snk-cli 0.7.1__tar.gz → 0.7.2__tar.gz

snk_cli-0.7.2/.github/workflows/tests.yml

@@ -0,0 +1,64 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches:
+      - "*"
+
+permissions:
+  contents: write
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, "3.10", 3.11, 3.12]
+        snakemake-version: ["==7.32.4", ">8"]
+        exclude:
+          # Exclude incompatible combinations
+          - python-version: 3.8
+            snakemake-version: ">8"
+          - python-version: 3.9
+            snakemake-version: ">8"
+          - python-version: "3.10"
+            snakemake-version: ">8"
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-activate-base: false
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+
+      - name: Install pip dependencies
+        run: |
+          pip install hatch
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y llvm clang build-essential graphviz
+
+      - name: Run tests
+        env:
+          AR: /usr/bin/ar
+        shell: bash
+        run: |
+          hatch python install ${{ matrix.python-version }}
+          hatch --env "snakemake.py${{ matrix.python-version }}-${{ matrix.snakemake-version }}" run cov
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          flags: ${{ matrix.python-version }}-snakemake-${{ matrix.snakemake-version }}

{snk_cli-0.7.1 → snk_cli-0.7.2}/PKG-INFO

@@ -1,11 +1,12 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: snk-cli
-Version: 0.7.1
+Version: 0.7.2
 Project-URL: Documentation, https://github.com/wytamma/snk-cli#readme
 Project-URL: Issues, https://github.com/wytamma/snk-cli/issues
 Project-URL: Source, https://github.com/wytamma/snk-cli
 Author-email: Wytamma Wirth <wytamma.wirth@me.com>
-License: MIT
+License-Expression: MIT
+License-File: LICENSE.txt
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3.8

{snk_cli-0.7.1 → snk_cli-0.7.2}/pyproject.toml

@@ -45,7 +45,12 @@ path = "src/snk_cli/__about__.py"
 
 
 [[tool.hatch.envs.snakemake.matrix]]
-snakemake = ["==7.32.4", ">8"]
+snakemake = ["==7.32.4"]  # Compatible with Python 3.9–3.12
+python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+[[tool.hatch.envs.snakemake.matrix]]
+snakemake = [">8"]  # Compatible only with Python 3.11 and 3.12
+python = ["3.11", "3.12"]
 
 [tool.hatch.envs.default]
 dependencies = [
@@ -66,7 +71,7 @@ cov = [
 ]
 
 [[tool.hatch.envs.all.matrix]]
-python = ["3.9", "3.10", "3.11", "3.12"]
+python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
 [tool.hatch.envs.types]
 dependencies = [

{snk_cli-0.7.1 → snk_cli-0.7.2}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.7.1"
+__version__ = "0.7.2"

{snk_cli-0.7.1 → snk_cli-0.7.2}/src/snk_cli/config/config.py

@@ -117,7 +117,7 @@ class SnkConfig:
         invalid_config_keys = set(snk_config_dict.keys()) - fields
         if invalid_config_keys:
             import warnings
-            warnings.warn(f"invalid keys in `snk.yaml` file: {invalid_config_keys}.")
+            warnings.warn(f"""invalid keys '{" ".join(invalid_config_keys)}' in {snk_config_path}.""")
         # filer out any invalid keys
         snk_config_dict = {k: v for k, v in snk_config_dict.items() if k in fields}
         snk_config = cls(**snk_config_dict)

{snk_cli-0.7.1 → snk_cli-0.7.2}/src/snk_cli/options/utils.py

@@ -1,11 +1,10 @@
-from typing import List, Tuple, get_origin
+from typing import Dict, List, Tuple, get_origin
 from ..config.config import SnkConfig
 from ..utils import get_default_type, flatten
 from .option import Option
 from pathlib import Path
-from enum import Enum
 
-types = {
+allowed_option_types = {
     "int": int,
     "integer": int,
     "float": float,
@@ -21,8 +20,8 @@ types = {
     "list[float]": List[float],
     "pair": Tuple[str, str],
     "dict": dict,
-    "dict[str, str]": dict[str, str],
-    "dict[str, int]": dict[str, int],
+    "dict[str,str]": Dict[str, str],
+    "dict[str,int]": Dict[str, int],
 }
 
 # Define the basic types for the combinations
@@ -31,7 +30,7 @@ basic_types = [int, str, bool, float]
 # Add the combinations of the basic types to the `types` dictionary
 for t1 in basic_types:
     for t2 in basic_types:
-        types[f"pair[{t1.__name__}, {t2.__name__}]"] = Tuple[t1, t2]
+        allowed_option_types[f"pair[{t1.__name__},{t2.__name__}]"] = Tuple[t1, t2]
 
 def get_keys_from_annotation(annotations):
     # Get the unique keys from the annotations
@@ -68,10 +67,10 @@ def create_option_from_annotation(
         updated = True
     annotation_type = annotation_values.get(f"{annotation_key}:type", None) 
     if annotation_type is not None:
-        annotation_type = annotation_type.lower()
-        assert annotation_type in types, f"Type '{annotation_type}' not supported."
+        annotation_type = annotation_type.lower().replace(" ", "")
+        assert annotation_type in allowed_option_types, f"Type '{annotation_type}' for '{annotation_key}' is not supported."
     annotation_type = (annotation_type or get_default_type(default)).lower()
-    annotation_type = types.get(
+    annotation_type = allowed_option_types.get(
         annotation_type, List[str] if "list" in annotation_type else str
     )
     name = annotation_values.get(

{snk_cli-0.7.1 → snk_cli-0.7.2}/src/snk_cli/validate.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 from typing import Any, Dict, Union, get_origin
 from .config import SnkConfig
-from .options.utils import types
+from .options.utils import allowed_option_types
 import inspect
 
 class ValidationError(Exception):
@@ -52,24 +52,35 @@ def validate_and_transform_in_place(config: Dict[str, Any], validation: Validati
         val_info = validation[key]
         if isinstance(val_info, dict) and 'type' in val_info:
             # Direct type validation
-            val_type = types.get(val_info["type"].lower(), None)
+            val_type = allowed_option_types.get(val_info["type"].lower().replace(" ", ""), None)
             if val_type is None:
                 raise ValueError(f"Unknown type '{val_info['type']}'")
             try:
                 if getattr(val_type, "__origin__", None) is list:
+                    # List e.g. List[str]
                     val_type = val_type.__args__[0]
                     if not isinstance(value, list):
                         raise ValueError(f"Expected a list for key '{key}'")
                     config[key] = [val_type(v) for v in value]
                 elif get_origin(val_type) is tuple:
-                    assert len(value) == 2, f"Expected a list of length 2 for key '{key}'"
+                    # Tuple e.g. Tuple[str, int]
+                    assert len(value) == 2, f"Tuple type should have 2 elements for key '{key}'"
                     key_type = val_type.__args__[0]
                     val_type = val_type.__args__[1]
                     config[key] = [key_type(value[0]), val_type(value[1])]
+                elif get_origin(val_type) is dict:
+                    # Dict e.g. Dict[str, int]
+                    if val_type.__args__ is None:
+                        config[key] = value
+                        continue
+                    assert len(val_type.__args__) == 2, f"Dict type should have 2 arguments for key '{key}'"
+                    val_type = val_type.__args__[1]
+                    config[key] = {k: val_type(v) for k, v in value.items()}
                 else:
+                    # basic
                     config[key] = val_type(value)
             except (ValueError, TypeError) as e:
-                raise ValueError(f"Type conversion error for key '{key}': {e}")
+                raise ValueError(f"Type conversion error for key '{key}' ({val_info['type']}). Could not convert value '{value}' to type '{val_type}'.") from e
         elif isinstance(value, dict):
             # Nested dictionary validation
             validate_and_transform_in_place(value, val_info)

snk_cli-0.7.1/.github/workflows/tests.yml

@@ -1,41 +0,0 @@
-
-name: tests 
-on:
-  push:
-    branches:
-      - master 
-      - main
-permissions:
-  contents: write
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - uses: "conda-incubator/setup-miniconda@v2"
-        with:
-          python-version: 3.11
-          auto-activate-base: false
-          miniforge-variant: Mambaforge
-          channels: conda-forge,bioconda,defaults
-          channel-priority: strict
-          auto-update-conda: true
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11' 
-      - uses: actions/cache@v2
-        with:
-          key: ${{ github.ref }}
-          path: .cache
-      - run: pip install hatch
-      - run: sudo apt-get update && sudo apt-get install -y llvm
-      - run: sudo apt-get -y install graphviz
-      - name: Run tests
-        shell: bash
-        run: hatch run snakemake:cov
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
-
-