diff --git a/CHANGELOG b/CHANGELOG index fddedc6..d193c8f 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -12,8 +12,10 @@ The rules for this file: use tabs but use spaces for formatting * accompany each entry with github issue/PR number (Issue #xyz) ------------------------------------------------------------------------------- -??/??/???? IAlibay, ollyfutur, conradolandia, orbeckst, PlethoraChutney, Pradyumn-cloud +------------------------------------------------------------------------------- +01/16/2026 IAlibay, ollyfutur, conradolandia, orbeckst, PlethoraChutney, + Pradyumn-cloud + * 1.1.0 Changes @@ -30,7 +32,7 @@ The rules for this file: (PR #142) * `Grid` now allows forcing MRC/CCP4 maps to be read as volumes even when the header indicates they are stacks of 2D images. (#150, PR #149) - * Added MRC file writing support (Issue #108) + * Added MRC file writing support (#108, PR #147) Fixes diff --git a/doc/source/gridData/core.rst b/doc/source/gridData/core.rst index 8f051b5..17c81df 100644 --- a/doc/source/gridData/core.rst +++ b/doc/source/gridData/core.rst @@ -1,2 +1,2 @@ .. automodule:: gridData.core - :members: + diff --git a/doc/source/gridData/formats.rst b/doc/source/gridData/formats.rst index 9e9e822..0680ac8 100644 --- a/doc/source/gridData/formats.rst +++ b/doc/source/gridData/formats.rst @@ -27,7 +27,7 @@ small number of file formats is directly supported. ============================ ========== ========= ===== ===== ========================================= :mod:`~gridData.OpenDX` OpenDX_ dx x x subset of OpenDX implemented :mod:`~gridData.gOpenMol` gOpenMol_ plt x - :mod:`~gridData.mrc` CCP4_ ccp4,mrc x subset implemented + :mod:`~gridData.mrc` CCP4_ ccp4,mrc x x subset implemented :class:`~gridData.core.Grid` pickle pickle x x standard Python pickle of the Grid class ============================ ========== ========= ===== ===== ========================================= diff --git a/doc/source/gridData/formats/OpenDX.rst b/doc/source/gridData/formats/OpenDX.rst index 8dde426..9a21b11 100644 --- a/doc/source/gridData/formats/OpenDX.rst +++ b/doc/source/gridData/formats/OpenDX.rst @@ -1,3 +1,3 @@ .. automodule:: gridData.OpenDX - :members: + diff --git a/doc/source/gridData/formats/gOpenMol.rst b/doc/source/gridData/formats/gOpenMol.rst index 029e3f5..0cd783f 100644 --- a/doc/source/gridData/formats/gOpenMol.rst +++ b/doc/source/gridData/formats/gOpenMol.rst @@ -1,2 +1,2 @@ .. automodule:: gridData.gOpenMol - :members: + diff --git a/doc/source/gridData/formats/mrc.rst b/doc/source/gridData/formats/mrc.rst index 352f040..e1e2f5a 100644 --- a/doc/source/gridData/formats/mrc.rst +++ b/doc/source/gridData/formats/mrc.rst @@ -1,2 +1,2 @@ .. automodule:: gridData.mrc - :members: + diff --git a/doc/source/index.rst b/doc/source/index.rst index a972d1f..f541d17 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -49,7 +49,7 @@ GridDataFormats is open source and welcomes your contributions. Fork the `GridDa .. Contents (sidebar) .. toctree:: - :maxdepth: 4 + :maxdepth: 3 :hidden: installation diff --git a/gridData/OpenDX.py b/gridData/OpenDX.py index 206501d..a081942 100644 --- a/gridData/OpenDX.py +++ b/gridData/OpenDX.py @@ -160,8 +160,46 @@ https://web.archive.org/web/20080808140524/http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm .. http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF -Classes and functions ---------------------- +Classes +------- + +DX field class +~~~~~~~~~~~~~~ + +The primary class is :class:`field`, which is a container for the other classes. +It contains the following classes: + +* :class:`gridpositions` +* :class:`gridconnections` +* :class:`array` + +The :class:`gridpositions` class contains the position of the grid cells. +The :class:`gridconnections` class contains the connections between the grid cells. +The :class:`array` class contains the data on the grid. + +.. autoclass:: field + :members: + +DX components +~~~~~~~~~~~~~ + +The :class:`field` class contains the following components: + +.. autoclass:: gridpositions + :members: + +.. autoclass:: gridconnections + :members: + +.. autoclass:: array + :members: + +DX parser +~~~~~~~~~~ +The :class:`DXParser` class is used to parse the DX file and construct the :class:`field` object. + +.. autoclass:: DXParser + :members: """ import numpy diff --git a/gridData/core.py b/gridData/core.py index 6813ac8..035d769 100644 --- a/gridData/core.py +++ b/gridData/core.py @@ -2,8 +2,8 @@ # Copyright (c) 2009-2014 Oliver Beckstein # Released under the GNU Lesser General Public License, version 3 or later. r""" -Core functionality for storing n-D grids --- :mod:`gridData.core` -================================================================= +Core functionality for storing n-D grids +======================================== The :mod:`core` module contains classes and functions that are independent of the grid data format. In particular this module @@ -19,10 +19,20 @@ g.load(filename) # populate with data from filename -Classes and functions ---------------------- +Classes +------- +.. autoclass:: Grid + :members: + :undoc-members: + :show-inheritance: + +Functions +--------- + +.. autofunction:: ndmeshgrid """ + import os import errno import pickle diff --git a/gridData/gOpenMol.py b/gridData/gOpenMol.py index 92faa04..3a2aa3c 100644 --- a/gridData/gOpenMol.py +++ b/gridData/gOpenMol.py @@ -126,6 +126,9 @@ Classes ------- +.. autoclass:: Plt + :members: + """ import warnings import struct diff --git a/gridData/mrc.py b/gridData/mrc.py index c81cd87..676d993 100644 --- a/gridData/mrc.py +++ b/gridData/mrc.py @@ -28,6 +28,10 @@ Classes ------- +.. autoclass:: MRC + :members: + + """ import numpy as np import mrcfile @@ -176,6 +180,7 @@ def write(self, filename): header information (including mapc, mapr, maps ordering) is preserved. Otherwise, standard ordering (mapc=1, mapr=2, maps=3) is used. + .. versionadded:: 1.1.0 """ if filename is not None: