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biogeme: deprecate as of oct 2018 #54717

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biogeme: deprecate as of oct 2018 #54717

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Amar1729
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  • Have you followed the guidelines for contributing?
  • Have you checked that there aren't other open pull requests for the same formula update/change?
  • Have you built your formula locally with brew install --build-from-source <formula>, where <formula> is the name of the formula you're submitting?
  • Is your test running fine brew test <formula>, where <formula> is the name of the formula you're submitting?
  • Does your build pass brew audit --strict <formula> (after doing brew install <formula>)?

According to biogeme's homepage, the command-line pythonbiogeme has been deprecated since late 2018. The new project, PandasBiogeme, is purely a pip package and is hosted on PyPI (release history).

From the homepage:

PythonBiogeme
    Around 2010, a more flexible version was designed for general purpose parametric models. 
    The modeling language was extended, and based on the Python language.
    A series of discrete choice models were precoded for an easy use.
    Also written in GNU C++, it is distributed on the homebrew package manager.
    The distributions can be found here. 

PandasBiogeme
    In 2018, a completely new version of the software was released.
    It was not anymore a standalone executable, but a Python package.
    The package is written in Python, with the exception of the core calculations of the models, that are written in C++ for the sake of efficiency.
    The motivation was to combine the simplicity of the usage (especially for teaching purposes), with the sophistication provided by Python (for research and applications purposes).
    Morever, the management of the data relies on the package Pandas, which has become the workhorse of data scientists.
    Therefore, the name PandasBiogeme has been adopted.
    It is distributed on the Python Package Index repository.

Tagging @michelbierlaire - user account that first introduced biogeme package. Is it ok to deprecate this from homebrew? Are most user-installs now focused on the PyPI-distributed PandasBiogeme rather than the command-line tool, or is PythonBiogeme still being used?

https://formulae.brew.sh/formula/biogeme#default

This is one of the formulae remaining before the python3.8 switch - #47274

@SMillerDev
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I'd say we should switch to the pypy package then.

@michelbierlaire
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michelbierlaire commented May 15, 2020 via email

@Amar1729
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@SMillerDev should this formula switch to the PyPI version, or should it be introduced as a new formula?

@iMichka iMichka mentioned this pull request May 15, 2020
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@bayandin
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@SMillerDev should this formula switch to the PyPI version, or should it be introduced as a new formula?

Switch it to pypi version, please

@Amar1729
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I'm having a bit of trouble converting this to the python, mostly because i can't quite seem to get the pandas dependency building properly with cython inside homebrew. Let's see how this works...

@michelbierlaire
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michelbierlaire commented May 23, 2020 via email

@Amar1729
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@michelbierlaire thanks for the offer - really I'm just not used to writing python packages as Homebrew formulae. If you're more comfortable with it feel free to update this formula otherwise I'll take another look at it when I can.

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@Amar1729 Well, no, I am not sufficiently familiar with Homebrew. I had in mind that, if you need any specific information about the package itself, let me know.

@Rylan12
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Rylan12 commented May 29, 2020

Is it worth having biogeme available from Homebrew if it's available through pip?

According to the Python for Formula Authors documentation page:

Homebrew generally won’t accept libraries that can be installed correctly with pip install foo.

As a user, I'm not sure that I see a benefit to having a pip package available through Homebrew. It seems that using pip install biogeme is a better option.

That being said, I'm not a maintainer nor do I use biogeme so take my opinion with a grain of salt.

@Amar1729
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@Rylan12 i agree, I'm not sure it's worth it to have biogeme provided by homebrew.

@Rylan12
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Rylan12 commented May 29, 2020

@SMillerDev Is it worth continuing to work on this or should it just be removed?

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Assuming this is still wanted, this should solve the problems.

The test should also be updated because the current one uses the old binary. Something like this might work:

  test do
    xy = Language::Python.major_minor_version Formula["python@3.8"].opt_bin/"python3"
    ENV.prepend_create_path "PYTHONPATH", libexec/"lib/python#{xy}/site-packages"
    system Formula["python@3.8"].opt_bin/"python3", "-c", "import biogeme"
  end

Formula/biogeme.rb
Comment on lines +45 to +47
%w[numpy scipy].each do |d|
ENV.prepend "PYTHONPATH", Formula[d].opt_lib/"python#{xy}/site-packages"
end
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Removing these lines did the trick for me

Suggested change
%w[numpy scipy].each do |d|
ENV.prepend "PYTHONPATH", Formula[d].opt_lib/"python#{xy}/site-packages"
end

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michelbierlaire commented May 30, 2020 via email

iMichka added a commit to iMichka/homebrew-core that referenced this pull request Jun 2, 2020
@iMichka
biogeme: delete
b111fed 
This was previously a c++ tool, but is now written in pure Python and
shipped through pypi.

As discussed in Homebrew#54717,
upstream is fine to remove this formula from homebrew.

This is the last formula blocking the python 3.8 migration.
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iMichka commented Jun 2, 2020 •
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As upstream is fine with deletion; and it is shipped on pypi, and this is now a pure Python package, and this is the last blocker for the Python 3.8 migration, let's delete this in #55702.

@iMichka iMichka closed this Jun 2, 2020
BrewTestBot pushed a commit that referenced this pull request Jun 2, 2020
@iMichka @BrewTestBot
biogeme: delete
1356373 
This was previously a c++ tool, but is now written in pure Python and
shipped through pypi.

As discussed in #54717,
upstream is fine to remove this formula from homebrew.

This is the last formula blocking the python 3.8 migration.

Closes #55702.

Signed-off-by: BrewTestBot <1589480+BrewTestBot@users.noreply.github.com>
@Amar1729 Amar1729 deleted the python3/biogeme branch June 3, 2020 04:27
@Moisan Moisan mentioned this pull request Apr 9, 2021
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@Amar1729 @SMillerDev @michelbierlaire @bayandin @Rylan12 @iMichka