Add MANIFEST.in for source distribution

[mrakitin]

This PR adds the MANIFEST.in file required to add necessary files into the source distribution uploaded to PyPI (those files are bundled in the .whl file via setup.py). It is based on https://github.com/NSLS-II/scientific-python-cookiecutter/blob/master/%7B%7B%20cookiecutter.repo_name%20%7D%7D/MANIFEST.in.

Comparison:

main branch:

$ tree lixtools-2021.2.21.1
lixtools-2021.2.21.1
├── PKG-INFO
├── README.md
├── lixtools
│   ├── __init__.py
│   ├── atsas.py
│   ├── hdf.py
│   ├── mailin.py
│   ├── modeling.py
│   └── notebooks.py
├── lixtools.egg-info
│   ├── PKG-INFO
│   ├── SOURCES.txt
│   ├── dependency_links.txt
│   ├── requires.txt
│   └── top_level.txt
├── setup.cfg
└── setup.py

this PR branch:

$ tree lixtools-2021.2.21.1
lixtools-2021.2.21.1
├── LICENSE
├── MANIFEST.in
├── PKG-INFO
├── README.md
├── lixtools
│   ├── __init__.py
│   ├── atsas.py
│   ├── hdf.py
│   ├── mailin.py
│   ├── modeling.py
│   ├── notebooks.py
│   ├── plate_label_template.html
│   └── template_report.ipynb
├── lixtools.egg-info
│   ├── PKG-INFO
│   ├── SOURCES.txt
│   ├── dependency_links.txt
│   ├── requires.txt
│   └── top_level.txt
├── setup.cfg
└── setup.py

[mrakitin]

I'd recommend using the https://github.com/NSLS-II/scientific-python-cookiecutter project to generate all infrastructure files for this project (docs, CI, etc.) Would you like to give it a try following the detailed instruction in https://nsls-ii.github.io/scientific-python-cookiecutter/preliminaries.html, @lyang11973?

[mrakitin]

I'd recommend using the https://github.com/NSLS-II/scientific-python-cookiecutter project to generate all infrastructure files for this project (docs, CI, etc.) Would you like to give it a try following the detailed instruction in https://nsls-ii.github.io/scientific-python-cookiecutter/preliminaries.html, @lyang11973?

I opened an issue #2 for this request, which should be done via a separate PR. This PR is targeting a fix for the missing files (LICENSE, plate_label_template.html, template_report.ipynb).

Also, I haven't observed any tags for this repo. It would be great to have a tag for each PyPI build. The procedure we follow is documented here: https://nsls-ii.github.io/scientific-python-cookiecutter/publishing-releases.html.

Please merge this PR, cut a new tag, and push to PyPI. Then I'll be able to build a conda package via https://github.com/nsls-ii-forge/lixtools-feedstock. Right now, with the missing files, the package is incomplete.

[lyang11973]

Hi Maxim, since I'm the only one contributing to this package, I would rather keep it simple for now. The files on PyPI are up to date.

…

On Wed, Feb 24, 2021, 6:18 PM Maksim Rakitin ***@***.***> wrote: I'd recommend using the https://github.com/NSLS-II/scientific-python-cookiecutter project to generate all infrastructure files for this project (docs, CI, etc.) Would you like to give it a try following the detailed instruction in https://nsls-ii.github.io/scientific-python-cookiecutter/preliminaries.html, @lyang11973 <https://github.com/lyang11973>? I opened an issue #2 <#2> for this request, which should be done via a separate PR. This PR is targeting a fix for the missing files (LICENSE, plate_label_template.html, template_report.ipynb). Also, I haven't observed any tags for this repo. It would be great to have a tag for each PyPI build. The procedure we follow is documented here: https://nsls-ii.github.io/scientific-python-cookiecutter/publishing-releases.html . Please merge this PR, cut a new tag, and push to PyPI. Then I'll be able to build a conda package via https://github.com/nsls-ii-forge/lixtools-feedstock. Right now, with the missing files, the package is incomplete. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFNJXDYUVTSEUWI3BN56OL3TAWCNRANCNFSM4YFNFF7Q> .

[mrakitin]

As explained in the description, there are missing files in the source distribution .tar.gz file. These updates from the present PR are needed to fix it for the next release.

[mrakitin]

Hi Maxim, since I'm the only one contributing to this package, I would rather keep it simple for now. The files on PyPI are up to date.

@lyang11973, by "simple", do you mean avoiding tags? I don't think they should be disregarded. How does one know what commit was used for a specific version on PyPI? From the packaging perspective that would be useful, for example, if we wanted to temporarily use the archived files from the GitHub tags instead of the sources on PyPI, to work-around the situation with the missing files in the source distribution on PyPI. Does it sound convincing?

From the DAMA perspective of maintaining the beamline-specific packages, anything that goes in the production conda environments on the experimental floor has to meet minimum requirements, and this PR is attempting to address some of them. Please accept and merge this PR, so that we could provide an expected package during the next deployment.

[mrakitin]

@lyang11973, I think the xlrd dependency should be removed from setup.py, as the package is not maintained for .xlsx files starting from v2. Here is my earlier investigation: NSLS-II-IOS/profile_collection#11 (comment). The openpyxl should be used for that purpose, which you already have in your requirements. I'll update the list here.

[mrakitin]

@lyang11973, I saw another release on PyPI today, which still does not contain these fixes: https://pypi.org/project/lixtools/2021.2.25.0/#files. You can verify it yourself by downloading https://files.pythonhosted.org/packages/c4/a0/c2a5deb94962e3966afc2049c94f52dcca8327fecf4178cf24906a0a0845/lixtools-2021.2.25.0.tar.gz and unpacking it. You will see that the package is incomplete:

$ tree lixtools-2021.2.25.0
lixtools-2021.2.25.0
├── PKG-INFO
├── README.md
├── lixtools
│   ├── __init__.py
│   ├── atsas.py
│   ├── hdf.py
│   ├── mailin.py
│   ├── modeling.py
│   ├── notebooks.py
│   ├── ot2.py
│   └── webcam.py
├── lixtools.egg-info
│   ├── PKG-INFO
│   ├── SOURCES.txt
│   ├── dependency_links.txt
│   ├── requires.txt
│   └── top_level.txt
├── setup.cfg
└── setup.py

The wheel file is OK though, as it's controlled by setup.py, not MANIFEST.in. I have to mention that if the .whl file exists on PyPI, it will be used during the pip installation. However, conda uses .tar.gz sources from PyPI, which is a cause of the problem (current build fails: nsls-ii-forge/lixtools-feedstock#3). Also, people may be interested in the source archive for code inspection, etc., so maintaining a proper package is critical. Please consider merging this update ASAP, so the conda packaging can be done flawlessly, and you get the package during the next deployment.