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pythonPackages.pymc3: init at 3.2 #32416

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pythonPackages.pymc3: init at 3.2 #32416

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1pakch
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@1pakch 1pakch commented Dec 7, 2017 •
edited

Motivation for this change

Adds the latest stable version of pymc3 to Python packages. This is one of the major Bayesian inference libraries (along with stan, BUGS, JAGS and, to a lesser extent, edward),

Things done
  • Tested using sandboxing
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested the library
  • Fits [CONTRIBUTING.md]

Edit: longer info

@1pakch 1pakch requested a review from FRidh as a code owner December 7, 2017 16:41
FRidh
FRidh requested changes Dec 7, 2017
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pkgs/development/python-modules/patsy/default.nix Outdated
sha256 = "1wkjd71rx1akfrk6iimi4zm783gagxmkxm3ppjyr2c98asni009c";
};

buildInputs = [ nose ];
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checkInputs

pkgs/development/python-modules/patsy/default.nix Outdated
propagatedBuildInputs = [
six
numpy
] ++ lib.optional (!isNull scipy) [ scipy ];
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that lib.optional needs to be removed

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Why? It's an optional dependency to patsy allowing for some optional features.

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Its no problem if one would pass in scipy = null;;

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Oh, I see! Of course then.

pkgs/development/python-modules/pymc3/default.nix Outdated
propagatedBuildInputs = [
Theano
gfortran
openblas
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numpy.blas or scipy.blas

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not needed, your concerns are very valid

pkgs/development/python-modules/pymc3/default.nix Outdated

propagatedBuildInputs = [
Theano
gfortran
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does it need to propagate gfortran and openblas?

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Definitely not needed. I found some existing nix expression where they were listed and did not think about it honestly.

pkgs/development/python-modules/pymc3/default.nix Outdated
patsy
tqdm
joblib
];
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several packages you mentioned here are dependencies of others. No need to repeat them, although it also doesn't hurt.

pkgs/development/python-modules/pymc3/default.nix Outdated
joblib
];

doCheck = false;
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Why? Leave a comment in the code.

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I made the tests work but they are quite computationally intensive and some of them fail. Maybe I can patch it so that only few specific tests are run.

Another issue is that the tests are being run in the install phase instead of the check phase. Is it normal?

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No, not really.

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I disabled the tests and left a note on this peculiarity.

pkgs/development/python-modules/patsy/default.nix Outdated
pname = "patsy";
version = "0.4.1";

src = fetchurl {
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why not from PyPI?

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I tried it actually but specifically patsy 0.4.1 is not found there

pkgs/development/python-modules/pymc3/default.nix Outdated

doCheck = false;

src = fetchurl {
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why not from PyPI?

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fixed

@1pakch
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1pakch commented Dec 10, 2017 •
edited

I used this package thoroughly and It’s fully functional. The test suite failures I mentioned above are not relevant for end users.

@1pakch 1pakch closed this Dec 10, 2017
@1pakch 1pakch reopened this Dec 10, 2017
FRidh
FRidh requested changes Dec 10, 2017
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pkgs/development/python-modules/pymc3/default.nix Outdated
, tqdm
, six
, h5py
, run-tests ? false # these are quite heavy
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This should not be an option. If one wants to change this value one can use overridePythonAttrs.

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fixed, thank you

matthewbauer and others added 20 commits April 8, 2018 21:37
@matthewbauer
Merge pull request NixOS#38521 from yesbox/nixos-18.03-backport
d74b169 
rclone: 1.39 -> 1.40
@Madouura @Mic92
terraria-server: 1.3.1.1 -> 1.3.5.3
61249b5
@NeQuissimus
sbt: 1.1.2 -> 1.1.3
40fd490 
(cherry picked from commit 3e88838f3f2fe4e56d10e5eb60d9d8b4c544fb17)
@domenkozar
xalanc: /usr -> /
1944dc7 
(cherry picked from commit 2e0dfb4)
Signed-off-by: Domen Kožar <domen@dev.si>
@jtojnar
gsmartcontrol: 0.8.7 → 1.1.3
0366747 
Closes: NixOS#37444

(cherry picked from commit 9acdfbf)
@NeQuissimus
sbt: 1.1.3 -> 1.1.4
fecaa54 
(cherry picked from commit 8322981)
@7c6f434c
libreoffice: wrap to set JAVA_HOME, SAL_USE_VCLPLUGIN and DBus sessio…
62658a3 
…n if not set

(cherry picked from commit 95a819c)
@Mic92
linuxPackages.{zfs,spl}{Stable,Unstable}: 0.7.7 -> 0.7.8; 2018-04-04 …
023feb5 
…-> 2018-04-10

(cherry picked from commit ad22967)
@ryantm @Mic92
nextcloud-news-updater: 10.0.0 -> 10.0.1
4dea3cf 
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:

- built on NixOS
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/.nextcloud-news-updater-wrapped -h` got 0 exit code
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/.nextcloud-news-updater-wrapped --help` got 0 exit code
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/.nextcloud-news-updater-wrapped -v` and found version 10.0.1
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/.nextcloud-news-updater-wrapped --version` and found version 10.0.1
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/nextcloud-news-updater -h` got 0 exit code
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/nextcloud-news-updater --help` got 0 exit code
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/nextcloud-news-updater -v` and found version 10.0.1
- ran `/nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1/bin/nextcloud-news-updater --version` and found version 10.0.1
- found 10.0.1 with grep in /nix/store/58kz8y29n2habv056d7iz20484rq87mr-nextcloud-news-updater-10.0.1
- directory tree listing: https://gist.github.com/ef3eb260a3fd46598a3b70c142c2ef2c

(cherry picked from commit a7046d5)
@eonpatapon @Mic92
nextcloud: 13.0.0 -> 13.0.1
fc403a8 
(cherry picked from commit ae3782b)

fixes NixOS#38550
@peterhoeg @Mic92
terraform: 0.11.3 -> 0.11.4
ad46d18 
(cherry picked from commit 059f33c)
@zimbatm @Mic92
terraform_0_11: 0.11.4 -> 0.11.5
a864266 
(cherry picked from commit 4009338)
@jbgi @Mic92
terraform_0_11: 0.11.5 -> 0.11.6
dcc85ff 
(cherry picked from commit d6e8371)
@adisbladis
nodejs-6_x: 6.13.0 -> 6.13.1
5a16d26 
(cherry picked from commit 0cadbb8)
@adisbladis
nodejs-6_x: 6.13.1 -> 6.14.1
29f1290 
(cherry picked from commit 042c001)
@adisbladis
nodejs-8_x: 8.9.4 -> 8.10.0
c00bfc1 
(cherry picked from commit a36ae7a)
@adisbladis
nodejs-8_x: 8.10.0 -> 8.11.1
46ed995 
(cherry picked from commit 017fffc)
@frontsideair @adisbladis
nodejs: 9.6.1 -> 9.7.1
3624a8f 
(cherry picked from commit 399edfe)
@adisbladis
nodejs-9_x: 9.7.1 -> 9.8.0
6089f8e 
(cherry picked from commit 03efbb0)
@adisbladis
nodejs-9_x: 9.8.0 -> 9.10.1
03cbd91 
(cherry picked from commit 357a2cc)
@1pakch 1pakch closed this Apr 28, 2018
@1pakch 1pakch mentioned this pull request Apr 28, 2018
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2.status: merge conflict 6.topic: erlang 6.topic: fetch 6.topic: GNOME GNOME desktop environment and its underlying platform 6.topic: golang 6.topic: haskell 6.topic: nixos 6.topic: printing 6.topic: python 6.topic: qt/kde 6.topic: ruby 6.topic: rust 6.topic: stdenv Standard environment 6.topic: steam 6.topic: vim 6.topic: xfce The Xfce Desktop Environment 8.has: changelog 8.has: documentation 8.has: module (update) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10
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