Modernize full

.github/workflows/cli-coverage.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.12"]
-        os: [ ubuntu-latest ] # can't use macOS when using service containers or container jobs
+        os: [ubuntu-latest] # can't use macOS when using service containers or container jobs
     runs-on: ${{ matrix.os }}
     services:
       postgres:
@@ -24,23 +24,17 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
 
       - name: Install uv
         run: pip install uv
 
-      - name: Install dev dependencies
-        run: if [ -f requirements/requirements-dev.txt ]; then uv pip install -r requirements/requirements-dev.txt --system; fi
-
-      - name: Install test dependencies
-        run: if [ -f requirements/requirements-test.txt ]; then uv pip install -r requirements/requirements-test.txt --system; fi
-
-      - name: Install package
-        run: uv pip install . --system
+      - name: Install package with test dependencies
+        run: uv pip install ".[test]" --system
 
       - name: Run tests
         run: coverage run -m pytest
@@ -55,4 +49,4 @@ jobs:
           SMOKESHOW_GITHUB_CONTEXT: coverage
           SMOKESHOW_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SMOKESHOW_GITHUB_PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}
+          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}

.github/workflows/black.yml → .github/workflows/format.yml

@@ -8,4 +8,8 @@ jobs:
     steps:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
-      - uses: psf/black@stable
+        with:
+          python-version: "3.12"
+      - run: pip install ruff
+      - run: ruff check .
+      - run: ruff format --check .

.github/workflows/python-publish.yml

@@ -6,24 +6,24 @@ on:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
     name: upload release to PyPI
     permissions:
-      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      contents: read
+      id-token: write
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      run: |
-        python setup.py sdist bdist_wheel
+
+    - name: Install build dependencies
+      run: python -m pip install --upgrade pip build
+
+    - name: Build package
+      run: python -m build
+
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run-pytest.yml

@@ -27,23 +27,18 @@ jobs:
           - 5432:5432
           options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - uses: actions/checkout@v6
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install uv
       run: pip install uv
 
-    - name: Install dev dependencies
-      run: if [ -f requirements/requirements-dev.txt ]; then uv pip install -r requirements/requirements-dev.txt --system; fi
-
-    - name: Install test dependencies
-      run: if [ -f requirements/requirements-test.txt ]; then uv pip install -r requirements/requirements-test.txt --system; fi
-
-    - name: Install package
-      run: uv pip install . --system
+    - name: Install package with test dependencies
+      run: uv pip install ".[test]" --system
 
     - name: Run pytest tests
-      run: pytest tests -x -vv
+      run: pytest tests -x -vv

README.md

@@ -12,9 +12,13 @@
 
 ## What is this?
 
-`bbconf` is a configuration and management tool for BEDbase, facilitating the reading of configuration files, 
-setting up connections to PostgreSQL, PEPhub, S3, and Qdrant databases, managing file paths, and storing transformer models. 
-It formalizes communication pathways for pipelines and downstream tools, ensuring seamless interaction."
+`bbconf` is a configuration and data management library for the [BEDbase](https://bedbase.org) platform. It serves as the central backbone for all BEDbase tools and pipelines by:
+
+- Reading and validating YAML configuration files
+- Setting up and managing connections to PostgreSQL, Qdrant, S3, and PEPHub
+- Loading ML models (Region2Vec, text embedders, sparse encoders, UMAP) used for BED file search
+- Providing high-level Python interfaces for querying and managing BED files and BED sets
+- Exposing a unified `BedBaseAgent` object that all downstream tools use to interact with the platform
 
 ---
 
@@ -28,10 +32,27 @@ It formalizes communication pathways for pipelines and downstream tools, ensurin
 
 To install `bbclient` use this command: 
 ```
-pip install bbclient
+pip install bbconf
 ```
 or install the latest version from the GitHub repository:
 ```
 pip install git+https://github.com/databio/bbconf.git
 ```
 
+
+## Quick start
+
+```python
+from bbconf import BedBaseAgent
+
+agent = BedBaseAgent(config="config.yaml")
+
+# Access submodules
+agent.bed        # BED file operations
+agent.bedset     # BED set operations
+agent.objects    # Generic object/file operations
+
+# Get platform statistics
+stats = agent.get_stats()
+print(stats.bedfiles_number, stats.bedsets_number)
+```

bbconf/__init__.py

@@ -4,10 +4,9 @@
 
 from bbconf.bbagent import BedBaseAgent
 
-from ._version import __version__
 from .const import PKG_NAME
 
-__all__ = ["BedBaseAgent", "__version__"]
+__all__ = ["BedBaseAgent"]
 
 _LOGGER = logging.getLogger(PKG_NAME)
 coloredlogs.install(