refurbishment

code/BacDup/__init__.py

@@ -0,0 +1,14 @@
+from pkg_resources import get_distribution
+try:
+    __version__ = get_distribution('BacDup').version
+except:
+    __version__ = 'local'
+
+__all__ = [
+	'modules',
+	'scripts',
+	'config'
+]
+
+from BacDup import *
+

code/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 JF Sanchez-Herrero and Alba Moya
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

code/devel/clean_devel.sh

@@ -0,0 +1,9 @@
+echo "######################################"
+echo "## Clean old folders"
+echo "rm -r build"
+rm -r build
+echo "rm -r dist"
+rm -r dist
+echo "rm -r BacDup.egg-info"
+rm -r BacDup.egg-info
+echo ""

code/devel/create_distro.sh

@@ -0,0 +1,4 @@
+echo "######################################"
+echo "## Create new distribution"
+python setup.py sdist bdist_wheel
+echo ""

code/devel/developer_guidelines.txt

@@ -0,0 +1,24 @@
+## clean distribution packages
+sh devel/clean_devel.sh
+
+## create distribution files
+sh devel/create_distro.sh
+
+## create .pypirc file
+
+$ nano .pypirc
+
+[distutils] 
+index-servers=pypi
+[pypi] 
+repository = https://upload.pypi.org/legacy/ 
+username =jfsanchezherrero
+
+## Upload using twine
+sh devel/upload_pypi.sh
+
+
+
+## references
+https://dzone.com/articles/executable-package-pip-install
+https://packaging.python.org/tutorials/packaging-projects/

code/devel/requirements.txt

@@ -0,0 +1,3 @@
+wheel
+twine
+setuptools

code/devel/test_module.sh

@@ -0,0 +1 @@
+sh devel/clean_devel.sh; sh devel/create_distro.sh; pip install -e ./

code/devel/upload_pypi.sh

@@ -0,0 +1 @@
+python -m twine upload dist/*

code/setup.py

@@ -0,0 +1,44 @@
+import setuptools
+import glob
+
+long_description_text = ""
+with open("README.md", "r") as fh:
+    long_description_text = fh.read()
+
+setuptools.setup(
+    name="BacDup",
+    version="0.1",
+
+    scripts=glob.glob('main/*'),
+    ## TODO: check add several authors
+    author="Jose F. Sanchez-Herrero and Alba Moya Garces",
+
+    author_email="jfbioinformatics@gmail.com",
+    description="Bacterial gene duplication analysis pipeline",
+
+    long_description_content_type="text/markdown",
+    long_description=long_description_text,
+    url="https://github.com/JFsanchezherrero/BacDup",
+    packages=setuptools.find_packages(),
+    license='MIT License',
+
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    include_package_data=True,
+
+    ## TODO: check
+    install_requires=[ 
+        'pandas', 'patool', 'termcolor', 
+	#'pysam', 'pybedtools', 'multiqc',
+	'bcbio-gff', 
+	'biopython', 'HCGB', 
+	'ftputil', 'numpy', 'python-dateutil', 'pytz', 'six', 'wget'
+    ],
+)
+
+
+
+