Update install docs for conda optional dependencies by taldcroft · Pull Request #10343 · astropy/astropy

taldcroft · 2020-05-12T16:41:52Z

Description

This pull request is to add explicit instructions for installing all the optional Python package
dependencies using conda. The instructions include specifying the conda channels pkgs/main and then conda-forge. I think this improves reproducibility in case users have messed with channel order in their .condarc. I've had problems in the past with getting confused by non-standard packages. I think pkgs/main is the right thing, but if someone knows better please chime in.

It also adds a comment about bintrees now being deprecated.

I'm not exactly sure how to milestone a docs update like this so I just picked 4.0.2.

pllim · 2020-05-12T16:48:24Z

+
+    conda install -c pkgs/main -c conda-forge \
+      scipy h5py beautifulsoup4 html5lib bleach pyyaml pandas sortedcontainers \
+      pytz matplotlib setuptools mpmath bottleneck jplephem asdf bintrees


Why still install bintrees when we warn that it is no longer maintained above?

Yeah, I thought about that. It is still supported in the code and listed as an optional dependency above, so it seems like it belongs in this list. In any case this is just a small package with no other dependencies.

I think we have an unspoken policy to not actively advertise deprecated things. I would prefer if it is removed, as people usually blindly copy-paste, but if you insist it should stay on the command, then so be it.

I'll change, I was on the fence.

pllim · 2020-05-12T16:49:05Z


+To install all of the optional dependencies using ``conda`` enter the following::
+
+    conda install -c pkgs/main -c conda-forge \


I think defaults is the user facing name for the main channel.

I was thinking that users can override the default channels, but I guess if they have gone to that length then they know what they are doing.

I'll change it.

taldcroft · 2020-05-12T18:03:44Z

@pllim - I pushed changes with your suggestions. I went one step further and put in the command line to optionally install pytest-astropy, which is necessary for the subsequent import astropy; astropy.test() to actually work.

taldcroft · 2020-05-12T19:11:16Z

This is failing html-docs in a way that makes no sense to me. Ideas @pllim??

pllim · 2020-05-12T19:18:47Z

I see the failures at my other PR too. And Travis CI is not reporting back. I don't have time to investigate today. I am hoping it is going to magically go away tomorrow.

pllim · 2020-05-13T16:21:40Z

@taldcroft , @astrofrog has a fix. Might need rebase after #10347 is merged.

astrofrog · 2020-05-13T17:13:51Z

@taldcroft - can you rebase now?

taldcroft · 2020-05-28T13:52:57Z

I rebased and made a minor new addition in 21b59cb.

taldcroft · 2020-06-04T12:38:50Z

 Installing ``astropy``
 ======================

+If you are new to Python and/or do not have familiarity with `Python virtual


I'm thinking of the new user that just comes to this page wanting to install astropy. What they'll likely run is the first command they see, which means opening a terminal window and typing pip install astropy. That will generally fail unless they have a non-root Python in their path.

astrofrog

Looks good to me, small question below about defaults, but don't mind either way if this is addressed or not.

astrofrog · 2020-06-04T13:35:39Z


+It is highly recommended that you install all of the optional dependencies with::
+
+    conda install -c astropy -c defaults \


if -c defaults actually needed?

Also as an aside, this is why we need conda to support optional extra dependencies. See conda/conda#7502 for a possible approach (using 'outputs'). We should really just be able to do conda install -c astropy astropy.all or something like that.

I worry that users will set up their .condarc in a way that might prefer other channels in particular conda-forge. I think it is relatively easy to accidentally get in that situation and start pulling core packages from conda-forge instead of defaults.

As a specific example, if a user does this seemingly innocuous command to add conda-forge to channels, then bad things happen:

conda config --add channels conda-forge conda update jplephem The following packages will be SUPERSEDED by a higher-priority channel: attrs pkgs/main --> conda-forge certifi pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.4.5.1-py37hc8dfbb8_0 importlib-metadata pkgs/main::importlib-metadata-1.6.0-p~ --> conda-forge::importlib-metadata-1.6.0-py37hc8dfbb8_0 importlib_metadata pkgs/main --> conda-forge jplephem astropy --> conda-forge kiwisolver pkgs/main::kiwisolver-1.2.0-py37h04f5~ --> conda-forge::kiwisolver-1.2.0-py37ha1cc60f_0 libgfortran pkgs/main::libgfortran-3.0.1-h93005f0~ --> conda-forge::libgfortran-3.0.1-0 libiconv pkgs/main::libiconv-1.16-h1de35cc_0 --> conda-forge::libiconv-1.15-h0b31af3_1006 mkl-service pkgs/main::mkl-service-2.3.0-py37hfbe~ --> conda-forge::mkl-service-2.3.0-py37h0b31af3_0 ncurses pkgs/main::ncurses-6.2-h0a44026_1 --> conda-forge::ncurses-6.1-h0a44026_1002 openssl pkgs/main::openssl-1.1.1g-h1de35cc_0 --> conda-forge::openssl-1.1.1g-h0b31af3_0 py pkgs/main --> conda-forge pyparsing pkgs/main::pyparsing-2.4.7-py_0 --> conda-forge::pyparsing-2.4.7-pyh9f0ad1d_0 pytest-arraydiff astropy --> conda-forge pytest-astropy-he~ astropy --> conda-forge pytest-doctestplus astropy --> conda-forge pytest-openfiles astropy --> conda-forge pytest-remotedata astropy --> conda-forge python pkgs/main::python-3.7.7-hc70fcce_0_cp~ --> conda-forge::python-3.7.6-cpython_h1fd5dd1_6 python-dateutil pkgs/main --> conda-forge readline pkgs/main::readline-8.0-h1de35cc_0 --> conda-forge::readline-8.0-hcfe32e1_0 soupsieve pkgs/main/noarch::soupsieve-2.0.1-py_0 --> conda-forge/osx-64::soupsieve-2.0.1-py37hc8dfbb8_0 sqlite pkgs/main::sqlite-3.31.1-h5c1f38d_1 --> conda-forge::sqlite-3.30.1-h93121df_0 tornado pkgs/main::tornado-6.0.4-py37h1de35cc~ --> conda-forge::tornado-6.0.4-py37h9bfed18_1 webencodings pkgs/main/osx-64::webencodings-0.5.1-~ --> conda-forge/noarch::webencodings-0.5.1-py_1 xz pkgs/main::xz-5.2.5-h1de35cc_0 --> conda-forge::xz-5.2.5-h0b31af3_0 zipp pkgs/main --> conda-forge zstd pkgs/main::zstd-1.4.4-h1990bb4_3 --> conda-forge::zstd-1.4.4-h4b3e974_3

Update install docs for conda optional dependencies

taldcroft added Docs no-changelog-entry-needed labels May 12, 2020

taldcroft added this to the v4.0.2 milestone May 12, 2020

pllim reviewed May 12, 2020

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pllim added the installation label May 12, 2020

taldcroft force-pushed the docs-conda-optional branch from 9cc91a5 to 767a0df Compare May 12, 2020 17:54

taldcroft added 3 commits May 28, 2020 09:51

Update install docs for conda opt deps [skip travis]

dd9f4f6

Add install command to allow running tests [skip travis]

d570fb0

Update instruction to support building docs as well

21b59cb

taldcroft force-pushed the docs-conda-optional branch from dc351da to 21b59cb Compare May 28, 2020 13:52

taldcroft mentioned this pull request May 29, 2020

Describe how to do development within a tox testing environment #10394

Closed

taldcroft added 2 commits June 3, 2020 18:45

Fix channel order

85b92cd

Add recommendation for new users to install Anaconda; more tweaks

0b16f16

taldcroft commented Jun 4, 2020

View reviewed changes

astrofrog approved these changes Jun 4, 2020

View reviewed changes

taldcroft merged commit 370bb94 into astropy:master Jun 4, 2020

taldcroft deleted the docs-conda-optional branch June 4, 2020 14:57

astrofrog pushed a commit that referenced this pull request Jun 5, 2020

Merge pull request #10343 from taldcroft/docs-conda-optional

895c070

Update install docs for conda optional dependencies

astrofrog pushed a commit that referenced this pull request Jun 5, 2020

Merge pull request #10343 from taldcroft/docs-conda-optional

977ff62

Update install docs for conda optional dependencies


		To install all of the optional dependencies using ``conda`` enter the following::

		conda install -c pkgs/main -c conda-forge \


		It is highly recommended that you install all of the optional dependencies with::

		conda install -c astropy -c defaults \

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taldcroft commented May 12, 2020

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taldcroft Jun 4, 2020 •

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