Release 0.1.2 — make geo-mcp actually work end-to-end

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  ci:
+    uses: MCPmed/.github/.github/workflows/reusable-python-ci.yml@main
+    with:
+      package-name: geomcp
+      python-versions: "['3.10','3.11','3.12']"
+      install-extras: "dev"
+      run-ruff: true
+      run-black: true
+      run-mypy: false
+      run-tests: true
+      coverage: true

.pre-commit-config.yaml

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+minimum_pre_commit_version: "3.5.0"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-added-large-files
+        args: ["--maxkb=1024"]
+      - id: mixed-line-ending
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.1.2] - 2026-04-17
+
+### Added
+
+- Regression test suite covering the import-time crash, URL scheme
+  handling for both `ftp://` and `https://`, `configure()` override
+  precedence, XDG defaults, and legacy config fallback.
+- `configure(**overrides)` runtime config API; CLI flags (`--email`,
+  `--api-key`, `--download-dir`, `--max-*`) now actually apply through
+  this path.
+- `GEOMCP_EMAIL`, `GEOMCP_API_KEY`, `GEOMCP_BASE_URL`, and
+  `GEOMCP_DOWNLOAD_DIR` environment variables as a config layer between
+  `config.json` and runtime overrides.
+- `.pre-commit-config.yaml`, `CHANGELOG.md`, `CONTRIBUTING.md`.
+- `.github/workflows/ci.yml` that delegates to the organization-wide
+  reusable Python CI workflow.
+
+### Changed
+
+- **Breaking (for the uncommon case):** default `download_dir` is now
+  `$XDG_DATA_HOME/geomcp/downloads` instead of `./downloads` resolved
+  relative to the installed package directory. Users with an existing
+  `~/.geo-mcp/config.json` are unaffected — that location is still
+  honored as a fallback, and an existing legacy file is also where
+  `geo-mcp --init` now writes to avoid orphaning existing installs.
+- `geo_downloader` config is now loaded lazily with four precedence
+  layers (runtime overrides → env vars → `config.json` → defaults).
+  Config is no longer read at module import time.
+- E-utilities calls (`esearch`, `efetch`, `esummary`) in both
+  `geo_downloader` and `geo_profiles` migrated from blocking `requests`
+  to `aiohttp`. The search path now shares the same config resolution
+  layer as the downloader (env vars, `configure()`, XDG `config.json`)
+  and no longer stalls the MCP stdio event loop on every tool call.
+- `geomcp.__version__` and `geo-mcp --version` are now read from
+  installed package metadata via `importlib.metadata`, so they stay in
+  sync with the wheel/tag instead of drifting from a hand-maintained
+  constant.
+- Classifier bumped from `Development Status :: 3 - Alpha` to
+  `Development Status :: 4 - Beta`.
+- License aligned: `pyproject.toml` and `README.md` badge now match
+  the BSD-3-Clause `LICENSE` file (they previously said MIT).
+
+### Fixed
+
+- **Downloads broken for every valid accession since mid-2024.** NCBI
+  retired its anonymous FTP endpoint and E-utilities now returns
+  `https://ftp.ncbi.nlm.nih.gov/...` URLs. The old regex only matched
+  `ftp://` and silently dropped every response, producing spurious
+  "no downloadable SOFT file exposed" errors. URL extraction now
+  accepts both schemes and normalises to `https://`.
+- **Package could not be imported without a pre-existing `config.json`.**
+  `geo_downloader` ran `_load_config()` at module scope and called
+  `sys.exit(1)` if `email` was missing, breaking pytest, mypy, and any
+  environment without a config file.
+- **First-run bootstrap was broken.** `main.setup_environment()`
+  tried to copy a `config_template.json` that does not exist in the
+  package, then `sys.exit(1)`ed.
+- `pytest.ini` `testpaths` pointed at `geo_mcp_server/test`, a
+  directory that no longer exists — pytest silently collected zero
+  tests. Repointed to `tests/`.
+- `asyncio.Semaphore` for concurrent downloads no longer lives at
+  module scope; it is now created per event loop, preventing
+  "attached to a different loop" errors under MCP stdio.
+- `main.py` no longer `os.chdir()`s the process into the install
+  directory or prepends a fictional `.venv/bin` to `PATH`.
+- Pre-existing ruff errors (`F401`, `F841`, `E401`) and black
+  formatting inconsistencies across the package were cleaned up so CI
+  is green on the first run.
+- README examples no longer reference the long-gone `geo_mcp_server/`
+  source layout, the pre-CLI `python main.py --mode stdio` invocation,
+  or port 8000 (the HTTP server runs on 8001).
+
+### Removed
+
+- Duplicate release workflow (`python-publish.yml` overlapped with
+  `pypi-publish.yml`; both fired on `release: published` and would
+  double-upload).
+- Broken `test.yml` workflow that invoked pytest against a
+  non-existent `geo_mcp_server/test/` directory.
+- Stale `.github/WORKFLOWS.md` that documented a workflow layout the
+  repo never actually had.
+- Dead download helpers in `geo_profiles` (legacy-FTP-URL
+  `download_geo_data`, `list_downloaded_datasets`, `get_download_stats`),
+  superseded by their async equivalents in `geo_downloader`.
+
+## [0.1.1] - 2025
+
+Initial tagged release on PyPI.