Initial commit

settings.ini

+[DEFAULT]
+# All sections below are required unless otherwise specified
+host = github
+lib_name = Iterative_masking
+# For Enterprise Git add variable repo_name and company name
+# repo_name = analytics
+# company_name = nike
+
+user = damiano-sg
+description = An iterative masking algorithm for MSA Transformer to generate synthetic protein sequences 
+keywords = MSA Transformer, Iterative masking, Protein sequence generation
+author = Damiano Sgarbossa
+author_email = damiano.sgarbossa@epfl.ch
+copyright = Damiano Sgarbossa
+branch = main
+version = 0.0.1
+min_python = 3.6
+audience = Researchers
+language = English
+# Set to True if you want to create a more fancy sidebar.json than the default
+custom_sidebar = False
+# Add licenses and see current list in `setup.py`
+license = apache2
+# From 1-7: Planning Pre-Alpha Alpha Beta Production Mature Inactive
+status = 2
+
+# Optional. Same format as setuptools requirements
+requirements = numpy numba scipy torch biopython fastcore fair-esm==0.4.0
+# Optional. Same format as setuptools console_scripts
+# console_scripts = 
+# Optional. Same format as setuptools dependency-links
+# dep_links = 
+
+###
+# You probably won't need to change anything under here,
+#   unless you have some special requirements
+###
+
+# Change to, e.g. "nbs", to put your notebooks in nbs dir instead of repo root
+nbs_path = .
+doc_path = docs
+
+# Whether to look for library notebooks recursively in the `nbs_path` dir
+recursive = False
+
+# Anything shown as '%(...)s' is substituted with that setting automatically
+doc_host =  https://%(user)s.github.io
+#For Enterprise Git pages use:  
+#doc_host = https://pages.github.%(company_name)s.com.  
+
+
+doc_baseurl = /%(lib_name)s/
+# For Enterprise Github pages docs use:
+# doc_baseurl = /%(repo_name)s/%(lib_name)s/
+
+git_url = https://github.com/%(user)s/%(lib_name)s/tree/%(branch)s/
+# For Enterprise Github use:
+#git_url = https://github.%(company_name)s.com/%(repo_name)s/%(lib_name)s/tree/%(branch)s/
+
+
+
+lib_path = %(lib_name)s
+title = %(lib_name)s
+
+#Optional advanced parameters
+#Monospace docstings: adds <pre> tags around the doc strings, preserving newlines/indentation.
+#monospace_docstrings = False
+#Test flags: introduce here the test flags you want to use separated by |
+#tst_flags = 
+#Custom sidebar: customize sidebar.json yourself for advanced sidebars (False/True)
+#custom_sidebar = 
+#Cell spacing: if you want cell blocks in code separated by more than one new line
+#cell_spacing = 
+#Custom jekyll styles: if you want more jekyll styles than tip/important/warning, set them here
+#jekyll_styles = note,warning,tip,important

setup.py

+from pkg_resources import parse_version
+from configparser import ConfigParser
+import setuptools,re,sys
+assert parse_version(setuptools.__version__)>=parse_version('36.2')
+
+# note: all settings are in settings.ini; edit there, not here
+config = ConfigParser(delimiters=['='])
+config.read('settings.ini')
+cfg = config['DEFAULT']
+
+cfg_keys = 'version description keywords author author_email'.split()
+expected = cfg_keys + "lib_name user branch license status min_python audience language".split()
+for o in expected: assert o in cfg, "missing expected setting: {}".format(o)
+setup_cfg = {o:cfg[o] for o in cfg_keys}
+
+if len(sys.argv)>1 and sys.argv[1]=='version':
+    print(setup_cfg['version'])
+    exit()
+
+licenses = {
+    'apache2': ('Apache Software License 2.0','OSI Approved :: Apache Software License'),
+    'mit': ('MIT License', 'OSI Approved :: MIT License'),
+    'gpl2': ('GNU General Public License v2', 'OSI Approved :: GNU General Public License v2 (GPLv2)'),
+    'gpl3': ('GNU General Public License v3', 'OSI Approved :: GNU General Public License v3 (GPLv3)'),
+    'bsd3': ('BSD License', 'OSI Approved :: BSD License'),
+}
+statuses = [ '1 - Planning', '2 - Pre-Alpha', '3 - Alpha',
+    '4 - Beta', '5 - Production/Stable', '6 - Mature', '7 - Inactive' ]
+py_versions = '2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 3.10'.split()
+
+lic = licenses.get(cfg['license'].lower(), (cfg['license'], None))
+min_python = cfg['min_python']
+
+requirements = ['pip', 'packaging']
+if cfg.get('requirements'): requirements += cfg.get('requirements','').split()
+if cfg.get('pip_requirements'): requirements += cfg.get('pip_requirements','').split()
+dev_requirements = (cfg.get('dev_requirements') or '').split()
+
+long_description = open('README.md').read()
+# ![png](docs/images/output_13_0.png)
+for ext in ['png', 'svg']:
+    long_description = re.sub(r'!\['+ext+'\]\((.*)\)', '!['+ext+']('+'https://raw.githubusercontent.com/{}/{}'.format(cfg['user'],cfg['lib_name'])+'/'+cfg['branch']+'/\\1)', long_description)
+    long_description = re.sub(r'src=\"(.*)\.'+ext+'\"', 'src=\"https://raw.githubusercontent.com/{}/{}'.format(cfg['user'],cfg['lib_name'])+'/'+cfg['branch']+'/\\1.'+ext+'\"', long_description)
+
+setuptools.setup(
+    name = cfg['lib_name'],
+    license = lic[0],
+    classifiers = [
+        'Development Status :: ' + statuses[int(cfg['status'])],
+        'Intended Audience :: ' + cfg['audience'].title(),
+        'Natural Language :: ' + cfg['language'].title(),
+    ] + ['Programming Language :: Python :: '+o for o in py_versions[py_versions.index(min_python):]] + (['License :: ' + lic[1] ] if lic[1] else []),
+    url = cfg['git_url'],
+    packages = setuptools.find_packages(),
+    include_package_data = True,
+    install_requires = requirements,
+    extras_require={ 'dev': dev_requirements },
+    python_requires  = '>=' + cfg['min_python'],
+    long_description = long_description,
+    long_description_content_type = 'text/markdown',
+    zip_safe = False,
+    entry_points = { 'console_scripts': cfg.get('console_scripts','').split() },
+    **setup_cfg)
+