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python3Packages.rdkit: init at 2020.09.3 #107268

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merged 4 commits into from Feb 4, 2021
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rmcgibbo
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Motivation for this change

RDKit is a very widely used package in computational chemistry.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@SuperSandro2000
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@rmcgibbo please fix the eval error of ofborg.

@rmcgibbo
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Thanks, @SuperSandro2000. Looks like I didn't structure the package correctly for ofborg given the fact that it needs sources from multiple repos. I'll try to follow this design pattern: https://discourse.nixos.org/t/how-to-create-package-with-multiple-sources/9308/3

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@jonringer jonringer left a comment

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please have a commit per package added, and do you mind linting the files?

@rmcgibbo
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@jonringer: Sure, will do.

I'm not totally sure how to reproduce the ofborg failure locally. First attempts to move the external sources into a single 'srcs' are failing with

error: cannot coerce a set to a string, at /home/mcgibbon/projects/nixpkgs/pkgs/development/interpreters/python/mk-python-derivation.nix:111:5
(use '--show-trace' to show detailed location information)

so i'll try to fix that.

@jonringer
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you pass it a list, not a set

@rmcgibbo
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rmcgibbo commented Dec 21, 2020

Looks like I'm still hitting an ofborg failure, where the builtins.fetchTarball (one of the srcs) won't pull down in restricted mode.

Fixed w/ force push.

pkgs/development/libraries/coordgenlibs/default.nix Outdated Show resolved Hide resolved
pkgs/development/libraries/coordgenlibs/default.nix Outdated Show resolved Hide resolved
pkgs/development/libraries/maeparser/default.nix Outdated Show resolved Hide resolved
pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
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Result of nixpkgs-review pr 107268 run on x86_64-darwin 1

3 packages failed to build:
  • python37Packages.rdkit
  • python38Packages.rdkit
  • python39Packages.rdkit
2 packages built:
  • coordgenlibs
  • maeparser
<1xyqxdqxwviq7b8jjxssxjlkldk01ms8dzqdjgvjs8n3fh7w0l11/details>
  100   391  100   391    0     0     73      0  0:00:05  0:00:05 --:--:-- 18619                                                                                                              100 2530k  100 2530k    0     0   378k      0  0:00:06  0:00:06 --:--:-- 4571k                                                                                                              unpacking source archive /private/tmp/nix-build-source.drv-0/AvalonToolkit_1.2.0.source.tar                                                                                                 error: zip file must contain a single file or directory.                                                                                                                                    hint: Pass stripRoot=false; to fetchzip to assume flat list of files

@rmcgibbo
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Thanks for the reviews. I think I've addressed all of the comments with the latest force-push.

@SuperSandro2000
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Can you please put the changes from the review commit into the corresponding init commits?

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Result of nixpkgs-review pr 107268 run on x86_64-darwin 1

3 packages failed to build:
  • python37Packages.rdkit
  • python38Packages.rdkit
  • python39Packages.rdkit
2 packages built:
  • coordgenlibs
  • maeparser

Fails to build on darwin because inchi failds to build:

these derivations will be built:
  /nix/store/93dwx0vanag5scwr3yf5818lzv8zzb0j-inchi-1.05.drv
building '/nix/store/93dwx0vanag5scwr3yf5818lzv8zzb0j-inchi-1.05.drv'...
unpacking sources
unpacking source archive /nix/store/7j8zpnzw37y1g3pwyv9ds718ljgjqjc9-INCHI-1-SRC.zip
source root is INCHI-1-SRC
setting SOURCE_DATE_EPOCH to timestamp 1486122502 of file INCHI-1-SRC/INCHI_BASE/src/runichi2.c
patching sources
configuring
no configure script, doing nothing
building
build flags: -j4 -l4 SHELL=/nix/store/drz9yxh2v1swn9yl88c8w5g0x69b8wk2-bash-4.4-p23/bin/bash
gcc -fPIC -DTARGET_API_LIB -DCOMPILE_ANSI_ONLY -ansi -O3 -c ../../../INCHI_BASE/src/ichican2.c
gcc -fPIC -DTARGET_API_LIB -DCOMPILE_ANSI_ONLY -ansi -O3 -c ../../../INCHI_BASE/src/ichicano.c
gcc -fPIC -DTARGET_API_LIB -DCOMPILE_ANSI_ONLY -ansi -O3 -c ../../../INCHI_BASE/src/ichi_io.c
gcc -fPIC -DTARGET_API_LIB -DCOMPILE_ANSI_ONLY -ansi -O3 -c ../../../INCHI_BASE/src/ichierr.c
/nix/store/drz9yxh2v1swn9yl88c8w5g0x69b8wk2-bash-4.4-p23/bin/bash: gcc: command not found
/nix/store/drz9yxh2v1swn9yl88c8w5g0x69b8wk2-bash-4.4-p23/bin/bash: gcc: command not found
make: *** [makefile:196: ichicano.o] Error 127
make: *** Waiting for unfinished jobs....
make: *** [makefile:196: ichican2.o] Error 127
/nix/store/drz9yxh2v1swn9yl88c8w5g0x69b8wk2-bash-4.4-p23/bin/bash: gcc: command not found
make: *** [makefile:196: ichi_io.o] Error 127
/nix/store/drz9yxh2v1swn9yl88c8w5g0x69b8wk2-bash-4.4-p23/bin/bash: gcc: command not found
make: *** [makefile:196: ichierr.o] Error 127
builder for '/nix/store/93dwx0vanag5scwr3yf5818lzv8zzb0j-inchi-1.05.drv' failed with exit code 2
error: build of '/nix/store/93dwx0vanag5scwr3yf5818lzv8zzb0j-inchi-1.05.drv' failed

@rmcgibbo
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Build fixed on darwin, and previous review comments incorporated into the per-package commits.

pkgs/development/libraries/coordgenlibs/default.nix Outdated Show resolved Hide resolved
pkgs/development/libraries/inchi/default.nix Outdated Show resolved Hide resolved
pkgs/development/libraries/maeparser/default.nix Outdated Show resolved Hide resolved
pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
@rmcgibbo
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@jonringer: Thanks. Fixes applied.

@SuperSandro2000
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Result of nixpkgs-review pr 107268 run on x86_64-darwin 1

6 packages built:
  • coordgenlibs
  • inchi
  • maeparser
  • python37Packages.rdkit
  • python38Packages.rdkit
  • python39Packages.rdkit

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Result of nixpkgs-review pr 107268 run on x86_64-linux 1

6 packages built:
  • coordgenlibs
  • inchi
  • maeparser
  • python37Packages.rdkit
  • python38Packages.rdkit
  • python39Packages.rdkit

@rmcgibbo
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rmcgibbo commented Jan 5, 2021

(Friendly ping on this PR)

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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 107268 run on x86_64-linux 1

6 packages built:
  • coordgenlibs
  • inchi
  • maeparser
  • python37Packages.rdkit
  • python38Packages.rdkit
  • python39Packages.rdkit

@SuperSandro2000
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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 107268 run on x86_64-darwin 1

6 packages built:
  • coordgenlibs
  • inchi
  • maeparser
  • python37Packages.rdkit
  • python38Packages.rdkit
  • python39Packages.rdkit

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We got a recent stdenv.lib deprecation so that occurrence needs to be removed.

pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
pkgs/development/python-modules/rdkit/default.nix Outdated Show resolved Hide resolved
pkgs/development/libraries/inchi/default.nix Outdated Show resolved Hide resolved
pkgs/development/libraries/inchi/default.nix Show resolved Hide resolved
pkgs/development/libraries/coordgenlibs/default.nix Outdated Show resolved Hide resolved
pkgs/development/libraries/coordgenlibs/default.nix Outdated Show resolved Hide resolved
@SuperSandro2000
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This is a semi-automatic executed nixpkgs-review with nixpkgs-review-checks extension. It 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 107268 run on x86_64-linux 1

5 packages built:
  • coordgenlibs
  • inchi
  • maeparser
  • python37Packages.rdkit
  • python38Packages.rdkit

@SuperSandro2000
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This is a semi-automatic executed nixpkgs-review with nixpkgs-review-checks extension. It 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 107268 run on x86_64-darwin 1

2 packages failed to build and are new build failures:

@rmcgibbo
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rmcgibbo commented Feb 3, 2021

Thanks for the report on Darwin, Sando. I think I've fix it now with some more darwin-specific fixups in libinchi.

@SuperSandro2000
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This is a semi-automatic executed nixpkgs-review with nixpkgs-review-checks extension. It 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 107268 run on x86_64-darwin 1

2 packages built:
  • python37Packages.rdkit
  • python38Packages.rdkit

@SuperSandro2000 SuperSandro2000 merged commit 70d71ec into NixOS:master Feb 4, 2021
@rmcgibbo rmcgibbo deleted the rdkit branch February 4, 2021 19:46
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