Merge pull request #41 from databio/dev

Release 0.4.1

.github/workflows/cli-coverage.yml

@@ -0,0 +1,54 @@
+name: test coverage
+
+on:
+  push:
+    branches: [master, dev]
+
+jobs:
+  cli-coverage-report:
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+        os: [ ubuntu-latest ] # can't use macOS when using service containers or container jobs
+    runs-on: ${{ matrix.os }}
+    services:
+      postgres:
+        image: postgres
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: dockerpassword
+          POSTGRES_DB: pipestat-test
+          POSTGRES_HOST: localhost
+        ports:
+          - 5432:5432
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v1
+        with:
+          python-version: '3.10'
+
+      - name: Install dev dependencies
+        run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
+
+      - name: Install test dependencies
+        run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
+
+      - run: pip install .
+
+      - name: Run tests
+        run: coverage run -m pytest
+
+      - name: build coverage
+        run: coverage html -i
+
+      - run: smokeshow upload htmlcov
+        env:
+          SMOKESHOW_GITHUB_STATUS_DESCRIPTION: Coverage {coverage-percentage}
+          SMOKESHOW_GITHUB_COVERAGE_THRESHOLD: 50
+          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 }}

.github/workflows/python-publish.yml

@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: Upload Python Package
 
 on:
@@ -11,21 +8,22 @@ jobs:
   deploy:
 
     runs-on: ubuntu-latest
+    name: upload release to PyPI
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
     - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -1,25 +1,36 @@
-# bbconf
+<h1 align="center">bbconf</h1>
 
 ![Run pytests](https://github.com/databio/bbconf/workflows/Run%20pytests/badge.svg)
-[![codecov](https://codecov.io/gh/databio/bbconf/branch/master/graph/badge.svg)](https://codecov.io/gh/databio/bbconf)
+[![pypi-badge](https://img.shields.io/pypi/v/bbconf?color=%2334D058)](https://pypi.org/batabio/bbconf)
+[![pypi-version](https://img.shields.io/pypi/pyversions/bbconf.svg?color=%2334D058)](https://pypi.org/databio/bbconf)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/databio/bbconf)
+[![coverage](https://coverage-badge.samuelcolvin.workers.dev/databio/bbconf.svg)](https://coverage-badge.samuelcolvin.workers.dev/redirect/databio/bbconf)
 
 
-*BEDBASE* project configuration package
+*BEDBASE* project configuration package (agent)
 
 ## What is this?
 
-`bbconf` standardizes reporting of [bedstat](https://github.com/databio/bedstat) and [bedbuncher](https://github.com/databio/bedsbuncher) results. It formalizes a way for these pipelines and downstream tools to communicate -- the produced results can easily and reliably become an
-input for the server ([bedhost](https://github.com/databio/bedhost)). The object exposes API for interacting with the results and is backed by a [PostgreSQL](https://www.postgresql.org/) database.
+`bbconf` is a configuration and management tool for BEDbase, facilitating the reading of configuration files, 
+setting up connections to PostgreSQL and Qdrant databases, managing file paths, and storing transformer models. 
+It formalizes communication pathways for pipelines and downstream tools, ensuring seamless interaction."
 
-## Installation
+---
+
+**Documentation**: <a href="https://docs.bedbase.org/bedboss" target="_blank">https://docs.bedbase.org/bedboss</a>
+
+**Source Code**: <a href="https://github.com/databio/bbconf" target="_blank">https://github.com/databio/bbconf</a>
+
+---
 
-Install from [GitHub releases](https://github.com/databio/bbconf/releases) or from PyPI using `pip`:
+## Installation
+To install `bbclient` use this command: 
+```
+pip install bbclient
+```
+or install the latest version from the GitHub repository:
 ```
-pip install --user bbconf
+pip install git+https://github.com/databio/bbconf.git
 ```
 
-## Documentation
-- [Bedbase configuration file](docs/config.ipynb)
-- [Usage demonstration](docs/demo.ipynb)
-- [Python API](docs/bbc_api.md)

bbconf/__init__.py

@@ -1,4 +1,15 @@
+import logging
+import coloredlogs
+
 from bbconf.bbconf import BedBaseConf, get_bedbase_cfg
 from ._version import __version__
+from .const import PKG_NAME
 
 __all__ = ["BedBaseConf", "get_bedbase_cfg", "__version__"]
+
+_LOGGER = logging.getLogger(PKG_NAME)
+coloredlogs.install(
+    logger=_LOGGER,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] [BBCONF] %(message)s",
+)

bbconf/bbconf.py

@@ -39,6 +39,7 @@
     DEFAULT_VEC2VEC_MODEL,
     DEFAULT_REGION2_VEC_MODEL,
     CFG_ACCESS_METHOD_KEY,
+    PKG_NAME,
 )
 from bbconf.exceptions import (
     BedBaseConfError,
@@ -56,7 +57,7 @@
 from geniml.region2vec import Region2VecExModel
 from geniml.io import RegionSet
 
-_LOGGER = getLogger(__name__)
+_LOGGER = getLogger(PKG_NAME)
 
 
 class BedBaseConf:
@@ -440,17 +441,17 @@ def select_bedfiles_from_bedset(
                     self.BedsetORM.record_identifier == bedset_record_id
                 )
                 results = session.exec(statement).one().bedfiles
-            bedfile_list = [bedfile.dict() for bedfile in results]
+            bedfile_list = [bedfile.model_dump() for bedfile in results]
         else:
             # Probably we can do it in more simple way
             with self.bed.backend.session as session:
                 statement = select(self.BedfileORM.record_identifier).where(
                     self.BedfileORM.id.in_(
                         select(self.rel_table.bedfile_id).where(
                             self.rel_table.bedset_id
-                            == select(self.BedsetORM.id).where(
-                                self.BedsetORM.record_identifier == bedset_record_id
-                            )
+                            == select(self.BedsetORM.id)
+                            .where(self.BedsetORM.record_identifier == bedset_record_id)
+                            .scalar_subquery()
                         )
                     )
                 )

bbconf/schemas/bedfiles_schema.yaml

@@ -12,6 +12,12 @@ properties:
       genome:
         type: object
         description: genome assembly of the BED files
+      bed_type:
+        type: string
+        description: type of BED file, eg. "bed3", "bed6+4"
+      bed_format:
+        type: string
+        description: format type of BED file, narrowpeak, broadpeak, or bed
       bedfile:
         $ref: "#/$defs/file"
         label: bedfile

docs/changelog.md

@@ -2,6 +2,12 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.4.2] - 2024-XX-XX
+### Change
+- Updated logger
+- Updated requirements
+
+
 ## [0.4.1] - 2024-01-01
 ### Fix
 - Requirements