Create doc files for h5pyd

README.md

@@ -66,7 +66,7 @@ variables are needed to be defined:
 To use "local" mode with S3, define these variables:
 
 * ``AWS_S3_GATEWAY`` - AWS S3 endpoint, e.g.: ``https://s3.us-west-2.amazonaws.com``
-* ``AWS_REGION`` - Region where the Lambda function is installed, e.g.: ``us-west-2``
+* ``AWS_REGION`` - Region where the S3 bucket is located, e.g.: ``us-west-2``
 * ``AWS_SECRET_ACCESS_KEY`` - Your AWS secret access AWS_SECRET_ACCESS_KEY
 * ``AWS_ACCESS_KEY_ID`` - Your AWS access key ID
 

docs/Makefile

@@ -1,4 +1,5 @@
 # Makefile for Sphinx documentation
+#
 
 # You can set these variables from the command line.
 SPHINXOPTS    = -W
@@ -84,17 +85,17 @@ qthelp:
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/h5py.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/h5pyd.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/h5py.qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/h5pyd.qhc"
 
 devhelp:
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/h5py"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/h5py"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/h5pyd"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/h5pyd"
 	@echo "# devhelp"
 
 epub:
@@ -174,3 +175,6 @@ pseudoxml:
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+show:
+	@python -m webbrowser -t "file://$(shell pwd)/_build/html/index.html"

docs/conf.py

@@ -1,6 +1,18 @@
+# -*- coding: utf-8 -*-
+#
+# h5pyd documentation build configuration file,
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
 import sys
 import os
-from importlib import metadata
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -21,12 +33,13 @@
     'sphinx.ext.mathjax',
 ]
 
-# intersphinx_mapping = {'low': ('https://api.h5py.org', None)}
+intersphinx_mapping = {'low': ('https://api.h5py.org', None)}
 
 extlinks = {
-    'issue': ('https://github.com/HDFGroup/h5pyd/issues/%s', 'GH'),
-    'pr': ('https://github.com/HDFGroup/h5pyd/pulls/%s', 'PR '),
+    'issue': ('https://github.com/h5py/h5pyd/issues/%s', 'GH%s'),
+    'pr': ('https://github.com/h5py/h5pyd/pull/%s', 'PR %s'),
 }
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -41,14 +54,14 @@
 
 # General information about the project.
 project = 'h5pyd'
-copyright = '2014 The HDF Group'
+copyright = '2017, The HDF Group'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = metadata.version('h5pyd')
+release = '0.20.0'
 # The short X.Y version.
 version = '.'.join(release.split('.')[:2])
 
@@ -95,7 +108,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'furo'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -174,3 +187,82 @@
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'h5pyddoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    ('index', 'h5pyd.tex', 'h5pyd Documentation',
+     'The HDF Group', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+# latex_appendices = []
+
+# If false, no module index is generated.
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'h5pyd', 'h5pyd Documentation',
+     ['The HDF Group'], 1)
+]
+
+# If true, show URL addresses after external links.
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    ('index', 'h5pyd', 'h5pyd Documentation',
+     'The HDF Group', 'h5pyd', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+# texinfo_no_detailmenu = False

docs/config.rst

@@ -27,50 +27,3 @@ attributes:
         particular container by specifying ``track_order`` argument to
         :class:`h5py.File`, :meth:`h5py.Group.create_group`,
         :meth:`h5py.Group.create_dataset`.  The default is ``False``.
-
-
-IPython
--------
-
-H5py ships with a custom ipython completer, which provides object introspection
-and tab completion for h5py objects in an ipython session. For example, if a
-file contains 3 groups, "foo", "bar", and "baz"::
-
-   In [4]: f['b<TAB>
-   bar   baz
-
-   In [4]: f['f<TAB>
-   # Completes to:
-   In [4]: f['foo'
-
-   In [4]: f['foo'].<TAB>
-   f['foo'].attrs            f['foo'].items            f['foo'].ref
-   f['foo'].copy             f['foo'].iteritems        f['foo'].require_dataset
-   f['foo'].create_dataset   f['foo'].iterkeys         f['foo'].require_group
-   f['foo'].create_group     f['foo'].itervalues       f['foo'].values
-   f['foo'].file             f['foo'].keys             f['foo'].visit
-   f['foo'].get              f['foo'].name             f['foo'].visititems
-   f['foo'].id               f['foo'].parent
-
-The easiest way to enable the custom completer is to do the following in an
-IPython session::
-
-   In  [1]: import h5py
-
-   In [2]: h5py.enable_ipython_completer()
-
-It is also possible to configure IPython to enable the completer every time you
-start a new session. For >=ipython-0.11, "h5py.ipy_completer" just needs to be
-added to the list of extensions in your ipython config file, for example
-:file:`~/.config/ipython/profile_default/ipython_config.py` (if this file does
-not exist, you can create it by invoking `ipython profile create`)::
-
-   c = get_config()
-   c.InteractiveShellApp.extensions = ['h5py.ipy_completer']
-
-For <ipython-0.11, the completer can be enabled by adding the following lines
-to the :func:`main` in :file:`.ipython/ipy_user_conf.py`::
-
-   def main():
-       ip.ex('from h5py import ipy_completer')
-       ip.ex('ipy_completer.load_ipython_extension()')

docs/faq.rst

@@ -80,6 +80,7 @@ family                              Multi-file driver
 mpio                                Parallel HDF5 file access
 =================================== =========================================== ============================
 
+.. _h5py_pytable_cmp:
 
 What's the difference between h5py and PyTables?
 ------------------------------------------------
@@ -202,15 +203,20 @@ To build from a Git checkout:
 
 Clone the project::
 
-    $ git clone https://github.com/HDFGroup/h5pyd.git
-    $ cd h5pyd
+    $ git clone https://github.com/h5py/h5py.git
+    $ cd h5py
 
-Build and install the project::
+(Optional) Choose which branch to build from (e.g. a stable branch)::
 
-    $ pip install .
+    $ git checkout 2.1
+
+Build the project. If given, /path/to/hdf5 should point to a directory
+containing a compiled, shared-library build of HDF5 (containing things like "include" and "lib")::
+
+    $ python setup.py build [--hdf5=/path/to/hdf5]
 
 (Optional) Run the unit tests::
 
-    $ python testall.py
+    $ python setup.py test
 
-Report any failing tests by filing a bug report at GitHub.
+Report any failing tests to the mailing list (h5py at googlegroups), or by filing a bug report at GitHub.

docs/high/attr.rst

@@ -29,6 +29,17 @@ dictionaries.
 The default ``track_order`` for all new groups and datasets can be
 specified globally with ``h5.get_config().track_order``.
 
+Large attributes
+----------------
+
+HDF5 allows attributes to be larger than 64 KiB, but these need to be stored in
+a different way. As of March 2024, the way HDF5 documentation suggests you
+configure this does not work. Instead, enable order tracking when creating the
+object you want to attach attributes to::
+
+    grp = f.create_group('g', track_order=True)
+    grp.attrs['large'] = np.arange(1_000_000, dtype=np.uint32)
+
 
 Reference
 ---------