Fix CI: install test deps and require Python 3.11+

.github/workflows/ci.yml

@@ -15,10 +15,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - run: python -m pip install -e '.[dev]'
       - run: make release-check

CHANGELOG.md

@@ -4,6 +4,20 @@ All notable changes to this project are documented in this file. The format
 follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and the
 project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Changed
+
+- Require Python 3.11+. `check_release_metadata.py` uses `tomllib`, which is in
+  the standard library only on Python 3.11 and newer. The CI matrix now covers
+  Python 3.11 through 3.13.
+
+### Fixed
+
+- CI installs the package and dev extras before `make release-check`, so the
+  release gate runs. Previously the workflow had no install step and stopped on
+  a missing `pytest`.
+
 ## [0.1.0] - 2026-05-26
 
 Initial public release. Agentic harness for discovering biosynthetic pathways

docs/AGENT_INSTALL.md

@@ -52,7 +52,7 @@ or `goal` for different orchestrator conventions.
 Any agent that can read repository files works the same way. Point it at
 the checkout, ask it to read `skills/bioprospector/SKILL.md`, `README.md`,
 and the docs index, then have it write outputs under `.runtime/`. The
-skill's CLIs run with stock Python 3.10+ and no third-party dependencies.
+skill's CLIs run with stock Python 3.11+ and no third-party dependencies.
 
 ## Quick Sanity Check
 

docs/OPTIONAL_TOOLS.md

@@ -1,6 +1,6 @@
 # Optional Tools
 
-BioProspector itself depends only on Python 3.10+ and a POSIX shell. The
+BioProspector itself depends only on Python 3.11+ and a POSIX shell. The
 local doctor reports the availability of several optional tools that the
 skill can use when present. None of them are required for the planning path
 or release checks; they unlock more lanes when an operator decides to run

docs/QUICKSTART.md

@@ -42,7 +42,7 @@ the skill.
 
 Prerequisites:
 
-- Python 3.10 or newer.
+- Python 3.11 or newer.
 - `make` and a POSIX shell for the bundled local command targets.
 - `git` for tracked-file hygiene checks.
 - Run commands from the repository root unless a command says otherwise.

pyproject.toml

@@ -7,7 +7,7 @@ name = "biosymphony-bioprospector"
 version = "0.1.0"
 description = "An agentic harness for discovering biosynthetic pathways to target molecules: enzyme mining, pathway stitching, host-fit review, construct hypotheses, and compute-portable work graphs."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = { file = "LICENSE" }
 authors = [{ name = "BioSymphony" }]
 keywords = [
@@ -22,7 +22,6 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: MIT License",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",

scripts/check_release_metadata.py

@@ -47,8 +47,8 @@ def issues(root: Path) -> list[str]:
             out.append(f"missing optional dependency group: {key}")
     if "biosymphony-bioprospector" != project.get("name"):
         out.append("unexpected project name")
-    if project.get("requires-python") != ">=3.10":
-        out.append("requires-python should stay >=3.10 unless CI/docs are updated")
+    if project.get("requires-python") != ">=3.11":
+        out.append("requires-python should stay >=3.11 unless CI/docs are updated")
     return out
 
 

skills/bioprospector/scripts/bioprospector_doctor.py

@@ -157,9 +157,9 @@ def doctor(root: Path, include_runtime: bool) -> dict[str, Any]:
     root = root.resolve()
     checks = {
         "python": {
-            "ok": sys.version_info >= (3, 10),
+            "ok": sys.version_info >= (3, 11),
             "version": f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}",
-            "minimum": "3.10",
+            "minimum": "3.11",
         },
         "schema": check_schema(root),
         "scripts": check_scripts(root),