# python — general data science + single-cell + cheminformatics (Python 3.11)
#
# This is the DEFAULT kernel env. It includes the portable top-level dependency
# intent from Claude Science's Python environment plus OpenAI4S's broader
# single-cell, cheminformatics, IO, and plotting stack. Conda resolves native
# and platform-specific transitive dependencies for the target machine; do not
# copy build strings or macOS-only toolchain packages into this shared spec.
name: python
channels:
  - conda-forge
  - bioconda
dependencies:
  - python=3.11
  # single-cell stack
  - anndata
  - leidenalg
  - python-igraph
  - umap-learn
  - numba
  # cheminformatics — conda-forge, NOT the pip `rdkit-pypi` wheel: that project
  # is frozen at 2022.9.5 and is built against the NumPy 1.x C ABI, so it
  # segfaults the kernel worker against the NumPy 2.x this spec now resolves.
  - rdkit
  # machine learning + numerics
  - scikit-learn
  - numpy
  - scipy
  - pandas<3
  # plotting
  - matplotlib
  - seaborn
  - plotly
  - pillow
  # bio + IO + web
  - biopython
  - h5py
  - zarr
  - pyarrow
  - openpyxl
  - pypdf
  - beautifulsoup4
  - httpx
  - socksio
  - pysocks
  - tqdm
  - statsmodels
  - networkx
  # pip-only packages
  - pip
  - pip:
      - fair-esm==2.0.0
      # Workflow-pinned CPU single-cell core. Pertpy (Milo DA) stays OUT of
      # the default env and the desktop bundle: its core hard-requires the
      # Flax/NumPyro/ott-jax stack. Install it via the optional `singlecell`
      # uv extra; the Skill degrades DA to failed_missing_dependency without it.
      - scanpy[harmony]==1.11.5
      # scikit-misc (seurat_v3 HVG's LOESS) publishes no linux-aarch64 wheel,
      # so the marker keeps `openai4s setup` working on Graviton/Jetson; the
      # Skill falls back to the log-normalized seurat HVG flavor without it.
      # Marker-carrying entries are platform-optional and excluded from the
      # readiness requirement list (openai4s/kernel/readiness.py).
      - scikit-misc==0.5.2; platform_machine != "aarch64"
      - pydeseq2==0.5.4
      # from PyPI so pip selects the bundled PDFium wheel matching this platform.
      - pypdfium2==5.9.0