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Deprecation warnings on testing #1664

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arokem opened this issue Nov 9, 2018 · 7 comments

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@arokem
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commented Nov 9, 2018

I am getting the following series of deprecation warnings while testing #1659:

/Users/arokem/source/dipy/dipy/io/trackvis.py:11: DeprecationWarning: The `dipy.io.trackvis` module is deprecated as of version 0.14 of Dipy and will be removed in a future version. Please use `dipy.io.streamline` module instead
  DeprecationWarning)
/Users/arokem/source/dipy/dipy/reconst/mapmri.py:1832: DeprecationWarning: invalid escape sequence \p
  """
/Users/arokem/source/dipy/dipy/reconst/mapmri.py:1853: DeprecationWarning: invalid escape sequence \p
  """
/Users/arokem/source/dipy/dipy/reconst/mapmri.py:1877: DeprecationWarning: invalid escape sequence \p
  """
/Users/arokem/source/dipy/dipy/reconst/qtdmri.py:2116: DeprecationWarning: invalid escape sequence \D

Opening this issue to keep track of that.

@abhayjindal51

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commented Nov 27, 2018

I want to work on this issue.

@jhlegarreta

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commented Dec 24, 2018

@arokem Are the trackvis deprecation and the issues reported in the mapmri and qtdmri related?

I'd dare to say that they are not: the latter seem to be related to LaTeX syntax not being understood by Sphinx.

@abhayjindal51 I could start solving these if you do not find enough time to devote to.

jhlegarreta added a commit to jhlegarreta/dipy that referenced this issue Dec 24, 2018
BUG: Fix `dipy.io.trackvis` deprecation warnings.
Fix `dipy.io.trackvis` deprecation warnings: substitute by
`dipy.io.streamline` as per the DIPY 0.14. API changes:
https://github.com/nipy/dipy/blob/master/doc/api_changes.rst

Partially addresses nipy#1664.
jhlegarreta added a commit to jhlegarreta/dipy that referenced this issue Dec 24, 2018
BUG: Fix Sphinx math notation documentation warnings.
Fix Sphinx math notation documentation warnings.

Partially addresses nipy#1664.
@arokem

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commented Dec 24, 2018

Unrelated. I believe that the latter would be fixed either by your commit here: jhlegarreta@8e1eb21, or by making the entire docstring a raw string (by adding an r before the triple quotes).

@arokem

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commented Dec 24, 2018

And your other commit: jhlegarreta@8df012e, would address the other issue, I believe.

@jhlegarreta

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commented Dec 24, 2018

So let's give a try then ! I'll open the PRs. Yes, I saw that using a raw string was another option; I just preferred to use :math: instead of a raw string, but if the latter are preferred, let me know.

jhlegarreta added a commit to jhlegarreta/dipy that referenced this issue Dec 30, 2018
BUG: Fix Sphinx math notation documentation warnings.
Fix Sphinx math notation documentation warnings.

Partially addresses nipy#1664.
@jhlegarreta

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commented Dec 31, 2018

Both PRs have been merged:

  • The math notation issue addressed by #1701 is not present in the master CI builds.
  • The dipy.io.trackvis deprecation warning issue addressed by #1702 is not present in the master build (there is still one such warning, but given that it stems from the trackvis package itself, that would not be an issue).

So I think the issue can be closed.

@arokem

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commented Dec 31, 2018

Wonderful. Thanks!

@arokem arokem closed this Dec 31, 2018

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