Add Biogeme #26374

FGarridoV · 2024-05-16T07:16:57Z

Checklist

conda-forge-webservices · 2024-05-16T07:17:51Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme, recipes/biogeme-optimization, recipes/cythonbiogeme) and found it was in an excellent condition.

conda-forge-webservices · 2024-05-21T07:01:16Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme) and found it was in an excellent condition.

moorepants · 2024-05-21T07:16:24Z

recipes/biogeme/meta.yaml

+    - scipy >=1.7.3
+    - tqdm >=4.64.1
+    - tomlkit >=0.11.5
+    - cythonbiogeme ==1.0.2


This is not present on conda forge, afaik. You should include a recipe for it in this PR also.

recipes/biogeme/meta.yaml

moorepants · 2024-05-21T07:19:16Z

recipes/biogeme/meta.yaml

+  home: http://biogeme.epfl.ch
+  summary: Estimation and application of discrete choice models
+  license: MIT
+  license_family: MIT


This license does not seem to be MIT: https://github.com/michelbierlaire/biogeme/blob/master/LICENSE

It seems to be a modification of the MIT license. I'm not sure we can actually distribute this package, given the license.

MIT license:

Copyright (c) <year> <copyright holders> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

License found in biogeme:

BIOGEME is distributed free of charge. We ask each user to register to Biogeme's users group, and to mention explicitly the use of the package when publishing results, using the following reference: For BisonBiogeme: Bierlaire, M. (2003). BIOGEME: A free package for the estimation of discrete choice models , Proceedings of the 3rd Swiss Transportation Research Conference, Ascona, Switzerland. For PythonBiogeme: Bierlaire, M. (2016) PythonBiogeme: a short introduction. Report TRANSP-OR 160706 ,Series on Biogeme. Transport and Mobility Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Switzerland. Disclaimer: This software is provided free of charge and "AS IS" WITHOUT ANY WARRANTY of any kind. The implied warranties of merchantability, fitness for a particular purpose and non-infringment are expressly disclaimed. In no event will the author (Michel Bierlaire) or his employer (EPFL) be liable to any party for any direct, indirect, special or other consequential damages for any use of the code including, without limitation, any lost profits, business interruption, loss of programs or other data on your information handling system or otherwise, even if we are expressly advised of the possibility of such damages.

Remove license and license_family since this is not the MIT license.

This needs to be license: Custom, same as I did in cythonbiogeme.

…cipes into biogeme

conda-forge-webservices · 2024-05-21T07:32:23Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme, recipes/biogeme-optimization, recipes/cythonbiogeme) and found some lint.

Here's what I've got...

For recipes/biogeme:

There are too few lines. There should be one empty line at the end of the file.

For recipes/biogeme-optimization:

There are too few lines. There should be one empty line at the end of the file.

For recipes/cythonbiogeme:

There are too few lines. There should be one empty line at the end of the file.

conda-forge-webservices · 2024-05-21T07:43:21Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme, recipes/biogeme-optimization, recipes/cythonbiogeme) and found some lint.

Here's what I've got...

For recipes/biogeme:

There are too few lines. There should be one empty line at the end of the file.

For recipes/cythonbiogeme:

There are too few lines. There should be one empty line at the end of the file.

conda-forge-webservices · 2024-05-21T07:45:50Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme, recipes/biogeme-optimization, recipes/cythonbiogeme) and found it was in an excellent condition.

moorepants · 2024-05-21T16:50:47Z

recipes/cythonbiogeme/meta.yaml

+  sha256: f139342944c849b47ce5aaa548e68aa179c195de93ab76be78353f4309684d0e
+
+build:
+  number: 3


Build number should start at 0.

moorepants · 2024-05-21T16:52:47Z

recipes/biogeme-optimization/meta.yaml

+  summary: Various optimization algorithms for teaching and research
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE.txt


This is the error from the linux build:

ValueError: License file given in about/license_file (/home/conda/staged-recipes-copy/recipes/biogeme-optimization/LICENSE.txt) does not exist in source root dir or in recipe root dir (with meta.yaml)

There is no license file in the source tarball for this package. In fact, there is no evidence of a license in the repo at all: https://github.com/michelbierlaire/optimization

If there is no license at all, I don't think we can add this to conda forge because no permission to redistribute is given. Maybe you can open an issue on the author's repository and ask if he will grant permission or add an OSS license to the repository.

moorepants · 2024-05-21T16:56:37Z

cythonbiogeme osx failure:

  In file included from /Users/runner/Miniforge3/conda-bld/cythonbiogeme_1716277750463/_build_env/bin/../include/c++/v1/__mbstate_t.h:45:
  /Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/sys/_types/_mbstate_t.h:31:9: error: unknown type name '__darwin_mbstate_t'
  typedef __darwin_mbstate_t mbstate_t;
          ^
  1 error generated.
  error: command '/Users/runner/Miniforge3/conda-bld/cythonbiogeme_1716277750463/_build_env/bin/clang++' failed with exit code 1
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

moorepants · 2024-05-21T16:58:23Z

recipes/cythonbiogeme/meta.yaml

+  summary: C++ part of the Biogeme package
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE.txt


Windows build error:

ValueError: License file given in about/license_file (D:\a\1\s\recipes\cythonbiogeme\LICENSE.txt) does not exist in source root dir or in recipe root dir (with meta.yaml)

moorepants · 2024-05-21T17:00:54Z

recipes/cythonbiogeme/meta.yaml

+  summary: C++ part of the Biogeme package
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE.txt


Suggested change

license_file: LICENSE.txt

license_file: LICENSE

moorepants · 2024-05-21T17:03:29Z

recipes/cythonbiogeme/meta.yaml

+
+build:
+  number: 3
+  script: /bin/rm -f pyproject.toml && {{ PYTHON }} -m pip install . -vv  # [unix]


Suggested change

script: /bin/rm -f pyproject.toml && {{ PYTHON }} -m pip install . -vv # [unix]

script: {{ PYTHON }} -m pip install . -vv

Should be able to keep pyproject.toml and this should run on windows too (at least to start to see if we need a special script.

moorepants · 2024-05-21T17:03:51Z

recipes/cythonbiogeme/meta.yaml

+build:
+  number: 3
+  script: /bin/rm -f pyproject.toml && {{ PYTHON }} -m pip install . -vv  # [unix]
+  skip: true  # [python_impl == 'pypy']


Remove this line, we'll see if it runs on pypy later.

moorepants · 2024-05-21T17:04:25Z

recipes/cythonbiogeme/meta.yaml

+    - pip
+  run:
+    - python
+    - cython >=0.29.16


Shouldn't need this a run dependency, remove.

Nevermind I see it in the setup.cfg:

install_requires =
cython >= 0.29.16
pandas >= 1.3.5

Does the package compile things at run time?

moorepants · 2024-05-21T18:34:18Z

cythonbiogeme builds for me locally on linux with the suggested changes I made above.

conda-forge-webservices · 2024-08-07T05:36:12Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme/meta.yaml, recipes/biogeme-optimization/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/biogeme/meta.yaml:

License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

For recipes/biogeme-optimization/meta.yaml:

License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

moorepants · 2024-08-07T06:07:53Z

recipes/biogeme/meta.yaml

+    - python-levenshtein >=0.25.1
+    - fuzzywuzzy >=0.18.0
+    - cythonbiogeme ==1.0.4
+    - biogeme_optimization ==0.0.10


Suggested change

- biogeme_optimization ==0.0.10

- biogeme-optimization ==0.0.10

FGarridoV · 2024-08-16T15:26:53Z

@moorepants Finally!! It seems that there no issues now!

sandervancranenburgh · 2024-08-16T15:41:14Z

Wonderful!!

FGarridoV · 2024-08-22T06:11:12Z

@conda-forge/help-python-c This is ready for review.

The license is a custom license that does not have an SPDX identifier. The author gave consent to package for conda forge in #27157. I used "Custom" as the license name and the license is packaged.

We are hoping to get this included in our annual software deployment at my university before classes start Sept 1, so if this can be merged soon, that would be much appreciated. I can iterate in the feedstock if there are any other issues.

@mwcraig I would like your assistance as you were involved in cythonbiogeme (a dependency of biogeme) Thank you!

conda-forge-webservices · 2024-08-23T11:13:17Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme/meta.yaml, recipes/biogeme-optimization/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/biogeme/meta.yaml:

License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

For recipes/biogeme-optimization/meta.yaml:

No valid build backend found for Python recipe for package biogeme-optimization using pip. Python recipes using pip need to explicitly specify a build backend in the host section. If your recipe has built with only pip in the host section in the past, you likely should add setuptools to the host section of your recipe.
License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

sandervancranenburgh · 2024-08-23T11:18:41Z

@moorepants
So, now we just need to wait for the conda-forge team to pull biogeme and biogeme-optimization. And, then we can test it?

moorepants · 2024-08-23T11:35:10Z

So, now we just need to wait for the conda-forge team to pull biogeme and biogeme-optimization. And, then we can test it?

Yes.

xhochy · 2024-08-29T13:36:38Z

recipes/biogeme-optimization/meta.yaml

+about:
+  home: http://biogeme.epfl.ch
+  summary: Various optimization algorithms for teaching and research
+  license: Custom


Please make it SPDX

Suggested change

license: Custom

license: LicenseRef-BIOGEME

The license has been updated, in line with the naming convention. Pls review

recipes/biogeme-optimization/meta.yaml

conda-forge-webservices · 2024-08-30T06:57:30Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme/meta.yaml, recipes/biogeme-optimization/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/biogeme/meta.yaml:

License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

For recipes/biogeme-optimization/meta.yaml:

No valid build backend found for Python recipe for package biogeme-optimization using pip. Python recipes using pip need to explicitly specify a build backend in the host section. If your recipe has built with only pip in the host section in the past, you likely should add setuptools to the host section of your recipe.

conda-forge-webservices · 2024-08-30T09:57:37Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme/meta.yaml, recipes/biogeme-optimization/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/biogeme-optimization/meta.yaml:

No valid build backend found for Python recipe for package biogeme-optimization using pip. Python recipes using pip need to explicitly specify a build backend in the host section. If your recipe has built with only pip in the host section in the past, you likely should add setuptools to the host section of your recipe.

conda-forge-webservices · 2024-08-30T11:04:10Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/biogeme/meta.yaml, recipes/biogeme-optimization/meta.yaml) and found it was in an excellent condition.

sandervancranenburgh · 2024-08-30T11:22:37Z

@xhochy it seems all remaining issues have been addressed. Please review to code to merge the PR.

mwcraig

This is almost ready to go -- just a couple version restrictions to fix, and ideally you would add the dev_url to each recipe.

The versions are important to get right to make sure the user doesn't end up with an unsupported combination (e.g. numpy 1.26)

mwcraig · 2024-08-30T16:58:35Z

recipes/biogeme-optimization/meta.yaml

+    - pip
+  run:
+    - python >=3.7
+    - numpy


Suggested change

- numpy

- numpy >=2

There is a version restriction in the biogeme-optimization dependencies: https://github.com/michelbierlaire/optimization/blob/main/pyproject.toml#L28

The author of biogeme compiled cythonbiogeme against numpy 2, so it should be fine with numpy 1. We really need to be able to install this with numpy 1 and that is why I recommended not following upstream. I've opened an issue upstream to see if the author will correct this.

I've opened both of these:

michelbierlaire/biogeme#40

michelbierlaire/cythonbiogeme#21

I will help manage this in the feedstock repo and if we really have to add a restriction to numpy 2 we will, but there should be no issues with this and if someone reports something on the feedstock I can give my word to help resolve it. Can that possibly be sufficient? I maintain many feedstocks and haven't had any past issues with similar decisions when upstream authors are a bit to heavy with the pins.

Ah, ok, thanks for the explanation.

Also @moorepants should I add you as a maintainer on this?

OK, and you have no objection to adding the dev_url, I assume? If not, then I'll wait a couple hours for @FGarridoV to chime, then push the necessary changes and merge. That way you can both start testing and tuning as needed. I know you have an imminent deadline.

mwcraig · 2024-08-30T17:00:55Z

recipes/biogeme-optimization/meta.yaml

+  home: http://biogeme.epfl.ch
+  summary: Various optimization algorithms for teaching and research
+  license: LicenseRef-BIOGEME-OPTIMIZATION
+  license_file: LICENSE


Suggested change

license_file: LICENSE

license_file: LICENSE

dev_url: https://github.com/michelbierlaire/optimization

This one took a little while to find 😀, so listing it explicitly would be helpful.

I have added this dev_url

mwcraig · 2024-08-30T17:02:29Z

recipes/biogeme/meta.yaml

+    - cythonbiogeme ==1.0.4
+    - biogeme-optimization ==0.0.10
+    - Jinja2 >=3.1.4
+    - ipython 


Suggested change

- ipython

- ipython >=8.25.0

Please include the version restriction

ipython isn't even really a dependency, it is never imported in the modules. I think this is also a mistake from the upstream author.

This one seems harmless to include now, and it can always be removed later.

mwcraig · 2024-08-30T17:03:39Z

recipes/biogeme/meta.yaml

+  home: http://biogeme.epfl.ch
+  summary: Estimation and application of discrete choice models
+  license: LicenseRef-BIOGEME
+  license_file: LICENSE


Suggested change

license_file: LICENSE

license_file: LICENSE

dev_url: https://github.com/michelbierlaire/biogeme

The dev URL is really handy for checking for dependency changes when the conda-forge bot opens pull requests for new versions.

I have added this dev_url

mwcraig · 2024-08-31T01:39:48Z

I wasn't able to add @moorepants as a maintainer, so I'll merge this and he can be added in the feedstock repos. Thanks everyone for wrapping this one up.

moorepants · 2024-08-31T04:28:32Z

Thanks!

EwoutH · 2024-08-31T06:32:41Z

Exciting to see this merged! And just in time for the new academic year.

Thanks for everyone’s efforts!

FGarridoV added 2 commits May 16, 2024 09:00

biogeme for conda-forge

a6618e0

biogeme for conda-forge

63659a1

FGarridoV added 4 commits May 21, 2024 08:19

Merge branch 'conda-forge:main' into biogeme

de7f8c3

updated cythonbiogeme

42135ff

updated cythonbiogeme v2

28e80ac

new test

f780af2

Merge branch 'conda-forge:main' into biogeme

677dd86

moorepants reviewed May 21, 2024

View reviewed changes

recipes/biogeme/meta.yaml Outdated Show resolved Hide resolved

biogeme v3

beb61a0

moorepants reviewed May 21, 2024

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FGarridoV added 2 commits May 21, 2024 09:26

Merge branch 'biogeme' of https://github.com/TUD-CityAI-Lab/staged-re…

4e0d84f

…cipes into biogeme

tester v3

f157eb3

FGarridoV added 3 commits May 21, 2024 09:42

Update meta.yaml

1d415c4

Update meta.yaml

a2a77a1

Update meta.yaml

77bed29

moorepants reviewed May 21, 2024

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moorepants reviewed Aug 7, 2024

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FGarridoV added 2 commits August 16, 2024 14:22

typo

29a7ba9

Adding ipython

8c45729

Merge branch 'main' into biogeme

edbd25b

xhochy requested changes Aug 29, 2024

View reviewed changes

Update license meta.yaml --> LicenseRef-BIOGEME

f7964d4

sandervancranenburgh added 4 commits August 30, 2024 09:24

Merge branch 'main' into biogeme

a759d95

Merge branch 'main' into biogeme

ca058c5

Update meta.yaml license --> LicenseRef-BIOGEME-OPTIMIZATION

ba9e2a2

Update meta.yaml license: --> LicenseRef-BIOGEME

0ee164b

Update meta.yaml Adding setuptools to host requirements

bd12db2

mwcraig requested changes Aug 30, 2024

View reviewed changes

sandervancranenburgh added 2 commits August 30, 2024 21:20

Update meta.yaml add dev_url

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Update meta.yaml add dev_url

0306cc3

mwcraig approved these changes Aug 31, 2024

View reviewed changes

mwcraig merged commit 2df8284 into conda-forge:main Aug 31, 2024
5 checks passed

	script: /bin/rm -f pyproject.toml && {{ PYTHON }} -m pip install . -vv # [unix]
	script: {{ PYTHON }} -m pip install . -vv

	- biogeme_optimization ==0.0.10
	- biogeme-optimization ==0.0.10

	license_file: LICENSE
	license_file: LICENSE
	dev_url: https://github.com/michelbierlaire/optimization

Add Biogeme #26374

Add Biogeme #26374

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FGarridoV commented May 16, 2024 • edited Loading

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mwcraig commented Aug 31, 2024

moorepants commented Aug 31, 2024

EwoutH commented Aug 31, 2024

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