update package dependencies

Author: n-gao

.github/workflows/precommit.yaml

@@ -16,6 +16,8 @@ jobs:
         with:
           version: "0.4.20"
           enable-cache: true
+      - name: Setup virtual environment
+        run: uv sync
       - name: Install pre-commit
         run: uv tool install pre-commit --with pre-commit-uv
       - name: Run pre-commit

.pre-commit-config.yaml

@@ -1,13 +1,6 @@
 repos:
-  - repo: local
-    hooks:
-      - id: sync-dependencies
-        name: update pre-commit-config
-        entry: uv run ci/scripts/pre_commit_sync_pyright_deps.py
-        language: system
-        files: "(pyproject.toml|scripts/.pre-commit-config.yaml.template|.pre-commit.config.yaml)" # the quotes are here to make sure that this stay in line for the formatter.
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-case-conflict
       - id: check-toml
@@ -20,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: trailing-whitespace
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
         name: pyupgrade
@@ -31,47 +24,20 @@ repos:
         args: [--py38-plus, --keep-runtime-typing]
         files: .*\/__main__.py # We run ruff after pyugprade to remove unused imports
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1
+    rev: v0.14.6
     hooks:
       - id: ruff # Run the linter.
         args: [--fix]
       - id: ruff # Sort improts
         name: sort imports with ruff
         args: [--select, I, --fix]
       - id: ruff-format # Run the formatter.
-  - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.377
+  - repo: local # Run pyright type checker
     hooks:
       - id: pyright
-        additional_dependencies: # these dependencies are synced via the first hook
-          - numpy>=1.15; python_version < '3.13'
-          - numpy>=2.1; python_version >= '3.13'
-          - pymongo>=4.1
-          - pandas>=2.2; python_version < '3.13'
-          - pandas>=2.2.3; python_version >= '3.13'
-          - sacred>=0.8.4
-          - pyyaml>=5.1
-          - jsonpickle>=2.2
-          - munch>=4.0
-          - debugpy>=1.2.1
-          - requests>=2.28.1
-          - typer>=0.12
-          - rich>=13.0,<14.1
-          - click>=8.0
-          - omegaconf>=2.3.0
-          - gitignore_parser>=0.1.11
-          - setuptools>=69.2.0
-          - importlib_resources>=5.7.0
-          - typing_extensions>=4.10; python_version < '3.13'
-          - typing_extensions>=4.12; python_version >= '3.13'
-          - deepdiff>=7.0.1
-          - ruff>=0.6.1
-          - pytest>=8.3.2
-          - pre-commit>=3.8.0
-          - filelock>=3.15.4
-          - sshtunnel>=0.4.0
-          - build>=1.2.1
-          - twine>=5.1.1
-          - backports-tarfile>=1.2.0
-          - tuna>=0.5.11
-        files: src/seml/.*\.py
+        name: pyright check
+        entry: uv run pyright src/
+        language: system
+        types: [python]
+        pass_filenames: false
+        always_run: true

ci/scripts/pre_commit_sync_pyright_deps.py

@@ -290,7 +290,7 @@
     "for i, exp in results.iterrows():\n",
     "    plt.plot(\n",
     "        exp[\"result.test_acc\"],\n",
-    "        label=f'{exp[\"config.hidden_sizes\"]} {exp[\"config.learning_rate\"]}',\n",
+    "        label=f\"{exp['config.hidden_sizes']} {exp['config.learning_rate']}\",\n",
     "    )\n",
     "plt.legend()\n",
     "plt.show()"

examples/tutorial/intro_slides.ipynb

@@ -50,7 +50,7 @@ dev = [
     "filelock>=3.15.4",
     "sshtunnel>=0.4.0",
 ]
-ssh_forward = ["sshtunnel>=0.4.0", "filelock>=3.13.3"]
+ssh_forward = ["sshtunnel>=0.4.0", "filelock>=3.13.3", "paramiko>=3.0,<4.0"]
 
 [project.urls]
 Homepage = "https://github.com/TUM-DAML/seml"
@@ -76,6 +76,7 @@ dev-dependencies = [
     "twine>=5.1.1",
     "backports-tarfile>=1.2.0",
     "tuna>=0.5.11",
+    "pyright>=1.1.407",
 ]
 
 [tool.ruff.format]
@@ -84,3 +85,5 @@ line-ending = "lf"
 
 [tool.pyright]
 typeCheckingMode = "standard"
+venvPath = "."
+venv = ".venv"

pyproject.toml

@@ -16,9 +16,9 @@
     TypeVar,
 )
 
+import typer
 from typing_extensions import Annotated, ParamSpec
 
-import seml.cli_utils.typer as typer
 from seml.cli_utils import AUTOCOMPLETING, cache_to_disk
 from seml.cli_utils.cli_states import CliStates as States
 from seml.document import SBatchOptions
@@ -196,7 +196,7 @@ def parse_optional_str_list(values: Optional[Sequence[str]]) -> List[str]:
     typer.Option(
         '-n',
         '--num-experiments',
-        help='Number of experiments to start. ' '0: all (staged) experiments ',
+        help='Number of experiments to start. 0: all (staged) experiments ',
     ),
 ]
 NoFileOutputAnnotation = Annotated[

src/seml/__main__.py

@@ -113,7 +113,7 @@ def add_configs(
         start_id = start_id + 1
 
     logging.info(
-        f"Adding {len(documents)} configs to the database (batch-ID {documents[0]['batch_id']})."
+        f'Adding {len(documents)} configs to the database (batch-ID {documents[0]["batch_id"]}).'
     )
 
     documents = [

src/seml/cli_utils/typer.py

@@ -65,8 +65,8 @@ def mongodb_configure(
         config['ssh_config'] = prompt_ssh_forward()
     config_string = yaml.dump(config)
     logging.info(
-        f"Saving the following configuration to {file_path}:\n"
-        f"{config_string.replace(f'{password}', '********')}"
+        f'Saving the following configuration to {file_path}:\n'
+        f'{config_string.replace(f"{password}", "********")}'
     )
     file_path.parent.mkdir(parents=True, exist_ok=True)
     with open(file_path, 'w') as f:

src/seml/commands/add.py

@@ -180,7 +180,7 @@ def cancel_experiment_by_id(
     # check if the job has been claimed and associated with a concrete job
     is_running = 'array_id' in exp['execution']
     if is_running:
-        job_strings = [f"{exp['execution']['array_id']}_{exp['execution']['task_id']}"]
+        job_strings = [f'{exp["execution"]["array_id"]}_{exp["execution"]["task_id"]}']
     else:
         job_strings = list(map(str, array_ids))
 
@@ -710,7 +710,7 @@ def detect_killed(db_collection_name: str, print_detected: bool = True):
                         # If the experiment is canceled before starting (e.g. when still queued), there is not output file.
                         logging.debug(f'File {output_file} could not be read.')
                 else:
-                    logging.debug(f"Output file not found in experiment {exp['_id']}.")
+                    logging.debug(f'Output file not found in experiment {exp["_id"]}.')
     updates = [
         UpdateMany(
             {'_id': {'$in': interrupted_exps}},