add RobustL(1|2)Loss aliases for backwards compatibility

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.2.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -42,7 +42,7 @@ repos:
       - id: format-ipy-cells
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]

aviary/losses.py

@@ -34,3 +34,8 @@ def robust_l2_loss(pred_mean: Tensor, pred_log_std: Tensor, target: Tensor) -> T
     """
     loss = 0.5 * (pred_mean - target) ** 2 * torch.exp(-2 * pred_log_std) + pred_log_std
     return torch.mean(loss)
+
+
+# aliases for backwards compatibility
+RobustL1Loss = robust_l1_loss
+RobustL2Loss = robust_l2_loss

aviary/wrenformer/data.py

@@ -178,7 +178,7 @@ def df_to_in_mem_dataloader(
     for idx, tensor in enumerate(initial_embeddings):
         inputs[idx] = tensor.to(device)
 
-    ids = (df[id_col] if id_col in df else df.index).to_numpy()
+    ids = df.get(id_col, df.index).to_numpy()
     return InMemoryDataLoader(
         [inputs, targets, ids], collate_fn=collate_batch, **kwargs
     )

examples/notebooks/Roost.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +74,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,7 +135,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [

examples/notebooks/Wren.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -69,7 +69,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -130,7 +130,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": null,
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [

pyproject.toml

@@ -72,7 +72,7 @@ no_implicit_optional = false
 [tool.ruff]
 target-version = "py38"
 include = ["**/pyproject.toml", "*.ipynb", "*.py", "*.pyi"]
-select = [
+lint.select = [
   "B",    # flake8-bugbear
   "C4",   # flake8-comprehensions
   "D",    # pydocstyle
@@ -103,7 +103,7 @@ select = [
   "W",    # pycodestyle warning
   "YTT",  # flake8-2020
 ]
-ignore = [
+lint.ignore = [
   "C408",  # Unnecessary dict call - rewrite as a literal
   "D100",  # Missing docstring in public module
   "D104",  # Missing docstring in public package
@@ -114,9 +114,9 @@ ignore = [
   "PLR",   # pylint refactor
   "PT006", # pytest-parametrize-names-wrong-type
 ]
-pydocstyle.convention = "google"
-isort.known-third-party = ["wandb"]
+lint.pydocstyle.convention = "google"
+lint.isort.known-third-party = ["wandb"]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*" = ["D"]
 "examples/notebooks/*.py" = ["E402"]