Merge pull request #21 from databio/dev

Release v0.1.0

Author: khoroshevskyi

.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

.github/workflows/run-pytest.yml

@@ -1,5 +1,5 @@
 ## we can't run test, but lets just install all dependencies and package
-name: Run instalation test
+name: Installation test
 
 on:
   push:
@@ -12,7 +12,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.10"]
+        python-version: ["3.8", "3.11"]
         os: [ubuntu-latest]
 
     steps:

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+.ruff_cache/
 build/
 develop-eggs/
 dist/
@@ -134,3 +135,8 @@ bedqc/*
 test/bedqc/*
 
 openSignalMatrix
+
+out2023/*
+
+# test data
+test/test_data/*

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  # Using this mirror lets us use mypyc-compiled black, which is about 2x faster
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.1.1
+    hooks:
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3.10

MANIFEST.in

@@ -4,4 +4,8 @@ include bedboss/*
 include bedboss/bedstat/*
 include bedboss/bedstat/tools/*
 include bedboss/bedmaker/*
-include bedboss/bedqc/*
+include bedboss/bedqc/*
+include bedboss/qdrant_index/*
+include bedboss/bedbuncher/*
+include bedboss/bedbuncher/tools/*
+include bedboss/bedclassifier/*

README.md

@@ -1,33 +1,58 @@
 # bedboss
 
----
+[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pep.databio.org/)
 ![Run pytests](https://github.com/bedbase/bedboss/workflows/Run%20instalation%20test/badge.svg)
-[![docs-badge](https://readthedocs.org/projects/bedboss/badge/?version=latest)](https://bedboss.databio.org/en/latest/)
-[![pypi-badge](https://img.shields.io/pypi/v/bedboss)](https://pypi.org/project/bedboss)
+[![pypi-badge](https://img.shields.io/pypi/v/bedboss?color=%2334D058)](https://pypi.org/project/bedboss)
+[![pypi-version](https://img.shields.io/pypi/pyversions/bedboss.svg?color=%2334D058)](https://pypi.org/project/bedboss)
 [![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/bedboss)
+
+---
+
+**Documentation**: <a href="https://docs.bedbase.org/bedboss" target="_blank">https://docs.bedbase.org/bedboss</a>
+
+**Source Code**: <a href="https://github.com/databio/bedboss" target="_blank">https://github.com/databio/bedboss</a>
+
+---
+
+bedboss is a command-line pipeline that filters, standardizes, and calculates statistics for genomic interval data, 
+and enters the results into a BEDbase database. 
+
+## Installation
+To install `bedboss` use this command: 
+```
+pip install bedboss
+```
+or install the latest version from the GitHub repository:
+```
+pip install git+https://github.com/databio/bedboss.git
+```
+
+## Development
+For development, you should install all the dependencies, create a virtual environment, and work on the local database.
+The workflow is described in the [development documentation](https://docs.bedbase.org/bedboss/development).
 
-bedboss is a command-line pipeline that standardizes and calculates statistics for genomic interval data, and enters the results into a BEDbase database. It has 3 components: 1) bedmaker (`bedboss make`); 2) bedqc (`bedboss qc`); and 3) bedstat `bedboss stat`. You may run all 3 pipelines separately, together (`bedbase all`).
 
-## 1) bedmaker
+## Testing
 
-Converts supported file types into BED and bigBed format. Currently supported formats:
-   - bedGraph
-   - bigBed
-   - bigWig
-   - wig
+### Requirements test:
 
-## 2) bedqc
+To test requirements, install bedboss and run: 
 
-Assess QC of BED files and flag potential problems for further evaluation so you can determine whether they should be included in downstream analysis. 
-Currently, it flags BED files that are larger than 2 GB, have over 5 milliom regions, or have mean region width less than 10 bp.
-These thresholds can be changed with pipeline arguments.
+```
+bedboss requirements-check
+```
 
-## bedstat
+### Smoke tests:
 
-Calculates statistics about BED files.
+Use this docs:
+- [./test/README.md](./test/README.md)
 
-# Documentation
 
-Detailed information about each pipeline can be found in the [bedboss Readme](./docs/README.md).
+## How to generate usage documentation:
 
-For the specific bedbase.org instance, see instructions in the bedbase.org repo.
+Run this command in the root of the repository:
+```
+cd scripts
+bash update_usage_docs.sh
+```

bedboss/__init__.py

@@ -1,14 +1,22 @@
 """ Package-level data """
+
 import logmuse
 import coloredlogs
+import logging
 
-from bedboss import *
 
 # from bedboss.bedqc.bedqc import bedqc
 # from bedboss.bedmaker.bedmaker import BedMaker
 # from bedboss.bedstat.bedstat import bedstat
 from bedboss._version import __version__
-from bedboss.bedboss import run_all, run_all_by_pep, bedqc, BedMaker, bedstat
+from bedboss.bedboss import (
+    run_all,
+    insert_pep,
+    bedqc,
+    bedstat,
+    run_bedbuncher,
+)
+from bedboss.bedmaker.bedmaker import BedMaker
 
 
 __package_name__ = "bedboss"
@@ -32,12 +40,41 @@
     "BedMaker",
     "bedstat",
     "run_all",
-    "run_all_by_pep",
+    "insert_pep",
+    "run_bedbuncher",
 ]
 
 _LOGGER = logmuse.init_logger("bedboss")
 coloredlogs.install(
     logger=_LOGGER,
     datefmt="%H:%M:%S",
-    fmt="[%(levelname)s] [%(asctime)s] %(message)s",
+    fmt="[%(levelname)s] [%(asctime)s] [BEDBOSS] %(message)s",
+)
+
+_LOGGER_PIPESTAT = logging.getLogger("pipestat")
+coloredlogs.install(
+    logger=_LOGGER_PIPESTAT,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] [PIPESTAT] %(message)s",
+)
+
+_LOGGER_GENIML = logging.getLogger("geniml")
+coloredlogs.install(
+    logger=_LOGGER_GENIML,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] [GENIML] %(message)s",
+)
+
+_LOGGER_BBCONF = logging.getLogger("bbconf")
+coloredlogs.install(
+    logger=_LOGGER_BBCONF,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] [BBCONF] %(message)s",
+)
+
+_LOGGER_BBCONF = logging.getLogger("pephubclient")
+coloredlogs.install(
+    logger=_LOGGER_BBCONF,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] [PEPHUBCLIENT] %(message)s",
 )

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.1.0a4"
+__version__ = "0.1.0"