Merge pull request #176 from BU-ISCIII/develop

PR for the v1.0.0 release

.github/workflows/python_lint.yml

@@ -0,0 +1,35 @@
+name: python_lint
+
+on:
+  push:
+    paths:
+      - '**.py'
+  pull_request:
+    paths:
+      - '**.py'
+
+jobs:
+  flake8_py3:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9.x
+          architecture: x64
+      - name: Checkout PyTorch
+        uses: actions/checkout@master
+      - name: Install flake8
+        run: pip install flake8
+      - name: Run flake8
+        run: flake8 --ignore E501,W503,E203,W605
+
+  black_lint:
+    runs-on: ubuntu-latest
+    steps:
+        - name: Setup
+          uses: actions/checkout@v2
+        - name: Install black in jupyter
+          run: pip install black[jupyter]
+        - name: Check code lints with Black
+          uses: psf/black@stable

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# (Ad-hoc files)
+.nextflow*

MANIFEST.in

@@ -0,0 +1,8 @@
+include LICENSE
+include README.md
+graft bu_isciii/templates
+graft bu_isciii/schemas
+graft bu_isciii/conf
+graft bu_isciii/assets
+include requirements.txt
+include environment.yml

README.md

@@ -1 +1,59 @@
-# buisciii-tools
+# buisciii-tools
+[![python_lint](https://github.com/BU-ISCIII/buisciii-tools/actions/workflows/python_lint.yml/badge.svg)](https://github.com/BU-ISCIII/buisciii-tools/actions/workflows/python_lint.yml)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+> THIS REPO IS IN ACTIVE DEVELOPMENT.
+
+BU-ISCIII provides a serie or services in its portfolio for supporting bioinformatics analysis to the labs in the Institute of Health Carlos III. bu-isciii tools is a set of helper tools for management of these bioinformatics analysis together with the LIMS ([iSkyLIMS](https://github.com/BU-ISCIII/iSkyLIMS))
+
+* [Installation](#installation)
+* [Usage](#usage)
+    * [list](#list)
+    * [new-service](#new-service)
+    * [scratch](#scratch)
+    * [clean](#clean)
+    * [copy_sfp](#copy_sftp)
+    * [archive](#archive)
+    * [bioinfo_doc](#bioinfo_doc)
+    * [autoclean_sftp](#autoclean_sftp)
+* [Aknowledgements](#aknowledgements)
+
+## Installation
+
+### Bioconda
+Soon
+
+### Pip
+Soon
+
+### Development version
+If you want to install the latest code in the repository:
+
+```
+conda create -n buisciii_dev pip
+pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/buisciii-tools.git@develop
+```
+
+## Usage
+
+### Command-line
+
+#### list
+
+#### new-service
+
+#### scratch
+
+#### clean
+
+#### copy_sftp
+
+#### archive
+
+#### bioinfo_doc
+
+#### autoclean_sftp
+
+
+## Acknowledgements
+Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools).

bu_isciii/__init__.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+""" Main bu_isciii package file.
+"""
+
+import pkg_resources
+
+__version__ = pkg_resources.get_distribution("bu_isciii").version