refactor: Merge branch 'dev' into fix_mvbs

Sync changes in dev to the branch
OSOceanAcoustics · Aug 25, 2023 · c75d9a2 · c75d9a2
2 parents f30df73 + 183cf7a
commit c75d9a2
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Showing 28 changed files with 13,799 additions and 2,361 deletions.
diff --git a/docs/source/_config.yml b/docs/source/_config.yml
@@ -18,8 +18,8 @@ execute:
 #     targetname: book.tex
 
 # Add a bibtex file so that we can create citations
-# bibtex_bibfiles:
-#   - references.bib
+bibtex_bibfiles:
+  - references.bib
 
 # Information about where the book exists on the web
 repository:
@@ -39,13 +39,15 @@ sphinx:
     'sphinx_automodapi.automodapi',
     'numpydoc',
     # 'sphinx.ext.autodoc',
+    'sphinxcontrib.bibtex',
     'sphinx.ext.intersphinx',
     'sphinx.ext.mathjax',
     'sphinx.ext.ifconfig',
     'sphinx.ext.githubpages',
     'sphinxcontrib.mermaid'
   ]
-  # config:
+  config:
+    bibtex_reference_style: author_year
   #   # https://github.com/executablebooks/jupyter-book/issues/1186
   #   # https://sphinx-book-theme.readthedocs.io/en/latest/customize/sidebar-secondary.html
   #   html_theme_options:

diff --git a/docs/source/_toc.yml b/docs/source/_toc.yml
@@ -12,13 +12,17 @@ parts:
   chapters:
   - file: convert
   - file: open-converted
-  - file: process
   - file: data-format
-    title: Data formats
+    title: Raw data formats
     sections:
+    - file: data-format-sonarnetcdf4
     - file: data-format-raw
-    - file: data-format-processed
     - file: data-format-5to6
+  - file: data-proc
+    title: Data processing
+    sections:
+    - file: data-proc-func
+    - file: data-proc-additional
   - file: viz
   - file: processing-levels
     title: Processing levels

diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -8,7 +8,7 @@ API components that most users will interact with.
    In echopype versions prior to 0.5.0, the API in this page focused
    on the ``convert`` and ``process`` subpackages. See the
    `0.4.1 API page <https://echopype.readthedocs.io/en/v0.4.1/api.html>`_
-   if you're using a previous release. That workflow is being deprecated.
+   if you're using a previous release. That workflow is now removed.
 
 **Content**
 
@@ -72,6 +72,13 @@ commongrid
    :no-inheritance-diagram:
    :no-heading:
 
+consolidate
+^^^^^^^^^^
+
+.. automodapi:: echopype.consolidate
+   :no-inheritance-diagram:
+   :no-heading:
+
 qc
 ^^^
 
@@ -86,6 +93,14 @@ mask
    :no-inheritance-diagram:
    :no-heading:
 
+metrics
+^^^^^^^
+
+.. automodapi:: echopype.metrics
+   :no-inheritance-diagram:
+   :no-heading:
+
+
 Utilities
 ---------
 

diff --git a/docs/source/data-format-processed.ipynb b/docs/source/data-format-processed.ipynb