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How to get rid of library root mark in PyCharm

I've started working on a Pyramid application, which requires setup.py usage, but as soon as I built the app, my app folder was marked as library root.
It is not convenient, because when I open a file, it is also opened under External Libraries unfolding it. This can be "fixed" by removing check on Always Select Opened File, but I like this feature, so I don't want to disable it.
I've also tried to tweak Project Structure in settings, but it didn't help.
How to get rid of this _library_root_ mark?
UPD. Contents of setup.py:
setup(
name='app',
version=0.1,
description='Blog with CMS',
classifiers=[
"Programming Language :: Python",
"Framework :: Pylons",
"Topic :: Internet :: WWW/HTTP",
"Topic :: Internet :: WWW/HTTP :: WSGI :: Application"
],
keywords="web services",
author='',
author_email='',
url='',
packages=find_packages(),
include_package_data=True,
zip_safe=False,
install_requires=['cornice', 'waitress'],
entry_points="""\
[paste.app_factory]
main=app:main
""",
paster_plugins=['pyramid']
)

The reason why it happens is PyCharm adds sd-blog/app to the interpreter paths once you pip install -e in order to be able to provide completion for app objects. Possible workaround:
remove app from the interpreter paths
mark sd-blog/app as a source root to restore the code insight broken in the step 1

Modules missing when installing python project using pip

I'm deploying my first python project, but having issues with installation. I've followed the practices outlined in https://packaging.python.org/guides/distributing-packages-using-setuptools/#uploading-your-project-to-pypi. My project is organized with a top-level executable script bin/gsat that calls imports other modules like so:
import gsat.input_validation as input_validation
The modules are in src/gsat/ , following the arrangement in the example project at https://github.com/pypa/sampleproject
If I install locally from the project source , using develop mode:
pip install -e .
... then I have no issues installing and the software works.
But if I install it from PyPI:
pip install "gsat"
... then it won't run because the import statements fail to find the modules. Error:
File "/Library/Frameworks/Python.framework/Versions/3.7/bin/gsat", line 10, in <module>
import gsat.input_validation as input_validation
ModuleNotFoundError: No module named 'gsat'
The full project is at https://github.com/MikeAxtell/gsat , commit c680172. The project is also on PyPI as "gsat". The distribution files are being made like:
python3 setup.py sdist bdist_wheel
... and the fun setup.py file is below. I'm sure this is some noob issue; I am new to python packaging and python programming in general, so thanks in advance for help!
setup.py:
with open("README.md", "r") as fh:
long_description = fh.read()
setuptools.setup(
name="gsat",
version="0.1a",
author="Michael J. Axtell",
author_email="mja18#psu.edu",
description="General Small RNA-seq Analysis Tool",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/MikeAxtell/gsat",
scripts=['bin/gsat'],
package_dir={'': 'src'},
packages=setuptools.find_packages(where='gsat'),
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
],
python_requires='>3.5, <4',
install_requires=['biopython','python-Levenshtein'],
)

Looks like there is an issue in this line:
packages=setuptools.find_packages(where='gsat'),
I believe it should read the following instead:
packages=setuptools.find_packages(where='src'),

Make my pypi script executable without the need to specify every time the path to the script

Recently I created a python script for PyPI. That you can download with pip install. The problem is you can only execute the script, that you downloaded with pip install, when you are in the Scripts folder which is where you python is localized (your_python_location/Scripts/myscript.py).
But this would be a hassle for the users. So I wanted to ask, how can I make it that you can execute the script from everywhere? (like you can do with pip without specifying the pip location). I also don't want that every user needs to set the path to the script.
My Setup.py (maybe its helpful):
import setuptools
with open("README.md", "r") as fh:
long_description = fh.read()
with open('requirements.txt') as f:
requirements = f.read().splitlines()
setuptools.setup(
name="boston-housing-prediction",
version="0.2.0a0",
author="xx",
author_email="xxx#gmail.com",
py_modules=["misc_libary", "polynomial_regression_libary", "linear_regression_libary"],
scripts=["boston-housing-main.py"],
description="Predict housing prices in boston.",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/XXX",
packages=setuptools.find_packages(),
classifiers=[
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7'
],
keywords="regression meachine-learning housing_prices_boston learning_purpose",
license="MIT",
install_requires=requirements,
python_requires='>=3.5',
)

You can specify entry_points in setup.py, like
setuptools.setup(
# ...
entry_points = {
'console_scripts': [
'boston_housing = boston-housing-main:main'
]
},
)
This will cause pip install to install a wrapper somewhere like /usr/local/bin/boston_housing which basically pulls in the module boston-housing-main and runs its main() function.
You probably want to replace the scripts entry with this, though there is no reason per se you could not have both.

One approach to making a globally accessible Python script is to have your users call the module itself. If your package is called 'boston-housing-prediction', your users will be able to call your script from anywhere using the following command:
python -m boston-housing-prediction
What this does is calls a __main__.py file inside your package. This is just like any other Python script, so it can take arguments normally. All you have to do is rename your script to __main__.py and drop it into the package directory (not the folder including setup.py, rather into the folder including the package scripts), or create a new __main__.py that calls your script (you can just import the script if they are in the same folder).
The benefit of this approach is that it is platform independent, relying only on the proper installation of the packages. It doesn't rely on the OS at all.

Changing console_script entry point interpreter for packaging

I'm packaging some python packages using a well known third party packaging system, and I'm encountering an issue with the way entry points are created.
When I install an entry point on my machine, the entry point will contain a shebang pointed at whatever python interpreter, like so:
in /home/me/development/test/setup.py
from setuptools import setup
setup(
entry_points={
"console_scripts": [
'some-entry-point = test:main',
]
}
)
in /home/me/.virtualenvs/test/bin/some-entry-point:
#!/home/me/.virtualenvs/test/bin/python
# EASY-INSTALL-ENTRY-SCRIPT: 'test==1.0.0','console_scripts','some-entry-point'
__requires__ = 'test==1.0.0'
import sys
from pkg_resources import load_entry_point
sys.exit(
load_entry_point('test==1.0.0', 'console_scripts', 'some-entry-point')()
)
As you can see, the entry point boilerplate contains a hard-coded path to the python interpreter that's in the virtual environment that I'm using to create my third party package.
Installing this entry point using my third-party packaging system results in the entry point being installed on the machine. However, with this hard-coded reference to a python interpreter which doesn't exist on the target machine, the user must run python /path/to/some-entry-point.
The shebang makes this pretty unportable. (which isn't a design goal of virtualenv for sure; but I just need to MAKE it a little more portable here.)
I'd rather not resort to crazed find/xargs/sed commands. (Although that's my fallback.)
Is there some way that I can change the interpreter path after the shebang using setuptools flags or configs?

You can customize the console_scripts' shebang line by setting 'sys.executable' (learned this from a debian bug report). That is to say...
sys.executable = '/bin/custom_python'
setup(
entry_points={
'console_scripts': [
... etc...
]
}
)
Better though would be to include the 'execute' argument when building...
setup(
entry_points={
'console_scripts': [
... etc...
]
},
options={
'build_scripts': {
'executable': '/bin/custom_python',
},
}
)

For future reference for someone who wants to do this at runtime without modifying the setup.py, it's possible to pass the interpreter path to setup.py build via pip with:
$ ./venv/bin/pip install --global-option=build \
--global-option='--executable=/bin/custom_python' .
...
$ head -1 ./venv/bin/some-entry-point
#!/bin/custom_python

Simply change the shebang of your setup.py to match the python you want your entry points to use:
#!/bin/custom_python
(I tried #damian answer but not working for me, maybe the setuptools version on Debian Jessie is too old)

using Mysql and SqlAlchemy in Pyramid Framework

Pyramid Framework comes with a sample tutorial of sql alchemy that uses sqlite. The problem is that i want to use mysql so i change this
sqlalchemy.url = sqlite:///%(here)s/tutorial.db
Into this
sqlalchemy.url = mysql://root:22password#localhost/alchemy
when i try to run
../bin/pserve development.ini --reload
It gives me the following error
File "build/bdist.linux-i686/egg/sqlalchemy/connectors/mysqldb.py", line 52, in dbapi
ImportError: No module named MySQLdb
I understand that i should include the dependecies of my app in setup.py but i don't know what to include right now some help please my setup.py looks like this
import os
import sys
from setuptools import setup, find_packages
here = os.path.abspath(os.path.dirname(__file__))
README = open(os.path.join(here, 'README.txt')).read()
CHANGES = open(os.path.join(here, 'CHANGES.txt')).read()
requires = [
'pyramid',
'SQLAlchemy',
'transaction',
'pyramid_tm',
'pyramid_debugtoolbar',
'zope.sqlalchemy',
]
if sys.version_info[:3] < (2,5,0):
requires.append('pysqlite')
setup(name='tutorial',
version='0.0',
description='tutorial',
long_description=README + '\n\n' + CHANGES,
classifiers=[
"Programming Language :: Python",
"Framework :: Pylons",
"Topic :: Internet :: WWW/HTTP",
"Topic :: Internet :: WWW/HTTP :: WSGI :: Application",
],
author='',
author_email='',
url='',
keywords='web wsgi bfg pylons pyramid',
packages=find_packages(),
include_package_data=True,
zip_safe=False,
test_suite='tutorial',
install_requires = requires,
entry_points = """\
[paste.app_factory]
main = tutorial:main
[console_scripts]
populate_tutorial = tutorial.scripts.populate:main
""",
)

Try adding "MySQLdb" to the requires list. It was fine with sqlite3 as that comes with python (as of version 2.5), MySQLdb doesn't and needs to be installed separately.
UPDATE:
Try "mysql-python" in the requires list instead.

Okay i Solved my own question by following the directions on this page
http://www.saltycrane.com/blog/2010/02/install-mysqldb-virtualenv-ubuntu-karmic/

There is the huge list of Unofficial Windows Binaries for Python Extension Packages which are extremely useful for Windows users.
http://www.lfd.uci.edu/~gohlke/pythonlibs/

Solved in ubuntu environment
sudo apt-get build-dep python-mysqldb
source /bin/active && pip install MySQL-python