Docs remove conda (#2516)

* General clean-up of docs

* Remove old example code from docs folder

For some reason some of the example models and code ended up in the docs folder rather than in the HELICS-Examples repo. This commit removes them from the main HELICS repo.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update docs/user-guide/installation/package_manager.md

Co-authored-by: Ryan Mast <3969255+nightlark@users.noreply.github.com>

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Ryan Mast <3969255+nightlark@users.noreply.github.com>

docs/HELICS2_CHANGELOG.md

@@ -6,7 +6,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 A note on future revisions.
-Everything within a major version number should be code compatible (with the exception of experimental interfaces). Everything within a single minor release should be network compatible with other federates on the same minor release number. Compatibility across minor release numbers may be possible in some situations but we are not going to guarantee this as those components are subject to performance improvements and may need to be modified at some point. Patch releases will be limited to bug fixes and other improvements not impacting the public API or network compatibility. Check the [Public API](./docs/Public_API.md) for details on what is included and excluded from the public API and version stability.
+Everything within a major version number should be code compatible (with the exception of experimental interfaces). Everything within a single minor release should be network compatible with other federates on the same minor release number. Compatibility across minor release numbers may be possible in some situations but we are not going to guarantee this as those components are subject to performance improvements and may need to be modified at some point. Patch releases will be limited to bug fixes and other improvements not impacting the public API or network compatibility. Check the [Public API](./Public_API.md) for details on what is included and excluded from the public API and version stability.
 
 ## [2.8.1][] - 2022-06-09
 
@@ -541,7 +541,7 @@ Minor release with bug fixes and a few additional features
 - helics apps tests is converted to use Google test and is now being run through the sanitizers
 - **BREAKING CHANGE** The C interface helics logging callback specifications now include a user data object. This is technically a breaking change, but there were a few issues with the current implementation so it is not entirely clear it was usable as it was. There are now some tests for the functionality. This log callback specification was not available in the language API's and the C++ API has not changed, only the C interface to specifying direct logging callbacks. This is considered a minor change due to no known users of this interface at present and as it was it wasn't entirely operational. No further changes are expected.
 - The use of Boost C++ in the helics core and application api are now limited to the IPC core(there are no plans to remove this usage) and an option to `DISABLE_BOOST` is available in the CMAKE files. This will turn off the IPC_CORE and any optional uses of boost in some of the libraries. Future features may use Boost but should retain the ability to disable its use.
-- **BREAKING CHANGE** Some function names in the C\+\+98 API were changed to better match the C\+\+ API and were documented more completely through doxygen, these were listed as potentially changing in the [Public API](/docs/Public_API.md) so this is not a consideration for semantic versioning. The C++98 API also has limited numbers of users at this point yet and may not be fully stable until HELICS 3.0 release
+- **BREAKING CHANGE** Some function names in the C\+\+98 API were changed to better match the C\+\+ API and were documented more completely through doxygen, these were listed as potentially changing in the [Public API](./Public_API.md) so this is not a consideration for semantic versioning. The C++98 API also has limited numbers of users at this point yet and may not be fully stable until HELICS 3.0 release
 - The doxygen CMake project was renamed from `doc` to `helics_doxygen`
 - several variables used by submodules in CMake were hidden
 - updated zmq subproject version to 4.3.2
@@ -739,7 +739,7 @@ This is a major revision so this changelog will not capture all the changes that
 - some additional tests for the shared library
 - TOML readers for interface description in Federates
 - interactive command line for helics_broker
-- a few new queries on brokers see [Queries](docs/user_guide/Queries.md)
+- a few new queries on brokers see [Queries](./user-guide/advanced_topics/queries.md)
 - CPACK can now build a dmg files
 - Players can have multiline comments in input file and omit the tag for repeated messages
 - marker option on player, recorder, tracer to print time advancement message

docs/developer-guide/index.md

@@ -15,4 +15,5 @@
    ../Public_API
    ../ROADMAP
    typeConversions
+   Notes
 ```

docs/user-guide/advanced_topics/advanced_topics_index.md

@@ -25,7 +25,8 @@
     iteration
     aliases
     callbacks
-    CallbackFederates
+    CallbackFederate
+    networking
     encrypted_communication
 ```
 
@@ -58,7 +59,8 @@ The Advanced Topics will cover:
 - [**Dynamic Federations**](./dynamic_federations.md) - Sometimes it is useful to have a federate that is not ready at the beginning of co-simulation. This is a dynamic federation. There are various levels of this (not all are available yet) and this document discusses some aspects of dynamic co-simulation.
 - [**Timeouts**](./timeouts.md) - HELICS includes a number of timeouts to prevent failed operations from continuing indefinitely, the various timeout options are discussed in this document.
 - [**Command Interface**](./commandInterface.md) - HELICS v3 introduced the command interface as a method of asynchronously communicating between federates.
-- [\*_Aliases_](./aliases.md) - HELICS 3.3 introduced the notion of aliases. Aliases allow a mapping of an interface key to a different string.
-- [\*_Callbacks_](./callbacks.md) - Over time a number of callbacks have been added for various operations and stages of the life cycle of a federate. This document describes the different callbacks available.
-- [\*_Callback Federates_](./CallbackFederate.md) - HELICS 3.3 introduced a beta test for callback federates which allow a federate to operate purely inline with a core based solely on callbacks. This can allow a much higher number of federates on a given system than was previously possible.
+- [**Aliases**](./aliases.md) - HELICS 3.3 introduced the notion of aliases. Aliases allow a mapping of an interface key to a different string.
+- [**Callbacks**](./callbacks.md) - Over time a number of callbacks have been added for various operations and stages of the life cycle of a federate. This document describes the different callbacks available.
+- [**Callback Federates**](./CallbackFederate.md) - HELICS 3.3 introduced a beta test for callback federates which allow a federate to operate purely inline with a core based solely on callbacks. This can allow a much higher number of federates on a given system than was previously possible.
+- [**Networking**](./CallbackFederate.md) - HELICS provides several ways of working in more restrictive networking environments.
 - [**Encrypted Communication**](./encrypted_communication.md) - How to encrypt communication between HELICS brokers/federates.

docs/user-guide/advanced_topics/commandInterface.md

@@ -50,29 +50,29 @@ The `commandStr` is a generic string, so can be anything that can be contained i
 The following queries are defined directly in HELICS. Federates may specify a callback function which allows arbitrary user-defined queries. The queries defined here are available inside of HELICS.
 
 ```{eval-rst}
-+---------------------------+------------------------------------------------------------------------------------------------+
-| Command String            | Description                                                                                    |
-+===========================+================================================================================================+
-| ``terminate``             | [all objects] disconnect the object from the federation                                        |
-+---------------------------+------------------------------------------------------------------------------------------------+
-| ``echo``                  | [all objects] send a command with a `commandStr`=`echo_reply` back to the sender               |
-+---------------------------+------------------------------------------------------------------------------------------------+
-| ``log <string>``          | [all objects] generate a log message in a particular object                                    |
-+---------------------------+------------------------------------------------------------------------------------------------+
-| ``logbuffer <size>``      | [all objects] set the log buffer to a particular size or `stop`                                |
-+---------------------------+------------------------------------------------------------------------------------------------+
-| ``monitor <args...>``     | [brokers] set up a federate as the time monitor <args...> = <federate names> <logperiod>       |
-+---------------------------+------------------------------------------------------------------------------------------------+
++---------------------------+-------------------------------------------------------------------------------------------------+
+| Command String            | Description                                                                                     |
++===========================+=================================================================================================+
+| ``terminate``             | [all objects] disconnect the object from the federation                                         |
++---------------------------+-------------------------------------------------------------------------------------------------+
+| ``echo``                  | [all objects] send a command with a `commandStr`=`echo_reply` back to the sender                |
++---------------------------+-------------------------------------------------------------------------------------------------+
+| ``log <string>``          | [all objects] generate a log message in a particular object                                     |
++---------------------------+-------------------------------------------------------------------------------------------------+
+| ``logbuffer <size>``      | [all objects] set the log buffer to a particular size or `stop`                                 |
++---------------------------+-------------------------------------------------------------------------------------------------+
+| ``monitor <args...>``     | [brokers] set up a federate as the time monitor <args...> = <federate names> <logperiod>        |
++---------------------------+-------------------------------------------------------------------------------------------------+
 | ``set barrier <args...>`` | [brokers,federates] set a time barrier <args...> = <time> <barrier_id*>                         |
-+---------------------------+------------------------------------------------------------------------------------------------+
-| ``clear barrier <id*>``   | [brokers,federates] clear a time barrier <barrier_id*>                         |
-+---------------------------+------------------------------------------------------------------------------------------------+
++---------------------------+-------------------------------------------------------------------------------------------------+
+| ``clear barrier <id*>``   | [brokers,federates] clear a time barrier <barrier_id*>                                          |
++---------------------------+-------------------------------------------------------------------------------------------------+
 | ``remotelog <level>``     | [all objects] instruct the object to send log messages to a remote location in addition to local|
-|                           |  logging.  The <level> is a [log level string](../fundamental_topics/logging.md) or `stop`     |
-+---------------------------+------------------------------------------------------------------------------------------------+
-| ``command_status``        | [federates] when received will send a string back to the source of the command                 |
-|                           | looking like \"X unprocessed commands\" where X is the number of unprocessed commands          |
-+---------------------------+------------------------------------------------------------------------------------------------+
+|                           |  logging.  The <level> is a [log level string](../fundamental_topics/logging.md) or `stop`      |
++---------------------------+-------------------------------------------------------------------------------------------------+
+| ``command_status``        | [federates] when received will send a string back to the source of the command                  |
+|                           | looking like \"X unprocessed commands\" where X is the number of unprocessed commands           |
++---------------------------+-------------------------------------------------------------------------------------------------+
 ```
 
 `*` argument is optional

docs/user-guide/advanced_topics/encrypted_communication.md

@@ -174,7 +174,7 @@ methods, there are a few settings that the encryption configuration file should
 
 The general outline of what the file looks is:
 
-```json
+```text
 {
     "encrypted": <true|false; this setting is optional and sort of an alternative to the --encrypted flag so can be omitted>,
     "verify_file": "<path to certificate authority (CA) file to verify connecting federates>",

docs/user-guide/advanced_topics/multiSourceInputs.md

@@ -42,7 +42,7 @@ The priority of the inputs is only applicable if the default operation to retrie
 +-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
 | ``helics_multi_input_or_operation``       | treat all inputs as boolean and perform an `or` operation                                                                                    |
 +-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
-|``helics_multi_input_sum_operation``       | sum all the inputs after converting to double vector, except if input type is string then concatenate all inputs as a single string        |
+|``helics_multi_input_sum_operation``       | sum all the inputs after converting to double vector, except if input type is string then concatenate all inputs as a single string          |
 +-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
 | ``helics_multi_input_diff_operation``     | if the input type is specified as a double subtract the sum of remaining values from the first, if it is a vector do a vector diff operation |
 +-------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+