biocomposer 0.1.0__tar.gz

biocomposer-0.1.0/.env.example

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+GEMINI_API_KEY=
+GOOGLE_API_KEY=        
+ANTHROPIC_API_KEY=
+OPENAI_API_KEY=
+
+
+PIPELINE_TEMP_DIR=.pipeline_temp          # scratch dir: downloads, connectors file
+PIPELINE_STATE_PATH=.pipeline_temp/pipeline_state.json   # persisted node I/O state
+PIPELINE_CONNECTORS=.pipeline_temp/connectors.py         # auto-generated connector functions
+PIPELINE_RESULTS_BASE=.pipeline_temp      # root dir for tool output subdirs
+
+BIOCOMPOSER_LOG_LEVEL=DEBUG

biocomposer-0.1.0/.github/workflows/docs.yml

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+name: Docs
+
+# Build the Sphinx docs and publish them to GitHub Pages.
+on:
+  push:
+    branches: [main, modal_bv_integration]   # build on pushes to these branches
+    paths: ["docs/**", "biocomposer/**", ".github/workflows/docs.yml"]
+  workflow_dispatch:                          # allow manual runs from the Actions tab
+
+# Permissions the Pages deploy needs.
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Only one Pages deploy at a time.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          pip install -r docs/requirements.txt
+          pip install -e .          # autodoc imports biocomposer at build time
+
+      - name: Build HTML
+        run: sphinx-build -b html docs docs/_build/html
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

biocomposer-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+# Publishes the biocomposer package to PyPI when a GitHub Release is published.
+# Auth uses PyPI Trusted Publishing (OIDC) — no API token stored. You must
+# register this repo as a trusted publisher once at:
+#   https://pypi.org/manage/project/biocomposer/settings/publishing/
+#   (or the "pending publisher" form if the project doesn't exist on PyPI yet)
+# with workflow filename "publish.yml" and environment "pypi".
+
+on:
+  release:
+    types: [published]
+  # Manual dry-run: Actions tab -> "Publish to PyPI" -> Run workflow.
+  # This builds and uploads to TestPyPI only (never real PyPI).
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # setuptools-scm needs full history + tags to derive the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build sdist and wheel
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Check distribution metadata
+        run: |
+          python -m pip install --upgrade twine
+          python -m twine check dist/*
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    # Real PyPI only on a published GitHub Release — never on the manual dry-run.
+    if: github.event_name == 'release'
+    # The environment name must match the one configured on PyPI's trusted publisher.
+    environment:
+      name: pypi
+      url: https://pypi.org/project/biocomposer/
+    permissions:
+      id-token: write  # required for OIDC trusted publishing
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  testpypi:
+    name: Publish to TestPyPI (dry-run)
+    needs: build
+    runs-on: ubuntu-latest
+    # Dry-run target — only the manual "Run workflow" dispatch hits TestPyPI.
+    if: github.event_name == 'workflow_dispatch'
+    # Needs its own trusted-publisher registration on test.pypi.org and a
+    # matching "testpypi" GitHub environment.
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/biocomposer/
+    permissions:
+      id-token: write  # required for OIDC trusted publishing
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

biocomposer-0.1.0/.gitignore

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+.env
+.env.local
+.pipeline_temp/
+__pycache__/
+*.pyc
+/project-context/
+candidate-model-library/colabfold_out/
+.venv/
+tools/__pycache__/
+.bv/
+.claude/
+bv_test.py
+bv.lock
+bv.toml
+fasttree_stdout.txt
+helpers/__pycache__/
+bvx-proto/bvx/__pycache__
+model_glue.egg-info/
+results/
+proteinmpnn_1.0.1.toml
+rfdiffusion_1.1.0.toml
+run/testing_if_new_tools_work.py
+# Sphinx build output
+docs/_build/
+ViennaRNA/
+fpocket/
+biocomposer.egg-info/
+biocomposer/_version.py
+autodockvina/
+acpype/
+pipeline_agent.py
+openbabel/
+gromacs/
+fpocket/

biocomposer-0.1.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

biocomposer-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: biocomposer
+Version: 0.1.0
+Summary: LLM-wired bioinformatics pipeline orchestration over containerised tools
+Requires-Python: >=3.10
+Requires-Dist: python-dotenv
+Requires-Dist: google-genai
+Requires-Dist: google-generativeai
+Requires-Dist: anthropic
+Requires-Dist: openai
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: tomli; python_version < "3.11"
+Requires-Dist: modal
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"

biocomposer-0.1.0/README.md

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+# Setup (both local and Modal)
+
+```
+pip install -e .
+mkdir inputs              # put your FASTA/PDB/etc. files here
+mkdir run                 # holds your pipeline script
+```
+
+Create a `.env` file in your working directory with the API key(s) you use
+(`GEMINI_API_KEY`, `GOOGLE_API_KEY`, `ANTHROPIC_API_KEY`, or `OPENAI_API_KEY`).
+
+Create `run/run_pipeline.py` to define your pipeline.
+
+# Running locally
+
+Prerequisites: Docker installed and running, `bv` installed (`cargo install biov`).
+
+```
+biocomp run run/run_pipeline.py --env .env
+```
+
+Outputs go to `./results/`.
+
+# Running on Modal
+
+```
+pip install modal
+modal setup
+biocomp run --modal run/run_pipeline.py --env .env
+modal volume get biocomp results/fasttree_output_1/stdout/fasttree_stdout.txt ./fasttree_stdout.txt
+```
+
+# Flags
+
+```
+--env <path>      [both]  env file with API keys (default .env)
+--clean           [both]  clear previous outputs first
+--modal           [both]  run on Modal instead of locally
+--gpu T4          [modal] GPU type (default A10G)
+--memory 32768    [modal] sandbox memory in MB (default 8192)
+--shell           [modal] drop into an interactive sandbox shell
+```
+
+# Overriding a tool's command
+
+By default a node runs the tool's entrypoint binary with its registry args.
+Override either when needed (slots like `{input}`/`{output}` map to the node's I/O):
+
+```python
+# run a different exposed binary instead of the entrypoint
+g.add_node("trimal", entrypoint_override="readal")
+
+# replace the argument template
+g.add_node("colabfold", args_override="--num-recycle 0 {fasta} {output_dir}")
+
+# both together (common for non-entrypoint binaries)
+g.add_node("trimal", entrypoint_override="readal",
+           args_override="-in {alignment} -out {trimmed} -fasta")
+```

biocomposer-0.1.0/ViennaRNA/2.7.2.toml

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+[tool]
+id          = "viennarna"
+version     = "2.7.2"
+description = "RNA secondary structure prediction and comparison: minimum free energy structures, partition function, base-pair probabilities, centroid/MEA structures, suboptimal and consensus structures (ViennaRNA Package)"
+homepage    = "https://www.tbi.univie.ac.at/RNA/"
+#   https://github.com/ViennaRNA/ViennaRNA/blob/master/license.txt
+license     = "custom"
+tier        = "community"
+maintainers = [ "github:ViennaRNA",]
+
+[[tool.inputs]]
+name        = "sequences"
+type        = "fasta"
+cardinality = "one"
+description = "RNA sequence(s) to fold. Plain (one sequence per line) or FASTA; the first word of each FASTA header is used as the output-file prefix. T is auto-converted to U unless --noconv is set. Sequences up to ~32,700 nt are supported."
+
+[[tool.inputs]]
+name        = "constraints"
+type        = "file"
+cardinality = "one"
+description = "Optional — structure-constraint command file (passed via --commands, or a pseudo-dot-bracket constraint string via -C/--constraint). Encodes hard/soft constraints, forced/prohibited pairs, ligand motifs, and unstructured-domain commands."
+
+[[tool.inputs]]
+name        = "shape_data"
+type        = "file"
+cardinality = "one"
+description = "Optional — experimental structure-probing reactivities (SHAPE/DMS), two-column text (1-based position, normalized reactivity). Consumed via --shape or --sp-data and converted to pseudo-energies by the chosen probing strategy."
+
+[[tool.inputs]]
+name        = "param_file"
+type        = "file"
+cardinality = "one"
+description = "Optional — energy-parameter set read via -P/--paramFile (e.g. rna_turner2004.par, rna_turner1999.par, rna_andronescou2007.par, dna_mathews2004.par). The literal placeholder 'DNA' loads built-in DNA parameters."
+
+[[tool.inputs]]
+name        = "mod_file"
+type        = "file"
+cardinality = "one"
+description = "Optional — JSON of modified-base energy corrections read via --mod-file (complements the built-in inosine, pseudouridine, m1Psi, m5C, m6A, 7DA, purine, dihydrouridine parameter sets)."
+
+[[tool.outputs]]
+name        = "structures"
+type        = "file"
+cardinality = "one"
+description = "Per-sequence results (stdout, redirected by the args_template): the MFE structure in dot-bracket notation with free energy, and — when partition-function mode is on — the pair-probability pseudo-bracket line with ensemble free energy, the centroid structure, the MEA structure, MFE frequency, and ensemble diversity."
+
+[[tool.outputs]]
+name        = "structure_plot"
+type        = "file"
+cardinality = "one"
+description = "PostScript drawing of the MFE secondary structure, written to the working directory as <prefix>_ss.ps. Suppress with --noPS."
+
+[[tool.outputs]]
+name        = "dot_plot"
+type        = "file"
+cardinality = "one"
+description = "PostScript base-pair probability 'dot plot' (<prefix>_dp.ps), produced in partition-function mode (-p). Upper-right triangle = pair probabilities, lower-left = MFE pairs. Suppress with --noDP; stack-probability plot (<prefix>_dp2.ps) is added with -p2."
+
+[tool.image]
+backend   = "docker"
+reference = "quay.io/biocontainers/viennarna:2.7.2--py311pl5321hb7402bf_1"
+
+[tool.hardware]
+cpu_cores = 4
+ram_gb    = 8.0
+disk_gb   = 2.0
+
+[tool.entrypoint]
+command = "RNAfold"
+args_template = "--partfunc --MEA --temp=37 --dangles=2 {sequences} > {structures}"
+
+
+[tool.binaries]
+exposed = [
+    "RNAfold",
+    "RNAcofold",
+    "RNAsubopt",
+    "RNAalifold",
+    
+    "RNALalifold",
+    "RNALfold",
+    "RNAplfold",
+    "RNAeval",
+    "RNAinverse",
+    "RNAduplex",
+    "RNAaliduplex",
+    "RNAplex",
+    "RNAsnoop",
+    "RNAup",
+    "RNAmultifold",
+    "RNAheat",
+    "RNAdos",
+    "RNA2Dfold",
+    "RNAdistance",
+    "RNApdist",
+    "RNApaln",
+    "RNAplot",
+    "RNApvmin",
+    "RNAPKplex",
+    "RNAparconv",
+    "AnalyseSeqs",
+    "AnalyseDists",
+]

biocomposer-0.1.0/biocomposer/__init__.py

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+from __future__ import annotations
+import logging
+import os
+
+# Version is written by setuptools-scm at build time to _version.py (gitignored).
+# In a plain source checkout that file won't exist yet — fall back gracefully.
+try:
+    from biocomposer._version import version as __version__
+except ImportError:  # pragma: no cover - source checkout without a build
+    __version__ = "0.0.0+unknown"
+
+# Library-level logger. Attaches a NullHandler by default so logs are silent
+# unless the caller configures logging. Set BIOCOMPOSER_LOG_LEVEL=DEBUG/INFO/WARNING
+# to emit logs to stderr without any extra setup.
+_log = logging.getLogger("biocomposer")
+_log.addHandler(logging.NullHandler())
+
+_level_name = os.environ.get("BIOCOMPOSER_LOG_LEVEL", "").upper()
+if _level_name:
+    _level = getattr(logging, _level_name, logging.DEBUG)
+    _handler = logging.StreamHandler()
+    _handler.setLevel(_level)
+    _handler.setFormatter(logging.Formatter("%(asctime)s  %(levelname)-8s  %(name)s  %(message)s"))
+    _log.addHandler(_handler)
+    _log.setLevel(_level)
+
+
+def __getattr__(name: str):
+    if name in ("Graph", "SubGraph"):
+        from biocomposer.graph import Graph, SubGraph
+        globals()["Graph"] = Graph
+        globals()["SubGraph"] = SubGraph
+        return globals()[name]
+    if name in ("Node", "InputNode", "OutputNode", "DecisionNode", "GatherNode"):
+        from biocomposer.node import Node, InputNode, OutputNode, DecisionNode, GatherNode
+        globals().update({"Node": Node, "InputNode": InputNode,
+                          "OutputNode": OutputNode, "DecisionNode": DecisionNode,
+                          "GatherNode": GatherNode})
+        return globals()[name]
+    if name == "Condition":
+        from biocomposer.helpers.condition import Condition
+        globals()["Condition"] = Condition
+        return Condition
+    raise AttributeError(f"module 'biocomposer' has no attribute {name!r}")
+
+
+__all__ = [
+    "Graph",
+    "SubGraph",
+    "Node",
+    "InputNode",
+    "OutputNode",
+    "DecisionNode",
+    "GatherNode",
+    "Condition",
+]

biocomposer-0.1.0/biocomposer/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.1.0'
+__version_tuple__ = version_tuple = (0, 1, 0)
+
+__commit_id__ = commit_id = 'g71d32aaaf'