mite-standard · mmzdouc · Jul 17, 2026 · Jul 14, 2026 · Jul 14, 2026 · Jul 14, 2026
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -22,6 +22,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          persist-credentials: false
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
@@ -35,4 +37,4 @@ jobs:
           pip install .[dev]
 
       - name: Run tests
-        run: pytest
+        run: pytest
diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -14,6 +14,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -51,4 +53,4 @@ jobs:
           name: python-package-distributions
           path: dist/
       - name: Publish distribution package to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,15 +1,15 @@
 fail_fast: true
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v6.0.0
   hooks:
     - id: check-yaml
 - repo: https://github.com/astral-sh/uv-pre-commit
-  rev: 0.9.5
+  rev: 0.11.28
   hooks:
     - id: uv-lock
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.0
+  rev: v0.15.21
   hooks:
     - id: ruff
       args: [ --fix ]
@@ -25,4 +25,4 @@ repos:
       name: pytest
       entry: uv run pytest
       language: system
-      pass_filenames: false
+      pass_filenames: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,8 @@
 All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
-This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+This project adheres to [Semantic
+Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [1.6.5] 25-10-2025
 
@@ -15,7 +16,8 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ### Changed
 
-- Missing/wrong Wikidata QID does not raise error, only logs warning (matches genpept/uniprot behavior)
+- Missing/wrong Wikidata QID does not raise error, only logs warning (matches
+  genpept/uniprot behavior)
 
 ## [1.6.3] 30-09-2025
 
@@ -29,20 +31,24 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ### Changed
 
-- `to_json()` and `to_html()` return changelog even if it is an empty list (compatibility with mite_web data submission)
+- `to_json()` and `to_html()` return changelog even if it is an empty list
+  (compatibility with mite_web data submission)
 
 ## [1.6.1] 29-08-2025
 
 ### Changed
 
-- Unpinned version of dependency of `mite_schema` to facilitate maintenance (should always pull the newest release)
+- Unpinned version of dependency of `mite_schema` to facilitate maintenance
+  (should always pull the newest release)
 
 ## [1.6.0] 28-08-2025
 
 ### Changed
 
-- In html_json generation, changed substrate from tuple to list of tuples to visualize substrates separately
-- Changed Wikidata QID checking from raise errror to log warning (frequent 403 errors)
+- In html_json generation, changed substrate from tuple to list of tuples to
+  visualize substrates separately
+- Changed Wikidata QID checking from raise error to log warning (frequent 403
+  errors)
 
 ## [1.5.1] 26-07-2025
 
@@ -74,8 +80,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 - Bumped `mite_schema` version to `1.7.0`
 - Reworked `ValidationManager`
-- Implemented option for intramolecular reactions (recognized from reaction SMARTS)
-- Pinned RDkit version to `2024.3.6` 
+- Implemented option for intramolecular reactions (recognized from reaction
+  SMARTS)
+- Pinned RDkit version to `2024.3.6`
 
 ## [1.3.1] 02-12-2024
 
@@ -142,4 +149,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ### Added
 
-- Initial version of `mite_extras`
+- Initial version of `mite_extras`
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -1,3 +1,4 @@
 # CODE OF CONDUCT
 
-See our organization-level [Code of Conduct](https://github.com/mite-standard/.github/blob/main/CODE_OF_CONDUCT.md).
+See our organization-level [Code of
+Conduct](https://github.com/mite-standard/.github/blob/main/CODE_OF_CONDUCT.md).
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,3 +1,4 @@
 # CONTRIBUTING
 
-See our organization-level document on [Contributing](https://github.com/mite-standard/.github/blob/main/CONTRIBUTING.md).
+See our organization-level document on
+[Contributing](https://github.com/mite-standard/.github/blob/main/CONTRIBUTING.md).
diff --git a/README.md b/README.md
@@ -1,12 +1,11 @@
-mite_extras
-==========
+# mite_extras
 
-[![DOI](https://zenodo.org/badge/804997522.svg)](https://doi.org/10.5281/zenodo.13941745) 
-[![PyPI version](https://badge.fury.io/py/mite-extras.svg)](https://badge.fury.io/py/mite-extras)
+[![DOI](https://zenodo.org/badge/804997522.svg)](https://doi.org/10.5281/zenodo.13941745)
+[![PyPI
+version](https://badge.fury.io/py/mite-extras.svg)](https://badge.fury.io/py/mite-extras)
 
+## Contents
 
-Contents
------------------
 - [Overview](#overview)
 - [Documentation](#documentation)
 - [System Requirements](#system-requirements)
@@ -17,27 +16,38 @@ Contents
 
 ## Overview
 
-**MITE** (Minimum Information about a Tailoring Enzyme) is a community-driven database for the characterization of tailoring enzymes.
-These enzymes play crucial roles in the biosynthesis of secondary or specialized metabolites, naturally occurring molecules with strong biological activities, such as antibiotic properties.
+**MITE** (Minimum Information about a Tailoring Enzyme) is a community-driven
+database for the characterization of tailoring enzymes. These enzymes play
+crucial roles in the biosynthesis of secondary or specialized metabolites,
+naturally occurring molecules with strong biological activities, such as
+antibiotic properties.
 
 This repository contains functionality to validate MITE entries in JSON format.
 
-For more information, visit the [MITE Data Standard Organization page](https://github.com/mite-standard) or read our [publication]( https://doi.org/10.1093/nar/gkaf969).
+For more information, visit the [MITE Data Standard Organization
+page](https://github.com/mite-standard) or read our
+[publication](https://doi.org/10.1093/nar/gkaf969).
 
 ## Documentation
 
-This repository provides validation functionality for verifying files following the MITE `JSON Schema` format, such as the files in the  **MITE** data repository [mite_data](https://github.com/mite-standard/mite_data).
+This repository provides validation functionality for verifying files following
+the MITE `JSON Schema` format, such as the files in the **MITE** data repository
+[mite_data](https://github.com/mite-standard/mite_data).
 
-The validation functionality includes:
-- Calling the `mite_schema` functionality
-- Validation of reaction SMARTS (does the reaction SMARTS lead to the expected product when applied to a specified substrate)
-- Sanitation of SMILES and reaction SMARTS
-- Fetching of NCBI GenPept/UniProtKB IDs
+The validation functionality includes: - Calling the `mite_schema` functionality
+- Validation of reaction SMARTS (does the reaction SMARTS lead to the expected
+product when applied to a specified substrate) - Sanitation of SMILES and
+reaction SMARTS - Fetching of NCBI GenPept/UniProtKB IDs
 
 `mite_extras` can be used as a CLI to automatically update MITE entries.
-Furthermore, this repository can also be used as a library. For examples, see [mite_data](https://github.com/mite-standard/mite_data) or [mite_web](https://github.com/mite-standard/mite_web).
+Furthermore, this repository can also be used as a library. For examples, see
+[mite_data](https://github.com/mite-standard/mite_data) or
+[mite_web](https://github.com/mite-standard/mite_web).
 
-For errors, feature requests, and suggestions, please open an [Issue](https://github.com/mite-standard/mite_extras/issues) or start a discussion in the [MITE Discussion Forum](https://github.com/orgs/mite-standard/discussions/).
+For errors, feature requests, and suggestions, please open an
+[Issue](https://github.com/mite-standard/mite_extras/issues) or start a
+discussion in the [MITE Discussion
+Forum](https://github.com/orgs/mite-standard/discussions/).
 
 ## System Requirements
 
@@ -49,7 +59,8 @@ Local installation was tested on:
 
 #### Python dependencies
 
-Dependencies including exact versions are specified in the [pyproject.toml](./pyproject.toml) file.
+Dependencies including exact versions are specified in the
+[pyproject.toml](./pyproject.toml) file.
 
 ## Installation Guide
 
@@ -59,35 +70,41 @@ Dependencies including exact versions are specified in the [pyproject.toml](./py
 
 ## Quick Start
 
-To validate MITE entries or update them to a new schema versiom, run:
+To validate MITE entries or update them to a new schema version, run:
 
 - `mite_extras -i <input/> -o <output/>`
 
 ## Attribution
 
 ### License
 
-`mite_extras` is an open source tool licensed under the MIT license (see [LICENSE](LICENSE)).
+`mite_extras` is an open source tool licensed under the MIT license (see
+[LICENSE](LICENSE)).
 
 ### Publications
 
-See [CITATION.cff](CITATION.cff) or [MITE online](https://mite.bioinformatics.nl/) for information on citing MITE.
+See [CITATION.cff](CITATION.cff) or [MITE
+online](https://mite.bioinformatics.nl/) for information on citing MITE.
 
 ### Acknowledgements
 
-This work was supported by the Netherlands Organization for Scientific Research (NWO) KIC grant KICH1.LWV04.21.013.
+This work was supported by the Netherlands Organization for Scientific Research
+(NWO) KIC grant KICH1.LWV04.21.013.
 
 ## For Developers
 
-*Nota bene: for details on how to contribute to the MITE project, please refer to [CONTRIBUTING](CONTRIBUTING.md).*
+*Nota bene: for details on how to contribute to the MITE project, please refer
+to [CONTRIBUTING](CONTRIBUTING.md).*
 
 ### Package Installation
 
-*Please note that the development installation is only tested and supported on (Ubuntu) Linux.*
+*Please note that the development installation is only tested and supported on
+(Ubuntu) Linux.*
 
 ### With `uv` from GitHub
 
-*Note: assumes that `uv` is installed locally - see the methods described [here](https://docs.astral.sh/uv/getting-started/installation/).* 
+*Note: assumes that `uv` is installed locally - see the methods described
+[here](https://docs.astral.sh/uv/getting-started/installation/).*
 
 ```commandline
 git clone https://github.com/mite-standard/mite_extras
@@ -96,6 +113,7 @@ uv run pre-commit install
 ```
 
 All tests should be passing
+
 ```commandline
 uv run pytest
 ```
@@ -104,4 +122,7 @@ uv run pytest
 
 CI/CD via GitHub Actions runs on every PR and push to the `main` branch.
 
-A new release created on the [mite_extras](https://github.com/mite-standard/mite_extras) GitHub page will automatically relay changes to [PyPI](https://pypi.org/project/mite-extras/) and [Zenodo](https://doi.org/10.5281/zenodo.13941744).
+A new release created on the
+[mite_extras](https://github.com/mite-standard/mite_extras) GitHub page will
+automatically relay changes to [PyPI](https://pypi.org/project/mite-extras/) and
+[Zenodo](https://doi.org/10.5281/zenodo.13941744).
diff --git a/_typos.toml b/_typos.toml
@@ -0,0 +1,5 @@
+# typos exceptions for this repository
+# Prevent typos from flagging project-specific tokens and acronyms
+[default.extend-words]
+sur = "sur"
+NWO = "NWO"
diff --git a/prek.toml b/prek.toml
@@ -0,0 +1,91 @@
+# Configuration file for `prek`, a git hook framework written in Rust.
+# See https://prek.j178.dev for more information.
+#:schema https://www.schemastore.org/prek.json
+
+[[repos]]
+repo = "https://github.com/pre-commit/pre-commit-hooks"
+rev = "v6.0.0"
+hooks = [
+  { id = "check-added-large-files" },
+  { id = "check-ast" },
+  { id = "check-builtin-literals" },
+  { id = "check-case-conflict" },
+  { id = "check-docstring-first" },
+  { id = "check-executables-have-shebangs" },
+  { id = "check-illegal-windows-names" },
+  { id = "check-merge-conflict" },
+  { id = "check-symlinks" },
+  { id = "check-shebang-scripts-are-executable" },
+  { id = "check-symlinks" },
+  { id = "check-toml" },
+  { id = "check-xml" },
+  { id = "check-yaml" },
+  { id = "check-json", exclude = "^.devcontainer/devcontainer.json" },
+  {
+    id = "pretty-format-json",
+    exclude = "^.devcontainer/devcontainer.json",
+    args = ["--autofix"]
+  },
+  { id = "debug-statements" },
+  { id = "end-of-file-fixer" },
+  { id = "mixed-line-ending" },
+  { id = "pretty-format-json" },
+  { id = "trailing-whitespace" }
+]
+
+[[repos]]
+repo = "https://github.com/fpgmaas/deptry"
+rev = "0.25.1"
+hooks = [
+  {
+    id = "deptry",
+    language = "python",
+    additional_dependencies = ["deptry"],
+    exclude = '^(?!.*\.py$).*$'
+  }
+]
+
+[[repos]]
+repo = "https://github.com/python-jsonschema/check-jsonschema"
+rev = "0.37.4"
+hooks = [{ id = "check-github-workflows" }, { id = "check-taskfile" }]
+
+[[repos]]
+repo = "https://github.com/asottile/pyupgrade"
+rev = "v3.21.2"
+hooks = [{ id = "pyupgrade" }]
+
+[[repos]]
+repo = "https://github.com/asottile/add-trailing-comma"
+rev = "v4.0.0"
+hooks = [{ id = "add-trailing-comma" }]
+
+[[repos]]
+repo = "https://github.com/astral-sh/ruff-pre-commit"
+rev = "v0.15.21"
+hooks = [{ id = "ruff-check", args = ["--fix"] }, { id = "ruff-format" }]
+
+[[repos]]
+repo = "https://github.com/tombi-toml/tombi-pre-commit"
+rev = "v1.2.0"
+hooks = [{ id = "tombi-format", exclude = '^uv\.lock$' }, { id = "tombi-lint" }]
+
+[[repos]]
+repo = "https://github.com/crate-ci/typos"
+rev = "v1.48.0"
+hooks = [{ id = "typos" }]
+
+[[repos]]
+repo = "https://github.com/astral-sh/uv-pre-commit"
+rev = "0.11.29"
+hooks = [{ id = "uv-lock" }]
+
+[[repos]]
+repo = "https://github.com/zizmorcore/zizmor-pre-commit"
+rev = "v1.27.0"
+hooks = [{ id = "zizmor", entry = "zizmor --fix=all ." }]
+
+[[repos]]
+repo = "https://github.com/jolars/panache-pre-commit"
+rev = "v2.61.0"
+hooks = [{ id = "panache-format" }, { id = "panache-lint" }]