diff --git a/docs/source/api.rst b/docs/source/api.rst index 97903fc..46cb119 100644 --- a/docs/source/api.rst +++ b/docs/source/api.rst @@ -8,8 +8,6 @@ API Documentation :Year: 2020 :Copyright: GNU Public License v3 -.. versionadded:: 1.0.0 - This toolkit provides an updated interface for the HOLE_ suite of tools :cite:p:`Smart1993,Smart1996` to analyse an ion channel pore or transporter pathway :cite:p:`Stelzl2014` as a function of time or arbitrary order diff --git a/mdahole2/analysis/__init__.py b/mdahole2/analysis/__init__.py index 8424adb..74c753b 100644 --- a/mdahole2/analysis/__init__.py +++ b/mdahole2/analysis/__init__.py @@ -28,8 +28,6 @@ :Year: 2020 :Copyright: GNU Public License v3 -.. versionadded:: 1.0.0 - """ from .hole import hole, HoleAnalysis from .utils import create_vmd_surface diff --git a/mdahole2/analysis/hole.py b/mdahole2/analysis/hole.py index 59ca1da..a5881ed 100644 --- a/mdahole2/analysis/hole.py +++ b/mdahole2/analysis/hole.py @@ -210,8 +210,6 @@ def hole(pdbfile, - HOLE is very picky and does not read all DCD-like formats [#HOLEDCD]_. If in doubt, look into the `outfile` for error diagnostics. - .. versionadded:: 1.0 - .. [#HOLEDCD] PDB files are not the only files that :program:`hole` can read. In principle, it is also able to read CHARMM DCD trajectories and generate a hole profile for each frame. However, @@ -394,19 +392,13 @@ class HoleAnalysis(AnalysisBase): results.sphpdbs: numpy.ndarray Array of sphpdb filenames - .. versionadded:: 2.0.0 - results.outfiles: numpy.ndarray Arrau of output filenames - .. versionadded:: 2.0.0 - results.profiles: dict Profiles generated by HOLE2. A dictionary of :class:`numpy.recarray`\ s, indexed by frame. - .. versionadded:: 2.0.0 - sphpdbs: numpy.ndarray Alias of :attr:`results.sphpdbs` @@ -428,13 +420,6 @@ class HoleAnalysis(AnalysisBase): This will be removed in MDAnalysis 3.0.0. Please use :attr:`results.profiles` instead. - .. versionadded:: 1.0 - - .. versionchanged:: 2.0.0 - :attr:`sphpdbs`, :attr:`outfiles` and :attr:`profiles ` - are now stored in a :class:`MDAnalysis.analysis.base.Results` - instance. - """ input_file = '{prefix}hole{i:03d}.inp' diff --git a/mdahole2/analysis/templates.py b/mdahole2/analysis/templates.py index 3ab83f1..8665e81 100644 --- a/mdahole2/analysis/templates.py +++ b/mdahole2/analysis/templates.py @@ -28,8 +28,6 @@ :Year: 2020 :Copyright: GNU Public License v3 -.. versionadded:: 1.0 - Templates used in :mod:`mdahole2.analysis.hole` """ diff --git a/mdahole2/analysis/utils.py b/mdahole2/analysis/utils.py index 8694d04..380f0b2 100644 --- a/mdahole2/analysis/utils.py +++ b/mdahole2/analysis/utils.py @@ -30,8 +30,6 @@ :Year: 2020 :Copyright: GNU Public License v3 -.. versionadded:: 1.0 - Helper functions used in :mod:`mdahole2.analysis.hole` """ import logging @@ -308,8 +306,6 @@ def set_up_hole_input(pdbfile, str input text to run HOLE - .. versionadded:: 1.0 - """.format(IGNORE_RESIDUES) short_filename = check_and_fix_long_filename(pdbfile, tmpdir=tmpdir) if vdwradii_file is not None: