=None
         )
     except FileNotFoundError:
         print(f"No checkpoint found at {model_version_path}")
@@ -143,8 +138,7 @@ def load_params(model_version_path: Path, best=True) -> FrozenDict:
 
 
 def restore_single_parameters(model_dir: Path) -> Tuple[Config, FrozenDict]:
-    """Load the config and parameters of a single model
-    """
+    """Load the config and parameters of a single model"""
     model_dir = Path(model_dir)
     model_config = parse_config(model_dir / "config.yaml")
 
@@ -200,6 +194,6 @@ def canonicalize_energy_grad_model_parameters(params):
 
     first_level = param_dict["params"]
     if "energy_model" not in first_level.keys():
-        params = {"params": {"energy_model" : first_level}}
+        params = {"params": {"energy_model": first_level}}
     params = freeze(params)
     return params

apax/train/trainer.py

@@ -109,12 +109,10 @@ def fit(
             epoch_loss["val_loss"] /= val_steps_per_epoch
             epoch_loss["val_loss"] = float(epoch_loss["val_loss"])
 
-            epoch_metrics.update(
-                {
-                    f"val_{key}": float(val)
-                    for key, val in val_batch_metrics.compute().items()
-                }
-            )
+            epoch_metrics.update({
+                f"val_{key}": float(val)
+                for key, val in val_batch_metrics.compute().items()
+            })
 
         epoch_metrics.update({**epoch_loss})
 

apax/utils/jax_md_reduced/README.md

@@ -17,4 +17,4 @@ We would like to thank the developers of `jax_md` for the work on this great pac
  volume = {33},
  year = {2020}
 }
-```
+```

docs/source/_tutorials/md_with_ase.rst

@@ -7,4 +7,4 @@ An ASE calculator of a trained model can be instantiated as follows
 
 CODE
 
-Please refer to the ASE documentation LINK to see how to use ASE calculators.
+Please refer to the ASE documentation LINK to see how to use ASE calculators.

docs/source/_tutorials/molecular_dynamics.rst

@@ -54,9 +54,6 @@ Congratulations, you have calculated the first observable from a trajectory gene
 
 ## Custom Simulation Loops
 
-More complex simulation loops are relatively easy to build yourself in JaxMD (see their colab notebooks for examples). 
+More complex simulation loops are relatively easy to build yourself in JaxMD (see their colab notebooks for examples).
 Trained apax models can of course be used as `energy_fn` in such custom simulations.
 If you have a suggestion for adding some MD feature or thermostat to the core of `apax`, feel free to open up an issue on Github LINK.
-
-
-

docs/source/_tutorials/training_a_model.rst

@@ -76,4 +76,4 @@ We provide a separate command for test set evaluation:
 
 TODO pretty print results to the terminal
 
-Congratulations, you have successfully trained and evaluated your fitrst apax model!
+Congratulations, you have successfully trained and evaluated your fitrst apax model!

docs/source/conf.py

@@ -37,4 +37,4 @@
 
 html_theme = "furo"
 
-html_theme_options = {}
+html_theme_options = {}

docs/source/getting_started/index.rst

@@ -4,4 +4,4 @@ Getting Started
 .. toctree::
    :maxdepth: 2
 
-   install
+   install

docs/source/getting_started/install.rst

@@ -47,4 +47,4 @@ If you want to enable GPU support, please overwrite the jaxlib version:
 See the `Jax installation instructions <https://github.com/google/jax#installation>`_ for more details.
 
 
-.. _Poetry: https://python-poetry.org/
+.. _Poetry: https://python-poetry.org/

docs/source/modules/md.rst

@@ -11,4 +11,4 @@ Molecular Dynamics
     :members:
 
 .. automodule:: apax.md.nvt
-    :members:
+    :members:

docs/source/modules/optimizer.rst

@@ -2,4 +2,4 @@ Optimizers
 ==========
 
 .. automodule:: apax.optimizer.get_optimizer
-    :members:
+    :members:

pyproject.toml

@@ -76,4 +76,3 @@ directory = "coverage_html_report"
 
 [tool.coverage.report]
 show_missing = true
-

tests/conftest.py

@@ -143,13 +143,11 @@ def modify_xyz_file(file_path, target_string, replacement_string):
 
 @pytest.fixture()
 def get_sample_input():
-    positions = np.array(
-        [
-            [1.0, 0.0, 0.0],
-            [0.0, 1.0, 0.0],
-            [0.0, 0.0, 1.0],
-        ]
-    )
+    positions = np.array([
+        [1.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0],
+        [0.0, 0.0, 1.0],
+    ])
     atomic_numbers = np.array([1, 1, 8])
     box = np.diag(np.zeros(3))
     offsets = np.full([3, 3], 0)

tests/integration_tests/bal/config.yaml

@@ -26,4 +26,4 @@ metrics:
 
 loss:
   - name: energy
-  - name: forces
+  - name: forces

tests/integration_tests/md/config.yaml

@@ -25,4 +25,4 @@ metrics:
 
 loss:
   - name: energy
-  - name: forces
+  - name: forces

tests/integration_tests/md/md_config.yaml

@@ -7,4 +7,4 @@ duration: 0.25
 n_inner: 1
 sampling_rate: 1
 checkpoint_interval: 2
-restart: True
+restart: True

tests/integration_tests/md/test_md.py

@@ -115,13 +115,11 @@ def test_ase_calc(get_tmp_path):
     model_config.dump_config(model_config.data.model_version_path)
 
     cell_size = 10.0
-    positions = np.array(
-        [
-            [1.0, 0.0, 0.0],
-            [0.0, 1.0, 0.0],
-            [0.0, 0.0, 1.0],
-        ]
-    )
+    positions = np.array([
+        [1.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0],
+        [0.0, 0.0, 1.0],
+    ])
     atomic_numbers = np.array([1, 1, 8])
     box = np.diag([cell_size] * 3)
     offsets = jnp.full([3, 3], 0)

tests/integration_tests/transfer_learning/config_base.yaml

@@ -26,4 +26,4 @@ optimizer:
   emb_lr: 0.001
   nn_lr: 0.001
   scale_lr: 0.0001
-  shift_lr: 0.001
+  shift_lr: 0.001

tests/integration_tests/transfer_learning/config_ft.yaml

@@ -29,4 +29,4 @@ optimizer:
   shift_lr: 0.001
 
 checkpoints:
-  base_model_checkpoint: null
+  base_model_checkpoint: null