replace .. SeeAlso:: with numpy section by kain88-de · Pull Request #1314 · MDAnalysis/mdanalysis

kain88-de · 2017-04-18T13:32:42Z

Changes made in this Pull Request:

replace .. SeeAlso:: with numpy section

I used the following command to replace all occurrences.

find . -name '*py' -exec sed -rie 's/^(( *).. SeeAlso::( *))/\2See Also\n\2--------\n\2/g' {} \;

Following a comment of @jbarnoud
#1240 (comment)

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

jbarnoud

I am surprised of how often sed did work. But some cases request some more attention.

jbarnoud · 2017-04-18T13:47:04Z

package/MDAnalysis/analysis/align.py

-.. SeeAlso::
+See Also
+--------
+


This one needs some further fixing.

jbarnoud · 2017-04-18T13:47:43Z

package/MDAnalysis/analysis/align.py

+    See Also
+    --------
+
       AlignTraj: More efficient method for RMSD-fitting trajectories.


Should be unindented

jbarnoud · 2017-04-18T13:47:55Z

package/MDAnalysis/analysis/align.py

+    See Also
+    --------
+
      :func:`sequence_alignment`, which does not require external


Should be unindented

jbarnoud · 2017-04-18T13:48:23Z

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

+        --------
+

           :meth:`_get_bonded_hydrogens_dist` and :meth:`_get_bonded_hydrogens_list`


Should be unindented

jbarnoud · 2017-04-18T13:51:55Z

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

+        See Also
+        --------
+        :meth:`HydrogenBondAnalysis.generate_table` for processing
                     the data into a different format.


Should be unindented

jbarnoud · 2017-04-18T13:54:45Z

package/MDAnalysis/topology/ExtendedPDBParser.py

+--------
+

   * :mod:`MDAnalysis.topology.PDBParser`


Should be unindented

jbarnoud · 2017-04-18T13:54:55Z

package/MDAnalysis/topology/PDBParser.py

+--------
+

   * :mod:`MDAnalysis.topology.ExtendedPDBParser`


Should be unindented

jbarnoud · 2017-04-18T13:55:29Z

package/MDAnalysis/topology/core.py

+See Also
+--------
+:mod:`MDAnalysis.topology.tables` for some hard-coded atom
   information that is used by functions such as :func:`guess_atom_type` and


Should be unindented

jbarnoud · 2017-04-18T13:55:41Z

package/MDAnalysis/topology/guessers.py

+    See Also
+    --------
+    :func:`guess_atom_element` and
                 :mod:`MDAnalysis.topology.tables`


Should be unindented

jbarnoud · 2017-04-18T13:55:47Z

package/MDAnalysis/topology/guessers.py

+    See Also
+    --------
+    :func:`guess_atom_type` and
                 :mod:`MDAnalysis.topology.tables` (where the data are stored)


Should be unindented

kain88-de · 2017-04-18T14:06:20Z

I am surprised of how often sed did work.

Yeah it's a super neat tool. But one line changes it has become my go to tool.

kain88-de

After checking every file that has been changed I still see some rendering issues.

kain88-de · 2017-04-20T11:06:09Z

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

-    .. SeeAlso:: Table :ref:`Default atom names for hydrogen bonding analysis`
+    See Also
+    --------
+    Table :ref:`Default atom names for hydrogen bonding analysis`


I don't get this reference to render a link correctly.

kain88-de · 2017-04-20T11:29:05Z

package/MDAnalysis/coordinates/core.py

+    For trajectory formats :class:`~DCD.DCDReader`, :class:`~XTC.XTCReader`,
+    :class:`~TRR.TRRReader`, :class:`~XYZ.XYZReader`. For single frame formats:
+    :class:`~CRD.CRDReader`, and :class:`~PDB.PDBReader`,
+    :class:`~GRO.GROReader`


The classes aren't linked.

Can it be that the tilde isn't expanded correctly?

kain88-de · 2017-04-20T11:35:17Z

package/MDAnalysis/lib/util.py

-    .. SeeAlso:: :func:`anyopen`
+    See Also
+    --------
+    :func:`anyopen`


I don't see this docstring rendered at all in the docs.

kain88-de · 2017-04-20T11:38:02Z

package/MDAnalysis/topology/ExtendedPDBParser.py

-    .. SeeAlso:: :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader`
+    See Also
+    --------
+    :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader`


also doesn't link correctly

This is fixed now

kain88-de · 2017-04-21T06:56:09Z

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

-    .. SeeAlso:: Table :ref:`Default atom names for hydrogen bonding analysis`
+    See Also
+    --------
+    Table :ref:`Default heavy atom names for CHARMM27 force field.`


I get everything to render with links except for this reference. Anyone a idea?

kain88-de · 2017-04-21T17:09:50Z

OK I think I fixed all issues. This is good for review from my side.

orbeckst

thank you!!

orbeckst · 2017-04-21T19:29:14Z

package/MDAnalysis/lib/util.py

-   Context manager to open a compressed (bzip2, gzip) or plain file
-   (uses :func:`anyopen`).
-
+.. autofunction:: openany


Does the context manager decorator preserve function docs nowadays (or is sphinx smarter)? I remember I wrote it explicitly because the decorator had mangled the docs.

Oh haven't checked

Context manager here is never used as a decorator. It can't mangle any docs.

When I look at the code I see
@contextmanager
def openany():

(Sorry difficult to link to code on mobile gh interface.)

If the docs look fine then it's not a problem, of course.

kain88-de · 2017-04-22T21:23:38Z

@jbarnoud any more changes you would like?

jbarnoud · 2017-04-25T12:37:39Z

I am at a conference. Sorry, I do not have the time to look. What I noticed seems fixed, I approve the PR as I have no reason to block it anymore, but I did not review it.

orbeckst · 2017-04-25T18:26:32Z

One of the travis runs just times out after passing the tests: https://travis-ci.org/MDAnalysis/mdanalysis/jobs/225668887

Ran 4504 tests in 1042.470s

OK (KNOWNFAIL=4, SKIP=3)

No output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself.

Check the details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#Build-times-out-because-no-output-was-received

The build has been terminated

I am now restarting a second time but if anyone else has any insights...

kain88-de · 2017-04-25T18:57:21Z

This happens a lot recently. Just restart the build.

orbeckst · 2017-04-26T00:15:37Z

I did and seemed to work on the third attempt.

replace .. SeeAlso:: with numpy section

5e6c23c

jbarnoud requested changes Apr 18, 2017

View reviewed changes

fix obvious formatting errors

2565849

orbeckst added the Component-Docs label Apr 19, 2017

kain88-de added 3 commits April 20, 2017 11:47

last fix of errors

c78f533

comments from jonathan

029f862

fix rendering issues

fb22350

kain88-de commented Apr 20, 2017

View reviewed changes

kain88-de added 3 commits April 21, 2017 07:24

some more usability changes

aee0265

add ExtendedPDBReader to docs

f2aa905

fix more rendering issues

a2a402e

kain88-de commented Apr 21, 2017

View reviewed changes

fix last link issue

cb52330

orbeckst approved these changes Apr 21, 2017

View reviewed changes

orbeckst mentioned this pull request Apr 21, 2017

Minor fixes #1247

Merged

jbarnoud approved these changes Apr 25, 2017

View reviewed changes

orbeckst merged commit 68e4c17 into develop Apr 25, 2017

orbeckst deleted the fix-see-also branch April 25, 2017 16:17

		--------


		:meth:`_get_bonded_hydrogens_dist` and :meth:`_get_bonded_hydrogens_list`

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kain88-de commented Apr 18, 2017

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kain88-de commented Apr 18, 2017

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kain88-de commented Apr 21, 2017

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kain88-de commented Apr 22, 2017

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orbeckst commented Apr 25, 2017

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kain88-de commented Apr 25, 2017

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orbeckst commented Apr 26, 2017

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