Minor improvements toBiocFrame class (#129).

- Major update to type hints throughout the module for better type safety and consistency.
- Fixed bug in slice operations where column indices might be incorrectly initialized.
- Added missing index validation in `get_row()` for integer row indices. Similar index validation in `remove_columns()` and `remove_rows()` for out-of-range indices.
- Accept a list of column values and column names to initialize a biocframe object.
- Implement empty, contains, head, tail,
- Coercion to list and `NamedList` from bioctuls.

Author: jkanche

.github/workflows/publish-pypi.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Publish to PyPI
 
 on:
@@ -19,10 +16,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install dependencies
         run: |
@@ -33,6 +30,14 @@ jobs:
         run: |
           tox
 
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      # This uses the trusted publisher workflow so no token is required.
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
       - name: Build docs
         run: |
           tox -e docs
@@ -45,11 +50,3 @@ jobs:
           branch: gh-pages # The branch the action should deploy to.
           folder: ./docs/_build/html
           clean: true # Automatically remove deleted files from the deploy branch
-
-      - name: Build Project and Publish
-        run: |
-          python -m tox -e clean,build
-
-      # This uses the trusted publisher workflow so no token is required.
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run-tests.yml

@@ -1,33 +1,73 @@
-name: Run tests
+name: Test the library
 
 on:
   push:
-    branches: [master]
+    branches:
+      - master # for legacy repos
+      - main
   pull_request:
-    branches: [master]
+    branches:
+      - master # for legacy repos
+      - main
+  workflow_dispatch: # Allow manually triggering the workflow
+  schedule:
+    # Run roughly every 15 days at 00:00 UTC
+    # (useful to check if updates on dependencies break the package)
+    - cron: "0 0 1,16 * *"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  test:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-
-    name: Python ${{ matrix.python-version }}
+        python: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        platform:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+    runs-on: ${{ matrix.platform }}
+    name: Python ${{ matrix.python }}, ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5
+        id: setup-python
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
+          python-version: ${{ matrix.python }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install tox
+          pip install tox coverage
 
-      - name: Test with tox
-        run: |
+      - name: Run tests
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
           tox
+          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
+
+      - name: Check for codecov token availability
+        id: codecov-check
+        shell: bash
+        run: |
+          if [ ${{ secrets.CODECOV_TOKEN }} != '' ]; then
+            echo "codecov=true" >> $GITHUB_OUTPUT;
+          else
+            echo "codecov=false" >> $GITHUB_OUTPUT;
+          fi
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v5
+        if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          slug: ${{ github.repository }}
+          flags: ${{ matrix.platform }} - py${{ matrix.python }}

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## Version 0.7.0
+
+- Major update to type hints throughout the module for better type safety and consistency.
+- Fixed bug in slice operations where column indices might be incorrectly initialized.
+- Added missing index validation in `get_row()` for integer row indices. Similar index validation in `remove_columns()` and `remove_rows()` for out-of-range indices.
+- Accept a list of column values and column names to initialize a biocframe object.
+- Implement empty, contains, head, tail,
+- Coercions to list and `NamedList` from bioctuls.
+
 ## Version 0.6.3
 - Implement `remove_rows()`.
 - Implement `has_row()`.

README.md

@@ -32,6 +32,106 @@ pip install biocframe
 pip install biocframe[optional]
 ```
 
+## Quick Examples
+
+### Genomic Annotation Data
+
+Genomic data often requires storing coordinates, annotations, and metadata together:
+
+```python
+# Gene annotation with nested structures
+gene_annotations = BiocFrame({
+    "gene_id": ["GENE1", "GENE2", "GENE3"],
+    "symbol": ["BRCA1", "TP53", "EGFR"],
+    "location": BiocFrame({
+        "chromosome": ["chr17", "chr17", "chr7"],
+        "start": [43044295, 7668422, 55019017],
+        "end": [43125483, 7687550, 55211628],
+        "strand": ["-", "-", "+"],
+    }),
+    "transcripts": [
+        ["NM_007294", "NM_007297", "NM_007300"],
+        ["NM_000546"],
+        ["NM_005228", "NM_201282"],
+    ],
+    "pathways": [
+        ["DNA repair", "Cell cycle"],
+        ["Apoptosis", "Cell cycle", "DNA repair"],
+        ["Cell growth", "Signal transduction"],
+    ],
+}, row_names=["ENSG00000012048", "ENSG00000141510", "ENSG00000146648"])
+
+print(gene_annotations)
+```
+
+### Multi-Omics Data Integration
+
+When combining different types of omics data with varying structures:
+
+```python
+# Multi-omics data with different measurement types
+multi_omics = BiocFrame({
+    "sample_id": ["S1", "S2", "S3"],
+    "rna_seq": np.array([
+        [100, 200, 150],
+        [300, 250, 180],
+        [120, 220, 160],
+    ], dtype=np.float32),
+    "methylation": BiocFrame({
+        "cg0001": [0.85, 0.92, 0.78],
+        "cg0002": [0.45, 0.38, 0.52],
+        "cg0003": [0.12, 0.15, 0.10],
+    }),
+    "clinical": BiocFrame({
+        "age": [45, 52, 38],
+        "gender": ["M", "F", "F"],
+        "diagnosis": ["Type A", "Type B", "Type A"],
+    }),
+}, column_data=BiocFrame({
+    "data_type": ["identifier", "expression", "epigenetic", "clinical"],
+    "source": ["lab", "sequencer", "array", "EHR"],
+}))
+
+print(multi_omics)
+print("\nColumn metadata:")
+print(multi_omics.get_column_data())
+```
+
+### Hierarchical Data Structures
+
+For data with natural hierarchies (e.g., samples → patients → cohorts):
+
+```python
+# Hierarchical clinical trial data
+clinical_trial = BiocFrame({
+    "patient_id": ["P001", "P002", "P003"],
+    "cohort": ["A", "A", "B"],
+    "samples": [
+        BiocFrame({
+            "sample_id": ["S001", "S002"],
+            "collection_date": ["2024-01-01", "2024-01-15"],
+            "vital_status": ["alive", "alive"],
+        }),
+        BiocFrame({
+            "sample_id": ["S003", "S004", "S005"],
+            "collection_date": ["2024-01-02", "2024-01-16", "2024-01-30"],
+            "vital_status": ["alive", "alive", "deceased"],
+        }),
+        BiocFrame({
+            "sample_id": ["S006"],
+            "collection_date": ["2024-01-03"],
+            "vital_status": ["alive"],
+        }),
+    ],
+}, metadata={
+    "trial_name": "PHASE_III_STUDY",
+    "start_date": "2024-01-01",
+    "status": "ongoing",
+})
+
+print(clinical_trial)
+```
+
 ## Construction
 
 To construct a `BiocFrame` object, simply provide the data as a dictionary.