Update docs references as I move SIERRA to my personal github

jharwell · Sep 11, 2022 · 3ee9432 · 3ee9432
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diff --git a/README.rst b/README.rst
@@ -21,25 +21,25 @@ SIERRA (reSearch pIpEline for Reproducibility, Reusability, and Automation)
    .. image:: https://img.shields.io/badge/python-3.9-blue.svg
       :target: https://www.python.org/downloads/release/python-390/
 
-.. |ci-integration-master| image:: https://github.com/swarm-robotics/sierra/actions/workflows/integration-all.yml/badge.svg?branch=master
-.. |ci-analysis-master| image:: https://github.com/swarm-robotics/sierra/actions/workflows/static-analysis.yml/badge.svg?branch=master
-.. |ci-coverage-master| image:: https://coveralls.io/repos/github/swarm-robotics/sierra/badge.svg?branch=master
+.. |ci-integration-master| image:: https://github.com/jharwell/sierra/actions/workflows/integration-all.yml/badge.svg?branch=master
+.. |ci-analysis-master| image:: https://github.com/jharwell/sierra/actions/workflows/static-analysis.yml/badge.svg?branch=master
+.. |ci-coverage-master| image:: https://coveralls.io/repos/github/jharwell/sierra/badge.svg?branch=master
 
-.. |ci-integration-devel| image:: https://github.com/swarm-robotics/sierra/actions/workflows/integration-all.yml/badge.svg?branch=devel
-.. |ci-analysis-devel| image:: https://github.com/swarm-robotics/sierra/actions/workflows/static-analysis.yml/badge.svg?branch=devel
-.. |ci-coverage-devel| image:: https://coveralls.io/repos/github/swarm-robotics/sierra/badge.svg?branch=devel
+.. |ci-integration-devel| image:: https://github.com/jharwell/sierra/actions/workflows/integration-all.yml/badge.svg?branch=devel
+.. |ci-analysis-devel| image:: https://github.com/jharwell/sierra/actions/workflows/static-analysis.yml/badge.svg?branch=devel
+.. |ci-coverage-devel| image:: https://coveralls.io/repos/github/jharwell/sierra/badge.svg?branch=devel
 
 .. |license| image:: https://img.shields.io/badge/License-GPLv3-blue.svg
              :target: https://www.gnu.org/licenses/gpl-3.0
 
 .. |doi| image:: https://zenodo.org/badge/125774567.svg
          :target: https://zenodo.org/badge/latestdoi/125774567
 
-.. |docs| image:: https://readthedocs.org/projects/swarm-robotics-sierra/badge/?version=master
-          :target: https://readthedocs.org/projects/swarm-robotics-sierra/master
+.. |docs| image:: https://readthedocs.org/projects/sierra/badge/?version=master
+          :target: https://readthedocs.org/projects/sierra/master
 
 .. |maintenance| image:: https://img.shields.io/badge/Maintained%3F-yes-green.svg
-                  :target: https://gitHub.com/swarm-robotics/sierra/graphs/commit-activity
+                  :target: https://gitHub.com/jharwell/sierra/graphs/commit-activity
 
 
 :Usage:
@@ -73,7 +73,7 @@ To install SIERRA (requires python 3.8+):
    pip3 install sierra-research
 
 To get started using SIERRA, see `getting started
-<https://swarm-robotics-sierra.readthedocs.io/en/master/getting_started.html>`_.
+<https://sierra.readthedocs.io/en/master/src/getting_started.html>`_.
 
 Want to cite SIERRA? See `Citing`_.
 
@@ -82,7 +82,7 @@ Have an issue using SIERRA? See `Troubleshooting`_.
 What is SIERRA?
 ===============
 
-.. figure:: https://raw.githubusercontent.com/swarm-robotics/sierra/master/docs/figures/architecture.png
+.. figure:: https://raw.githubusercontent.com/jharwell/sierra/master/docs/figures/architecture.png
 
    SIERRA architecture, organized by pipeline stage. Stages are listed left to
    right, and an approximate joint architectural/functional stack is top to
@@ -147,7 +147,7 @@ cases:
 
 If aspects of either use case sound familiar, then there is a strong chance
 SIERRA could help you! SIERRA is well documented--see the `SIERRA docs
-<https://swarm-robotics-sierra.readthedocs.io/en/master/>`_ to get started.
+<https://sierra.readthedocs.io/en/master/>`_ to get started.
 
 Use Case #1: Alice The Robotics Researcher
 ------------------------------------------
@@ -262,160 +262,133 @@ SIERRA Support Matrix
 =====================
 
 SIERRA supports multiple `platforms
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/platform/index.html>`_
-which researchers can write code to target. In SIERRA terminology, a platform is
-a "thing" (usually a simulator or robot) that you want to write to code to run
+<https://sierra.readthedocs.io/en/master/src/platform/index.html>`_ which
+researchers can write code to target. In SIERRA terminology, a platform is a
+"thing" (usually a simulator or robot) that you want to write to code to run
 on. Note that platform != OS, in SIERRA terminology. If a SIERRA platform runs
 on a given OS, then SIERRA supports doing so; if it does not, then SIERRA does
 not. For example, SIERRA does not support running ARGoS on windows, because
 ARGoS does not support windows.
 
-If your desired platform is not listed, see the `plugin tutorials
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/tutorials.html>`_
-for how to add it via a plugin.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 50,50
-
-   * - Platform
-
-     - Description
-
-   * - `ARGoS <https://www.argos-sim.info/index.php>`_
-
-     - Simulator for fast simulation of large swarms. Requires ARGoS >=
-       3.0.0-beta59.
-
-   * - `ROS1 <https://ros.org)+[Gazebo](https://www.gazebosim.org>`_
-
-     - Using ROS1 with the Gazebo simulator. Requires Gazebo >= 11.9.0, ROS1
-       Noetic or later.
-
-   * - `ROS1+Robot <https://ros.org>`_
-
-     - Using ROS1 with a real robot platform of your choice. ROS1 Noetic or
-       later is required.
-
 SIERRA supports multiple execution environments for execution of experiments,
 such as `High Performance Computing (HPC) environments
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/exec_env/hpc.html>`_
-and `real robots
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/exec_env/robots.html>`_.
+<https://sierra.readthedocs.io/en/master/src/exec_env/hpc.html>`_ and `real
+robots <https://sierra.readthedocs.io/en/master/src/exec_env/robots.html>`_.
 Which execution environment experiments targeting a given platform is (somewhat)
-independent of the platform itself (see below). If your desired execution
-environment is not listed, see the `plugin tutorials
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/tutorials.html>`_
-for how to add it via a plugin.
-
-
-.. list-table::
-   :header-rows: 1
-   :widths: 50,50
-
-   * - Execution Environment
-
-     - Description
-
-   * - `SLURM <https://slurm.schedmd.com/documentation.html>`_
-
-     - An HPC cluster managed by the SLURM scheduler
-
-   * - `Torque/MOAB <https://adaptivecomputing.com/cherry-services/torque-resource-manager>`_
-
-     - An HPC cluster managed by the Torque/MOAB scheduler
-
-   * - Adhoc
-
-     - Miscellaneous collection of networked HPC compute nodes or random
-       servers; not managed by a scheduler
-
-   * - HPC local
-
-     - The SIERRA host machine,e.g., a researcher's laptop
-
-   * - `Turtlebot3 <https://emanual.robotis.com/docs/en/platform/turtlebot3/overview>`_
-
-     - Real turtlebot3 robots
-
-
-SIERRA also supports multiple output formats for experimental outputs. If the
-format for your experimental outputs is not listed, see the `tutorials
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/tutorials.html>`_
-for how to add it via a plugin. SIERRA currently only supports XML experimental
-inputs.
-
-.. list-table::
-   :header-rows: 1
-   :widths: 50,50
-
-   * - Experimental Output Format
-
-     - Scope
-
-   * - CSV file
+independent of the platform itself (see below).
 
-     - Raw experimental outputs, transforming into heatmap images.
-
-   * - PNG file
-
-     - Stitching images together into videos.
+SIERRA also supports multiple output formats for experimental outputs, as shown
+below. SIERRA currently only supports XML experimental inputs.
 
 SIERRA supports (mostly) mix-and-match between platforms, execution
 environments, experiment input/output formats as shown in its support matrix
-below. This is one of the most powerful features of SIERRA!
+below. This is one of the most powerful features of SIERRA!  If your desired
+platform/execution environment is not listed, see the `plugin tutorials
+<https://sierrap.readthedocs.io/en/master/src/tutorials.html>`_ for how to add
+it via a plugin.
 
 .. list-table::
    :header-rows: 1
    :widths: 25,25,25,25
 
    * - Execution Environment
+
      - Platform
 
      - Experimental Input Format
 
      - Experimental Output Format
 
-   * - SLURM
+   * - `SLURM <https://slurm.schedmd.com/documentation.html>`_: An HPC cluster
+       managed by the SLURM scheduler.
 
      - ARGoS, ROS1+Gazebo
 
      - XML
 
      - CSV, PNG
 
-   * - Torque/MOAB
+   * - `Torque/MOAB
+       <https://adaptivecomputing.com/cherry-services/torque-resource-manager>`_:
+       An HPC cluster managed by the Torque/MOAB scheduler.
 
      - ARGoS, ROS1+Gazebo
 
      - XML
 
      - CSV, PNG
 
-   * - ADHOC
+   * - ADHOC: A miscellaneous collection of networked HPC compute nodes or
+       random servers; not managed by a scheduler.
+
 
      - ARGoS, ROS1+Gazebo
 
      - XML
 
      - CSV, PNG
 
-   * - Local
+   * - Local: The SIERRA host machine,e.g., a researcher's laptop.
 
      - ARGoS, ROS1+Gazebo
 
      - XML
 
      - CSV, PNG
 
-   * - ROS1+Turtlebot3
+   * - ROS1+Turtlebot3: `Turtlebot3
+       <https://emanual.robotis.com/docs/en/platform/turtlebot3/overview>`_
+       robots with ROS1.
 
      - ROS1+Gazebo, ROS1+robot
 
      - XML
 
      - CSV, PNG
 
+For more details about the platforms out experimental output formats, see below.
+
+.. list-table::
+   :header-rows: 1
+   :widths: 50,50
+
+   * - Platform
+
+     - Description
+
+   * - `ARGoS <https://www.argos-sim.info/index.php>`_
+
+     - Simulator for fast simulation of large swarms. Requires ARGoS >=
+       3.0.0-beta59.
+
+   * - `ROS1 <https://ros.org>`_ + `Gazebo <https://www.gazebosim.org>`_
+
+     - Using ROS1 with the Gazebo simulator. Requires Gazebo >= 11.9.0, ROS1
+       Noetic or later.
+
+   * - `ROS1+Robot <https://ros.org>`_
+
+     - Using ROS1 with a real robot platform of your choice. ROS1 Noetic or
+       later is required.
+
+
+.. list-table::
+   :header-rows: 1
+   :widths: 50,50
+
+   * - Experimental Output Format
+
+     - Scope
+
+   * - CSV file
+
+     - Raw experimental outputs, transforming into heatmap images.
+
+   * - PNG file
+
+     - Stitching images together into videos.
+
+
 Requirements To Use SIERRA
 ==========================
 
@@ -437,7 +410,7 @@ The basic requirements are:
 
 For more details, including the requirements for researcher code, see the
 `SIERRA requirements
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/requirements.html>`_.
+<https://sierra.readthedocs.io/en/master/src/requirements.html>`_.
 
 Citing
 ======
@@ -467,5 +440,5 @@ Contributing
 
 I welcome all types of contributions, no matter how large or how small, and if
 you have an idea, I'm happy to talk about it at any point :-). See `here
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/contributing.html>`_
+<https://sierra.readthedocs.io/en/master/src/contributing.html>`_
 for the general procedure.
diff --git a/docs/conf.py b/docs/conf.py
@@ -160,12 +160,12 @@
                    "https://www.cs.unm.edu/~wjust/CS523/S2018/Readings/Hecker_Beyond_Pheromones_Swarm_Intelligence.pdf"),
     "Rosenfeld2006": ("Rosenfeld2006",
                       "http://users.umiacs.umd.edu/~sarit/data/articles/rosenfeldetalbook06.pdf"),
-    "SIERRA_GITHUB": ("https://github.com:swarm-robotics/sierra.git",
-                      "https://github.com:swarm-robotics/sierra.git"),
-    "SIERRA_SAMPLE_PROJECT": ("https://github.com:swarm-robotics/sierra-sample-project.git",
-                              "https://github.com:swarm-robotics/sierra-sample-project.git"),
-    "SIERRA_DOCS": ("https://swarm-robotics-sierra.readthedocs.io/en/master",
-                    "https://swarm-robotics-sierra.readthedocs.io/en/master"),
+    "SIERRA_GITHUB": ("https://github.com:jharwell/sierra.git",
+                      "https://github.com:jharwell/sierra.git"),
+    "SIERRA_SAMPLE_PROJECT": ("https://github.com:jharwell/sierra-sample-project.git",
+                              "https://github.com:jharwell/sierra-sample-project.git"),
+    "SIERRA_DOCS": ("https://sierra.readthedocs.io/en/master",
+                    "https://sierra.readthedocs.io/en/master"),
     "FORDYCA": ("FORDYCA", "https://swarm-robotics-fordyca.readthedocs.io"),
     "PRISM": ("PRISM", "https://swarm-robotics-prism.readthedocs.io"),
     "LIBRA": ("LIBRA", "https://swarm-robotics-libra.readthedocs.io"),

diff --git a/docs/src/matrix.rst b/docs/src/matrix.rst
@@ -96,7 +96,7 @@ listed, see the :ref:`ln-sierra-tutorials` for how to add it via a plugin.
 
 SIERRA also supports multiple output formats for experimental outputs. If the
 format for your experimental outputs is not listed, see the `docs
-<https://swarm-robotics-sierra.readthedocs.io/en/master/src/tutorials.html>`_
+<https://sierra.readthedocs.io/en/master/src/tutorials.html>`_
 for how to add it via a plugin. SIERRA currently only supports XML experimental
 inputs.
 

diff --git a/docs/src/packages.rst b/docs/src/packages.rst
@@ -53,7 +53,7 @@ SIERRA provides a :term:`ROS1` package containing functionality it uses to
 manage simulations and provide run-time support to :term:`projects<Project>`
 using a :term:`Platform` built on ROS. To use SIERRA with a ROS platform, you
 need to setup the SIERRA ROSbridge package here (details in README):
-`<https://github.com/swarm-robotics/sierra_rosbridge.git>`_.
+`<https://github.com/jharwell/sierra_rosbridge.git>`_.
 
 This package provides the following nodes:
 

diff --git a/docs/src/requirements.rst b/docs/src/requirements.rst
@@ -210,7 +210,7 @@ These requirements apply to any :term:`Platform` which uses :term:`ROS1` (e.g.,
    the elapsed time in seconds, and which exits (and takes down the roslaunch
    when it does) after the specified experiment time has elapsed. This node is
    inserted into all ``.launch`` files. All ROS projects must depend on this
-   `ROS bridge <https://github.com/swarm-robotics/sierra_rosbridge.git>`_
+   `ROS bridge <https://github.com/jharwell/sierra_rosbridge.git>`_
    package so the necessary nodes can be found by ROS at runtime.
 
 

diff --git a/docs/src/trial.rst b/docs/src/trial.rst
@@ -91,10 +91,10 @@ you clone things somewhere else.
 
             Where ``<distro>`` is replaced by your ROS distro.
 
-         #.  Install the `SIERRA ROSBridge <https:github.com/swarm-robotics/sierra_rosbridge.git>`_::
+         #.  Install the `SIERRA ROSBridge <https:github.com/jharwell/sierra_rosbridge.git>`_::
 
                pip3 install catkin_tools
-               git clone https://github.com/swarm-robotics/sierra_rosbridge.git
+               git clone https://github.com/jharwell/sierra_rosbridge.git
                cd sierra_rosbridge
                catkin init
                catkin config --extend /opt/ros/<distro>
@@ -117,7 +117,7 @@ you clone things somewhere else.
          Based on the `foraging example
          <https://www.argos-sim.info/examples.php>`_ from the ARGoS website::
 
-           git clone https://github.com/swarm-robotics/sierra-sample-project.git
+           git clone https://github.com/jharwell/sierra-sample-project.git
            cd sierra-sample-project/argos
            git checkout devel
            mkdir -p build && cd build
@@ -135,7 +135,7 @@ you clone things somewhere else.
          Based on one of the turtlebot3 `intro tutorials
          <https://github.com:ROBOTIS-GIT/turtlebot3_simulations.git>`_::
 
-           git clone https://github.com/swarm-robotics/sierra-sample-project.git
+           git clone https://github.com/jharwell/sierra-sample-project.git
            cd sierra-sample-project/ros1gazebo
            git checkout devel
            catkin init

diff --git a/setup.py b/setup.py
@@ -41,7 +41,7 @@
     description="Automation framework for the scientific method in AI research",
     long_description=readme,
     long_description_content_type="text/x-rst",
-    url="https://github.com/swarm-robotics/sierra",
+    url="https://github.com/jharwell/sierra",
     author="John Harwell",
     author_email="[email protected]",
     license="GPLv3+",