melib 1.1.1

Library functions to help with machine element design projects.

pip install melib

Documentation : https://melib.readthedocs.io/en/latest/

There are three files in this package:

• library.py -- a collection of small functions that can be used to execute small tasks associated with the design of mechanical components such as belts and chains, gears, rotating shafts, keys, bearings, welded joints, welded structures, fasteners, etc. The module is designed to be used in teaching machine element design to second-year mechanical students. To motivate learning of procedures and relevant standards, there are no pushbutton complete designs. Unless otherwise specified, the formula and data reference is ‘Machine Elements in Mechanical Design’ by Mott. There is a collection of Excel data files that are accessed by the library. These files are in the data folder. This is not a comprehensive machine design library but sufficient for preparing assignments, examples and exam questions.
• xt.py -- Functions that can be called upon to generate jupyter notebooks for documenting the mechanical design tasks. It also has functions to create pdf documents
• excel.py -- functions to read and write Microsoft Excel files. It uses the python package openpyxl.

This was the first project I registered in PyPi uploaded to GitHub with documentation atuomatically generated using ReadTheDocs. I document every step to help others and future self in similar endeavours.

Construct local repository

I create a local folder melib and copy LICENSE, pyproject.toml and setup.cfg into this folder.

• mkdir melib
• cd melib
• copy the python libraries and the data folder into melib
• mkdir docs

This is the folder structure at this stage:

• cd docs
• sphinx-quickstart

  Separate source and build directories (y/n)[n]: Pick the default ([n])  
  Project name: hgdemo  
  Author name(s): H Gurgenci  
  Project release []: June 2021  
  Project language [en]: __  

This creates an intial directory structure as seen below:

The next step is to edit the files index.rst and conf.py (they are two files sphinx created in the docs folder and are marked in the figure above. We will also create a new file api.rst in the same folder. Incidentally, the VS Code, did not automatically update the folder pane after sphinx-quickstart. One needs to refresh to see the new files and folders in docs.

index.rst This is the file after I edit it:

.. melib documentation master file, created by
   sphinx-quickstart on Tue Jun  8 09:34:23 2021.

Welcome to melib's documentation!
=================================
The melib package has three files: library, xt, and excel.
The first one is a library of functions that can be used
to do machine element design computations.  It was created
to help teach a second year design course at the University
of Queensland.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   api.rst


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

conf.py First, I add the path for the package files:

import os
import sys
sys.path.insert(0, os.path.abspath('..'))

Then the extensions. I copied the extension list from the conf file in the psf/requests repository on github. I probably did not need them all. Anyway, here they are.

extensions = [
    "sphinx.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.todo",
    "sphinx.ext.viewcode",
]

api.rst This is a new file:

melib API reference
===================

.. module:: melib

.. automodule:: melib.library
    :members:

.. automodule:: melib.xt
    :members:

.. automodule:: melib.excel
    :members:

The data folder has design data that are needed by the functions in the library.py file.

Before running ./make html to generate the local documentation pages, I copy the image files I need into the assets folder. These image files are referred to by doc strings in the library and xt files. For example, the reference to the file shoulderscf.png in library.py is

            .. image:: ../../assets/shoulderscf.png

The local addressing is all with respect to the docs folder.

This completes the local documentation. Let us now generate a github repository.

IMPORTANT Make sure you import the mock repository. Otherwise, ./make html will not work after we do the mock imports of the next section below. In VS Code Powershell terminal, enter py -m pip install mock and it will install mock in the python kernel that is used by VS Code. Incidentally, py -m pip is always better than just pip because it makes sure that the packe is imported into the python kernek you are using. Otherwise, confusion may occur when you have multiple python versions installed on your computer.

Construct remote repository

git add -A
git commit -am 'the first commit'
git branch -M main
git remote add origin https://github.com/Gurgenci/melib.git
git push -u origin main

Remote documentation

I will generate documentation using ReadtheDocs. For a package like melib that needs to import other packages, the dependencies need to be stated up front. Otherwise, ReadtheDocs will fail.

I create a new file called requirements.txt in the docs folder:

numpy>=1.0
pylatex>=1.0
openpyxl>=1.0

Now add this file to the git repository:

git add -A
git commit -am 'with the new file requirements.txt'
git push -u origin main

• Log in to ReadtheDocs.org
• Import a repository (melib should appear as an available option) The import click will invoke the following menu.

Simply press the Next button to get to

Then click on the Build version button. When the Build is finished, click on the View docs button.

Unfortunately, this did not work. The document generator failed to import my files library, xt, and excel and issued the following warnings:

WARNING: autodoc: failed to import module 'library' from module 'melib'; the following exception was raised:
No module named 'numpy'
WARNING: autodoc: failed to import module 'xt' from module 'melib'; the following exception was raised:
No module named 'pylatex'
WARNING: autodoc: failed to import module 'excel' from module 'melib'; the following exception was raised:
No module named 'openpyxl'
looking for now-outdated files... none found

This was a surprise because I tested the use of a requirements.txt in a simpler package, hgdemo. There, ReadtheDocs managed to import a module that
referenced numpy after I included a requirements.txt file with a numpy line.

This approach did not work for melib.

I decided to try an approach suggested in http://blog.rtwilson.com/how-to-make-your-sphinx-documentation-compile-with-readthedocs-when-youre-using-numpy-and-scipy/. The suggestion is to include the following code at the top of the conf.py file:

import mock

MOCK_MODULES = ['numpy', 'scipy', 'matplotlib', 'matplotlib.pyplot', 'scipy.interpolate',
                'pylatex', 'openpyxl',
                'pylatex.Document',
                ]
for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = mock.Mock()

This made the No module named 'pylatex' and similar messages disappear from the raw log. But the documentation still did not include anything on library, xt and excel contents.

I then realised that it is not enough to mock a package but you need to mock every module you import from it. For example, for pylatex.utils you get

No module named 'pylatex.utils'; 'pylatex' is not a package

All packages and its sub-packages must be added to the 'MOCK-MODULES' in conf.py. The objects imported from those packages do not need to be included in MOCK-MODULES. For example, if 'pylatex.utils' in MOCK_MODULES, then the line from openpyxl.utils import get_column_letter is safe. However, from openpyxl.utils.cell import coordinate_from_string is not acceptable. One needs to add openpyxl.utils.cell to MOCK_MODULES

Incidentally, when you do a rebuild in ReadtheDocs, you must make sure that ReadtheDocs is project database is updated with your latest git push. Otherwise, Build Docs will fail and it is an ugly process to recover from it. So make sure that the time since last built is as you expect it:

Sometimes, it takes a relatively long time for this time to reset to your last commit. Once it was 15 minutes for me.

If all works well, the documentation will be created on http://hgdemo.readthedocs.io/

Upload to PyPi

Finally, the melib package is uploaded to PyPi so that it can be pipped by others. This is done through the following process:

• Start an account with https://pypi.org/ if you do not have one already
• Once you have your PyPi account, create an API token through https://pypi.org/manage/account/ (scroll down that page and you will see the section)

If you follow the PyPi defaults, this token is stored in $HOME/.pypirc, on my system the token file name was C:\Users\e4hgurge\.pypirc

• The root folder for the following steps is "git/melib" in my system.
• Create two files in the root folder: setup.cfg and pyproject.toml (see the github repository for the contants of these files)
• Create a file called LICENSE (no extensions)
  • I use GNU General Public License (from https://choosealicense.com/). I copied the license text to the clipboard on this page and pasted it into the file setup.cfg.
• Increment the version in setup.cfg
• Make sure that we running the latest version of pip:
  • py -m pip install --upgrade pip
• Make sure that we running the latest version of build:
  • py -m pip install --upgrade build
• Now run build in the root folder
  • py -m build
• This will generate the dist folder with the following two files in it:
  • dist\hgdemo-0.0.1-py3-none-any.whl
  • dist\hgdemo-0.0.1.tar.gz
• If you are using VS Code, refresh the folder pane contents to see the changes.
• Now run twine to upload these two files to TestPyPi:
  • py -m twine upload --repository testpypi dist/* This worked. Now let us do the same for PyPi:
• py -m twine upload dist/* This sometime gives HTTPError: 400 Bad Request ... Even when you change your version, this sometimes happens.
• py -m twine upload --skip-existing dist/* sometimes works.

Including the data files in PyPi upload

https://packaging.python.org/guides/using-manifest-in/ lists the following files as those included in a source distribution by default:

• all Python and C source files
• files specified in scripts_setup(), package_data, and data_files setup()
• license_file and license_files as specified in setup.cfg
• all files test/test*.py, setup.py and/or setup.cfg
• README.md and some other README extensions, and
• MANIFEST.in. I have a data directory with five Excel files. I tried a few things to include them in the PyPi distribution and the following addition to setup.cfg worked:

[options.data_files]
data = melib/data/mats.xlsx, melib/data/bearing.xlsx, melib/data/sgear.xlsx, melib/data/shaft.xlsx,melib/data/vbelt.xlsx

I included the files all one line and with no spaces after the commas. But I do not think this matters. Incidentally, using wild cars like melib/data/*.xlsx ibstead of listing all five files separately did not work.

Final Steps

• Go to the root directory of the package
• git status
• git add -A
• git commit -am "Final Commit for the version 1.0.0 following the pypi upload"
• git push -u origin main
• Log in to https://readthedocs.org/dashboard/ and clock on the project melib
• Click on [Build Version] after making sure that the last built is the one you just pushed. The only way you can tell is by the time (e.g. 3 minutes ago). Refresh the page if necessary.
• Documentation will be created on https://melib.readthedocs.io

Additional issues

PyPi Upload Failure

I have already mentioned the occasional error message:

HTTPError: 400 Bad Request from https://upload.pypi.org/legacy/
File already exists. See https://pypi.org/help/#file-name-reuse for more information.

This happens when I fail to change the version number in setup.cfg (for example, if I try to upload version 1.0.11 again). When I change the version number (e.g. 1.0.12), I occasionally still get the same error. Deleting the dist and melib.egg-info folders before the build work in such circumstances. At the end, I get into the habit of deleting the dist and melib.eff-info folders after every upload - just in case.

PIP Failure

Sometimes, pip decides not to download the new version. It says that the version I have is already current and no update is needed. In such instances, deleting the local version always work.

I have two python installations: one was generated when I installed anaconda and the other through VS code. They are in two separate site-packages folders:

• ...\Anaconda3\Lib\site-packages and
• ...\.julia\conda\3\Lib\site-packages

I delete both melib folders in both of them because I read somewhere that sometimes pip decides to save on communications bandwidth and installs a local version of the library rather than going to PyPi. I have not experienced it (I think) but I playe it safe just in case.

VS Code and spyder

Finally, I do all PyPi builds and twine uploading in VS Code and then go to spyder, pip the new melib library and test it there. I hardly use python in VS Code.