My python project installs via setup.py. The project structure looks like:
├── Makefile
├── README.rst
├── circle.yml
├── docs
│ ├── Makefile
│ ├── conf.py
│ ├── deps.txt
│ ├── guide_installation.rst
│ ├── guide_model.rst
│ ├── guide_transliteration.rst
│ ├── index.rst
│ ├── make.bat
│ └── module_trans.rst
├── indictrans
│ ├── __init__.py
│ ├── _decode
│ ├── _utils
│ ├── base.py
│ ├── iso_code_transformer.py
│ ├── libindic_
│ ├── mappings
│ ├── models
│ ├── polyglot_tokenizer
│ ├── script_transliterate.py
│ ├── test.py
│ ├── tests
│ ├── transliterator.py
│ ├── trunk
│ └── unicode_marks.py
├── requirements.txt
├── setup.cfg
├── setup.py
├── test-requirements.txt
└── tox.ini
where the subfolder indictrans/models looks like
├── ben-eng
│ ├── classes.npy
│ ├── coef.npy
│ ├── intercept_final.npy
│ ├── intercept_init.npy
│ ├── intercept_trans.npy
│ └── sparse.vec
├── ben-guj
│ ├── classes.npy
│ ├── coef.npy
│ ├── intercept_final.npy
│ ├── intercept_init.npy
│ ├── intercept_trans.npy
│ └── sparse.vec
so I have .npy and .vec files to be included in the project.
In my setup.py I'm trying to explicitly include this folder models via the include_package_data directive like:
setup(
setup_requires=['pbr'],
pbr=True,
packages=find_packages(),
include_package_data=True,
package_data={'models': ['*.npy','*.vec']},
ext_modules=cythonize(extensions)
)
and in the setup.cfg I have
[files]
packages =
indictrans
but running python setup.py install does not copy the models folder to the installation folder /usr/local/lib/python2.7/dist-packages/indictrans/.
If I print the it is the output of the find_packages I get
['indictrans', 'indictrans.tests', 'indictrans.libindic_', 'indictrans._utils', 'indictrans._decode', 'indictrans.polyglot_tokenizer', 'indictrans.models', 'indictrans.trunk', 'indictrans.libindic_.utils', 'indictrans.libindic_.soundex', 'indictrans.libindic_.utils.tests', 'indictrans.libindic_.soundex.utils', 'indictrans.libindic_.soundex.tests', 'indictrans.libindic_.soundex.utils.tests', 'indictrans.polyglot_tokenizer.tests', 'indictrans.trunk.tests']
so I will assume that indictrans/models would be included, but it is not.
Add include_package_data=True to your setup-function (you already did that).
Create a file MANIFEST.in in the same directory as setup.py
MANIFEST.in can look as follows:
include indictrans/models/ben-eng/*
include indictrans/models/ben-guj/*
You don't need setup.cfg for doing this.
Source: This great writeup of python packaging
EDIT about recursive-include:
According to the documentation this should also work:
recursive-include indictrans/models *.npy *.vec
include_package_data=True requires MANIFEST.in.
To include data for the module indictrans.models you have to provide the full name:
package_data={'indictrans.models': ['*.npy','*.vec']},
Related
I am playing around with Sphinx 4.4.0 in a test project. I use sphinx.ext.autodoc and sphinx-apidoc.
But not all py files are recognized. It seams like that files with a starting _ in filename are ignored (e.g. _mypackage.py). But i am not sure if that character is the cause or something else.
Are you aware of an option to modify that behavior?
This is the project structure
sphinx_versuch
├── docs
│ ├── make.bat
│ ├── Makefile
│ └── source
│ ├── conf.py
│ ├── index.rst
│ ├── modules.rst
│ ├── mypackage.rst
│ ├── _static
│ └── _templates
├── LICENSE
├── README.md
├── src
│ ├── mypackage
│ │ ├── a.py
│ │ ├── b.py
│ │ ├── __init__.py
│ │ └── _mypackage.py
│ ├── setup.cfg
│ └── setup.py
└── tests
├── __init__.py
├── test_a.py
├── test_b.py
└── test_mypackage.py
The option --private or -P for sphinx-apidoc make sure that private files (which start with an underscore by convention) are included also.
See also
https://www.sphinx-doc.org/en/master/man/sphinx-apidoc.html#cmdoption-sphinx-apidoc-P
I'm trying to run my tests using python -m pytest but I get an error that
ModuleNotFoundError: No module named 'sample'
When using nosetests or anything else it works fine, but when trying to use pytest, it doesn't work.
My tree looks like below, do you have any advice why it doesn't work?
├── LICENSE.txt
├── README.md
├── data
│ └── data_file
├── exported_register.csv
├── pyproject.toml
├── requirements.txt
├── setup.cfg
├── setup.py
├── src
│ └── sample
│ ├── __init__.py
│ ├── __pycache__
│ │ ├── __init__.cpython-39.pyc
│ │ ├── dziennik.cpython-39.pyc
│ │ ├── przedmiot.cpython-39.pyc
│ │ ├── simple.cpython-39.pyc
│ │ └── uczen.cpython-39.pyc
│ ├── dziennik.py
│ ├── package_data.dat
│ ├── przedmiot.py
│ ├── simple.py
│ └── uczen.py
├── tests
│ ├── __init__.py
│ ├── __pycache__
│ │ ├── __init__.cpython-39.pyc
│ │ ├── test_ASSERTPY_uczen.cpython-39-pytest-6.2.1.pyc
│ │ ├── test_ASSERTPY_uczen.cpython-39-pytest-6.2.5.pyc
│ │ ├── test_ASSERTPY_uczen.cpython-39.pyc
│ │ ├── test_PYHAMCREST_uczen.cpython-39-pytest-6.2.1.pyc
│ │ ├── test_PYHAMCREST_uczen.cpython-39-pytest-6.2.5.pyc
│ │ ├── test_PYHAMCREST_uczen.cpython-39.pyc
│ │ ├── test_UNITTEST_register.cpython-39-pytest-6.2.1.pyc
│ │ ├── test_UNITTEST_register.cpython-39-pytest-6.2.5.pyc
│ │ ├── test_UNITTEST_register.cpython-39.pyc
│ │ ├── test_UNITTEST_uczen.cpython-39-pytest-6.2.1.pyc
│ │ ├── test_UNITTEST_uczen.cpython-39-pytest-6.2.5.pyc
│ │ ├── test_UNITTEST_uczen.cpython-39.pyc
│ │ ├── test_simple.cpython-39-pytest-6.2.1.pyc
│ │ ├── test_simple.cpython-39-pytest-6.2.5.pyc
│ │ └── test_simple.cpython-39.pyc
│ ├── test_ASSERTPY_uczen.py
│ ├── test_PYHAMCREST_uczen.py
│ ├── test_UNITTEST_register.py
│ ├── test_UNITTEST_uczen.py
│ └── test_simple.py
└── tox.ini
When you run pytest with python -m pytest it uses the current directory as it its working dir, which doesn't contain the sample module (located inside ./src). The way I deal with this is I have a conftest.py inside my tests directory where I add my source dir to python path something like this:
import sys
from pathlib import Path
source_path = Path(__file__).parents[1].joinpath("src").resolve()
sys.path.append(str(source_path))
I've recently started using pytorch and have had similar problems. Couple steps come to mind:
How are you writing the .py file that contains the tests? It may simply be that you need to change up how you import sample within the unit test file. I would expect that you need something like import src.sample.simple. In other words, could be just a pathing issue.
Try a (much) simpler folder structure and try again. If that doesn't work, try to just copy an example of a simple scheme that someone has posted. That is, just get python -m pytest to run somehow, then start slowly adding the complexities of your project.
I'm trying to generate documentation for my library. Since the library directory structure is quite big, I want Sphinx to generate the .rst files as a nested directory that mirrors the package and module structure.
The library structure:
pyflocker/
├── __init__.py
├── ciphers/
│ ├── __init__.py
│ ├── backends/
│ │ ├── __init__.py
│ │ ├── _asymmetric.py
│ │ ├── _symmetric.py
│ │ ├── cryptodome_/
│ │ │ ├── AES.py
│ │ │ ├── ChaCha20.py
│ │ │ ├── ECC.py
│ │ │ ├── Hash.py
│ │ │ ├── RSA.py
│ │ │ ├── __init__.py
│ │ │ ├── _serialization.py
│ │ │ └── _symmetric.py
│ │ └── cryptography_/
│ │ ├── AES.py
│ │ ├── Camellia.py
│ │ ├── ChaCha20.py
│ │ ├── DH.py
│ │ ├── ECC.py
│ │ ├── Hash.py
│ │ ├── RSA.py
│ │ ├── __init__.py
│ │ ├── _serialization.py
│ │ └── _symmetric.py
│ ├── base.py
│ ├── exc.py
│ ├── interfaces/
│ │ ├── AES.py
│ │ ├── Camellia.py
│ │ ├── ChaCha20.py
│ │ ├── DH.py
│ │ ├── ECC.py
│ │ ├── Hash.py
│ │ ├── RSA.py
│ │ └── __init__.py
│ └── modes.py
└── locker.py
Till now I was using sphinx-apidoc -e -o ... to generate the documentation within the docs/source/ folder.
But this doesn't work as expected.
Expected Results:
Documentation generated as a nested directory. The files have been removed to keep the backbone only.
docs/source/
└── ciphers/
└── backends/
├── cryptodome_/
└── cryptography_/
Actual results:
The whole module name is retained.
docs/source/
├── ... # skipping boilerplate files
├── pyflocker.ciphers.backends.cryptodome_.AES.rst
├── pyflocker.ciphers.backends.cryptodome_.ChaCha20.rst
├── pyflocker.ciphers.backends.cryptodome_.ECC.rst
├── pyflocker.ciphers.backends.cryptodome_.Hash.rst
├── pyflocker.ciphers.backends.cryptodome_.RSA.rst
├── pyflocker.ciphers.backends.cryptodome_.rst
├── pyflocker.ciphers.backends.cryptography_.AES.rst
├── pyflocker.ciphers.backends.cryptography_.Camellia.rst
├── pyflocker.ciphers.backends.cryptography_.ChaCha20.rst
├── pyflocker.ciphers.backends.cryptography_.DH.rst
├── pyflocker.ciphers.backends.cryptography_.ECC.rst
├── pyflocker.ciphers.backends.cryptography_.Hash.rst
├── pyflocker.ciphers.backends.cryptography_.RSA.rst
├── pyflocker.ciphers.backends.cryptography_.rst
├── pyflocker.ciphers.backends.rst
├── pyflocker.ciphers.base.rst
├── pyflocker.ciphers.exc.rst
├── pyflocker.ciphers.interfaces.AES.rst
├── pyflocker.ciphers.interfaces.Camellia.rst
├── pyflocker.ciphers.interfaces.ChaCha20.rst
├── pyflocker.ciphers.interfaces.DH.rst
├── pyflocker.ciphers.interfaces.ECC.rst
├── pyflocker.ciphers.interfaces.Hash.rst
├── pyflocker.ciphers.interfaces.RSA.rst
├── pyflocker.ciphers.interfaces.rst
├── pyflocker.ciphers.modes.rst
├── pyflocker.ciphers.rst
├── pyflocker.locker.rst
└── pyflocker.rst
Is there any way to generate the doc as a directory tree?
What you specify isn't currently possible.
sphinx-apidoc will not create directories mirroring your package/file structure.
sphinx-apidoc will not distribute .rst files along several directories mirroring your package/file structure.
Notice the sphinx-apidoc signature, you can specify one input path for modules, and one output path for the .rst files:
Synopsis
sphinx-apidoc [OPTIONS] -o <OUTPUT_PATH> <MODULE_PATH> [EXCLUDE_PATTERN …]
You'll have to write your own script to recurse into your file system and execute sphinx-apidoc once for every package/directory with <MODULE_PATH> mirroring <OUTPUT_PATH>.
This may seem counter-intuitive, however the Python philosophy is:
The Zen of Python - PEP 20
Flat is better than nested.
Arguably it is more convenient to have sphinx-apidoc produce the .rst files with dotted names mirroring the package/module structure, because you get an overview of the packages at a glance and it tends to save clicking.
If you want to organize some .rst files into directories afterwards it is possible to link them, at the time of this writing it is however not possible to generate such a tree automatically using sphinx-apidoc in a single execution.
It is possible to do so using sphinx-nested-apidoc.
It mirrors the original package structure and generates appropriate files.
Note that it does not edit the files or the links within it. It just renames or moves them.
I have a Scrapy project that need to be build, below the project structure:
.
├── cli.py
├── docs
│ ├── README.md
│ └── README.md.html
├── __init__.py
├── my_scrapy_project
│ ├── exporters.py
│ ├── __init__.py
│ ├── items.py
│ ├── middlewares
│ │ ├── __init__.py
│ │ ├── randomproxy.py
│ │ └── random_user_agent.py
│ ├── middlewares.py
│ ├── pipelines.py
│ ├── settings.py
│ ├── signals.py
│ └── spiders
│ ├── website_extractor_1.py
│ ├── __init__.py
│ └── website_extractor_2.py
├── MANIFEST.in
├── requirements.txt
├── scrapy.cfg
├── setup.py
└── VERSION
Scrapy spiders are executed by cli.py, when I try to build this package it's doesn't inlcude the cli.py, if I put this file cli.py in scripts key in setup.py it doesn't found Scrapy settings when I use get_project_settings
Any help please?
I want to make python package with C extensions. I want this to be done with cython. My structure is:
.
├── build
│ ├── lib.linux-i686-2.7
│ │ └── pyA13SOM
│ │ ├── cython
│ │ │ └── spi.so
│ │ └── __init__.py
│ └── temp.linux-i686-2.7
│ └── pyA13SOM
│ └── cython
│ ├── my_test.o
│ └── spi.o
├── CHANGES.txt
├── Makefile
├── MANIFEST
├── pyA13SOM
│ ├── cython
│ │ ├── clibraries
│ │ │ └── spi_test.c
│ │ ├── __init__.py
│ │ ├── __init__.pyc
│ │ ├── spi.c
│ │ ├── spi.pyx
│ │ └── spi.so
│ ├── gpio
│ │ ├── gpio.c
│ │ ├── gpio_lib.c
│ │ ├── gpio_lib.h
│ │ ├── __init__.py
│ │ └── __init__.pyc
│ ├── i2c
│ │ ├── i2c.c
│ │ ├── i2c_lib.c
│ │ ├── i2c_lib.h
│ │ ├── __init__.py
│ │ └── __init__.pyc
│ ├── __init__.py
│ ├── __init__.pyc
│ ├── spi
│ │ ├── __init__.py
│ │ ├── __init__.pyc
│ │ ├── spi.c
│ │ ├── spi_lib.c
│ │ └── spi_lib.h
│ └── utilities
│ └── color.h
├── README.txt
└── setup.py
My setup file is:
from distutils.core import setup
from distutils.core import Extension
from Cython.Build import cythonize
from Cython.Distutils import build_ext
module_gpio = Extension('pyA13SOM.gpio',
sources=['pyA13SOM/gpio/gpio_lib.c', 'pyA13SOM/gpio/gpio.c'])
module_i2c = Extension('pyA13SOM.i2c',
sources=['pyA13SOM/i2c/i2c_lib.c', 'pyA13SOM/i2c/i2c.c'])
module_spi = Extension('pyA13SOM.spi',
define_macros=[('CYTHON_IN_USE', '1')],
sources=['pyA13SOM/spi/spi_lib.c', 'pyA13SOM/spi/spi.c'])
setup(
name='pyA13SOM',
version='0.2.0',
packages=['pyA13SOM'],
# ext_modules=[module_gpio, module_i2c, module_spi],
cmdclass={'build_ext': build_ext},
ext_modules=cythonize("pyA13SOM/cython/*.pyx"),
)
The tree is in ~/mydir/. I go to ~/mydir/ and do: python setup.py install.
Everything in the build process is OK. Next I try to test import. When I import pyA13SOM.cython.spi, it should give me "Hello world" message. And it does.
~/mydir/$ **python -c "import pyA13SOM.cython.spi"**
Test:
Hellowwwwwwwwwww!
But when I do this from another directory:
~/someotherdir/$ **python -c "import pyA13SOM.cython.spi"**
ImportError: No module named cython.spi
Any idea why does this happen?
You might need to include the directory in which your newly built .spi file is located into your $PYTHONPATH. Otherwise python cannot find the file to import it. While you are in ~/mydir/, python searches the local path if I am not mistaken...
Depending on the shell you are using, you can include the ~/mydir/ directory into the pythonpath with the following:
for the bash and sh shells:
PYTHONPATH=$PYTHONPATH:~/mydir/
export $PYTHONPATH
for the csh/tcsh environment:
set PYTHONPATH = ($PYTHONPATH ~/mydir/)
These two commands add the ~/mydir/ temporarily to your $PYTHONPATH. If you want to add the path permanently, you will have to add the above commands to your ~/.bashrc or ~/.tcshrc, respectively.
Hope this helps...