Dependency updates and unit test fixes

.coveragerc

@@ -17,4 +17,4 @@ exclude_lines =
     pragma: no cover
     raise NotImplementedError
     except ImportError
-    if __name__ == .__main__.:
+    if __name__ == .__main__.:

.gitattributes

@@ -1,2 +1,2 @@
 # Vendor files (not to be indexed)
-isa-cookbook/_static/**/* linguist-vendored
+isa-cookbook/_static/**/* linguist-vendored

.github/workflows/buildandtestpython.yml

@@ -21,8 +21,8 @@ jobs:
         cache-dependency-glob: uv.lock
     - name: Sync dependencies
       run: |
-        uv python pin ${{ matrix.python-version }} 
-        uv sync --group dev
+        uv python pin ${{ matrix.python-version }}
+        uv sync --extra database --extra dev
     - uses: astral-sh/ruff-action@v3
     - run: ruff check
     - run: ruff format

.github/workflows/pythonpublish.yml

@@ -2,7 +2,7 @@ name: Upload Python Package
 
 on:
   release:
-    types: [published]
+    types: [ published ]
 
 jobs:
   deploy:
@@ -20,7 +20,7 @@ jobs:
         cache-dependency-glob: uv.lock
     - name: Sync dependencies
       run: |
-        uv sync --no-dev
+        uv sync --extra database
     - name: Build
       run: |
         echo "Running uv build..."

.gitignore

@@ -144,4 +144,4 @@ isa-reports/*
 isaRDF/
 venv*/
 instance/*
-instance/
+instance/

.pre-commit-config.yaml

@@ -7,43 +7,43 @@ repos:
   - id: validate-pyproject
     name: 🔍 Validate pyproject.toml
 - repo: https://github.com/gitleaks/gitleaks
-  rev: v8.28.0
+  rev: v8.30.0
   hooks:
   - id: gitleaks
     name: "🔒 Security · Detect hardcoded secrets"
-- repo: https://github.com/hukkin/mdformat
-  rev: 0.7.22
-  hooks:
-  - id: mdformat
-    name: "🟢  Markdown · Format markdown"
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v6.0.0
   hooks:
   - id: check-added-large-files
     name: 🟢  Check large files
+    exclude: features/.+|isa-cookbook/.+|docs/.+|isatools/net/.+|isatools/resources/.+|tests/data/.+
     args: [ "--maxkb=2000" ]
   - id: check-toml
     name: 🟢  Check toml files
+    exclude: features/.+|isa-cookbook/.+|docs/.+|isatools/net/.+|isatools/resources/.+|tests/data/.+
   - id: check-json
     name: 🟢  Check json files
+    exclude: features/.+|isa-cookbook/.+|docs/.+|isatools/net/.+|isatools/resources/.+|tests/data/.+
   - id: pretty-format-json
     name: 🟢  Format json files
+    exclude: features/.+|isa-cookbook/.+|docs/.+|isatools/net/.+|isatools/resources/.+|tests/data/.+
     args:
     - "--autofix"
     - "--indent=4"
     - "--no-sort-keys"
   - id: check-yaml
     name: 🟢  Check yaml files
+    exclude: features/.+|isa-cookbook/.+|docs/.+|isatools/net/.+|isatools/resources/.+|tests/data/.+
     args:
     - --unsafe
   - id: end-of-file-fixer
     name: 🟢 Check end of file character
-    exclude: resources/.+\.(js|css)$
+    exclude: features/.+|isa-cookbook/.+|docs/.+|isatools/net/.+|isatools/resources/.+|tests/data/.+
   - id: trailing-whitespace
     name: 🟢  Check trailing whitespaces
-    exclude: (tests/data/.+|resources/.+\.(js|css))$
+    exclude: features/.+|isa-cookbook/.+|docs/.+|isatools/net/.+|isatools/resources/.+|tests/data/.+
 - repo: https://github.com/astral-sh/uv-pre-commit
-  rev: 0.9.1
+  rev: 0.9.15
   hooks:
   - id: uv-lock
     name: ✅ Check uv.lock file
@@ -54,7 +54,7 @@ repos:
     name: 🔍 Detect missing __init__.py files
     args: [ "--create", "--track", "--python-folders", "isatools" ]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.14.0
+  rev: v0.14.7
   hooks:
   - id: ruff-check
     name: 🔍 Check Format with Ruff
@@ -64,7 +64,7 @@ repos:
   - id: ruff-format
     name: 🐍 python · Format with Ruff
 - repo: https://github.com/seddonym/import-linter.git
-  rev: "v2.5.2"
+  rev: "v2.7"
   hooks:
   - id: import-linter
     name: 🪵 architecture and package structure check (lint-imports)

LICENSE.txt

@@ -100,4 +100,4 @@ EXHIBIT B. Attribution Information
 Attribution Copyright Notice: Copyright (c) 2015-Present ISA Team
 Attribution Phrase: Developed by the ISA Team
 Attribution URL: http://www.isa-tools.org
-Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL.
+Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL.

get_test_data.sh

@@ -1,9 +1,9 @@
 #!/bin/bash
-
+rm -rf tests/data
 if [ "$TRAVIS_BRANCH" = "develop" ]; then
   git clone -b tests --single-branch http://github.com/ISA-tools/ISAdatasets tests/data
 else
   git clone -b tests --single-branch http://github.com/ISA-tools/ISAdatasets tests/data
 fi
 
-ls -la tests/data/mtbls
+ls -la tests/data/mtbls

isatools/.gitignore

@@ -58,4 +58,3 @@ docs/_build/
 target/
 
     Status API Training Shop Blog About Pricing
-

isatools/constants.py

@@ -23,7 +23,7 @@
     "Acquisition Parameter Data File",
     "Metabolite Assignment File",
     "Metabolite Identification File",
-    "Normalization Name"
+    "Normalization Name",
 ]
 
 _LABELS_DATA_NODES = [

isatools/convert/isatab2cedar.py

@@ -142,7 +142,7 @@ def createCEDARjson(self, work_dir, json_dir, inv_identifier):
                 error_file_name = os.path.join(json_dir, "error.log")
                 with open(error_file_name, "w") as errorfile:
                     errorfile.write(e.message)
-#                    errorfile.write(e.cause)
+                    #                    errorfile.write(e.cause)
                     errorfile.close()
 
             if inv_identifier:

isatools/convert/magetab2json.py

@@ -22,5 +22,5 @@ def convert(idf_file_path):
             ISA = isatab.load(isa_inv_fp)
     finally:
         shutil.rmtree(tmp)
-        if ISA is not None:
-            return json.loads(json.dumps(ISA, cls=ISAJSONEncoder))
+    if ISA is not None:
+        return json.loads(json.dumps(ISA, cls=ISAJSONEncoder))

isatools/create/__init__.py

@@ -1 +0,0 @@
-

isatools/create/model.py

@@ -254,7 +254,7 @@ def __repr__(self):
 
     def __str__(self):
         return """"{0}
-        (type={1}, 
+        (type={1},
         factor_values={2})
         """.format(self.__class__.__name__, self.type, sorted(self.factor_values, key=lambda x: repr(x)))
 
@@ -327,8 +327,8 @@ def __repr__(self):
 
     def __str__(self):
         return """{0}(
-               name={name}, 
-               elements={elements_count} items, 
+               name={name},
+               elements={elements_count} items,
                )""".format(self.__class__.__name__, name=self.name, elements_count=len(self.elements))
 
     def __hash__(self):
@@ -799,12 +799,12 @@ def __repr__(self):
 
     def __str__(self):
         return """{0}(
-        id={1.id}, 
-        name={1.name}, 
-        protocol_type={1.protocol_type}, 
-        uri={1.uri}, 
-        description={1.description}, 
-        version={1.version}, 
+        id={1.id},
+        name={1.name},
+        protocol_type={1.protocol_type},
+        uri={1.uri},
+        description={1.description},
+        version={1.version},
         parameter_values={1.parameter_values})
         """.format(self.__class__.__name__, self)
 
@@ -1011,7 +1011,7 @@ def __repr__(self):
     def __str__(self):
         return """{0}(
         pre_run_sample_type={1}
-        post_run_sample_type={2} 
+        post_run_sample_type={2}
         interspersed_sample_types={3}
         )""".format(
             self.__class__.__name__,
@@ -1410,9 +1410,9 @@ def __str__(self):
         links = [(start_node.id, end_node.id) for start_node, end_node in self.links]
         return """"{0}(
         id={1.id}
-        measurement_type={1.measurement_type} 
+        measurement_type={1.measurement_type}
         technology_type={1.technology_type}
-        nodes={1.nodes} 
+        nodes={1.nodes}
         links={2}
         )""".format(self.__class__.__name__, self, sorted(links, key=lambda link: (link[0], link[1])))
 
@@ -1604,7 +1604,7 @@ def __repr__(self):
     def __str__(self):
         return """{0}(
         name={1.name},
-        sample_plan={1.sample_plan}, 
+        sample_plan={1.sample_plan},
         assay_plan={1.assay_plan}
         )""".format(self.__class__.__name__, self)
 
@@ -1848,7 +1848,7 @@ def __str__(self):
         return """{0}(
                name={name},
                source_type={source_type},
-               group_size={group_size}, 
+               group_size={group_size},
                no. cells={cells},
                no. sample_assay_plans={sample_assay_plans}
                )""".format(
@@ -2773,7 +2773,7 @@ def __repr__(self):
 
     def __str__(self):
         return """{0}(
-               identifier={identifier}, 
+               identifier={identifier},
                name={name},
                description={description},
                study_arms={study_arms}

isatools/database/models/constraints.py

@@ -63,6 +63,6 @@ def build_material_constraints() -> CheckConstraint:
 
     :return: A CheckConstraint object used to validate the Material table.
     """
-    statement = """NOT (material_type IS NOT NULL 
+    statement = """NOT (material_type IS NOT NULL
                 AND material_type != 'Extract Name' AND material_type != 'Labeled Extract Name')"""
     return CheckConstraint(statement, name="material_type_must_be_extract_name_or_labeled_extract_name")