openbabel: 2.4 -> 3.1.1 #107845

danielbarter · 2020-12-28T21:56:08Z

Motivation for this change

In my current job, openbabel is used quite heavily. The current nixpkgs version is out of date, and doesn't include the python bindings which are heavily used in theoretical chemistry (in pymatgen, for example). I felt like my openbabel nix expressions might be useful for others.

Things done

Bumped openbabel to latest version (3.1.1)
Build the python bindings. It would be relatively easy to include an argument pythonBindings ? True, but as far as I am aware, openbabel is predominantly used as a python module these days. Moreover, there is no appreciable difference in compile time.
from openbabel import openbabel is working correctly, but from openbabel import pybel needs some environment variables to be set as in openbabel-bindings/default.nix. I have been working around this by setting them explicitly in my working shell.nix. Fixing this would probably require a patch to openbabel itself.

This is my first PR to nixpkgs, so any feedback and suggestions would be be greatly appreciated!

SuperSandro2000

Please squash the commits into one named openbabel: 2.4 -> 3.1.1.

pkgs/development/libraries/openbabel/default.nix

pkgs/development/python-modules/openbabel-bindings/default.nix

pkgs/development/libraries/openbabel/builder_python_bindings_enabled.sh

danielbarter · 2020-12-29T18:32:06Z

OK, all the changes suggested by @SuperSandro2000 have been made. Thanks for the feedback :D

SuperSandro2000

Please orient your formatting on other packages in nixpkgs. It is not optional and makes reviewing packages easier if they all follow a somewhat uniform style.

pkgs/development/libraries/openbabel/default.nix

pkgs/development/python-modules/openbabel-bindings/default.nix

pkgs/top-level/python-packages.nix

danielbarter · 2021-01-01T19:44:39Z

All second round of changes have been made! I'll rebase once there are no further suggestions

maintainers/maintainer-list.nix

pkgs/development/libraries/openbabel/default.nix

pkgs/development/python-modules/openbabel-bindings/default.nix

SuperSandro2000 · 2021-01-11T01:01:37Z

This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or pytorch)
If you find some bugs or got suggestions for further things to search or run please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 107845 run on x86_64-darwin 1

1 package marked as broken and skipped:

avogadro

4 packages built:

openbabel
python37Packages.openbabel-bindings
python38Packages.openbabel-bindings
python39Packages.openbabel-bindings

The following issues got detected with the above build packages.
Please fix at least the ones listed with your changed packages:

python37Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

python38Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

python39Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

SuperSandro2000 · 2021-01-11T01:06:24Z

This is a semi-automatic executed nixpkgs-review which does not build all packages (e.g. lumo, tensorflow or pytorch)
If you find some bugs or got suggestions for further things to search or run please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 107845 run on x86_64-linux 1

1 package failed to build and are new build failure:

avogadro: log https://termbin.com/uybu

7 packages built:

libsForQt5.kalzium (kdeApplications.kalzium ,libsForQt515.kalzium)
libsForQt512.kalzium
libsForQt514.kalzium
openbabel
python37Packages.openbabel-bindings
python38Packages.openbabel-bindings
python39Packages.openbabel-bindings

The following issues got detected with the above build packages.
Please fix at least the ones listed with your changed packages:

python37Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

python38Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

python39Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

danielbarter · 2021-01-16T18:34:05Z

seems like avogadro is no longer being maintained and has openbabel2 as a dependency. I revived the old openbabel nix expression and called it openbabel2 to feed into avogadro. Let me know what you think

jonringer · 2021-01-16T18:38:55Z

please fix conflicts :(

danielbarter · 2021-01-16T18:41:42Z

Working on conflicts now 👍

SuperSandro2000

Sorry that this takes so long. I hope this is the final around after which we can finally merge.

We are currently doing several treewide changes which sadly delay this PR a bit again. Sorry about that.

pkgs/applications/science/chemistry/avogadro/default.nix

pkgs/development/libraries/openbabel/default.nix

pkgs/development/libraries/openbabel2/default.nix

pkgs/development/python-modules/openbabel-bindings/default.nix

pkgs/top-level/all-packages.nix

danielbarter · 2021-01-17T18:04:18Z

No need to apologize @SuperSandro2000, you are doing an amazing job! keep up the good work 👍. All changes have been made

SuperSandro2000

Sorry I found another nit but after that LGTM

pkgs/development/python-modules/openbabel-bindings/default.nix

SuperSandro2000 · 2021-01-17T22:28:46Z

This is a semi-automatic executed nixpkgs-review which is checked by a human on a best effort basis and does not build all packages (e.g. lumo, tensorflow or pytorch).
If you have any questions or problems please reach out to SuperSandro2000 on IRC.

Result of nixpkgs-review pr 107845 run on x86_64-darwin 1

4 packages built:

openbabel2
python37Packages.openbabel-bindings
python38Packages.openbabel-bindings
python39Packages.openbabel-bindings

The following issues got detected with the above build packages.
Please fix at least the ones listed with your changed packages:

python37Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

python38Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

python39Packages.openbabel-bindings:

Zero tests run by pytest got detected: 'Ran 0 tests in 0.000s'
You have the following options to fix this:

Tell pytest(CheckHook) where to find the tests included in the package
Check if the GitHub Repo contains tests but they are not shipped with Pypi. If so please switch to fetchFromGitHub.
If the Packages does not contain any tests add 'doCheck = false;'and apythonImportsCheck`.

pkgs/development/python-modules/openbabel-bindings/default.nix

danielbarter requested review from FRidh and jonringer as code owners December 28, 2020 21:56

ofborg bot added the 6.topic: python label Dec 28, 2020

danielbarter changed the title ~~Openbabel3~~ Openbabel 2.4 -> Openbabel 3.1.1 Dec 28, 2020

danielbarter changed the title ~~Openbabel 2.4 -> Openbabel 3.1.1~~ Openbabel 2.4 -> 3.1.1 Dec 28, 2020

danielbarter changed the title ~~Openbabel 2.4 -> 3.1.1~~ openbabel 2.4 -> 3.1.1 Dec 28, 2020

danielbarter changed the title ~~openbabel 2.4 -> 3.1.1~~ openbabel: 2.4 -> 3.1.1 Dec 28, 2020

ofborg bot added 8.has: package (new) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Dec 28, 2020

SuperSandro2000 requested changes Dec 28, 2020

View reviewed changes

danielbarter force-pushed the openbabel3 branch 6 times, most recently from eaa462c to 090a1ec Compare December 29, 2020 18:30

danielbarter requested a review from SuperSandro2000 December 29, 2020 18:36

SuperSandro2000 requested changes Jan 1, 2021

View reviewed changes

danielbarter requested a review from SuperSandro2000 January 1, 2021 19:47

ofborg bot added the 11.by: package-maintainer label Jan 1, 2021

SuperSandro2000 reviewed Jan 10, 2021

View reviewed changes

danielbarter force-pushed the openbabel3 branch 2 times, most recently from c17c9c4 to 23683e2 Compare January 15, 2021 23:37

ofborg bot added the 2.status: merge conflict label Jan 16, 2021

ofborg bot added 8.has: clean-up and removed 2.status: merge conflict labels Jan 16, 2021

maintainers: add danielbarter

30b4664

danielbarter force-pushed the openbabel3 branch from 72dc1d0 to 9bf6b78 Compare January 16, 2021 19:12

SuperSandro2000 reviewed Jan 17, 2021

View reviewed changes

danielbarter force-pushed the openbabel3 branch from fdf084b to ca4b9e9 Compare January 17, 2021 18:02

SuperSandro2000 approved these changes Jan 17, 2021

View reviewed changes

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danielbarter force-pushed the openbabel3 branch from c75e5ae to d8b8ab6 Compare January 17, 2021 19:31

SuperSandro2000 reviewed Jan 17, 2021

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danielbarter and others added 3 commits January 18, 2021 00:21

openbabel: 2.4 -> 3.1.1

a8bb8fc

openbabel2: init at 2.4.1

aadf7a5

avogadro: update maintainers

197eace

SuperSandro2000 force-pushed the openbabel3 branch from d8b8ab6 to 197eace Compare January 17, 2021 23:23

SuperSandro2000 merged commit fe2882e into NixOS:master Jan 17, 2021

Janik-Haag added the 12. first-time contribution label Jun 12, 2023

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openbabel: 2.4 -> 3.1.1 #107845

openbabel: 2.4 -> 3.1.1 #107845

danielbarter commented Dec 28, 2020 •

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openbabel: 2.4 -> 3.1.1 #107845

openbabel: 2.4 -> 3.1.1 #107845

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danielbarter commented Dec 28, 2020 • edited

Motivation for this change

Things done

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