involve-benchling 0.1.0a1__tar.gz

involve_benchling-0.1.0a1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: Install
+        run: pip install -e ".[dev]"
+      - name: Lint
+        run: |
+          ruff check src tests
+          ruff format --check src tests
+      - name: Type check
+        run: mypy
+      - name: Unit tests
+        run: pytest --cov --cov-report=term-missing

involve_benchling-0.1.0a1/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+venv/
+.venv/
+.mypy_cache/
+.ruff_cache/
+.pytest_cache/
+.coverage
+htmlcov/
+.test.env
+.env
+.DS_Store
+.benchling-cache/
+CLAUDE.local.md
+.claude/settings.local.json

involve_benchling-0.1.0a1/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: detect-private-key

involve_benchling-0.1.0a1/.test.env.template

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+# Copy to .test.env and fill in. Never commit .test.env.
+BENCHLING_BASE_URL=https://yourtenant.benchling.com
+BENCHLING_API_KEY=
+# or OAuth:
+BENCHLING_OAUTH_CLIENT_ID=
+BENCHLING_OAUTH_CLIENT_SECRET=
+BENCHLING_REGISTRY_NAME=

involve_benchling-0.1.0a1/AGENTS.md

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+# Agent guide
+
+Instructions for AI coding agents working in this repository. Human
+contributors should read [CONTRIBUTING.md](CONTRIBUTING.md), which this file
+follows.
+
+## Project
+
+involve-benchling is a typed Python library over `benchling-v3-sdk-python`.
+It adds caching, name resolution, dataframes, read-only clients and pytest
+utilities, and it never hides the SDK. Functions accept and return SDK
+objects.
+
+| Path | Contents |
+|---|---|
+| `src/involve_benchling/core/` | `BenchlingConfig`, `connect()`, the read-only `httpx` transport |
+| `src/involve_benchling/cache/` | Cache facade, policy, memory and disk backends |
+| `src/involve_benchling/resolve/` | Generic lookups over any `list` resource |
+| `src/involve_benchling/dataframes.py` | pandas adapters (optional extra) |
+| `src/involve_benchling/testing/` | pytest plugin and `ResourceTracker` |
+| `tests/fixtures/` | Shared fakes, builders and a canned tenant |
+| `docs/design/` | Design documents for planned modules |
+
+## Commands
+
+```bash
+make install   # editable install with dev extras
+make lint      # ruff
+make type      # mypy --strict
+make test      # unit tests; no credentials
+```
+
+Run `make lint type test` before you finish. All three must pass.
+
+## Rules
+
+- Pass SDK models through. Don't add wrapper dataclasses for Benchling
+  resources.
+- Keep helpers generic over resources rather than writing one per resource.
+- Type and document every public function. mypy runs in strict mode.
+- Never use pickle. Cached values are JSON.
+- Core depends only on the SDK, `httpx` and `pydantic`. Anything else is an
+  optional extra imported inside the function that needs it.
+- Unit tests must not touch the network or need credentials. Use the
+  fixtures in `tests/fixtures/` instead of new fakes.
+- Mark tests that need a tenant `@pytest.mark.integration`. Never run them
+  unless asked, because they write to the tenant.
+- Add a `docs/CHANGELOG.md` entry for every user-visible change.
+- Never commit `.test.env`, credentials, tenant URLs or data from a real
+  tenant. Examples use `example.benchling.com`.
+
+## Style
+
+- Line length is 100. Ruff formats the code.
+- Write docstrings in plain present tense, saying what the function does.
+- Keep comments short and about current behaviour.

involve_benchling-0.1.0a1/CLAUDE.md

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+@AGENTS.md

involve_benchling-0.1.0a1/CONTRIBUTING.md

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+# Contributing
+
+Thanks for helping. Bug reports, fixes and new helpers are all welcome. For a
+larger change, open an issue first so we can agree on the shape before you
+write it.
+
+## Ground rules
+
+- **Pass through SDK models.** Never introduce wrapper dataclasses for
+  Benchling resources.
+- **Generic over bespoke.** Prefer helpers that work on any resource to
+  per-resource code.
+- **Every public function is typed and documented.** CI runs mypy
+  `--strict` and ruff.
+- **Unit tests run with zero credentials.** Anything touching a real
+  tenant is marked `@pytest.mark.integration`.
+- **Optional dependencies stay optional.** Import them inside the function
+  that needs them and declare them as an extra in `pyproject.toml`.
+
+## Setup
+
+```bash
+python -m venv venv && source venv/bin/activate
+make install          # pip install -e ".[dev]"
+pre-commit install    # optional: ruff and file checks on every commit
+```
+
+## Checks
+
+```bash
+make lint             # ruff check and ruff format --check
+make type             # mypy --strict
+make test             # unit tests, no credentials needed
+make test-all         # unit and integration tests
+```
+
+Integration tests need a tenant. Copy `.test.env.template` to `.test.env`
+and fill it in. Use a sandbox tenant, because the tests create and archive
+resources.
+
+## Pull requests
+
+A pull request needs:
+
+- passing CI
+- a test for every behaviour change
+- an entry under `docs/CHANGELOG.md`
+- docstrings for any new public function
+
+Keep each pull request to one change.
+
+## Test fixtures
+
+Shared fixtures live in `tests/fixtures/` and are registered by
+`tests/conftest.py`. Use them instead of defining fakes inside test files.
+
+| Module | Provides |
+|---|---|
+| `builders` | V3 wire-format payloads (`text_value`, `link_value`, `custom_entity_payload`, ...) and real SDK models built from them (`custom_entity`, `field_definitions`) |
+| `fakes` | `FakeResource` (applies `name_any_of`, `id_any_of`, `schema_eq` and records calls), `UnfilteredResource`, `FakeSchemaResource`, `FakeClock` |
+| `config` | `clean_env`, `api_key_env`, `api_key_config`, `oauth_config` |
+| `cache` | `clock` (freezes cache time; `clock.advance(s)` expires entries), `cache_dir`, `memory_backend`, `disk_backend`, `tiered_backend`, `cache_policy`, `memory_cache`, `disk_cache` |
+| `tenant` | A canned plasmid tenant: `plasmid_field_definitions`, `plasmids`, `entity_resource`, `unfiltered_resource`, `schema_resource` |
+
+Unit tests run with every `BENCHLING_*` variable removed
+(`tests/unit/conftest.py`). Use `clock` rather than `time.sleep` for TTL
+tests.
+
+These fixtures are private to this repo. The shipped
+`involve_benchling.testing` plugin provides the live-tenant fixtures
+(`benchling_config`, `benchling`, `benchling_tracker`) for integration tests.
+
+## Security
+
+Report vulnerabilities privately, as described in [SECURITY.md](SECURITY.md).

involve_benchling-0.1.0a1/LICENSE

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involve_benchling-0.1.0a1/Makefile

@@ -0,0 +1,20 @@
+.PHONY: install lint type test test-all cov
+
+install:
+	pip install -e ".[dev]"
+
+lint:
+	ruff check src tests
+	ruff format --check src tests
+
+type:
+	mypy
+
+test:
+	pytest
+
+test-all:
+	pytest -m ""
+
+cov:
+	pytest --cov --cov-report=term-missing

involve_benchling-0.1.0a1/PKG-INFO

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+Metadata-Version: 2.5
+Name: involve-benchling
+Version: 0.1.0a1
+Summary: Caching, name resolution, dataframes, read-only clients and testing utilities for the Benchling V3 Python SDK.
+Project-URL: Homepage, https://github.com/involvedata/involve-benchling
+Project-URL: Repository, https://github.com/involvedata/involve-benchling.git
+Project-URL: Issues, https://github.com/involvedata/involve-benchling/issues
+Project-URL: Changelog, https://github.com/involvedata/involve-benchling/blob/main/docs/CHANGELOG.md
+Author: Involve Data
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: api,benchling,biology,biotech,laboratory,lims,sdk
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: benchling-v3-sdk-python>=15.0.0
+Requires-Dist: httpx>=0.27
+Requires-Dist: pydantic>=2.0
+Provides-Extra: dev
+Requires-Dist: mypy>=1.11; extra == 'dev'
+Requires-Dist: pandas>=2.0; extra == 'dev'
+Requires-Dist: pre-commit>=3.0; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Provides-Extra: pandas
+Requires-Dist: pandas>=2.0; extra == 'pandas'
+Provides-Extra: testing
+Requires-Dist: pytest>=8.0; extra == 'testing'
+Description-Content-Type: text/markdown
+
+# involve-benchling
+
+**The toolkit the official Benchling SDK doesn't give you.**
+
+A thin, composable layer over [`benchling-v3-sdk-python`](https://pypi.org/project/benchling-v3-sdk-python/)
+— it never hides the SDK. You keep Benchling's typed models, pagination,
+and full API surface; this library adds what's missing around them.
+
+> **Status: alpha.** The API may change before 1.0. See the [changelog](https://github.com/involvedata/involve-benchling/blob/main/docs/CHANGELOG.md).
+
+involve-benchling is an independent project. It is not affiliated with or endorsed by
+Benchling, Inc.
+
+## Why
+
+The Benchling V3 SDK is a complete API client. Teams that build on it tend to
+rebuild the same pieces around it:
+
+| Pillar | Module | What it gives you |
+|---|---|---|
+| **Caching** | `involve_benchling.cache` | Tiered (memory + disk, shared across processes), pickle-free JSON serialisation of SDK models, per-category TTLs. Reference data (schemas, dropdowns, registries) goes from ~500ms to <1ms. |
+| **Resolution** | `involve_benchling.resolve` | Generic `get_by_name` / `find_one` over *any* V3 resource, with typed `NotFoundError` / `AmbiguousError` instead of silent first-match. |
+| **DataFrames** | `involve_benchling.dataframes` | Explicit `to_dataframe()` that expands V3 `schemaFields` into one typed, named column per field. Optional extra. |
+| **Read-only clients** | `involve_benchling.core.readonly` | A client that cannot change tenant data, enforced in the HTTP transport below every SDK method. |
+| **Testing** | `involve_benchling.testing` | pytest plugin: env-based config/client fixtures and a `benchling_tracker` that cleans up every resource a test created — even on failure. |
+
+## Install
+
+```bash
+pip install involve-benchling              # core (the SDK and its own dependencies)
+pip install "involve-benchling[pandas]"    # + dataframe support
+```
+
+## Quick start
+
+```python
+from involve_benchling import BenchlingConfig, connect, resolve
+
+config = BenchlingConfig.from_env()   # BENCHLING_BASE_URL, BENCHLING_API_KEY, ...
+benchling = connect(config)           # a plain benchling_v3_sdk.Benchling
+
+# The SDK is right there — use it directly:
+for seq in benchling.dna_sequence.list(page_size=50):
+    print(seq.id, seq.name)
+
+# Resolution with typed errors, over any resource:
+plasmid = resolve.get_by_name(benchling.custom_entity, "pEX-001")
+schema_id = resolve.get_id_by_name(benchling.entity_schema, "Plasmid")
+
+# Caching reference data:
+from involve_benchling.cache import BenchlingCache
+
+cache = BenchlingCache.from_policy(config.cache, namespace=config.base_url)
+schemas = cache.get_or_fetch(
+    "schemas:entity",
+    category="schema",
+    fetch=lambda: list(benchling.entity_schema.list()),
+)
+
+# Analysis-ready dataframes:
+from involve_benchling.dataframes import field_names, to_dataframe
+
+df = to_dataframe(
+    benchling.custom_entity.list(schema_eq=schema_id),
+    field_names=field_names(benchling.custom_entity_schema, schema_id),
+)
+```
+
+### Read-only clients
+
+```python
+config = BenchlingConfig.from_env(read_only=True)   # or BENCHLING_READ_ONLY=1
+benchling = connect(config)
+
+benchling.folder.list()                     # fine
+benchling.folder.create(name="x", parent_id="lib_1")
+# ReadOnlyViolationError: Read-only client blocked POST .../api/v3/folder/items
+```
+
+The check sits in the `httpx` transport, below every SDK method. A
+read-only client sends only `GET`, `HEAD` and `OPTIONS`, plus `POST` to the
+OAuth token exchange and `/api/v3/search`, which read without changing data.
+Raw-response calls and methods added in later SDK releases are covered without
+a list of write verbs to maintain.
+
+### Cache storage
+
+The disk tier defaults to `.benchling-cache/` in the working directory. It
+creates the directory and its files readable only by the current user, and
+writes a `.gitignore` into it so the cache is never committed. Cached
+responses can hold sensitive data, so point `CachePolicy.directory` somewhere
+protected.
+
+The cache is keyed by `namespace` (usually the tenant URL), not by
+credential. Don't share one cache directory between credentials with
+different access, or a narrower credential can read what a broader one
+cached.
+
+### Testing your own Benchling integrations
+
+```python
+import pytest
+
+@pytest.mark.integration
+def test_my_workflow(benchling, benchling_tracker):
+    entity = benchling.custom_entity.create(...)
+    benchling_tracker.track(
+        f"custom_entity {entity.id}",
+        lambda: benchling.custom_entity.update(
+            entity.id, archived=True, archive_reason="Made in error"
+        ),
+    )
+    # ... test things; cleanup happens even if assertions fail
+```
+
+## Design principles
+
+1. **Pass through SDK models.** No parallel dataclass universe; functions
+   accept and return `benchling_v3_sdk` types.
+2. **Generic over bespoke.** One `get_by_name` for 100+ resources, not
+   one service class per resource.
+3. **Explicit APIs.** No magic kwargs, no hidden state. Strictly typed
+   (`py.typed`, mypy `--strict`).
+4. **Everything optional is an extra.** Core depends on the SDK and
+   nothing else.
+5. **No pickle.** Cached values are JSON documents; a shared cache
+   directory is never a code-execution vector.
+
+## Roadmap
+
+- `config` — configuration as code: export, plan and apply tenant configuration from
+  YAML state files. Design: [`docs/design/config-as-code.md`](https://github.com/involvedata/involve-benchling/blob/main/docs/design/config-as-code.md).
+- `tools.discovery` — tenant environment discovery: schemas, dropdowns,
+  relationships; ERD and documentation generation.
+- `tools.entry_search` — entry search with automatic user/project
+  resolution.
+- Cache invalidation hooks for write operations.
+- Async parity helpers for `AsyncBenchling`.
+
+## Development
+
+```bash
+python -m venv venv && source venv/bin/activate
+make install   # pip install -e ".[dev]"
+make lint type test
+```
+
+Integration tests need a tenant. Copy `.test.env.template` to `.test.env`,
+fill it in, then run `pytest -m integration`. See [CONTRIBUTING.md](https://github.com/involvedata/involve-benchling/blob/main/CONTRIBUTING.md)
+for the full workflow.
+
+## License
+
+Apache-2.0 © Involve Data