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The TF mirror of the torch reader change. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
hdwig is internal and not on PyPI, so a hard dependency made `pip install baskerville` unresolvable. Mirrors baskerville-torch: the import moves into CovFace.__init__, and the pin becomes a `hdwig` extra on the git URL. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Superseded by the PyTorch baskerville, which takes over the name. The distribution becomes baskerville-tf; the import name stays baskerville. - Fix undefined names (missing sys imports, nonexistent PolyReLU/Exp/ transformer_lambda branches, num_targets in hound_eval_genes). - Ruff clean; black 23 formatting. - CI: current runners/actions, run on PRs, Python 3.10/3.11, add ruff, docs deps via a docs extra. - Apache license classifier; drop env_vars.sh and docs/requirements.txt. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
0.10.0 is sdist-only and its setup.py needs pkg_resources, removed in setuptools 81, so pip install failed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
From #42: h5py, intervaltree, joblib, matplotlib, google-cloud-storage, tabulate, tqdm, pytest. Numeric stack, TensorFlow, and lint pins unchanged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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# Conflicts: # docs/transfer/transfer.md # pyproject.toml
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This repo is superseded by the PyTorch baskerville (currently
calico/baskerville-torch), which will take over thebaskervillename. This PR prepares the TF version to becomecalico/baskerville-tf.Changes
baskerville-tf, and the code still imports asbaskerville, so borzoi keeps working. The README, docs config and transfer tutorial point atcalico/baskerville-tf. The README has a "superseded" banner.sysimports inblocks.pyandtrainer.pypolyrelu/expactivation branches and thelambdatransformer branch, which referenced classes and functions that don't existnum_targetsbeing used before it's defined inhound_eval_genes.pyruff checkpasses clean, including on the newly mergedhound_predvcf.py. It removes unused imports and variables and fixes== Noneand type comparisons.ubuntu-latest, checkout v4, setup-python v5, and the workflows also run on pull requestsrequires-python >= 3.10)devextra, followingmaindocsextrapybedtools~=0.10.0→~=0.12.1. 0.10.0 exists only as source on PyPI, and itssetup.pyimportspkg_resources, which setuptools 81 removed, sopip installfailed. 0.12.1 ships wheels and works with the pinned numpy 1.24.Also relaxed to minor-compatible, from relax #42: h5py, intervaltree, joblib, matplotlib, google-cloud-storage, tabulate, tqdm, pytest. The numeric stack, TensorFlow, and lint pins are unchanged.
hound_data_read.pyreads.hw/.w5coverage throughhdwig, an optional[hdwig]extra imported lazily. These are commits 0c563a2 and 8e54b46, which weren't onmainyet.docs/transfer_human,docs/transfer_mouse, and thedocs/transfer/transfer.mdredirect) point at baskerville-tf.env_vars.sh(it had hardcoded user paths) andsrc/docs/requirements.txt(stale duplicate dependency pins).Testing
Local unit tests (TF 2.15.1, Python 3.10): 29 passed, 2 skipped, the same as
main. CI (lint and pytest on 3.10/3.11) passes on this branch.After merge
calico/baskerville-tf, then re-run the docs workflow so the docs publish atcalico.github.io/baskerville-tf.baskerville-torchtobaskerville.🤖 Generated with Claude Code