Migrate conda to pip#21
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- Drop unused conda-only pdbfixer and the erroneous mamba (conda manager) deps - Move torch/esm/transformers into optional [embeddings] extra (used only by the embedding path, which already imports lazily) - Move pytest/pytest-order into [test]; add [dev] aggregate extra - Replace bs4 with beautifulsoup4; drop redundant bio (biopython kept) - Add PyPI metadata (description, license, authors, classifiers, urls) - Guard embedder lazy imports with a clear 'pip install FRIdata[embeddings]' hint
…er-agnostic - setup_env.sh now creates a python -m venv and pip-installs FRIdata[dev] (editable), then calls install_pytorch.sh for a CUDA-matched torch build - install_pytorch.sh accepts a PYTHON env var to target a specific interpreter and no longer requires an active conda environment
- initialize_slurm.sh creates a python -m venv, pip-installs FRIdata, and uses install_pytorch.sh for a CUDA-matched torch build (no GROUP_DIR/.conda needed) - common_slurm.sh loads a Python module and activates the venv (VENV_PATH, default $DEEPFRI_PATH/.venv) instead of conda - Module name candidate lists flagged as cluster-specific for easy adjustment
- actions/setup-python with a 3.10/3.11/3.12 matrix and pip caching - Install CPU torch from the PyTorch index first, then FRIdata[embeddings,test] - Drops the entire micromamba/libmamba caching dance (~60 lines -> ~15)
- MANIFEST.in now ships only LICENSE/README/example config/scripts and prunes tests, docs, reports and large data files (*.h5/*.cif/*.idx) from the sdist (was 'global-include *', which bundled the whole repo) - Remove committed-on-disk FRIdata.egg-info (stale requires.txt) and __pycache__ - Ignore .DS_Store
- README install section rewritten around python -m venv + pip and the [embeddings] extra; PyPI install instructions added; conda/mamba/libmamba troubleshooting removed - HPC prerequisites updated (Python module + VENV_PATH instead of miniconda) - demo.ipynb cells activate .venv instead of a conda environment
- Delete fridata_env_conda.yml and requirements-fridata.txt (deps now live solely in pyproject.toml) - Add .github/workflows/publish.yml: build sdist+wheel, twine check, and publish to PyPI via OIDC Trusted Publishing on GitHub Release
Core-only checkouts (pip install -e .[test] without [embeddings]) previously failed the entire pytest run at collection time on a top-level 'import torch'. Guard with pytest.importorskip so the rest of the suite still runs.
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