Improve query ops API, update deps (#477)

.github/workflows/docs_build.yml

@@ -38,6 +38,17 @@ jobs:
           # pandoc README.md -f markdown -t rst -s -o docs/source/intro.rst
           cd docs && rm -rf source/reference/api/_autosummary && make html
           cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m
+      - name: Upload coverage to Codecov
+        uses: Wandalen/wretry.action@v1.0.36
+        with:
+          action: codecov/codecov-action@v3.1.3
+          with: |
+            token: ${{ secrets.CODECOV_TOKEN }}
+            file: ./coverage.xml
+            name: codecov-umbrella
+            fail_ci_if_error: true
+          attempt_limit: 5
+          attempt_delay: 30000
       - uses: actions/setup-node@v3
         with:
           node-version: 18

.github/workflows/integration_tests.yml

@@ -51,7 +51,6 @@ jobs:
           poetry install --without dev,docs,interface
           coverage run -m pytest -m integration_test && coverage xml && coverage report -m
       - name: Upload coverage to Codecov
-        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
         uses: Wandalen/wretry.action@v1.0.36
         with:
           action: codecov/codecov-action@v3.1.3

codecov.yml

@@ -0,0 +1,22 @@
+codecov:
+  after_n_builds: 2
+  require_ci_to_pass: true
+comment:
+  behavior: default
+  layout: reach,diff,flags,tree,reach
+  show_carryforward_flags: false
+  require_changes: true
+coverage:
+  precision: 2
+  range:
+  - 55.0
+  - 100.0
+  round: down
+  status:
+    changes: true
+    default_rules:
+      flag_coverage_not_uploaded_behavior: include
+    patch: true
+    project: true
+github_checks:
+  annotations: true

cyclops/evaluate/metrics/utils.py

@@ -135,7 +135,7 @@ def common_input_checks_and_format(
 def sigmoid(arr: npt.ArrayLike) -> npt.NDArray[np.float_]:
     """Sigmoid function."""
     arr = np.asanyarray(arr)
-    return 1 / (1 + np.exp(-arr))
+    return 1 / (1 + np.exp(-arr))  # type: ignore
 
 
 def check_topk(top_k: int, type_preds: str, type_target: str, n_classes: int) -> None:

cyclops/monitor/utils.py

@@ -373,23 +373,26 @@ def __init__(
         x_ref_preprocessed: bool = False,
         preprocess_at_init: bool = True,
         update_x_ref: Optional[Dict[str, int]] = None,
-        preprocess_fn: Optional[Callable[..., Any]] = None,
+        preprocess_fn: Optional[Callable] = None,
         n_permutations: int = 100,
+        batch_size_permutations: int = 1000000,
         var_reg: float = 1e-5,
-        reg_loss_fn: Callable[..., Any] = (lambda kernel: 0),
+        reg_loss_fn: Callable = (lambda kernel: 0),
         train_size: Optional[float] = 0.75,
         retrain_from_scratch: bool = True,
-        optimizer: Optional[Callable[..., Any]] = None,
+        optimizer: Optional[Callable] = None,
         learning_rate: float = 1e-3,
         batch_size: int = 32,
-        preprocess_batch_fn: Optional[Callable[..., Any]] = None,
+        batch_size_predict: int = 32,
+        preprocess_batch_fn: Optional[Callable] = None,
         epochs: int = 3,
+        num_workers: int = 0,
         verbose: int = 0,
-        train_kwargs: Optional[Dict[str, Any]] = None,
-        device: Optional[str] = None,
-        dataset: Optional[Callable[..., Any]] = None,
-        dataloader: Optional[Callable[..., Any]] = None,
-        input_shape: Optional[Tuple[int, ...]] = None,
+        train_kwargs: Optional[dict] = None,
+        device: str = None,
+        dataset: Optional[Callable] = None,
+        dataloader: Optional[Callable] = None,
+        input_shape: Optional[tuple] = None,
         data_type: Optional[str] = None,
         kernel_a: Optional[nn.Module] = None,
         kernel_b: Optional[nn.Module] = None,
@@ -411,15 +414,18 @@ def __init__(
             update_x_ref,
             preprocess_fn,
             n_permutations,
+            batch_size_permutations,
             var_reg,
             reg_loss_fn,
             train_size,
             retrain_from_scratch,
             optimizer,
             learning_rate,
             batch_size,
+            batch_size_predict,
             preprocess_batch_fn,
             epochs,
+            num_workers,
             verbose,
             train_kwargs,
             device,

cyclops/query/interface.py

@@ -25,7 +25,7 @@ class QueryInterface:
 
     Parameters
     ----------
-    database: cyclops.orm.Database
+    database
         Database object to create ORM, and query data.
     query: cyclops.query.util.TableTypes
         The query.