From 08b7288d4dae2a6088084f3e001995353be016ec Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 11 Oct 2018 12:25:57 -0700 Subject: [PATCH] doc fixes - include nhaa_equilibrium in docs... - minor fixes --- MDAnalysisData/base.py | 9 ++++++--- MDAnalysisData/descr/nhaa_equilibrium.rst | 2 +- docs/helpers.rst | 2 +- docs/index.rst | 1 + 4 files changed, 9 insertions(+), 5 deletions(-) diff --git a/MDAnalysisData/base.py b/MDAnalysisData/base.py index a388e0f..416d59e 100644 --- a/MDAnalysisData/base.py +++ b/MDAnalysisData/base.py @@ -37,8 +37,10 @@ from pkg_resources import resource_string #: Default value for the cache directory. It can be changed by setting -#: The environment variable :envvar:`MDANALYSIS_DATA`. The current +#: the environment variable :envvar:`MDANALYSIS_DATA`. The current #: value should be queried with :func:`get_data_home`. +#: +#: .. SeeAlso:: :ref:`managing-data`. DEFAULT_DATADIR = join('~', 'MDAnalysis_data') class Bunch(dict): @@ -186,7 +188,7 @@ def _fetch_remote(remote, dirname=None): def _read_description(filename, description_dir='descr'): - """Read the description from restructured text file `descr`. + """Read the description from restructured text file. Arguments --------- @@ -196,9 +198,10 @@ def _read_description(filename, description_dir='descr'): Note ---- All description files are supposed to be stored in the directory - ``description_dir`="descr"` that lives in the same directory as + `description_dir` ``="descr"`` that lives in the same directory as the :mod:`MDAnalysisData.base` module file. All descriptions are assumed to be in restructured text format and in UTF-8 encoding. + """ # The descr directory should be in the same directory as this file base.py. # `resource_string` returns bytes, which we need to decode to UTF-8 diff --git a/MDAnalysisData/descr/nhaa_equilibrium.rst b/MDAnalysisData/descr/nhaa_equilibrium.rst index 12d0234..35d3f47 100644 --- a/MDAnalysisData/descr/nhaa_equilibrium.rst +++ b/MDAnalysisData/descr/nhaa_equilibrium.rst @@ -3,7 +3,7 @@ .. _`nhaa-equilibrium-dataset`: NhaA equilibrium trajectory dataset -================================== +=================================== Molecular dynamics (MD) trajectory of the NhaA membrane protein in a POPE:POPG 4:1 model membrane. The equilibrium simulation was performed diff --git a/docs/helpers.rst b/docs/helpers.rst index ae316df..52b5f86 100644 --- a/docs/helpers.rst +++ b/docs/helpers.rst @@ -17,7 +17,7 @@ For users .. autoclass:: Bunch :members: -.. data:: DEFAULT_DATADIR +.. autodata:: DEFAULT_DATADIR .. autofunction:: get_data_home diff --git a/docs/index.rst b/docs/index.rst index 46f299f..e85f306 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -87,4 +87,5 @@ of pull requests are very welcome. adk_equilibrium adk_transitions ifabp_water + nhaa_equilibrium vesicles