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IPython installs without a lexar entry point for pygments #1430

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ResidentMario opened this issue Feb 7, 2017 · 3 comments

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@ResidentMario
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@ResidentMario ResidentMario commented Feb 7, 2017

I had an issue with the nbconvert component of jupyter, whereupon my code blocks were "swallowed" upon emission to HTML in sphinx. I filed this as an issue over at nbconvert, and it was fixed by running:

conda update ipython -c conda-forge

E.g. moving ipython over to the conda-forge build.

@takluyver hypothesizes this is because of a configuration miss on the default channel:

I don't think it's an issue with pygments, but the IPython package from the default channel appears to be built in a way that doesn't install the entry points (which are how we register lexers for pygments). In conda-forge, where we control the ipython package, it is built using pip, which works.

For more details see the bug report and fix over @ nbconvert.

@takluyver

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@takluyver takluyver commented Feb 8, 2017

I'd be happy for Anaconda to use the conda-forge recipe for IPython, if that's easy for you.

danking added a commit to danking/hail that referenced this issue Apr 19, 2017
danking added a commit to danking/hail that referenced this issue Apr 19, 2017
tpoterba added a commit to hail-is/hail that referenced this issue Apr 19, 2017
* eliminate warning in getting_started.rst

* all warnings are errors

* use anonymous links instead of named links

* fix indentation of list item

* fix a variety of list item syntax issues

* remove illegal excess indentation

* several list item syntax fixes

* variety of list item fixes and a link fix

* remove extraneous character from string [] docs

* favicons must end in ico

* work around a bug in conda

Discussion of issue:

  spatialaudio/nbsphinx#24 (comment)

Root cause:

  ContinuumIO/anaconda-issues#1430

* fix link to tutorial

* fix broken links

* remove broken link to sample

* remove more broken links to sample

* remove references to sec-objects

* fix bad reference syntax

* two small fixes

1. Remove reference to sample
2. Move ico to correct directory

* remove unnecessary html_extra_path entry

* fix doctest skip syntax
cseed added a commit to hail-is/hail that referenced this issue Apr 21, 2017
…1691)

* eliminate warning in getting_started.rst

* all warnings are errors

* use anonymous links instead of named links

* fix indentation of list item

* fix a variety of list item syntax issues

* remove illegal excess indentation

* several list item syntax fixes

* variety of list item fixes and a link fix

* remove extraneous character from string [] docs

* favicons must end in ico

* work around a bug in conda

Discussion of issue:

  spatialaudio/nbsphinx#24 (comment)

Root cause:

  ContinuumIO/anaconda-issues#1430

* fix link to tutorial

* fix broken links

* remove broken link to sample

* remove more broken links to sample

* remove references to sec-objects

* fix bad reference syntax

* two small fixes

1. Remove reference to sample
2. Move ico to correct directory

* remove unnecessary html_extra_path entry

* initial attempt

* add missing file

* improve hailType blurb

* further improvements from tpoterba

* Update hailType.rst

* sphinx lists must not have leading space

This triggers an error message:

    Error in "include" directive: no content permitted.

because the one-space-indented text is assumed to be an argument to the
`.. include` directive

Also fix location of hailType.rst

* use anonymous links instead of named links

* simplify docs
liameabbott added a commit to liameabbott/hail that referenced this issue May 3, 2017
* eliminate warning in getting_started.rst

* all warnings are errors

* use anonymous links instead of named links

* fix indentation of list item

* fix a variety of list item syntax issues

* remove illegal excess indentation

* several list item syntax fixes

* variety of list item fixes and a link fix

* remove extraneous character from string [] docs

* favicons must end in ico

* work around a bug in conda

Discussion of issue:

  spatialaudio/nbsphinx#24 (comment)

Root cause:

  ContinuumIO/anaconda-issues#1430

* fix link to tutorial

* fix broken links

* remove broken link to sample

* remove more broken links to sample

* remove references to sec-objects

* fix bad reference syntax

* two small fixes

1. Remove reference to sample
2. Move ico to correct directory

* remove unnecessary html_extra_path entry

* fix doctest skip syntax
liameabbott added a commit to liameabbott/hail that referenced this issue May 3, 2017
…ail-is#1691)

* eliminate warning in getting_started.rst

* all warnings are errors

* use anonymous links instead of named links

* fix indentation of list item

* fix a variety of list item syntax issues

* remove illegal excess indentation

* several list item syntax fixes

* variety of list item fixes and a link fix

* remove extraneous character from string [] docs

* favicons must end in ico

* work around a bug in conda

Discussion of issue:

  spatialaudio/nbsphinx#24 (comment)

Root cause:

  ContinuumIO/anaconda-issues#1430

* fix link to tutorial

* fix broken links

* remove broken link to sample

* remove more broken links to sample

* remove references to sec-objects

* fix bad reference syntax

* two small fixes

1. Remove reference to sample
2. Move ico to correct directory

* remove unnecessary html_extra_path entry

* initial attempt

* add missing file

* improve hailType blurb

* further improvements from tpoterba

* Update hailType.rst

* sphinx lists must not have leading space

This triggers an error message:

    Error in "include" directive: no content permitted.

because the one-space-indented text is assumed to be an argument to the
`.. include` directive

Also fix location of hailType.rst

* use anonymous links instead of named links

* simplify docs
@fperez

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@fperez fperez commented Sep 5, 2017

ping on this... I just ran into this same issue and the only workaround was to use the conda-forge channel as @takluyver suggested. It's a bummer that the default IPython package seems to have this problem; anything we can do to help?

@csoja

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@csoja csoja commented Nov 16, 2017

@mingwandroid or @msarahan this should be fixed for the packages in main now, right?

leezu added a commit to leezu/gluon-nlp that referenced this issue Apr 28, 2018
szhengac added a commit to dmlc/gluon-nlp that referenced this issue Apr 29, 2018
* Fix pygments lexers

`log` (used in beam_search_generator.rst) is not a valid lexer. `bash` is for
shell scripts. We are presenting interactive sessions and should use `console`.

* Add .ipynb_checkpoints to sphinx exclude_patterns

This is required: https://media.readthedocs.org/pdf/nbsphinx/latest/nbsphinx.pdf
Otherwise we will get a lot of warnings if the environment contains
ipynb_checkpoints..

* Declare development requirements

This may not be exhaustive yet, but are the requirements needed on my machine to
build the documentation.

* Make CI deploy stage fail if there are any Sphinx warnings

* Add 'release' dependency to 'docs' in Makefile

'docs' depends on .zip archives created in the 'release' step

* Declare word embedding evaluation extended_results.ipynb as orphan

Sphinx won't warn about orphan elements not being included in the TOC.

* Fix docstrings causing sphinx warnings

* Install ipython from conda-forge

Workaround ContinuumIO/anaconda-issues#1430
cgraywang pushed a commit to cgraywang/gluon-nlp-1 that referenced this issue May 2, 2018
* Fix pygments lexers

`log` (used in beam_search_generator.rst) is not a valid lexer. `bash` is for
shell scripts. We are presenting interactive sessions and should use `console`.

* Add .ipynb_checkpoints to sphinx exclude_patterns

This is required: https://media.readthedocs.org/pdf/nbsphinx/latest/nbsphinx.pdf
Otherwise we will get a lot of warnings if the environment contains
ipynb_checkpoints..

* Declare development requirements

This may not be exhaustive yet, but are the requirements needed on my machine to
build the documentation.

* Make CI deploy stage fail if there are any Sphinx warnings

* Add 'release' dependency to 'docs' in Makefile

'docs' depends on .zip archives created in the 'release' step

* Declare word embedding evaluation extended_results.ipynb as orphan

Sphinx won't warn about orphan elements not being included in the TOC.

* Fix docstrings causing sphinx warnings

* Install ipython from conda-forge

Workaround ContinuumIO/anaconda-issues#1430
bryanwweber added a commit to bryanwweber/thermostate that referenced this issue Oct 20, 2018
The issue described in
spatialaudio/nbsphinx#24 seems to be
resolved by ContinuumIO/anaconda-issues#1430
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