From cff6858c9d733f53687d73507ba7c497b56046c0 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:33:51 +0200
Subject: [PATCH 01/15] Remove fastobo dependency and add pytest marker for
 remote tests in pyproject.toml

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c2cf37b..0990a88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,6 @@ dependencies = [
     "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 +43,9 @@ v1 = [
 ]
 copasi = ["copasi-basico>=0.85"]
 
+[tool.pytest.ini_options]
+markers = ["remote: tests that require network access to external services"]
+
 [tool.uv]
 
 [build-system]

From 0de25cbf350f3e63882b2b1a2e98ac40a34d36b9 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:34:10 +0200
Subject: [PATCH 02/15] Update GitHub Actions workflows to include Python 3.14
 in test matrix

---
 .github/workflows/remote-tests.yaml | 2 +-
 .github/workflows/unit-tests.yaml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/remote-tests.yaml b/.github/workflows/remote-tests.yaml
index 84d8719..39e065c 100644
--- a/.github/workflows/remote-tests.yaml
+++ b/.github/workflows/remote-tests.yaml
@@ -9,7 +9,7 @@ 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
diff --git a/.github/workflows/unit-tests.yaml b/.github/workflows/unit-tests.yaml
index eb10321..6696bc8 100644
--- a/.github/workflows/unit-tests.yaml
+++ b/.github/workflows/unit-tests.yaml
@@ -9,7 +9,7 @@ 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

From a7a1e7a152398bf7fa3eeea8364b953bdf562255 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:34:20 +0200
Subject: [PATCH 03/15] Update versioning to use importlib.metadata for dynamic
 version retrieval

---
 pyenzyme/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyenzyme/__init__.py b/pyenzyme/__init__.py
index 3d248d5..73ba22b 100644
--- a/pyenzyme/__init__.py
+++ b/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")

From 98b11b26644a4919b0c41afb68c68c134772f2b4 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:38:27 +0200
Subject: [PATCH 04/15] Add pydantic dependency to pyproject.toml

This update includes the addition of the pydantic package with a version constraint of >=2,<3 to the dependencies list in pyproject.toml, enhancing type validation capabilities.
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 0990a88..89048df 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,6 +10,7 @@ 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",

From b61b8174183e25510d9c164e12cc120a796c1da6 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:39:58 +0200
Subject: [PATCH 05/15] fix(composer): surface real fetcher errors instead of
 swallowing them

_fetch_with_fetchers caught every exception and discarded it, so a
failing fetch reported only "no fetcher found" with no cause. Collect
each fetcher's actual error and include them in the raised ValueError.
---
 pyenzyme/composer.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/pyenzyme/composer.py b/pyenzyme/composer.py
index a623b6a..e3b45e1 100644
--- a/pyenzyme/composer.py
+++ b/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}"
     )
 
 

From cbac15b67f77daead991bbc36de876b83332a917 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:40:35 +0200
Subject: [PATCH 06/15] fix(fetcher): accept integer PubMed IDs from PDB API

PDB returns pdbx_database_id_PubMed as an int, but the Citation model
typed pubmed_id as str
---
 pyenzyme/fetcher/pdb.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/pyenzyme/fetcher/pdb.py b/pyenzyme/fetcher/pdb.py
index f241240..7914694 100644
--- a/pyenzyme/fetcher/pdb.py
+++ b/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

From d26217d99a1c0e01c4b2d907b4e4cd7aa4377a30 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:41:56 +0200
Subject: [PATCH 07/15] fix(sbml): flush model.xml before adding it to OMEX
 archive

add_entry copies the SBML file from disk, but was called inside the
open() block before the write flushed. On Python 3.14 this produced a
0-byte model.xml, breaking every SBML round-trip. Close the file first.
---
 pyenzyme/sbml/omex.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/pyenzyme/sbml/omex.py b/pyenzyme/sbml/omex.py
index 7d32f01..be7a641 100644
--- a/pyenzyme/sbml/omex.py
+++ b/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"

From eaf7efbea954cf5250927698f6becbc2c6eb2fd3 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:42:32 +0200
Subject: [PATCH 08/15] Add unit tests for composer fetcher functionality and
 mark integration tests as remote

This commit introduces a new unit test file for the composer module, which includes tests for handling successful and failed fetcher scenarios. Additionally, the integration test for the composer has been marked with the pytest remote marker to indicate its dependency on external resources.
---
 tests/integration/test_composer.py |  1 +
 tests/unit/test_composer.py        | 30 ++++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+)
 create mode 100644 tests/unit/test_composer.py

diff --git a/tests/integration/test_composer.py b/tests/integration/test_composer.py
index c7b2e63..1770459 100644
--- a/tests/integration/test_composer.py
+++ b/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
diff --git a/tests/unit/test_composer.py b/tests/unit/test_composer.py
new file mode 100644
index 0000000..61cc0e5
--- /dev/null
+++ b/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

From 55e6dcd90b36a2f876784b0312fb18faab19525c Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:46:40 +0200
Subject: [PATCH 09/15] Update expected JSON fixtures to include additional
 PubMed reference

This commit adds a new PubMed reference (https://pubmed.ncbi.nlm.nih.gov/9572841) to the expected JSON fixtures for both `expected_compose.json` and `expected_compose_no_vessel.json`, enhancing the citation information for the sequences.
---
 tests/fixtures/compose/expected_compose.json           | 3 ++-
 tests/fixtures/compose/expected_compose_no_vessel.json | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/fixtures/compose/expected_compose.json b/tests/fixtures/compose/expected_compose.json
index a6cb4a2..93d80c6 100644
--- a/tests/fixtures/compose/expected_compose.json
+++ b/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"
       ]
     }
   ],
diff --git a/tests/fixtures/compose/expected_compose_no_vessel.json b/tests/fixtures/compose/expected_compose_no_vessel.json
index 77905f6..cc03bf1 100644
--- a/tests/fixtures/compose/expected_compose_no_vessel.json
+++ b/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"
       ]
     }
   ],

From c141f538c286ffa37d8ede546881fce19726970c Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 13:48:50 +0200
Subject: [PATCH 10/15] Bump version to 2.2.3 and update fastobo dependency to
 0.14.1 in pyproject.toml and uv.lock

This commit updates the project version in pyproject.toml to 2.2.3 and modifies the fastobo dependency version in uv.lock to 0.14.1, ensuring compatibility with the latest features and fixes.
---
 pyproject.toml |  2 +-
 uv.lock        | 52 ++++++++++++++++++++++++++++++--------------------
 2 files changed, 32 insertions(+), 22 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 89048df..b57b459 100644
--- a/pyproject.toml
+++ b/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"
diff --git a/uv.lock b/uv.lock
index 2c9f675..224e726 100644
--- a/uv.lock
+++ b/uv.lock
@@ -370,25 +370,35 @@ wheels = [
 
 [[package]]
 name = "fastobo"
-version = "0.13.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/9f/29/db8cb028855907b06faa360fdefe6412879f279f00e31e3153940411a8b1/fastobo-0.13.0.tar.gz", hash = "sha256:c4548bcfb7f9f87188bf5d8e4c7fd530162707265a8d644ee75259d305cd6964", size = 1727619, upload-time = "2025-02-14T00:41:30.66Z" }
-wheels = [
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 ]
 
 [[package]]
@@ -1474,13 +1484,13 @@ source = { editable = "." }
 dependencies = [
     { name = "bokeh" },
     { name = "dill" },
-    { name = "fastobo" },
     { name = "httpx" },
     { name = "joblib" },
     { name = "loguru" },
     { name = "matplotlib" },
     { name = "mdmodels" },
     { name = "pandas" },
+    { name = "pydantic" },
     { name = "pydantic-xml" },
     { name = "pymetadata" },
     { name = "python-libsbml" },
@@ -1520,7 +1530,6 @@ requires-dist = [
     { name = "deepdiff", marker = "extra == 'v1'", specifier = ">=8.5.0,<9" },
     { name = "deprecation", marker = "extra == 'v1'", specifier = ">=2.1.0,<3" },
     { name = "dill", specifier = ">=0.3.9,<0.5.0" },
-    { name = "fastobo", specifier = ">=0.13.0,<0.14" },
     { name = "httpx", specifier = ">=0.27" },
     { name = "joblib", specifier = ">=1.5.0,<2" },
     { name = "lmfit", marker = "extra == 'pysces'", specifier = ">=1.3.3,<2" },
@@ -1530,6 +1539,7 @@ requires-dist = [
     { name = "numexpr", marker = "extra == 'v1'", specifier = ">=2.11.0,<3" },
     { name = "openpyxl", marker = "extra == 'excel'", specifier = ">=3.1.4,<4" },
     { name = "pandas", specifier = ">=2.0.0" },
+    { name = "pydantic", specifier = ">=2,<3" },
     { name = "pydantic-xml", specifier = ">=2.17.0,<3" },
     { name = "pymetadata", specifier = ">=0.5.3,<0.6" },
     { name = "pysces", marker = "extra == 'pysces'", specifier = ">=1.2.3,<2" },

From e44f88be69aef3a2faec1903a0e98efd235f925d Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 14:12:00 +0200
Subject: [PATCH 11/15] Update GitHub Actions workflows to use
 actions/checkout@v7 and actions/setup-python@v7, and upgrade
 astral-sh/setup-uv to v9.0.0. This ensures consistency across workflows and
 leverages the latest features and improvements in the actions used.

---
 .github/workflows/docs.yml          |  2 +-
 .github/workflows/lint.yml          |  2 +-
 .github/workflows/publish.yaml      | 20 +++++++++++++++++---
 .github/workflows/remote-tests.yaml |  6 +++---
 .github/workflows/test-publish.yaml |  6 +++---
 .github/workflows/unit-tests.yaml   | 10 ++++++----
 6 files changed, 31 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index a48d39c..b25f547 100644
--- a/.github/workflows/docs.yml
+++ b/.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
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index bb6ae08..a8d77a0 100644
--- a/.github/workflows/lint.yml
+++ b/.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'
diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
index 0844148..660c5f2 100644
--- a/.github/workflows/publish.yaml
+++ b/.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:
diff --git a/.github/workflows/remote-tests.yaml b/.github/workflows/remote-tests.yaml
index 39e065c..4333273 100644
--- a/.github/workflows/remote-tests.yaml
+++ b/.github/workflows/remote-tests.yaml
@@ -13,15 +13,15 @@ jobs:
 
     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
diff --git a/.github/workflows/test-publish.yaml b/.github/workflows/test-publish.yaml
index 423be2c..d967ce8 100644
--- a/.github/workflows/test-publish.yaml
+++ b/.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:
diff --git a/.github/workflows/unit-tests.yaml b/.github/workflows/unit-tests.yaml
index 6696bc8..6237aad 100644
--- a/.github/workflows/unit-tests.yaml
+++ b/.github/workflows/unit-tests.yaml
@@ -1,6 +1,8 @@
 name: Unit Tests
 
-on: [push]
+on:
+  push:
+  workflow_call:
 
 jobs:
   build:
@@ -13,13 +15,13 @@ jobs:
 
     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

From 2061d5d674592abb188089dde4977e824e9035d2 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 14:15:36 +0200
Subject: [PATCH 12/15] Sync uv.lock project version to 2.2.3

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 uv.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/uv.lock b/uv.lock
index 224e726..ccabeb5 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1479,7 +1479,7 @@ wheels = [
 
 [[package]]
 name = "pyenzyme"
-version = "2.2.2"
+version = "2.2.3"
 source = { editable = "." }
 dependencies = [
     { name = "bokeh" },

From 4a9b34d2c2c1688f76ba933b5d9d9bd25498bd29 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 14:39:31 +0200
Subject: [PATCH 13/15] Add pre-commit hooks for uv-lock and ruff

uv-lock re-locks uv.lock when pyproject.toml changes to prevent drift;
ruff mirrors the lint.yml gate (scoped to pyenzyme/ and tests/).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .pre-commit-config.yaml | 14 ++++++++++++++
 README.md               |  6 ++++++
 2 files changed, 20 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..6fc4ef3
--- /dev/null
+++ b/.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)/
diff --git a/README.md b/README.md
index 1620135..6920bda 100644
--- a/README.md
+++ b/README.md
@@ -139,6 +139,12 @@ 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 run pre-commit install
+```
+
 In order to run tests there are two different ways. First you can utilize `pytest` directly by running the following:
 
 ```bash

From 01c1e9419b3f903d5215c21e5ccd85fdba30de60 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 14:41:16 +0200
Subject: [PATCH 14/15] Fix pre-commit install instructions to use uv tool
 install

pre-commit is a standalone tool, not a project dependency, so 'uv run'
cannot find it. Use 'uv tool install pre-commit' instead.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6920bda..4366e69 100644
--- a/README.md
+++ b/README.md
@@ -142,7 +142,8 @@ For new projects, we recommend utilizing the updated API available in the packag
 Contributors should install the pre-commit hooks once per clone (keeps `uv.lock` in sync and runs the linter before each commit):
 
 ```bash
-uv run pre-commit install
+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:

From 03bd2d12c0ae9ca1ad3cccfefe956fc6b5958369 Mon Sep 17 00:00:00 2001
From: Max Haeussler <max.haeussler@gmail.com>
Date: Thu, 23 Jul 2026 14:46:26 +0200
Subject: [PATCH 15/15] Remove remote-tests CI workflow

Remote tests hit external APIs (e.g. RHEA-DB) that block CI datacenter
IPs with 403, making CI permanently red for reasons unrelated to the
code. They still run locally via 'pytest' (or 'pytest -m remote'); CI's
unit-tests already excludes them with -m 'not remote'.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .github/workflows/remote-tests.yaml | 30 -----------------------------
 1 file changed, 30 deletions(-)
 delete mode 100644 .github/workflows/remote-tests.yaml

diff --git a/.github/workflows/remote-tests.yaml b/.github/workflows/remote-tests.yaml
deleted file mode 100644
index 4333273..0000000
--- a/.github/workflows/remote-tests.yaml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: Remote Tests
-
-on: [push]
-
-jobs:
-  remote-tests:
-    runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 4
-      fail-fast: false
-      matrix:
-        python-version: ['3.11', '3.12', '3.13', '3.14']
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v7
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v7
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@v9.0.0
-
-      - name: Install the project
-        run: uv sync --locked --all-extras --all-groups
-
-      - name: Run remote tests
-        run: uv run pytest -vv -m "remote"