sim-atlas 0.0.1__tar.gz

sim_atlas-0.0.1/.gitignore

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+*.json
+*.pkl
+
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+# pdm
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+# Celery stuff
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+# SageMath parsed files
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+# Environments
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+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
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+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
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+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,python,node
+.sim_atlas/
+
+*.toml

sim_atlas-0.0.1/.gitlab-ci.yml

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+workflow:
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "push"'
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+
+variables:
+  SIM_ATLAS_JWT_SECRET: "ci-dummy-secret"
+  SIM_ATLAS_LLM_API_KEY: "ci-dummy-api-key"
+  SIM_ATLAS_LLM_BASE_URL: "http://localhost:11434/v1"
+  SIM_ATLAS_LLM_EMBEDDING_MODEL: "ci-dummy-embedding-model"
+  SIM_ATLAS_LLM_CHAT_MODEL: "ci-dummy-chat-model"
+  SIM_ATLAS_VOYAGE_API_KEY: "ci-dummy-voyage-api-key"
+
+default:
+  interruptible: true
+
+backend_lint_and_type_check:
+  image: python:3.12
+  before_script:
+    - python -m pip install --upgrade pip
+    - python -m pip install uv
+  script:
+    - cd backend
+    - uv sync --dev
+    - uv run ruff check .
+    - uv run ruff format --check .
+    - uv run pyright
+
+backend_test_and_coverage:
+  image: python:3.12
+  before_script:
+    - python -m pip install --upgrade pip
+    - python -m pip install uv
+  script:
+    - cd backend
+    - uv sync --dev
+    - uv run coverage run -m pytest
+    - uv run coverage report
+    - uv run coverage html
+  coverage: '/TOTAL.*\s+(\d+%)$/'
+  artifacts:
+    paths:
+      - backend/htmlcov/
+    expose_as: Coverage Report

sim_atlas-0.0.1/AGENTS.md

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+# backend
+
+FastAPI REST API with MCP tool exposure and AI integration.
+
+## Commands
+
+```bash
+uv run pytest                           # run tests
+uv run coverage run -m pytest           # run tests with coverage
+uv run ruff check .                     # lint
+uv run ruff format --check .            # check formatting
+uv run pyright                          # type-check (strict mode)
+```
+
+## Key Patterns
+
+- **Storage**: always interact via `storage_interface.py` (`StorageInterface`), never directly via `file_system_storage.py`; use `get_storage_backend()` (also in `storage_interface.py`) to instantiate the backend
+- **Dependency injection**: use `Depends()` for storage (`get_storage` in `main.py`) and auth (`get_current_user` in `security.py`); settings are NOT injected via `Depends()` — call `load_settings()` directly (it is `lru_cache`-cached)
+- **Models**: Pydantic v2; all schemas in `models.py`; three distinct types: `NodeRequest` (API write input), `NodeMetadata` (internal storage schema), `NodeResponse` (API read output); `NdArray` is a custom Pydantic type for gzip-compressed numpy arrays (embeddings)
+- **Auth**: JWT tokens carried in `x-api-key` header; `get_current_user` dependency enforces auth on write routes; read routes are public
+- **MCP**: only `semantic_search`, `hybrid_search`, and `agent_stream` are exposed as MCP tools (see `include_operations` in `main.py`); keep those route signatures clean — they double as tool signatures
+- **AI**: docstring enrichment via OpenAI-compatible API (`ai.py`); embeddings via VoyageAI (`voyage_ai.py`); agent in `agent/` — SSE streaming (`_sse.py`), agentic loop (`_runner.py`), system prompt (`_prompt.py`), observability (`_observability.py`), tools in `agent/tools/`; all AI features raise `AINotConfiguredError` (from `exceptions.py`) when the required settings are absent
+- **Config**: all settings via `settings.py` (`pydantic-settings`); loaded from TOML files at `/etc/sim_atlas/config.toml`, `~/.sim_atlas/config.toml`, or `.sim_atlas/config.toml`; never hardcode secrets or URLs
+- **CLI**: entry points live in `cli/` (`server.py` starts the server, `token.py` issues JWT tokens)
+
+## Libraries
+
+- **pydantic**: [Documentation](https://pydantic.dev/docs/validation/latest/llms.txt)
+- **pydantic-settings**: [Documentation](https://pydantic.dev/docs/validation/latest/llms.txt)
+- **langfuse**: [Documentation](https://langfuse.com/llms-docs.txt)
+
+## Think Before Coding
+
+**Don't assume. Don't hide confusion. Surface tradeoffs.**
+
+Before implementing:
+- State your assumptions explicitly. If uncertain, ask.
+- If multiple interpretations exist, present them - don't pick silently.
+- If a simpler approach exists, say so. Push back when warranted.
+- If something is unclear, stop. Name what's confusing. Ask.
+
+## Simplicity First
+
+**Minimum code that solves the problem. Nothing speculative.**
+
+- No features beyond what was asked.
+- No abstractions for single-use code.
+- No "flexibility" or "configurability" that wasn't requested.
+- No error handling for impossible scenarios.
+- If you write 200 lines and it could be 50, rewrite it.
+
+Ask yourself: "Would a senior engineer say this is overcomplicated?" If yes, simplify.
+
+## Surgical Changes
+
+**Touch only what you must. Clean up only your own mess.**
+
+When editing existing code:
+- Don't "improve" adjacent code, comments, or formatting.
+- Don't refactor things that aren't broken.
+- Match existing style, even if you'd do it differently.
+- If you notice unrelated dead code, mention it - don't delete it.
+
+When your changes create orphans:
+- Remove imports/variables/functions that YOUR changes made unused.
+- Don't remove pre-existing dead code unless asked.
+
+The test: Every changed line should trace directly to the user's request.
+
+## Code Quality — Write It Right First Time
+
+**Run `uv run ruff check . && uv run ruff format --check . && uv run pyright` before declaring done. Fix all errors before moving on.**
+
+### Type safety (Pyright strict)
+- Annotate every function parameter and return type — no implicit `Any`.
+- Use `X | Y` union syntax (Python 3.10+), never `Optional[X]` or `Union[X, Y]`.
+- Prefer `X | None` over wrapping in `Optional`.
+- Use `list[X]`, `dict[K, V]`, `tuple[X, ...]` (lowercase), not `List`, `Dict`, `Tuple` from `typing`.
+- Only import from `typing` what has no builtin equivalent: `TypeVar`, `Protocol`, `TypedDict`, `Literal`, `overload`, `cast`, `TYPE_CHECKING`.
+- Narrow types explicitly with `isinstance` checks or `assert` before use; don't cast blindly.
+- Never use `# type: ignore` without a specific error code and a comment explaining why.
+
+### Ruff lint rules enforced (see pyproject.toml)
+- **UP**: use modern Python syntax — `X | Y`, `type` aliases, `match` where appropriate.
+- **I**: imports are sorted — stdlib → third-party → local, one blank line between groups.
+- **F**: no unused imports or variables; remove them (don't comment them out).
+- **B**: no mutable default arguments, no `assert` in production logic.
+- **SIM**: simplify boolean returns, `if`/`else` chains, and `with` blocks.
+- **C4**: prefer comprehensions over `map`/`filter`; avoid unnecessary `list()` wrapping.
+- **ERA**: no commented-out code.
+- **PL**: Pylint rules — avoid too-many-branches, too-many-return-statements, etc.
+
+### Formatting (ruff format)
+- 88-character line limit (E501 is ignored so long lines won't error, but keep them readable).
+- Use double quotes for strings.
+- Trailing commas in multi-line collections.
+
+## Goal-Driven Execution
+
+**Define success criteria. Loop until verified.**
+
+Transform tasks into verifiable goals:
+- "Add validation" → "Write tests for invalid inputs, then make them pass"
+- "Fix the bug" → "Write a test that reproduces it, then make it pass"
+- "Refactor X" → "Ensure tests pass before and after"
+
+For multi-step tasks, state a brief plan:
+```
+1. [Step] → verify: [check]
+2. [Step] → verify: [check]
+3. [Step] → verify: [check]
+```
+
+Strong success criteria let you loop independently. Weak criteria ("make it work") require constant clarification.

sim_atlas-0.0.1/CLAUDE.md

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+AGENTS.md

sim_atlas-0.0.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, Sebastian Eibl
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

sim_atlas-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: sim-atlas
+Version: 0.0.1
+Summary: Search and discovery platform for simulation nodes — Python functions, workflow definitions, and pyiron nodes used in scientific computing.
+Author-email: Sebastian Eibl <sebastian.eibl@mpcdf.mpg.de>
+Maintainer-email: Sebastian Eibl <sebastian.eibl@mpcdf.mpg.de>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: pyiron
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Web Environment
+Classifier: Framework :: FastAPI
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.12
+Requires-Dist: fastapi-mcp>=0.4.0
+Requires-Dist: fastapi[standard]>=0.122.0
+Requires-Dist: langfuse>=4.6.1
+Requires-Dist: numpy>=1.21
+Requires-Dist: openai>=2.8.1
+Requires-Dist: pydantic-settings[toml]>=2.13.1
+Requires-Dist: pyjwt>=2.12.1
+Requires-Dist: python-workflow-definition>=0.1.2
+Requires-Dist: tqdm>=4.67.3
+Requires-Dist: voyageai>=0.3.7

sim_atlas-0.0.1/pyproject.toml

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+[project]
+name = "sim-atlas"
+version = "0.0.1"
+description = "Search and discovery platform for simulation nodes — Python functions, workflow definitions, and pyiron nodes used in scientific computing."
+authors = [
+  { name = "Sebastian Eibl", email = "sebastian.eibl@mpcdf.mpg.de"},
+]
+maintainers = [
+  { name = "Sebastian Eibl", email = "sebastian.eibl@mpcdf.mpg.de"},
+]
+readme = "README.md"
+requires-python = ">=3.12"
+license = "BSD-3-Clause"
+license-files = ["LICEN[CS]E*"]
+keywords = ["pyiron"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Web Environment",
+    "Framework :: FastAPI",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+dependencies = [
+    "fastapi-mcp>=0.4.0",
+    "fastapi[standard]>=0.122.0",
+    "langfuse>=4.6.1",
+    "numpy>=1.21",
+    "openai>=2.8.1",
+    "pydantic-settings[toml]>=2.13.1",
+    "pyjwt>=2.12.1",
+    "python-workflow-definition>=0.1.2",
+    "tqdm>=4.67.3",
+    "voyageai>=0.3.7",
+]
+
+[dependency-groups]
+dev = [
+    "coverage>=7.13.5",
+    "pyright>=1.1.407",
+    "pytest>=9.0.2",
+    "ruff>=0.14.6",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project.scripts]
+sim-atlas-access-token = "sim_atlas.cli:token"
+sim-atlas = "sim_atlas.cli:backend"
+
+[tool.fastapi]
+entrypoint = "sim_atlas.main:app"
+
+[tool.ruff.lint]
+select = [
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # flake8-comprehensions
+    "C4",
+    # eradicate
+    "ERA",
+    # pylint
+    "PL",
+]
+ignore = [
+    "E501",  # line too long
+    "PLR0912", # Too many branches
+    "PLR0915", # Too many statements
+    "PLR0913", # Too many arguments in function definition
+]
+
+[tool.pyright]
+typeCheckingMode = "strict"
+reportMissingTypeStubs = false
+
+[pytest]
+strict = true
+
+[[tool.uv.index]]
+name = "testpypi"
+url = "https://test.pypi.org/simple/"
+publish-url = "https://test.pypi.org/legacy/"
+explicit = true

sim_atlas-0.0.1/src/sim_atlas/agent/__init__.py

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+from ._runner import run_agent_stream
+
+__all__ = ["run_agent_stream"]