Test/filipps update deps

.github/workflows/build-binary.yml

@@ -21,9 +21,9 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-          pip install --no-deps -r requirements.txt
-          pip install -r requirements.txt --no-cache-dir
+          pip install uv
+          uv pip sync --system --no-build pylock.toml
+          uv pip install --system -e .
 
       - name: Build Binary (Linux)
         if: runner.os == 'Linux'

.github/workflows/build-version.yml

@@ -19,9 +19,9 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-          pip install --no-deps -r requirements.txt
-          pip install -r requirements.txt --no-cache-dir
+          pip install uv
+          uv pip sync --system --no-build pylock.toml
+          uv pip install --system -e .
       - name: Update CDISC standards cache
         env:
           CDISC_LIBRARY_API_KEY: ${{ secrets.CDISC_LIBRARY_API_KEY }}
@@ -73,9 +73,9 @@ jobs:
 #       - name: Install dependencies
 #         run: |
 #           python -m pip install --upgrade pip
-#           pip install setuptools wheel twine
-#           pip install --no-deps -r requirements.txt
-#           pip install -r requirements.txt --no-cache-dir
+#           pip install uv
+#           uv pip sync --system pylock.toml
+#           uv pip install --system -e .
 #       - name: Update CDISC standards cache
 #         env:
 #           CDISC_LIBRARY_API_KEY: ${{ secrets.CDISC_LIBRARY_API_KEY }}
@@ -117,9 +117,9 @@ jobs:
 #       - name: Install dependencies
 #         run: |
 #           python -m pip install --upgrade pip
-#           pip install setuptools wheel twine
-#           pip install --no-deps -r requirements.txt
-#           pip install -r requirements.txt --no-cache-dir
+#           pip install uv
+#           uv pip sync --system pylock.toml
+#           uv pip install --system -e .
 #       - name: Update CDISC standards cache
 #         env:
 #           CDISC_LIBRARY_API_KEY: ${{ secrets.CDISC_LIBRARY_API_KEY }}

.github/workflows/lint-format.yml

@@ -49,7 +49,7 @@ jobs:
           python-version: "3.12"
       - name: Install linters
         run: |
-          pip install black flake8 -c requirements-dev.txt
+          pip install black flake8
       - name: Run flake8
         run: |
           flake8 ${{needs.get_changed_files.outputs.py}} --count --select=E9,F63,F7,F82 --show-source --statistics

.github/workflows/prerelease-update-cache.yml

@@ -23,7 +23,10 @@ jobs:
           python-version: "3.12"
 
       - name: Install requirements
-        run: pip install -r requirements.txt
+        run: |
+          pip install uv
+          uv pip sync --system --no-build pylock.toml
+          pip install -e .
 
       - name: Run Update Cache Script
         run: python core.py update-cache

.github/workflows/release.yml

@@ -102,8 +102,9 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build setuptools wheel twine
-          pip install -r requirements.txt
+          pip install uv build twine
+          uv pip sync --system --no-build pylock.toml
+          uv pip install --system -e .
       - name: Build package
         run: |
           python -m build

.github/workflows/test-release.yml

@@ -81,8 +81,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build setuptools wheel twine
-          pip install -r requirements.txt
+          pip install uv build twine
+          uv pip sync --system --no-build pylock.toml
+          uv pip install --system -e .
+
 
       - name: Build package
         run: |

.github/workflows/test-suite.yml

@@ -28,7 +28,9 @@ jobs:
           python-version: "3.12"
       - name: Install dependencies
         run: |
-          pip install -r requirements.txt
+          pip install uv
+          uv pip sync --system --no-build pylock.toml
+          uv pip install --system -e .
       - name: Update rules cache
         env:
           CDISC_LIBRARY_API_KEY: ${{ secrets.CDISC_LIBRARY_API_KEY }}

.github/workflows/test-unit.yml

@@ -16,8 +16,9 @@ jobs:
           python-version: "3.12"
       - name: Install requirements
         run: |
-          pip install -r requirements-dev.txt
-          pip install -e .
+          pip install uv
+          uv pip sync --system --no-build pylock.dev.toml
+          uv pip install --system -e .
       - name: Running Tests
         env:
           CDISC_LIBRARY_API_KEY: fakekey12341234

.github/workflows/validate-published-rules.yml

@@ -80,9 +80,9 @@ jobs:
       - name: Install engine dependencies
         run: |
           python -m venv venv
-          ./venv/bin/pip install --upgrade pip
-          ./venv/bin/pip install -r engine/requirements.txt
-
+          venv/bin/pip install uv
+          venv/bin/uv pip sync --no-build pylock.dev.toml
+          venv/bin/uv pip install -e .
       # -----------------------------------------------------------------------
       # 5. Run validation for every Published rule
       # -----------------------------------------------------------------------

cdisc_rules_engine/dataset_builders/contents_define_vlm_dataset_builder.py

@@ -66,7 +66,7 @@ def build(self):
         data_contents_with_vlm["variable_value_length"] = data_contents_with_vlm.data[
             ["variable_value", "define_vlm_data_type"]
         ].apply(
-            lambda row: self.calculate_variable_value_length(
+            lambda row: ValuesDatasetBuilder.calculate_variable_value_length(
                 row["variable_value"], row["define_vlm_data_type"]
             ),
             axis=1,

cdisc_rules_engine/operations/codelist_extensible.py

@@ -32,6 +32,10 @@ def _handle_multiple_versions(self) -> pd.Series:
                 "codelist_code": "string",
             }
         )
+        cast_cols = {self.params.ct_version: str}
+        if self.params.codelist_code in self.evaluation_dataset.columns:
+            cast_cols[self.params.codelist_code] = str
+        self.evaluation_dataset = self.evaluation_dataset.astype(cast_cols)
         if self.params.codelist_code in self.evaluation_dataset.columns:
             is_extensible = self.evaluation_dataset.merge(
                 ct_df.data,

cdisc_rules_engine/operations/codelist_terms.py

@@ -60,10 +60,14 @@ def _handle_multiple_versions(self) -> pd.Series:
         ct_df = self.evaluation_dataset.__class__.from_dict(ct_data)
         ct_df = ct_df.astype(
             {
-                "version": "string",
-                "codelist_code": "string",
+                "version": str,
+                "codelist_code": str,
             }
         )
+        cast_cols = {self.params.ct_version: "string"}
+        if self.params.codelist_code in self.evaluation_dataset.columns:
+            cast_cols[self.params.codelist_code] = "string"
+        self.evaluation_dataset = self.evaluation_dataset.astype(cast_cols)
         if self.params.codelist_code in self.evaluation_dataset.columns:
             result = self.evaluation_dataset.merge(
                 ct_df.data,

cdisc_rules_engine/services/data_readers/csv_reader.py

@@ -1,6 +1,6 @@
 import tempfile
 
-from dask.dataframe import dd
+import dask.dataframe as dd
 
 from cdisc_rules_engine.exceptions.custom_exceptions import InvalidCSVFile
 from cdisc_rules_engine.interfaces import DataReaderInterface

cdisc_rules_engine/services/data_services/usdm_data_service.py

@@ -399,8 +399,8 @@ def __read_node_metadata(
         }
 
     @staticmethod
-    def __get_full_path(node: DatumInContext):
-        return f"{node.full_path}".replace(".[", "[")
+    def __get_full_path(node: DatumInContext) -> str:
+        return str(node.full_path).replace(".[", "[")
 
     def __get_datasets_content_index(self) -> List[dict]:
         """

cdisc_rules_engine/services/datasetxpt_metadata_reader.py

@@ -61,7 +61,7 @@ def read(self) -> dict:
             "variable_labels": list(metadata.column_labels),
             "variable_names": list(metadata.column_names),
             "variable_formats": [
-                "" if data_type == "NULL" else data_type
+                "" if (data_type == "NULL" or data_type is None) else data_type
                 for data_type in metadata.original_variable_types.values()
             ],
             "variable_name_to_label_map": metadata.column_names_to_labels,

core.py

@@ -357,15 +357,13 @@ def load_custom_dotenv_from_data_options(_ctx, _param, value):
     "-s",
     "--standard",
     required=True,
-    default=None,
     help="CDISC standard to validate against",
     envvar="PRODUCT",
 )
 @click.option(
     "-v",
     "--version",
     required=True,
-    default=None,
     help="Standard version to validate against",
     envvar="VERSION",
 )

docs/contributing.md

@@ -34,7 +34,7 @@ This project enforces consistent formatting and linting via pre-commit hooks.
 - [`flake8`](https://flake8.pycqa.org/) — Python linter
 - [`prettier`](https://prettier.io/) — JSON, YAML, and Markdown formatter
 
-Both `black` and `flake8` are included in `requirements-dev.txt`. After installing dependencies, install the pre-commit hooks:
+Both `black` and `flake8` are included in the `dev` dependency group in `pyproject.toml`. After installing dependencies, install the pre-commit hooks:
 
 ```bash
 pre-commit install

docs/development.md

@@ -46,10 +46,21 @@ source venv/bin/activate
 # Activate (Windows)
 .\venv\Scripts\Activate
 
-# Install dependencies
-python -m pip install -r requirements-dev.txt
+# Install uv (if not already installed)
+pip install uv
+
+# Install pinned dependencies from the primary & dev lockfiles
+uv pip sync pylock.dev.toml
+
+# Install the package itself in editable mode
+pip install -e.
 ```
 
+> **Note:** `pylock.toml` and `pylock.dev.toml` are standard lockfiles (PEP 751) and can be used
+> with any compatible tool. If you prefer not to use uv, you can install core dependencies via
+> standard pip (`pip install .`), though dev dependencies will need to be installed separately
+> and exact version pinning is only guaranteed when using a tool that supports `pylock.toml`.
+
 ---
 
 ## Running Tests

docs/quick-start.md

@@ -125,9 +125,15 @@ python -m venv venv
 ### 3. Install Dependencies
 
 ```bash
-python -m pip install -r requirements-dev.txt
+pip install uv
+uv pip sync pylock.toml
 ```
 
+> **Note:** `pylock.toml` is a standard format (PEP 751) and can be used with any compatible tool.
+> If you prefer not to use uv, you can install directly from `pyproject.toml` using standard pip
+> (`pip install .`) or any other PEP 517-compatible tool such as pip-tools or Poetry. Note that
+> exact version pinning is only guaranteed when using a tool that supports `pylock.toml`.
+
 ### 4. Populate the Cache
 
 ```bash