pythonPackages.pymc3 init at 3.2 #39660

1pakch · 2018-04-28T19:12:43Z

This is an updated version of #32416 rebased onto release-18.03 branch.

Motivation for this change

Adds the latest stable version of pymc3 to Python packages and update patsy (required by it) from 0.3.0 to 0.5.0. pymc3 of the major Bayesian inference libraries (along with stan, BUGS, JAGS and, to a lesser extent, edward).

Things done

dotlambda · 2018-04-28T19:37:58Z

pkgs/development/python-modules/patsy/default.nix

+    sha256 = "0fw888zd2s7f5zxm9f98ss93qhwv0sqnbdy21ipj33ccqgakhpz0";
+  };
+
+  doCheck = true;


no need for this, it is set automatically

dotlambda · 2018-04-28T19:38:47Z

pkgs/development/python-modules/pymc3/0001-strip-pytest-cov.patch

+     install_reqs.append('enum34')
+
+-test_reqs = ['pytest', 'pytest-cov']
+test_reqs = ['pytest'] # no need for test coverage info in Nix builds


I'd prefer using substituteInPlace in postPatch, because a patch generally requires more maintenance work.

dotlambda · 2018-04-28T19:40:24Z

@GrahamcOfBorg build python2.pkgs.patsy python3.pkgs.patsy

GrahamcOfBorg · 2018-04-28T19:42:35Z

Success on x86_64-linux (full log)

Attempted: python2.pkgs.patsy, python3.pkgs.patsy

Partial log (click to expand)

patsy.test_state.test_Center ... ok
patsy.test_state.test_stateful_transform_wrapper ... ok
patsy.test_state.test_Standardize ... ok

----------------------------------------------------------------------
Ran 39 tests in 33.753s

OK
/nix/store/x6r0qj5rscq34c376n7hdf1yx57v6ii9-python2.7-patsy-0.5.0
/nix/store/yrvb6iqlk8n8kjc6pc4hdybhmmcz2prc-python3.6-patsy-0.5.0

GrahamcOfBorg · 2018-04-28T19:46:09Z

Success on aarch64-linux (full log)

Attempted: python2.pkgs.patsy, python3.pkgs.patsy

Partial log (click to expand)

patsy.test_state.test_Center ... ok
patsy.test_state.test_stateful_transform_wrapper ... ok
patsy.test_state.test_Standardize ... ok

----------------------------------------------------------------------
Ran 39 tests in 288.422s

OK
/nix/store/jm12dwf2c6qlk80w8xnfwnp0gw136h6w-python2.7-patsy-0.5.0
/nix/store/bdqklw1sv1rvisahhx5gb5dn7l8c7cs7-python3.6-patsy-0.5.0

dotlambda · 2018-04-28T19:49:24Z

@GrahamcOfBorg build python2.pkgs.pymc3 python3.pkgs.pymc3

GrahamcOfBorg · 2018-04-28T19:50:53Z

Failure on x86_64-linux (full log)

Attempted: python2.pkgs.pymc3, python3.pkgs.pymc3

Partial log (click to expand)

Installing collected packages: pymc3
Successfully installed pymc3-3.2
/build/pymc3-3.2
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/4nvjvgb3sphyvilgzyvnv5gin9ck4g6m-python3.6-pymc3-3.2
strip is /nix/store/b0zlxla7dmy1iwc3g459rjznx59797xy-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/4nvjvgb3sphyvilgzyvnv5gin9ck4g6m-python3.6-pymc3-3.2/lib
patching script interpreter paths in /nix/store/4nvjvgb3sphyvilgzyvnv5gin9ck4g6m-python3.6-pymc3-3.2
checking for references to /build in /nix/store/4nvjvgb3sphyvilgzyvnv5gin9ck4g6m-python3.6-pymc3-3.2...
error: build of '/nix/store/9qd72anisb68aa83gqkz60aj8mpb080q-python2.7-pymc3-3.2.drv' failed

dotlambda · 2018-04-28T20:13:38Z

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

+  postPatch = ''
+    substituteInPlace setup.py --replace \
+      "test_reqs = ['pytest', 'pytest-cov']" \
+      "test_reqs = ['pytest']"


It will require even less maintenance if using

substituteInPlace setup.py --replace ", 'pytest-cov'" ""

dotlambda · 2018-04-28T20:21:45Z

pkgs/top-level/python-packages.nix

@@ -10135,7 +10135,9 @@ in {

  pygraphviz = callPackage ../development/python-modules/pygraphviz { };

-  pymc3 = callPackage ../development/python-modules/pymc3 { };
+  pymc3 = if pythonAtLeast "3.5"


Please use disabled = pythonOlder "3.5" instead.

This reverts commit 7a8fd03.

dotlambda

You should

base your PR on master instead
turn your 6 commits into 2 (one for each package)

GrahamcOfBorg · 2018-04-28T20:50:10Z

Failure on aarch64-linux (full log)

Attempted: python2.pkgs.pymc3, python3.pkgs.pymc3

Partial log (click to expand)

../../nix/store/ky7ygianva07b30vg7vp4n2i398msaf2-python2.7-pandas-0.22.0/lib/python2.7/site-packages/pandas/tests/indexing/test_partial.py . [ 56%]
..........                                                               [ 56%]
../../nix/store/ky7ygianva07b30vg7vp4n2i398msaf2-python2.7-pandas-0.22.0/lib/python2.7/site-packages/pandas/tests/indexing/test_scalar.py . [ 56%]
......                                                                   [ 56%]
../../nix/store/ky7ygianva07b30vg7vp4n2i398msaf2-python2.7-pandas-0.22.0/lib/python2.7/site-packages/pandas/tests/indexing/test_timedelta.py . [ 56%]
building of '/nix/store/r3z8101j41yiia5b6iaddapips5h4l1h-python2.7-pandas-0.22.0.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/dx0r3fqkqlk4755cckrfvlp232mwp7cj-python2.7-pymc3-3.2.drv': 2 dependencies couldn't be built
building of '/nix/store/xkvpfql5vfpyfijz4vsr1yccw7k2wnwv-python3.6-pandas-0.22.0.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/fhd7hsh98fpbrzj71306pwdp2f5a4pyh-python3.6-pymc3-3.2.drv': 2 dependencies couldn't be built
�[31;1merror:�[0m build of '/nix/store/dx0r3fqkqlk4755cckrfvlp232mwp7cj-python2.7-pymc3-3.2.drv', '/nix/store/fhd7hsh98fpbrzj71306pwdp2f5a4pyh-python3.6-pymc3-3.2.drv' failed

1pakch · 2018-04-28T20:52:02Z

The manual here should be updated as it explicitly asks not to work with the master branch (contradicting what is written in the repo's README).

Speaking of commits granularity, isn't it easy for a reviewer to squash when accepting? I thought it is easier to see how the review comments are acted upon when one add commits on top instead of force pushing.

I guess I should make another PR based on master then.

dotlambda · 2018-04-28T20:55:06Z

The last bullet point in the manual section you linked to clearly states

Rebase you branch against current master.

1pakch · 2018-04-28T21:14:41Z

Indeed, TLDR on my side. Rebased and collapsed PR is at #39662

1pakch added 2 commits April 28, 2018 21:02

pythonPackages.patsy: 0.3.0 -> 0.5.0

66cf0c3

pythonPackages.pymc3: init at 3.2

f924077

1pakch requested a review from FRidh as a code owner April 28, 2018 19:12

GrahamcOfBorg added 6.topic: python 8.has: package (new) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Apr 28, 2018

dotlambda requested changes Apr 28, 2018

View reviewed changes

1pakch added 2 commits April 28, 2018 22:09

remove redundant doCheck in patsy

df94f31

substituteInPlace instead of a patch in pymc3

fecd366

dotlambda reviewed Apr 28, 2018

View reviewed changes

require python>=3.5 for pymc3

7a8fd03

dotlambda reviewed Apr 28, 2018

View reviewed changes

1pakch added 3 commits April 28, 2018 22:26

explicitly strip pytest-cov via substituteInPlace

3c93a09

Revert "require python>=3.5 for pymc3"

7ca9811

This reverts commit 7a8fd03.

pymc3: disabled for python<3.5

6237aef

dotlambda requested changes Apr 28, 2018

View reviewed changes

1pakch mentioned this pull request Apr 28, 2018

pythonPackages.pymc3: init at 3.2 #39662

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1pakch closed this Apr 28, 2018

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pythonPackages.pymc3 init at 3.2 #39660

pythonPackages.pymc3 init at 3.2 #39660

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pythonPackages.pymc3 init at 3.2 #39660

pythonPackages.pymc3 init at 3.2 #39660

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1pakch commented Apr 28, 2018

Motivation for this change

Things done

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