update dependencies (#272)

* update dependencies

* fix `report_to`

* Update optimizer_config.schema.json

* fix ruff

* fix typing

* bump uv

* try to fix typing

* add more python versions

* up to 3.13

* up to 3.13

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

Author: Samoed

.github/workflows/build-docs.yaml

@@ -45,7 +45,7 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v6
         with:
-          version: "0.8.8"
+          version: "0.10.0"
 
       - name: Install dependencies
         run: |

.github/workflows/check-schema.yaml

@@ -19,7 +19,7 @@ jobs:
     - name: Install uv
       uses: astral-sh/setup-uv@v6
       with:
-        version: "0.8.8"
+        version: "0.10.0"
 
     - name: Install dependencies
       run: |

.github/workflows/reusable-test.yaml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13", ]
         include:
           - os: windows-latest
             python-version: "3.10"
@@ -34,7 +34,7 @@ jobs:
     - name: Install uv
       uses: astral-sh/setup-uv@v6
       with:
-        version: "0.8.8"
+        version: "0.10.0"
 
     - name: Install dependencies for Python ${{ matrix.python-version }}
       run: |

.github/workflows/ruff.yml

@@ -7,4 +7,4 @@ jobs:
       - uses: actions/checkout@v4
       - uses: astral-sh/ruff-action@v2
         with:
-          version: "0.8.4"
+          version: "0.15.0"

.github/workflows/typing.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v6
         with:
-          version: "0.8.8"
+          version: "0.10.0"
 
       - name: Install dependencies
         run: |

docs/optimizer_config.schema.json

@@ -393,7 +393,8 @@
                                 "enum": [
                                     "wandb",
                                     "tensorboard",
-                                    "codecarbon"
+                                    "codecarbon",
+                                    "none"
                                 ],
                                 "type": "string"
                             },
@@ -403,7 +404,9 @@
                             "type": "null"
                         }
                     ],
-                    "default": null,
+                    "default": [
+                        "none"
+                    ],
                     "description": "List of callbacks to report to. If None, no callbacks will be used",
                     "title": "Report To"
                 },
@@ -489,7 +492,9 @@
                 "run_name": null,
                 "dump_modules": false,
                 "clear_ram": false,
-                "report_to": null,
+                "report_to": [
+                    "none"
+                ],
                 "log_interval_time": 0.1
             }
         },

docs/source/docs_utils/versions_generator.py

@@ -12,7 +12,7 @@
 def get_sorted_versions(repo_root: Path, base_url: str) -> list[dict]:
     os.chdir(repo_root)
     # Fetch tags and branches
-    tags_output = subprocess.check_output(["git", "tag"], text=True).strip().split("\n")  # noqa: S603, S607
+    tags_output = subprocess.check_output(["git", "tag"], text=True).strip().split("\n")  # noqa: S607
     tag_regex = re.compile(r"^v\d+\.\d+\.\d+$")  # Matches tags like v0.0.1
     tags = [tag for tag in tags_output if tag_regex.match(tag)]
 
@@ -37,7 +37,7 @@ def get_sorted_versions(repo_root: Path, base_url: str) -> list[dict]:
         versions.append({"version": tag, "url": f"{base_url}/{tag}/"})  # noqa: PERF401
 
     # Get branches
-    branches_output = subprocess.check_output(["git", "branch", "-r"], text=True).strip().split("\n")  # noqa: S603, S607
+    branches_output = subprocess.check_output(["git", "branch", "-r"], text=True).strip().split("\n")  # noqa: S607
     dev_branches = [
         branch.strip().split("/")[-1] for branch in branches_output if "origin/dev" in branch and "HEAD" not in branch
     ]

pyproject.toml

@@ -29,9 +29,9 @@ classifiers=[
     'Framework :: Sphinx',
     'Typing :: Typed',
 ]
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.10,<3.14"
 dependencies = [
-    "sentence-transformers (>=3,<4)",
+    "sentence-transformers (>=3,<6)",
     "scikit-learn (>=1.5,<2.0)",
     "scikit-multilearn (==0.2.0)",
     "appdirs (>=1.4,<2.0)",
@@ -40,10 +40,10 @@ dependencies = [
     "pydantic (>=2.10.5,<3.0.0)",
     "faiss-cpu (>=1.9.0,<2.0.0)",
     "openai (>=1.59.6,<2.0.0)",
-    "datasets (>=3.2.0,<4.0.0)",
+    "datasets (>=3.2.0,<5.0.0)",
     "xxhash (>=3.5.0,<4.0.0)",
     "python-dotenv (>=1.0.1,<2.0.0)",
-    "transformers[torch] (>=4.49.0,<5.0.0)",
+    "transformers[torch] (>=4.49.0,<6.0.0)",
     "peft (>= 0.10.0, !=0.15.0, !=0.15.1, <1.0.0)",
     "catboost (>=1.2.8,<2.0.0)",
     "aiometer (>=1.0.0,<2.0.0)",
@@ -89,7 +89,7 @@ nb = [
     "ipywidgets (>=8.1.5,<9.0.0)",
 ]
 lint = [
-    "ruff (==0.8.4)",
+    "ruff (==0.15.0)",
 ]
 sentencepiece = [
     "sentencepiece (>=0.2.0,<0.3.0)",
@@ -156,6 +156,7 @@ ignore = [
     "ERA001",  # commented code
     "FBT",     # boolean trap
     "RUF001",  # ambiguous unicode character
+    "PLC0415",  # import outside top-level
 ]
 
 [tool.ruff.lint.per-file-ignores]

src/autointent/_callbacks/__init__.py

@@ -8,7 +8,7 @@
 
 REPORTERS = {cb.name: cb for cb in [WandbCallback, TensorBoardCallback, EmissionsTrackerCallback]}
 
-REPORTERS_NAMES = Literal[tuple(REPORTERS.keys())]  # type: ignore[valid-type]
+REPORTERS_NAMES = Literal[(*tuple(REPORTERS.keys()), "none")]  # type: ignore[valid-type]
 
 
 def get_callbacks(reporters: list[str] | None) -> CallbackHandler:
@@ -25,6 +25,8 @@ def get_callbacks(reporters: list[str] | None) -> CallbackHandler:
 
     reporters_cb = []
     for reporter in reporters:
+        if reporter == "none":
+            continue
         if reporter not in REPORTERS:
             msg = f"Reporter {reporter} not supported. Supported reporters {','.join(REPORTERS)}"
             raise ValueError(msg)

src/autointent/_callbacks/tensorboard.py

@@ -53,11 +53,11 @@ def start_module(self, module_name: str, num: int, module_kwargs: dict[str, Any]
         """
         module_run_name = f"{self.run_name}_{module_name}_{num}"
         log_dir = Path(self.dirpath) / module_run_name
-        self.module_writer = self.writer(log_dir=log_dir)  # type: ignore[no-untyped-call]
+        self.module_writer = self.writer(log_dir=log_dir)
 
-        self.module_writer.add_text("module_info", f"Starting module {module_name}_{num}")  # type: ignore[no-untyped-call]
+        self.module_writer.add_text("module_info", f"Starting module {module_name}_{num}")
         for key, value in module_kwargs.items():
-            self.module_writer.add_text(f"module_params/{key}", str(value))  # type: ignore[no-untyped-call]
+            self.module_writer.add_text(f"module_params/{key}", str(value))
 
     def log_value(self, **kwargs: dict[str, int | float | Any]) -> None:
         """Logs scalar or text values.
@@ -69,7 +69,7 @@ def log_value(self, **kwargs: dict[str, int | float | Any]) -> None:
             if isinstance(value, int | float):
                 self.module_writer.add_scalar(key, value)
             else:
-                self.module_writer.add_text(key, str(value))  # type: ignore[no-untyped-call]
+                self.module_writer.add_text(key, str(value))
 
     def log_metrics(self, metrics: dict[str, Any]) -> None:
         """Logs training metrics.
@@ -79,9 +79,9 @@ def log_metrics(self, metrics: dict[str, Any]) -> None:
         """
         for key, value in metrics.items():
             if isinstance(value, int | float):
-                self.module_writer.add_scalar(key, value)  # type: ignore[no-untyped-call]
+                self.module_writer.add_scalar(key, value)
             else:
-                self.module_writer.add_text(key, str(value))  # type: ignore[no-untyped-call]
+                self.module_writer.add_text(key, str(value))
 
     def log_final_metrics(self, metrics: dict[str, Any]) -> None:
         """Logs final metrics at the end of training.
@@ -97,13 +97,13 @@ def log_final_metrics(self, metrics: dict[str, Any]) -> None:
             raise RuntimeError(msg)
 
         log_dir = Path(self.dirpath) / "final_metrics"
-        self.module_writer = self.writer(log_dir=log_dir)  # type: ignore[no-untyped-call]
+        self.module_writer = self.writer(log_dir=log_dir)
 
         for key, value in metrics.items():
             if isinstance(value, int | float):
-                self.module_writer.add_scalar(key, value)  # type: ignore[no-untyped-call]
+                self.module_writer.add_scalar(key, value)
             else:
-                self.module_writer.add_text(key, str(value))  # type: ignore[no-untyped-call]
+                self.module_writer.add_text(key, str(value))
 
     def end_module(self) -> None:
         """Ends the current module and closes the TensorBoard writer.
@@ -115,8 +115,8 @@ def end_module(self) -> None:
             msg = "start_run must be called before end_module."
             raise RuntimeError(msg)
 
-        self.module_writer.add_text("module_info", "Ending module")  # type: ignore[no-untyped-call]
-        self.module_writer.close()  # type: ignore[no-untyped-call]
+        self.module_writer.add_text("module_info", "Ending module")
+        self.module_writer.close()
 
     def end_run(self) -> None:
         """Ends the current run. This method is currently a placeholder."""