Bug 712378 – sci-mathematics/pymc3-3.8 version bump

• Status: RESOLVED OBSOLETE
• Product: Gentoo Linux

[Description Erik Quaeghebeur 2020-03-13 14:45:13 UTC]

The current version of pymc3 in portage (3.1) is a bit outdated. Lots of nice fixes and features have been added. Please update the ebuild to a recent version. Currently, the most recent stable versions of dev-python/commonmark and dev-python/recommonmark cannot be installed because of dependency of the outdates pymc3 version.

Reproducible: Always

[Comment 1 Othremgliz 2020-03-13 16:18:25 UTC]

It also requires arviz, which isn't currently packaged (we need also another ebuild). I checked dependencies.

[Comment 2 Othremgliz 2020-03-13 17:10:12 UTC]

DEPEND="
    >=dev-python/arviz-0.4.1[${PYTHON_USEDEP}]
    >=dev-python/theano-1.0.4[${PYTHON_USEDEP}]
    >=dev-python/numpy-1.13[${PYTHON_USEDEP}]
    >=dev-python/scipy-0.18.1[${PYTHON_USEDEP}]
    >=dev-python/pandas-0.18[${PYTHON_USEDEP}]
    >=dev-python/patsy-0.4[${PYTHON_USEDEP}]
    >=dev-python/tqdm-4.8.4[${PYTHON_USEDEP}]
    >=dev-python/h5py-2.7[${PYTHON_USEDEP}]
"
RDEPEND="${DEPEND}
    test? (
        >=dev-python/bokeh-0.12.13[${PYTHON_USEDEP}]
        >=media-gfx/graphviz-0.8.3[${PYTHON_USEDEP}]
        dev-python/ipython[${PYTHON_USEDEP}]
        >=dev-python/Keras-2.0.8[${PYTHON_USEDEP}]
        >=dev-python/numpydoc-0.9.1[${PYTHON_USEDEP}]
        >=dev-python/pycodestyle-2.3.1[${PYTHON_USEDEP}]
        >=dev-python/pyflakes-1.5.0[${PYTHON_USEDEP}]
        >=dev-python/pylint-1.7.4[${PYTHON_USEDEP}]
        >=dev-python/pytest-cov-2.5.1[${PYTHON_USEDEP}]
        >=dev-python/pytest-3.0.7[${PYTHON_USEDEP}]
        >=dev-python/recommonmark-0.4.0[${PYTHON_USEDEP}]
        >=dev-python/seaborn-0.8.1[${PYTHON_USEDEP}]
        =dev-python/sphinx-autobuild-0.7.1[${PYTHON_USEDEP}]
        >=dev-python/sphinx-1.5.5[${PYTHON_USEDEP}]
    )
"

Missing deps in Portage tree:
dev-python/arviz

For test IUSE:
>=dev-python/bokeh-0.12.13
dev-python/Keras
dev-python/sphinx-autobuild

[Comment 3 Othremgliz 2020-03-13 17:56:56 UTC]

Also these are missing from RDEPEND:
   
    test? (
        >=dev-python/nbsphinx-0.4.2[${PYTHON_USEDEP}]
        >=dev-python/nose-1.3.7[${PYTHON_USEDEP}]
        =dev-python/nose-parameterized-0.6.0[${PYTHON_USEDEP}]
    )

nbsphinx-0.4.2 and nose-parameterized-0.6.0 are also missing from Portage.

[Comment 4 Erik Quaeghebeur 2020-07-16 11:37:22 UTC]

As a workaround, I've created an ebuild for 3.1 that excludes the (re)commonmark deps. It's available in my overlay (equaeghe):

https://github.com/equaeghe/gentoo-overlay/tree/master/sci-mathematics/pymc3

[Comment 5 Michał Górny 2020-09-21 14:27:50 UTC]

package(s) removed.