Fix/issue 100 python 314

.github/workflows/docs.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout your repository using git
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Install, build, and upload your site
         uses: withastro/action@v5

.github/workflows/lint.yml

@@ -4,7 +4,7 @@ jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - uses: chartboost/ruff-action@v1
         with:
           src: './pyenzyme'

.github/workflows/publish.yaml

@@ -5,14 +5,28 @@ on:
     types: [released]
 
 jobs:
-  deploy:
+  check-version:
     runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - name: Verify release tag matches package version
+        run: |
+          TAG="${GITHUB_REF_NAME#v}"
+          VER="$(grep -m1 '^version = ' pyproject.toml | sed -E 's/.*"([^"]+)".*/\1/')"
+          echo "tag=$TAG  pyproject=$VER"
+          test "$TAG" = "$VER"
 
+  test:
+    uses: ./.github/workflows/unit-tests.yaml
+
+  publish:
+    needs: [check-version, test]
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v7
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v9.0.0
 
       - name: Publish Package
         env:

.github/workflows/test-publish.yaml

@@ -7,15 +7,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v7
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v7
         with:
           python-version: '3.11'
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v9.0.0
 
       - name: Publish Package
         env:

.github/workflows/unit-tests.yaml

@@ -1,6 +1,8 @@
 name: Unit Tests
 
-on: [push]
+on:
+  push:
+  workflow_call:
 
 jobs:
   build:
@@ -9,17 +11,17 @@ jobs:
       max-parallel: 4
       fail-fast: false
       matrix:
-        python-version: ['3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v9.0.0
       - name: Install the project
         run: uv sync --locked --all-extras --all-groups
       - name: Run tests

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+# Run once per clone:  uv run pre-commit install
+repos:
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.11.31
+    hooks:
+      # Re-locks uv.lock whenever pyproject.toml changes, so the two can't drift.
+      - id: uv-lock
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.22
+    hooks:
+      # Same lint gate CI runs (lint.yml lints ./pyenzyme and ./tests only).
+      - id: ruff-check
+        files: ^(pyenzyme|tests)/

README.md

@@ -139,6 +139,13 @@ For new projects, we recommend utilizing the updated API available in the packag
 
 ## 🧪 Testing
 
+Contributors should install the pre-commit hooks once per clone (keeps `uv.lock` in sync and runs the linter before each commit):
+
+```bash
+uv tool install pre-commit
+pre-commit install
+```
+
 In order to run tests there are two different ways. First you can utilize `pytest` directly by running the following:
 
 ```bash

pyenzyme/__init__.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from importlib.metadata import version
+
 from mdmodels.units.unit_definition import UnitDefinition, UnitType
 
 from .composer import compose
@@ -45,4 +47,4 @@
     "group_measurements",
 ]
 
-__version__ = "2.2.2"
+__version__ = version("pyenzyme")

pyenzyme/composer.py

@@ -197,16 +197,18 @@ def _fetch_with_fetchers(
     Raises:
         ValueError: If no fetcher can handle the given entity ID
     """
+    errors = []
     for fetcher in fetchers:
         try:
             return fetcher(entity_id)
-        except Exception:
+        except Exception as e:
+            errors.append(f"{fetcher.__name__}: {type(e).__name__}: {e}")
             continue
 
-    fetcher_names = ", ".join(f.__name__ for f in fetchers)
+    detail = "; ".join(errors)
     raise ValueError(
-        f"No {entity_type} fetcher found for {entity_id}. "
-        f"Supported fetchers: {fetcher_names}"
+        f"No {entity_type} fetcher succeeded for {entity_id}. "
+        f"Tried: {detail}"
     )
 
 

pyenzyme/fetcher/pdb.py

@@ -24,7 +24,7 @@ class Citation(BaseModel):
     journal_name: Optional[str] = Field(default=None, alias="journal_abbrev")
     year: Optional[int] = None
     doi: Optional[str] = None
-    pubmed_id: Optional[str] = Field(default=None, alias="pdbx_database_id_PubMed")
+    pubmed_id: Optional[int] = Field(default=None, alias="pdbx_database_id_PubMed")
 
 
 class StructInfo(BaseModel):
@@ -261,9 +261,8 @@ def fetch_pdb(
     if pdb_response.citation and pdb_response.citation[0].doi:
         protein.references.append(f"https://doi.org/{pdb_response.citation[0].doi}")
 
-    if pdb_response.citation and pdb_response.citation[0].pubmed_id:
-        protein.references.append(
-            f"https://pubmed.ncbi.nlm.nih.gov/{pdb_response.citation[0].pubmed_id}"
-        )
+    if pdb_response.citation and pdb_response.citation[0].pubmed_id is not None:
+        pubmed_id = str(pdb_response.citation[0].pubmed_id)
+        protein.references.append(f"https://pubmed.ncbi.nlm.nih.gov/{pubmed_id}")
 
     return protein

pyenzyme/sbml/omex.py

@@ -114,14 +114,15 @@ def create_sbml_omex(
         sbml_path = f"{temp_dir}/model.xml"
         with open(sbml_path, "w") as f:
             f.write(sbml_doc)
-            omex.add_entry(
-                entry_path=Path(sbml_path),
-                entry=ManifestEntry(
-                    location="./model.xml",
-                    format=EntryFormat.SBML,
-                    master=True,
-                ),
-            )
+        # add_entry copies from entry_path, so the file must be closed/flushed first
+        omex.add_entry(
+            entry_path=Path(sbml_path),
+            entry=ManifestEntry(
+                location="./model.xml",
+                format=EntryFormat.SBML,
+                master=True,
+            ),
+        )
 
         if data is not None:
             data_path = f"{temp_dir}/data.tsv"

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pyenzyme"
-version = "2.2.2"
+version = "2.2.3"
 description = "A Python library for EnzymeML"
 authors = [{ name = "Jan Range", email = "range.jan@web.de" }]
 requires-python = ">=3.11,<4"
@@ -10,11 +10,11 @@ dependencies = [
     "python-libsbml>=5.20.2,<6",
     "rich>=13.7.1,<14",
     "pandas>=2.0.0",
+    "pydantic>=2,<3",
     "pydantic-xml>=2.17.0,<3",
     "loguru>=0.7.2,<0.8",
     "rdflib==7.0.0",
     "sympy>=1.12.1,<2",
-    "fastobo>=0.13.0,<0.14",
     "pymetadata>=0.5.3,<0.6",
     "httpx>=0.27",
     "mdmodels>=0.2.4,<0.3",
@@ -44,6 +44,9 @@ v1 = [
 ]
 copasi = ["copasi-basico>=0.85"]
 
+[tool.pytest.ini_options]
+markers = ["remote: tests that require network access to external services"]
+
 [tool.uv]
 
 [build-system]

tests/fixtures/compose/expected_compose.json

@@ -93,7 +93,8 @@
       "sequence": "AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK",
       "vessel_id": "vessel",
       "references": [
-        "https://www.rcsb.org/structure/1A23"
+        "https://www.rcsb.org/structure/1A23",
+        "https://pubmed.ncbi.nlm.nih.gov/9572841"
       ]
     }
   ],

tests/fixtures/compose/expected_compose_no_vessel.json

@@ -57,7 +57,8 @@
       "constant": true,
       "sequence": "AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK",
       "references": [
-        "https://www.rcsb.org/structure/1A23"
+        "https://www.rcsb.org/structure/1A23",
+        "https://pubmed.ncbi.nlm.nih.gov/9572841"
       ]
     }
   ],

tests/integration/test_composer.py

@@ -3,6 +3,7 @@
 from pyenzyme.tools import to_dict_wo_json_ld
 
 
+@pytest.mark.remote
 class TestComposer:
     def test_compose(self):
         # Act

tests/unit/test_composer.py

@@ -0,0 +1,30 @@
+import pytest
+
+from pyenzyme.composer import _fetch_with_fetchers
+
+
+def test_returns_first_successful_fetcher():
+    def boom(_):
+        raise ConnectionError("down")
+
+    def ok(entity_id):
+        return f"fetched:{entity_id}"
+
+    assert _fetch_with_fetchers("X1", [boom, ok], "protein") == "fetched:X1"
+
+
+def test_error_aggregates_every_fetcher_reason():
+    def bad_request(_):
+        raise ValueError("400 Bad Request")
+
+    def not_found(_):
+        raise KeyError("404")
+
+    with pytest.raises(ValueError) as exc:
+        _fetch_with_fetchers("X1", [bad_request, not_found], "protein")
+
+    msg = str(exc.value)
+    # names the entity, the type, and each fetcher's real failure reason
+    assert "No protein fetcher succeeded for X1" in msg
+    assert "bad_request: ValueError: 400 Bad Request" in msg
+    assert "not_found: KeyError" in msg