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DOC: add conda-forge install instructions #1006

Merged
merged 2 commits into from
Jan 27, 2020
Merged

DOC: add conda-forge install instructions #1006

merged 2 commits into from
Jan 27, 2020

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raybellwaves
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@raybellwaves raybellwaves commented Jan 19, 2020 •
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What does this PR do?

Add conda-forge install instructions

Where should the reviewer start?

#1005, #165

How should this PR be tested?

Ensure it looks pretty on the website.
Test the conda forge install

Any background context you want to provide?

NA

What are the relevant issues?

[you can link directly to issues by entering # then the number of the issue, for example, #3 links to issue 3]

Screenshots (if appropriate)

``` (tpot) ray@ray-MS-7B43:~/Documents/PYTHON_dev/tpot/docs_sources$ conda install -c conda-forge tpot xgboost dask dask-ml scikit-mdr skrebate Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/ray/local/bin/anaconda3/envs/tpot

added / updated specs:
- dask
- dask-ml
- scikit-mdr
- skrebate
- tpot
- xgboost

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
certifi-2019.11.28         |           py37_0         148 KB  conda-forge
dask-ml-1.2.0              |             py_0          89 KB  conda-forge
llvmlite-0.31.0            |   py37h8b12597_0         325 KB  conda-forge
numba-0.47.0               |   py37hb3f55d8_0         3.4 MB  conda-forge
scikit-mdr-0.4.4           |             py_0          11 KB  conda-forge
skrebate-0.6               |             py_0          19 KB  conda-forge
------------------------------------------------------------
                                       Total:         4.0 MB

The following NEW packages will be INSTALLED:

_py-xgboost-mutex conda-forge/linux-64::_py-xgboost-mutex-2.0-cpu_0
bokeh conda-forge/linux-64::bokeh-1.4.0-py37_0
cffi conda-forge/linux-64::cffi-1.13.2-py37h8022711_0
chardet conda-forge/linux-64::chardet-3.0.4-py37_1003
click conda-forge/noarch::click-7.0-py_0
cloudpickle conda-forge/noarch::cloudpickle-1.2.2-py_1
cryptography conda-forge/linux-64::cryptography-2.8-py37h72c5cf5_1
cycler conda-forge/noarch::cycler-0.10.0-py_2
cytoolz conda-forge/linux-64::cytoolz-0.10.1-py37h516909a_0
dask conda-forge/noarch::dask-2.9.2-py_0
dask-core conda-forge/noarch::dask-core-2.9.2-py_0
dask-glm conda-forge/noarch::dask-glm-0.2.0-py_1
dask-ml conda-forge/noarch::dask-ml-1.2.0-py_0
dbus conda-forge/linux-64::dbus-1.13.6-he372182_0
deap conda-forge/linux-64::deap-1.3.0-py37hb3f55d8_0
distributed conda-forge/noarch::distributed-2.9.3-py_0
expat conda-forge/linux-64::expat-2.2.5-he1b5a44_1004
fontconfig conda-forge/linux-64::fontconfig-2.13.1-he4413a7_1000
freetype conda-forge/linux-64::freetype-2.10.0-he983fc9_1
fsspec conda-forge/noarch::fsspec-0.6.2-py_0
gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
glib conda-forge/linux-64::glib-2.58.3-py37h6f030ca_1002
gst-plugins-base conda-forge/linux-64::gst-plugins-base-1.14.5-h0935bb2_0
gstreamer conda-forge/linux-64::gstreamer-1.14.5-h36ae1b5_0
heapdict conda-forge/noarch::heapdict-1.0.1-py_0
icu conda-forge/linux-64::icu-58.2-hf484d3e_1000
idna conda-forge/linux-64::idna-2.8-py37_1000
jinja2 conda-forge/noarch::jinja2-2.10.3-py_0
joblib conda-forge/noarch::joblib-0.14.1-py_0
jpeg conda-forge/linux-64::jpeg-9c-h14c3975_1001
kiwisolver conda-forge/linux-64::kiwisolver-1.1.0-py37hc9558a2_0
libblas conda-forge/linux-64::libblas-3.8.0-14_openblas
libcblas conda-forge/linux-64::libcblas-3.8.0-14_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_4
libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1005
liblapack conda-forge/linux-64::liblapack-3.8.0-14_openblas
libllvm8 conda-forge/linux-64::libllvm8-8.0.1-hc9558a2_0
libopenblas conda-forge/linux-64::libopenblas-0.3.7-h5ec1e0e_6
libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_0
libtiff conda-forge/linux-64::libtiff-4.1.0-hc3755c2_3
libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002
libxgboost conda-forge/linux-64::libxgboost-0.90-he1b5a44_4
libxml2 pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1
llvmlite conda-forge/linux-64::llvmlite-0.31.0-py37h8b12597_0
locket conda-forge/noarch::locket-0.2.0-py_2
lz4-c conda-forge/linux-64::lz4-c-1.8.3-he1b5a44_1001
markupsafe conda-forge/linux-64::markupsafe-1.1.1-py37h516909a_0
matplotlib pkgs/main/linux-64::matplotlib-3.1.1-py37h5429711_0
msgpack-python conda-forge/linux-64::msgpack-python-0.6.2-py37hc9558a2_0
multipledispatch conda-forge/noarch::multipledispatch-0.6.0-py_0
numba conda-forge/linux-64::numba-0.47.0-py37hb3f55d8_0
numpy conda-forge/linux-64::numpy-1.17.3-py37h95a1406_0
olefile conda-forge/noarch::olefile-0.46-py_0
packaging conda-forge/noarch::packaging-20.0-py_0
pandas conda-forge/linux-64::pandas-0.25.3-py37hb3f55d8_0
partd conda-forge/noarch::partd-1.1.0-py_0
pcre conda-forge/linux-64::pcre-8.43-he1b5a44_0
pillow pkgs/main/linux-64::pillow-7.0.0-py37hb39fc2d_0
psutil conda-forge/linux-64::psutil-5.6.7-py37h516909a_0
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
py-xgboost conda-forge/linux-64::py-xgboost-0.90-py37_4
pycparser conda-forge/linux-64::pycparser-2.19-py37_1
pyopenssl conda-forge/linux-64::pyopenssl-19.1.0-py37_0
pyparsing conda-forge/noarch::pyparsing-2.4.6-py_0
pyqt conda-forge/linux-64::pyqt-5.9.2-py37hcca6a23_4
pysocks conda-forge/linux-64::pysocks-1.7.1-py37_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
pytz conda-forge/noarch::pytz-2019.3-py_0
pyyaml conda-forge/linux-64::pyyaml-5.3-py37h516909a_0
qt conda-forge/linux-64::qt-5.9.7-h52cfd70_2
requests conda-forge/linux-64::requests-2.22.0-py37_1
scikit-learn conda-forge/linux-64::scikit-learn-0.22.1-py37hcdab131_1
scikit-mdr conda-forge/noarch::scikit-mdr-0.4.4-py_0
scipy conda-forge/linux-64::scipy-1.4.1-py37h921218d_0
sip pkgs/main/linux-64::sip-4.19.8-py37hf484d3e_0
six conda-forge/linux-64::six-1.14.0-py37_0
skrebate conda-forge/noarch::skrebate-0.6-py_0
sortedcontainers conda-forge/noarch::sortedcontainers-2.1.0-py_0
stopit conda-forge/noarch::stopit-1.1.2-py_0
tblib conda-forge/noarch::tblib-1.6.0-py_0
toolz conda-forge/noarch::toolz-0.10.0-py_0
tornado conda-forge/linux-64::tornado-6.0.3-py37h516909a_0
tpot conda-forge/noarch::tpot-0.11.1-py_0
tqdm conda-forge/noarch::tqdm-4.41.1-py_0
update_checker conda-forge/noarch::update_checker-0.16-py_0
urllib3 conda-forge/linux-64::urllib3-1.25.7-py37_0
xgboost conda-forge/linux-64::xgboost-0.90-py37he1b5a44_4
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
yaml conda-forge/linux-64::yaml-0.2.2-h516909a_1
zict conda-forge/noarch::zict-1.0.0-py_0
zstd conda-forge/linux-64::zstd-1.4.4-h3b9ef0a_1

</details>

## Questions:

- Do the docs need to be updated?
- Does this PR add new (Python) dependencies?

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Coverage Status

Coverage remained the same at 96.747% when pulling a43d1e4 on raybellwaves:add-cf-install-doc into aea42a5 on EpistasisLab:master.

@raybellwaves
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raybellwaves commented Jan 19, 2020 •
edited
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@bollwyvl how's this for a first stab?

Regarding your comments in #1005 (comment)
relating to conda installations e.g. tpot-full
Perhaps that can be a separate issue in here or in the feedstock?

I'm also not sure what the difference is between https://anaconda.org/conda-forge/xgboost and https://anaconda.org/anaconda/py-xgboost. I see your tests use py-xgboost (https://github.com/regro-cf-autotick-bot/tpot-feedstock/blob/b716a1df7ea2ea8a90c855e2d9fb2af06f7e1ddf/recipe/meta.yaml#L42_ Should I use this instead of xgboost for the extended conda-forge install command?

@bollwyvl
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bollwyvl commented Jan 19, 2020 via email

@bollwyvl
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bollwyvl commented Jan 19, 2020 via email

@raybellwaves
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Created a feature request here conda-forge/tpot-feedstock#19

I’ll do some further testing on the blanket conda install statement above to see how good/bad it is and ensure it still gives a working version of tpot with the other packages.

@weixuanfu
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weixuanfu commented Jan 21, 2020 •
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Thank both of you for updating docs and conda recipes of TPOT. Please update this PR once tpot-full's recipe works in both Windows and Linux. If xgboost is not working with conda-forge in Windows, we can add a note for windows users about installing xgboost from anaconda instead.

Please also use mkdocs build --clean commend to update docs after adding instructions of tpot-full.

@weixuanfu
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I will merge this PR for now. Please reopen another PR for instruction of installing tpot-full. Thank you again!

weixuanfu added a commit that referenced this pull request Jan 27, 2020
@weixuanfu
update docs #1006
c19b58b
@weixuanfu weixuanfu merged commit a43d1e4 into EpistasisLab:master Jan 27, 2020
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4 participants
@raybellwaves @coveralls @bollwyvl @weixuanfu