docs: Update links

Update various links after moving `shell-logger` out onto GitHub.

doc/source/abstract_method.rst

@@ -2,4 +2,3 @@ AbstractMethod
 ==============
 
 .. autoexception:: shell_logger.abstract_method.AbstractMethod
-   :noindex:

doc/source/html_utilities.rst

@@ -4,5 +4,38 @@ HTML Utilities
 The following are a number of utility functions used to generate the HTML log
 file produced by :class:`ShellLogger`.
 
-.. automodule:: shell_logger.html_utilities
-   :noindex:
+.. autofunction:: shell_logger.html_utilities.append_html
+.. autofunction:: shell_logger.html_utilities.child_logger_card
+.. autofunction:: shell_logger.html_utilities.child_logger_card_html
+.. autofunction:: shell_logger.html_utilities.closing_html_text
+.. autofunction:: shell_logger.html_utilities.command_card
+.. autofunction:: shell_logger.html_utilities.command_card_html
+.. autofunction:: shell_logger.html_utilities.command_detail
+.. autofunction:: shell_logger.html_utilities.command_detail_list
+.. autofunction:: shell_logger.html_utilities.diagnostics_card
+.. autofunction:: shell_logger.html_utilities.disk_time_series_plot
+.. autofunction:: shell_logger.html_utilities.embed_html
+.. autofunction:: shell_logger.html_utilities.embed_script
+.. autofunction:: shell_logger.html_utilities.embed_style
+.. autofunction:: shell_logger.html_utilities.fixed_width
+.. autofunction:: shell_logger.html_utilities.flatten
+.. autofunction:: shell_logger.html_utilities.get_human_time
+.. autofunction:: shell_logger.html_utilities.html_encode
+.. autofunction:: shell_logger.html_utilities.html_header
+.. autofunction:: shell_logger.html_utilities.html_message_card
+.. autofunction:: shell_logger.html_utilities.load_template
+.. autofunction:: shell_logger.html_utilities.message_card
+.. autofunction:: shell_logger.html_utilities.nested_simplenamespace_to_dict
+.. autofunction:: shell_logger.html_utilities.opening_html_text
+.. autofunction:: shell_logger.html_utilities.output_block
+.. autofunction:: shell_logger.html_utilities.output_block_card
+.. autofunction:: shell_logger.html_utilities.output_block_html
+.. autofunction:: shell_logger.html_utilities.output_line_html
+.. autofunction:: shell_logger.html_utilities.parent_logger_card_html
+.. autofunction:: shell_logger.html_utilities.sgr_24bit_color_to_html
+.. autofunction:: shell_logger.html_utilities.sgr_4bit_color_and_style_to_html
+.. autofunction:: shell_logger.html_utilities.sgr_8bit_color_to_html
+.. autofunction:: shell_logger.html_utilities.sgr_to_html
+.. autofunction:: shell_logger.html_utilities.split_template
+.. autofunction:: shell_logger.html_utilities.stat_chart_card
+.. autofunction:: shell_logger.html_utilities.time_series_plot

doc/source/index.rst

@@ -19,16 +19,18 @@ while logging various metadata, statistics, and trace information.  Any time
 you're tempted to write your own wrapper around things like
 :class:`subprocess.Popen` or :func:`subprocess.run`, consider using
 :func:`ShellLogger.log` instead.  If you're familiar with `the Unix script
-command <https://man7.org/linux/man-pages/man1/script.1.html>`_, this is
-similar in principle, but with substantially more functionality.  If you're
-familiar with `Python's logging module
-<https://docs.python.org/3/library/logging.html>`_, the motivation is similar,
-but this intends to capture what's happening *in the shell* rather than in
-Python itself.
+command`_, this is similar in principle, but with substantially more
+functionality.  If you're familiar with `Python's logging module`_, the
+motivation is similar, but this intends to capture what's happening *in the
+shell* rather than in Python itself.
 
-The following talk from the `US-RSE Virtual Workshop 2021
-<https://us-rse.org/virtual-workshop-2021/>`_ illustrates the module's
-functionality.
+.. _the Unix script command: https://man7.org/linux/man-pages/man1/script.1.html
+.. _Python's logging module: https://docs.python.org/3/library/logging.html
+
+The following talk from the `US-RSE Virtual Workshop 2021`_ illustrates the
+module's functionality.
+
+.. _US-RSE Virtual Workshop 2021: https://us-rse.org/virtual-workshop-2021/
 
 .. raw:: html
 
@@ -53,11 +55,12 @@ functionality.
 Where to Get shell-logger
 -------------------------
 
-The source repository for this module can be found `here
-<https://internal.gitlab.server/ShellLogger/ShellLogger>`_.  See the project's
-`README.md
-<https://internal.gitlab.server/ShellLogger/ShellLogger/-/blob/master/README.md>`_
-for details on how to clone, install, and otherwise interact with the project.
+The source repository for this module can be found `on GitHub`_.  See the
+project's `README`_ for details on how to clone, install, and otherwise
+interact with the project.
+
+.. _on GitHub: https://github.com/sandialabs/shell-logger
+.. _README: https://github.com/sandialabs/shell-logger/blob/master/README.md
 
 Using shell-logger
 ------------------
@@ -105,17 +108,16 @@ the following:
 .. literalinclude:: ../../example/hello_world_html.py
    :language: python
    :linenos:
+   :lines: 11-
    :caption: ``example/hello_world_html.py``
 
 Running the script yields
 
 .. code-block::
 
    This example demonstrates logging information solely to the HTML log file.
-   Open /Users/jmgate/workspace/shell-logger/example/log_hello_world_html/2021-09-22_14.56.42.558599_szt68acx/Hello_ShellLogger.html to view the log.
+   Open <path-to-example-dir>/log_hello_world_html/<timestamp>_<unique-str>/Hello_ShellLogger.html to view the log.
 
-You can view the generated HTML log file `here
-<http://shelllogger.internal.gitlab.pages/shell-logger/example/Hello_World_HTML.html>`__.
 When you open that file, you'll see something like
 
 .. image:: images/html_log.png
@@ -175,12 +177,10 @@ highlighted lines below.
 .. literalinclude:: ../../example/hello_world_html_and_console.py
    :language: python
    :linenos:
-   :emphasize-lines: 11, 13
+   :lines: 11-
+   :emphasize-lines: 15-16, 22-23
    :caption: ``example/hello_world_html_and_console.py``
 
-You can view the generated HTML log file `here
-<http://shelllogger.internal.gitlab.pages/shell-logger/example/Hello_World_HTML_and_Console.html>`__.
-
 Example 3:  Collecting Statistics
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -191,12 +191,10 @@ and **Example 1** are the highlighted lines below.
 .. literalinclude:: ../../example/hello_world_html_with_stats.py
    :language: python
    :linenos:
-   :emphasize-lines: 12, 14
+   :lines: 11-
+   :emphasize-lines: 16, 22
    :caption: ``example/hello_world_html_with_stats.py``
 
-You can view the generated HTML log file `here
-<http://shelllogger.internal.gitlab.pages/shell-logger/example/Hello_World_HTML_with_Stats.html>`__.
-
 Example 4:  Building a Code
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -215,11 +213,9 @@ The equivalent Python script using ``shell-logger`` is the following:
 .. literalinclude:: ../../example/build_flex.py
    :language: python
    :linenos:
+   :lines: 11-
    :caption: ``example/build_flex.py``
 
-You can view the generated HTML log file `here
-<http://shelllogger.internal.gitlab.pages/shell-logger/example/Build_Flex.html>`__.
-
 More Details
 ------------
 

doc/source/shell.rst

@@ -1,5 +1,4 @@
 Shell
 =====
 
-.. automodule:: shell_logger.shell
-   :noindex:
+.. autoclass:: shell_logger.shell.Shell

doc/source/shell_logger.rst

@@ -2,18 +2,15 @@ ShellLogger
 ===========
 
 .. autoclass:: shell_logger.ShellLogger
-   :noindex:
 
 JSON Serialization
 ------------------
 
 .. autoclass:: shell_logger.ShellLoggerDecoder
-   :noindex:
 
 .. todo::
 
    Figure out why the documentation below is pulling in the docstring for the
    base class as well.
 
 .. autoclass:: shell_logger.ShellLoggerEncoder
-   :noindex:

doc/source/stats_collector.rst

@@ -2,25 +2,20 @@ StatsCollector
 ==============
 
 .. autoclass:: shell_logger.stats_collector.StatsCollector
-   :noindex:
 
 .. automethod:: shell_logger.stats_collector::stats_collectors
-   :noindex:
 
 DiskStatsCollector
 ------------------
 
 .. autoclass:: shell_logger.stats_collector.DiskStatsCollector
-   :noindex:
 
 CPUStatsCollector
 -----------------
 
 .. autoclass:: shell_logger.stats_collector.CPUStatsCollector
-   :noindex:
 
 MemoryStatsCollector
 --------------------
 
 .. autoclass:: shell_logger.stats_collector.MemoryStatsCollector
-   :noindex:

doc/source/trace.rst

@@ -2,19 +2,15 @@ Trace
 =====
 
 .. autoclass:: shell_logger.trace.Trace
-   :noindex:
 
 .. automethod:: shell_logger.trace::trace_collector
-   :noindex:
 
 STrace
 ------
 
 .. autoclass:: shell_logger.trace.STrace
-   :noindex:
 
 LTrace
 ------
 
 .. autoclass:: shell_logger.trace.LTrace
-   :noindex: