Sphinx Documentation: Restructure (#1821)

The big restructuring & streamlining of our documentation.

Author: ax3l

CODE_OF_CONDUCT.md

@@ -0,0 +1,61 @@
+.. _coc:
+
+Code of Conduct
+===============
+
+Our Pledge
+----------
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to creating a positive environment include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
+
+Our Responsibilities
+--------------------
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+Scope
+-----
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community.
+Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+Representation of a project may be further defined and clarified by project maintainers.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at warpx-coc@lbl.gov.
+All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances.
+The project team is obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the `Contributor Covenant <https://www.contributor-covenant.org>`_, version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

CODE_OF_CONDUCT.rst

@@ -0,0 +1 @@
+../../CODE_OF_CONDUCT.rst

Docs/source/building/cori.rst

@@ -2,14 +2,13 @@ Advanced yt visualization, for developers (for plotfiles)
 =========================================================
 
 This sections contains yt commands for advanced users. The Particle-In-Cell methods uses a
-staggered grid (see :doc:`../theory/picsar_theory`), so that the x, y, and z components of the
+staggered grid (see :ref:`particle-in-cell theory <theory-pic>`), so that the x, y, and z components of the
 electric and magnetic fields are all defined at different locations in space. Regular output
 (see the :doc:`yt` page, or the notebook at ``WarpX/Tools/PostProcessing/Visualization.ipynb`` for an example)
 returns cell-centered data for convenience, which involves an additional operation. It is sometimes
 useful to access the raw data directly. Furthermore,
 the WarpX implementation for mesh refinement contains a number of grids for each level (coarse,
-fine and auxiliary, see
-:doc:`../theory/theory` for more details), and it is sometimes useful to access each of
+fine and auxiliary, see :ref:`the theory <theory>` for more details), and it is sometimes useful to access each of
 them (regular output return the auxiliary grid only). This page provides information to read
 raw data of all grids.
 
@@ -27,7 +26,7 @@ with parameters (``warpx.plot_rho`` only when using back-transformed diagnostics
     warpx.plot_dive = 1
     warpx.plot_rho = 1
 
-see :doc:`../running_cpp/parameters` for more information on these parameters.
+see :ref:`the input parameter section <running-cpp-parameters>` for more information.
 
 Read raw data
 -------------

Docs/source/coc.rst

@@ -1,5 +1,7 @@
-Visualizing back-transformed diagnostics
-========================================
+.. _dataanalysis-btd:
+
+Back-Transformed Diagnostics
+============================
 
 When running a simulation in a boosted frame, WarpX has the capability to
 back-transform the simulation results to the laboratory frame of reference, which