Merge pull request #16 from pfizer-opensource/release

Release to pypi

Author: jorenretel

.github/workflows/release.yaml

@@ -0,0 +1,54 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+env:
+  FORCE_COLOR: "1"
+
+jobs:
+  build:
+    name: build wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.10
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+      - name: Install pep517
+        run: |
+          python -m pip install --user build
+      - name: Build a source tarball
+        run: |
+          python -m build --sdist --no-deps .
+      - uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+          if-no-files-found: error
+  release:
+    needs: [build]
+    if: github.event_name == 'release'
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+      url: https://pypi.org/p/bigwig-loader
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run_tests.yaml

@@ -21,6 +21,7 @@ jobs:
           python-version: "3.10"
       - name: Install dependencies
         run: |
+          sed -i '0,/^ *"cupy",/s///' pyproject.toml
           python -m pip install --upgrade pip
           python -m pip install -e .[dev]
       - name: Run mypy

MANIFEST.in

@@ -0,0 +1,16 @@
+# MANIFEST.in
+exclude .gitignore
+exclude .github/*
+exclude .egg-info/*
+exclude benchmark/*
+exclude docs/*
+exclude examples/*
+exclude example_data/
+exclude images/*
+exclude .flake8
+exclude .pre-commit-config.yaml
+exclude environment.yml
+exclude tmp/*
+
+include example_data/some_intervals.tsv
+include example_data/some_positions.tsv

README.md

@@ -38,12 +38,12 @@ dataset = BigWigDataset(
     reference_genome_path=reference_genome,
     sequence_length=1000,
     center_bin_to_predict=1000,
+    window_size=1,
     batch_size=256,
     super_batch_size=1024,
     batches_per_epoch=20,
     maximum_unknown_bases_fraction=0.1,
     sequence_encoder="onehot",
-    use_cufile=True,
 )
 
 for encoded_sequences, epigenetics_profiles in dataset:

bigwig_loader/batch.py

@@ -1,3 +1,4 @@
+from pathlib import Path
 from typing import Any
 from typing import Sequence
 from typing import Union
@@ -51,6 +52,7 @@ def __init__(
         track_indices: IntSequenceType | None = None,
         sequences: StrSequenceType | None = None,
         values: cp.ndarray | None = None,
+        track_names: Sequence[str | Path] | None = None,
         other_batched: Sequence[Sequence[Any] | npt.NDArray[np.generic] | cp.ndarray]
         | None = None,
         other: Any = None,
@@ -63,6 +65,7 @@ def __init__(
         self.values = values
         self.other_batched = other_batched
         self.other = other
+        self.track_names = track_names
 
     @classmethod
     def from_args(cls, args: Union["Batch", IntervalType, dict[str, Any]]) -> "Batch":
@@ -88,6 +91,7 @@ def __getitem__(self, item: slice) -> "Batch":
             track_indices=self.track_indices,
             sequences=self.sequences[item] if self.sequences is not None else None,
             values=self.values[item] if self.values is not None else None,
+            track_names=self.track_names,
             other_batched=[x[item] for x in self.other_batched]
             if self.other_batched is not None
             else None,