diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 4cd89fbd2..2f6c89e5a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -209,3 +209,23 @@ jobs:
     with:
       docs-directory: docs/
       pip-install-target: .[dev]
+
+  check-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v5
+
+      - uses: actions/checkout@v4
+
+      - run: pip install .[dev]
+
+      - run: ./devel/generate-developer-api-docs
+
+      - name: Check for changes
+        run: |
+          if [[ -n $(git status --porcelain) ]]; then
+            git add .
+            git diff --staged >&2
+            echo "There are changes to the developer API docs. Please regenerate, commit, and push the changes." >&2
+            exit 1
+          fi
diff --git a/augur/argparse_.py b/augur/argparse_.py
index 6a535b430..6f0ee5e72 100644
--- a/augur/argparse_.py
+++ b/augur/argparse_.py
@@ -40,7 +40,7 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
         The special subparsers action object created by the parent parser
         via `parser.add_subparsers()`.
 
-    commands: list[ModuleType]
+    commands: list[types.ModuleType]
         A list of modules that are commands that require their own subparser.
         Each module is required to have a `register_parser` function to add its own
         subparser and arguments.
diff --git a/augur/curate/__init__.py b/augur/curate/__init__.py
index c8aacbbc5..d7afd9f3e 100644
--- a/augur/curate/__init__.py
+++ b/augur/curate/__init__.py
@@ -37,7 +37,7 @@ def create_shared_parser():
     that are intended to be shared across the subcommands.
 
     Note that any options strings used here cannot be used in individual subcommand
-    subparsers unless the subparser specifically sets `conflict_handler='resolve'`²,
+    subparsers unless the subparser specifically sets `conflict_handler='resolve'` ²,
     then the subparser option will override the option defined here.
 
     Based on https://stackoverflow.com/questions/23296695/permit-argparse-global-flags-after-subcommand/23296874#23296874
diff --git a/augur/curate/apply_geolocation_rules.py b/augur/curate/apply_geolocation_rules.py
index 7c167a9cf..e14974890 100644
--- a/augur/curate/apply_geolocation_rules.py
+++ b/augur/curate/apply_geolocation_rules.py
@@ -15,6 +15,9 @@ def load_geolocation_rules(geolocation_rules_file):
     """
     Loads the geolocation rules from the provided *geolocation_rules_file*.
     Returns the rules as a dict:
+
+.. code-block:: text
+
     {
         regions: {
             countries: {
diff --git a/devel/generate-developer-api-docs b/devel/generate-developer-api-docs
new file mode 100755
index 000000000..235464bdb
--- /dev/null
+++ b/devel/generate-developer-api-docs
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+sphinx-apidoc \
+  --force \
+  --module-first \
+  --separate \
+  --no-toc \
+  --output-dir docs/api/developer \
+  augur
diff --git a/docs/api/developer/augur.align.rst b/docs/api/developer/augur.align.rst
index 08c87d3c1..8d6393108 100644
--- a/docs/api/developer/augur.align.rst
+++ b/docs/api/developer/augur.align.rst
@@ -1,5 +1,5 @@
-augur.align
-===========
+augur.align module
+==================
 
 .. automodule:: augur.align
    :members:
diff --git a/docs/api/developer/augur.ancestral.rst b/docs/api/developer/augur.ancestral.rst
index 4bae58280..8a25bd315 100644
--- a/docs/api/developer/augur.ancestral.rst
+++ b/docs/api/developer/augur.ancestral.rst
@@ -1,5 +1,5 @@
-augur.ancestral
-===============
+augur.ancestral module
+======================
 
 .. automodule:: augur.ancestral
    :members:
diff --git a/docs/api/developer/augur.argparse_.rst b/docs/api/developer/augur.argparse_.rst
new file mode 100644
index 000000000..e24668843
--- /dev/null
+++ b/docs/api/developer/augur.argparse_.rst
@@ -0,0 +1,7 @@
+augur.argparse\_ module
+=======================
+
+.. automodule:: augur.argparse_
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.clades.rst b/docs/api/developer/augur.clades.rst
index 34e5fa013..738727997 100644
--- a/docs/api/developer/augur.clades.rst
+++ b/docs/api/developer/augur.clades.rst
@@ -1,5 +1,5 @@
-augur.clades
-============
+augur.clades module
+===================
 
 .. automodule:: augur.clades
    :members:
diff --git a/docs/api/developer/augur.curate.abbreviate_authors.rst b/docs/api/developer/augur.curate.abbreviate_authors.rst
new file mode 100644
index 000000000..f41729bd0
--- /dev/null
+++ b/docs/api/developer/augur.curate.abbreviate_authors.rst
@@ -0,0 +1,7 @@
+augur.curate.abbreviate\_authors module
+=======================================
+
+.. automodule:: augur.curate.abbreviate_authors
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.apply_geolocation_rules.rst b/docs/api/developer/augur.curate.apply_geolocation_rules.rst
new file mode 100644
index 000000000..fa6e95c8e
--- /dev/null
+++ b/docs/api/developer/augur.curate.apply_geolocation_rules.rst
@@ -0,0 +1,7 @@
+augur.curate.apply\_geolocation\_rules module
+=============================================
+
+.. automodule:: augur.curate.apply_geolocation_rules
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.apply_record_annotations.rst b/docs/api/developer/augur.curate.apply_record_annotations.rst
new file mode 100644
index 000000000..8d360eade
--- /dev/null
+++ b/docs/api/developer/augur.curate.apply_record_annotations.rst
@@ -0,0 +1,7 @@
+augur.curate.apply\_record\_annotations module
+==============================================
+
+.. automodule:: augur.curate.apply_record_annotations
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.format_dates.rst b/docs/api/developer/augur.curate.format_dates.rst
new file mode 100644
index 000000000..35e697563
--- /dev/null
+++ b/docs/api/developer/augur.curate.format_dates.rst
@@ -0,0 +1,7 @@
+augur.curate.format\_dates module
+=================================
+
+.. automodule:: augur.curate.format_dates
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.format_dates_directives.rst b/docs/api/developer/augur.curate.format_dates_directives.rst
new file mode 100644
index 000000000..80891975d
--- /dev/null
+++ b/docs/api/developer/augur.curate.format_dates_directives.rst
@@ -0,0 +1,7 @@
+augur.curate.format\_dates\_directives module
+=============================================
+
+.. automodule:: augur.curate.format_dates_directives
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.normalize_strings.rst b/docs/api/developer/augur.curate.normalize_strings.rst
new file mode 100644
index 000000000..19de55aa0
--- /dev/null
+++ b/docs/api/developer/augur.curate.normalize_strings.rst
@@ -0,0 +1,7 @@
+augur.curate.normalize\_strings module
+======================================
+
+.. automodule:: augur.curate.normalize_strings
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.parse_genbank_location.rst b/docs/api/developer/augur.curate.parse_genbank_location.rst
new file mode 100644
index 000000000..cbad6ee2b
--- /dev/null
+++ b/docs/api/developer/augur.curate.parse_genbank_location.rst
@@ -0,0 +1,7 @@
+augur.curate.parse\_genbank\_location module
+============================================
+
+.. automodule:: augur.curate.parse_genbank_location
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.passthru.rst b/docs/api/developer/augur.curate.passthru.rst
new file mode 100644
index 000000000..87e481733
--- /dev/null
+++ b/docs/api/developer/augur.curate.passthru.rst
@@ -0,0 +1,7 @@
+augur.curate.passthru module
+============================
+
+.. automodule:: augur.curate.passthru
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.rst b/docs/api/developer/augur.curate.rst
new file mode 100644
index 000000000..529991e6f
--- /dev/null
+++ b/docs/api/developer/augur.curate.rst
@@ -0,0 +1,24 @@
+augur.curate package
+====================
+
+.. automodule:: augur.curate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   augur.curate.abbreviate_authors
+   augur.curate.apply_geolocation_rules
+   augur.curate.apply_record_annotations
+   augur.curate.format_dates
+   augur.curate.format_dates_directives
+   augur.curate.normalize_strings
+   augur.curate.parse_genbank_location
+   augur.curate.passthru
+   augur.curate.titlecase
+   augur.curate.transform_strain_name
diff --git a/docs/api/developer/augur.curate.titlecase.rst b/docs/api/developer/augur.curate.titlecase.rst
new file mode 100644
index 000000000..3580664a8
--- /dev/null
+++ b/docs/api/developer/augur.curate.titlecase.rst
@@ -0,0 +1,7 @@
+augur.curate.titlecase module
+=============================
+
+.. automodule:: augur.curate.titlecase
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.curate.transform_strain_name.rst b/docs/api/developer/augur.curate.transform_strain_name.rst
new file mode 100644
index 000000000..60cac247d
--- /dev/null
+++ b/docs/api/developer/augur.curate.transform_strain_name.rst
@@ -0,0 +1,7 @@
+augur.curate.transform\_strain\_name module
+===========================================
+
+.. automodule:: augur.curate.transform_strain_name
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.data.rst b/docs/api/developer/augur.data.rst
new file mode 100644
index 000000000..6594d4b8c
--- /dev/null
+++ b/docs/api/developer/augur.data.rst
@@ -0,0 +1,7 @@
+augur.data package
+==================
+
+.. automodule:: augur.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.dates.ambiguous_date.rst b/docs/api/developer/augur.dates.ambiguous_date.rst
index 2471f3e8f..8d807ef38 100644
--- a/docs/api/developer/augur.dates.ambiguous_date.rst
+++ b/docs/api/developer/augur.dates.ambiguous_date.rst
@@ -1,5 +1,5 @@
-augur.dates.ambiguous\_date
-=======================================
+augur.dates.ambiguous\_date module
+==================================
 
 .. automodule:: augur.dates.ambiguous_date
    :members:
diff --git a/docs/api/developer/augur.dates.errors.rst b/docs/api/developer/augur.dates.errors.rst
index d4da219fc..a7fae8e9d 100644
--- a/docs/api/developer/augur.dates.errors.rst
+++ b/docs/api/developer/augur.dates.errors.rst
@@ -1,5 +1,5 @@
-augur.dates.errors
-==================
+augur.dates.errors module
+=========================
 
 .. automodule:: augur.dates.errors
    :members:
diff --git a/docs/api/developer/augur.dates.rst b/docs/api/developer/augur.dates.rst
index 5f314f3ce..5f73f4cc0 100644
--- a/docs/api/developer/augur.dates.rst
+++ b/docs/api/developer/augur.dates.rst
@@ -1,12 +1,16 @@
-augur.dates
-===========
+augur.dates package
+===================
 
 .. automodule:: augur.dates
    :members:
    :undoc-members:
    :show-inheritance:
 
+Submodules
+----------
+
 .. toctree::
+   :maxdepth: 4
 
    augur.dates.ambiguous_date
    augur.dates.errors
diff --git a/docs/api/developer/augur.distance.rst b/docs/api/developer/augur.distance.rst
index a93e87060..849f73212 100644
--- a/docs/api/developer/augur.distance.rst
+++ b/docs/api/developer/augur.distance.rst
@@ -1,5 +1,5 @@
-augur.distance
-==============
+augur.distance module
+=====================
 
 .. automodule:: augur.distance
    :members:
diff --git a/docs/api/developer/augur.errors.rst b/docs/api/developer/augur.errors.rst
index b35076ca3..3b6964961 100644
--- a/docs/api/developer/augur.errors.rst
+++ b/docs/api/developer/augur.errors.rst
@@ -1,5 +1,5 @@
-augur.errors
-============
+augur.errors module
+===================
 
 .. automodule:: augur.errors
    :members:
diff --git a/docs/api/developer/augur.export.rst b/docs/api/developer/augur.export.rst
index 1941432a8..cbfd13529 100644
--- a/docs/api/developer/augur.export.rst
+++ b/docs/api/developer/augur.export.rst
@@ -1,5 +1,5 @@
-augur.export
-============
+augur.export module
+===================
 
 .. automodule:: augur.export
    :members:
diff --git a/docs/api/developer/augur.export_v1.rst b/docs/api/developer/augur.export_v1.rst
index f743ee776..7cde9fb15 100644
--- a/docs/api/developer/augur.export_v1.rst
+++ b/docs/api/developer/augur.export_v1.rst
@@ -1,5 +1,5 @@
-augur.export\_v1
-================
+augur.export\_v1 module
+=======================
 
 .. automodule:: augur.export_v1
    :members:
diff --git a/docs/api/developer/augur.export_v2.rst b/docs/api/developer/augur.export_v2.rst
index 885607702..d08be029a 100644
--- a/docs/api/developer/augur.export_v2.rst
+++ b/docs/api/developer/augur.export_v2.rst
@@ -1,5 +1,5 @@
-augur.export\_v2
-================
+augur.export\_v2 module
+=======================
 
 .. automodule:: augur.export_v2
    :members:
diff --git a/docs/api/developer/augur.filenames.rst b/docs/api/developer/augur.filenames.rst
index 0eedd7018..34be1fd42 100644
--- a/docs/api/developer/augur.filenames.rst
+++ b/docs/api/developer/augur.filenames.rst
@@ -1,5 +1,5 @@
-augur.filenames
-===============
+augur.filenames module
+======================
 
 .. automodule:: augur.filenames
    :members:
diff --git a/docs/api/developer/augur.filter._run.rst b/docs/api/developer/augur.filter._run.rst
deleted file mode 100644
index 989429705..000000000
--- a/docs/api/developer/augur.filter._run.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-augur.filter._run
-=================
-
-.. automodule:: augur.filter._run
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/api/developer/augur.filter.constants.rst b/docs/api/developer/augur.filter.constants.rst
new file mode 100644
index 000000000..d0551e5d5
--- /dev/null
+++ b/docs/api/developer/augur.filter.constants.rst
@@ -0,0 +1,7 @@
+augur.filter.constants module
+=============================
+
+.. automodule:: augur.filter.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.filter.include_exclude_rules.rst b/docs/api/developer/augur.filter.include_exclude_rules.rst
index 07801f93d..6c62dd6b1 100644
--- a/docs/api/developer/augur.filter.include_exclude_rules.rst
+++ b/docs/api/developer/augur.filter.include_exclude_rules.rst
@@ -1,5 +1,5 @@
-augur.filter.include_exclude_rules
-==================================
+augur.filter.include\_exclude\_rules module
+===========================================
 
 .. automodule:: augur.filter.include_exclude_rules
    :members:
diff --git a/docs/api/developer/augur.filter.io.rst b/docs/api/developer/augur.filter.io.rst
index e86915ce3..6e74a4db7 100644
--- a/docs/api/developer/augur.filter.io.rst
+++ b/docs/api/developer/augur.filter.io.rst
@@ -1,5 +1,5 @@
-augur.filter.io
-===============
+augur.filter.io module
+======================
 
 .. automodule:: augur.filter.io
    :members:
diff --git a/docs/api/developer/augur.filter.rst b/docs/api/developer/augur.filter.rst
index c8fab2d7e..44942a2fd 100644
--- a/docs/api/developer/augur.filter.rst
+++ b/docs/api/developer/augur.filter.rst
@@ -1,14 +1,18 @@
-augur.filter
-============
+augur.filter package
+====================
 
 .. automodule:: augur.filter
    :members:
    :undoc-members:
    :show-inheritance:
 
+Submodules
+----------
+
 .. toctree::
+   :maxdepth: 4
 
-   augur.filter._run
+   augur.filter.constants
    augur.filter.include_exclude_rules
    augur.filter.io
    augur.filter.subsample
diff --git a/docs/api/developer/augur.filter.subsample.rst b/docs/api/developer/augur.filter.subsample.rst
index 64bc10d7b..af826b05d 100644
--- a/docs/api/developer/augur.filter.subsample.rst
+++ b/docs/api/developer/augur.filter.subsample.rst
@@ -1,5 +1,5 @@
-augur.filter.subsample
-======================
+augur.filter.subsample module
+=============================
 
 .. automodule:: augur.filter.subsample
    :members:
diff --git a/docs/api/developer/augur.filter.validate_arguments.rst b/docs/api/developer/augur.filter.validate_arguments.rst
index a91c9d11d..af5fe79ff 100644
--- a/docs/api/developer/augur.filter.validate_arguments.rst
+++ b/docs/api/developer/augur.filter.validate_arguments.rst
@@ -1,5 +1,5 @@
-augur.filter.validate_arguments
-===============================
+augur.filter.validate\_arguments module
+=======================================
 
 .. automodule:: augur.filter.validate_arguments
    :members:
diff --git a/docs/api/developer/augur.frequencies.rst b/docs/api/developer/augur.frequencies.rst
index 266a564a5..e45b7fdd4 100644
--- a/docs/api/developer/augur.frequencies.rst
+++ b/docs/api/developer/augur.frequencies.rst
@@ -1,5 +1,5 @@
-augur.frequencies
-=================
+augur.frequencies module
+========================
 
 .. automodule:: augur.frequencies
    :members:
diff --git a/docs/api/developer/augur.frequency_estimators.rst b/docs/api/developer/augur.frequency_estimators.rst
index b48df2f28..0d1ec6489 100644
--- a/docs/api/developer/augur.frequency_estimators.rst
+++ b/docs/api/developer/augur.frequency_estimators.rst
@@ -1,5 +1,5 @@
-augur.frequency\_estimators
-===========================
+augur.frequency\_estimators module
+==================================
 
 .. automodule:: augur.frequency_estimators
    :members:
diff --git a/docs/api/developer/augur.import.rst b/docs/api/developer/augur.import.rst
deleted file mode 100644
index d53159955..000000000
--- a/docs/api/developer/augur.import.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-augur.import
-============
-
-.. automodule:: augur.import_
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-.. toctree::
-
-   augur.import.beast
diff --git a/docs/api/developer/augur.import.beast.rst b/docs/api/developer/augur.import_.beast.rst
similarity index 61%
rename from docs/api/developer/augur.import.beast.rst
rename to docs/api/developer/augur.import_.beast.rst
index 72910cfaa..c33a9c9c8 100644
--- a/docs/api/developer/augur.import.beast.rst
+++ b/docs/api/developer/augur.import_.beast.rst
@@ -1,5 +1,5 @@
-augur.import.beast
-==================
+augur.import\_.beast module
+===========================
 
 .. automodule:: augur.import_.beast
    :members:
diff --git a/docs/api/developer/augur.import_.rst b/docs/api/developer/augur.import_.rst
new file mode 100644
index 000000000..741f610bf
--- /dev/null
+++ b/docs/api/developer/augur.import_.rst
@@ -0,0 +1,15 @@
+augur.import\_ package
+======================
+
+.. automodule:: augur.import_
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   augur.import_.beast
diff --git a/docs/api/developer/augur.index.rst b/docs/api/developer/augur.index.rst
index 65f8c9c9d..f8b1f4a10 100644
--- a/docs/api/developer/augur.index.rst
+++ b/docs/api/developer/augur.index.rst
@@ -1,5 +1,5 @@
-augur.index
-===========
+augur.index module
+==================
 
 .. automodule:: augur.index
    :members:
diff --git a/docs/api/developer/augur.io.file.rst b/docs/api/developer/augur.io.file.rst
index 82b052327..54e8056a0 100644
--- a/docs/api/developer/augur.io.file.rst
+++ b/docs/api/developer/augur.io.file.rst
@@ -1,5 +1,5 @@
-augur.io.file
-=============
+augur.io.file module
+====================
 
 .. automodule:: augur.io.file
    :members:
diff --git a/docs/api/developer/augur.io.json.rst b/docs/api/developer/augur.io.json.rst
index ee0811783..b6adbe1d8 100644
--- a/docs/api/developer/augur.io.json.rst
+++ b/docs/api/developer/augur.io.json.rst
@@ -1,5 +1,5 @@
-augur.io.json
-=============
+augur.io.json module
+====================
 
 .. automodule:: augur.io.json
    :members:
diff --git a/docs/api/developer/augur.io.metadata.rst b/docs/api/developer/augur.io.metadata.rst
index bdc462596..caaa0c910 100644
--- a/docs/api/developer/augur.io.metadata.rst
+++ b/docs/api/developer/augur.io.metadata.rst
@@ -1,5 +1,5 @@
-augur.io.metadata
-=================
+augur.io.metadata module
+========================
 
 .. automodule:: augur.io.metadata
    :members:
diff --git a/docs/api/developer/augur.io.print.rst b/docs/api/developer/augur.io.print.rst
index 536977d3e..6f73b5a71 100644
--- a/docs/api/developer/augur.io.print.rst
+++ b/docs/api/developer/augur.io.print.rst
@@ -1,5 +1,5 @@
-augur.io.print
-==============
+augur.io.print module
+=====================
 
 .. automodule:: augur.io.print
    :members:
diff --git a/docs/api/developer/augur.io.rst b/docs/api/developer/augur.io.rst
index 13c044f60..d6db9a2b2 100644
--- a/docs/api/developer/augur.io.rst
+++ b/docs/api/developer/augur.io.rst
@@ -1,13 +1,16 @@
-augur.io
-========
+augur.io package
+================
 
 .. automodule:: augur.io
    :members:
    :undoc-members:
    :show-inheritance:
-   :noindex:
+
+Submodules
+----------
 
 .. toctree::
+   :maxdepth: 4
 
    augur.io.file
    augur.io.json
@@ -15,4 +18,5 @@ augur.io
    augur.io.print
    augur.io.sequences
    augur.io.shell_command_runner
+   augur.io.strains
    augur.io.vcf
diff --git a/docs/api/developer/augur.io.sequences.rst b/docs/api/developer/augur.io.sequences.rst
index 1ed60dd4b..da25ac1c9 100644
--- a/docs/api/developer/augur.io.sequences.rst
+++ b/docs/api/developer/augur.io.sequences.rst
@@ -1,5 +1,5 @@
-augur.io.sequences
-==================
+augur.io.sequences module
+=========================
 
 .. automodule:: augur.io.sequences
    :members:
diff --git a/docs/api/developer/augur.io.shell_command_runner.rst b/docs/api/developer/augur.io.shell_command_runner.rst
index b77af7ab9..97f286186 100644
--- a/docs/api/developer/augur.io.shell_command_runner.rst
+++ b/docs/api/developer/augur.io.shell_command_runner.rst
@@ -1,5 +1,5 @@
-augur.io.shell_command_runner
-=============================
+augur.io.shell\_command\_runner module
+======================================
 
 .. automodule:: augur.io.shell_command_runner
    :members:
diff --git a/docs/api/developer/augur.io.strains.rst b/docs/api/developer/augur.io.strains.rst
new file mode 100644
index 000000000..92133034e
--- /dev/null
+++ b/docs/api/developer/augur.io.strains.rst
@@ -0,0 +1,7 @@
+augur.io.strains module
+=======================
+
+.. automodule:: augur.io.strains
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.io.vcf.rst b/docs/api/developer/augur.io.vcf.rst
index d75bddf1d..16ee195b1 100644
--- a/docs/api/developer/augur.io.vcf.rst
+++ b/docs/api/developer/augur.io.vcf.rst
@@ -1,5 +1,5 @@
-augur.io.vcf
-============
+augur.io.vcf module
+===================
 
 .. automodule:: augur.io.vcf
    :members:
diff --git a/docs/api/developer/augur.lbi.rst b/docs/api/developer/augur.lbi.rst
index 70599bde1..c58ef36cc 100644
--- a/docs/api/developer/augur.lbi.rst
+++ b/docs/api/developer/augur.lbi.rst
@@ -1,5 +1,5 @@
-augur.lbi
-=========
+augur.lbi module
+================
 
 .. automodule:: augur.lbi
    :members:
diff --git a/docs/api/developer/augur.mask.rst b/docs/api/developer/augur.mask.rst
index 8d1f5c250..27dc7e357 100644
--- a/docs/api/developer/augur.mask.rst
+++ b/docs/api/developer/augur.mask.rst
@@ -1,5 +1,5 @@
-augur.mask
-==========
+augur.mask module
+=================
 
 .. automodule:: augur.mask
    :members:
diff --git a/docs/api/developer/augur.measurements.concat.rst b/docs/api/developer/augur.measurements.concat.rst
index 1a257f323..a446e4e57 100644
--- a/docs/api/developer/augur.measurements.concat.rst
+++ b/docs/api/developer/augur.measurements.concat.rst
@@ -1,5 +1,5 @@
-augur.measurements.concat
-=========================
+augur.measurements.concat module
+================================
 
 .. automodule:: augur.measurements.concat
    :members:
diff --git a/docs/api/developer/augur.measurements.export.rst b/docs/api/developer/augur.measurements.export.rst
index 8850aea05..b0ac57198 100644
--- a/docs/api/developer/augur.measurements.export.rst
+++ b/docs/api/developer/augur.measurements.export.rst
@@ -1,5 +1,5 @@
-augur.measurements.export
-=========================
+augur.measurements.export module
+================================
 
 .. automodule:: augur.measurements.export
    :members:
diff --git a/docs/api/developer/augur.measurements.rst b/docs/api/developer/augur.measurements.rst
index e9f59e79f..a7e32f7c1 100644
--- a/docs/api/developer/augur.measurements.rst
+++ b/docs/api/developer/augur.measurements.rst
@@ -1,12 +1,16 @@
-augur.measurements
-==================
+augur.measurements package
+==========================
 
 .. automodule:: augur.measurements
    :members:
    :undoc-members:
    :show-inheritance:
 
+Submodules
+----------
+
 .. toctree::
+   :maxdepth: 4
 
    augur.measurements.concat
    augur.measurements.export
diff --git a/docs/api/developer/augur.parse.rst b/docs/api/developer/augur.parse.rst
index 071c89262..fb1511e75 100644
--- a/docs/api/developer/augur.parse.rst
+++ b/docs/api/developer/augur.parse.rst
@@ -1,5 +1,5 @@
-augur.parse
-===========
+augur.parse module
+==================
 
 .. automodule:: augur.parse
    :members:
diff --git a/docs/api/developer/augur.reconstruct_sequences.rst b/docs/api/developer/augur.reconstruct_sequences.rst
index f10ed1632..deb7ec700 100644
--- a/docs/api/developer/augur.reconstruct_sequences.rst
+++ b/docs/api/developer/augur.reconstruct_sequences.rst
@@ -1,5 +1,5 @@
-augur.reconstruct\_sequences
-============================
+augur.reconstruct\_sequences module
+===================================
 
 .. automodule:: augur.reconstruct_sequences
    :members:
diff --git a/docs/api/developer/augur.refine.rst b/docs/api/developer/augur.refine.rst
index d3a036248..409b23939 100644
--- a/docs/api/developer/augur.refine.rst
+++ b/docs/api/developer/augur.refine.rst
@@ -1,5 +1,5 @@
-augur.refine
-============
+augur.refine module
+===================
 
 .. automodule:: augur.refine
    :members:
diff --git a/docs/api/developer/augur.rst b/docs/api/developer/augur.rst
index d7fc72359..1afda35bc 100644
--- a/docs/api/developer/augur.rst
+++ b/docs/api/developer/augur.rst
@@ -1,32 +1,47 @@
-augur
-=====
+augur package
+=============
 
 .. automodule:: augur
    :members:
    :undoc-members:
    :show-inheritance:
 
+Subpackages
+-----------
+
 .. toctree::
+   :maxdepth: 4
+
+   augur.curate
+   augur.data
+   augur.dates
+   augur.filter
+   augur.import_
+   augur.io
+   augur.measurements
+   augur.util_support
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
 
    augur.align
    augur.ancestral
+   augur.argparse_
    augur.clades
-   augur.dates
    augur.distance
    augur.errors
    augur.export
    augur.export_v1
    augur.export_v2
    augur.filenames
-   augur.filter
    augur.frequencies
    augur.frequency_estimators
-   augur.import
    augur.index
-   augur.io
    augur.lbi
    augur.mask
-   augur.measurements
    augur.parse
    augur.reconstruct_sequences
    augur.refine
@@ -37,7 +52,6 @@ augur
    augur.translate
    augur.tree
    augur.types
-   augur.util_support
    augur.utils
    augur.validate
    augur.validate_export
diff --git a/docs/api/developer/augur.sequence_traits.rst b/docs/api/developer/augur.sequence_traits.rst
index 33316abba..39f2faccf 100644
--- a/docs/api/developer/augur.sequence_traits.rst
+++ b/docs/api/developer/augur.sequence_traits.rst
@@ -1,5 +1,5 @@
-augur.sequence\_traits
-======================
+augur.sequence\_traits module
+=============================
 
 .. automodule:: augur.sequence_traits
    :members:
diff --git a/docs/api/developer/augur.titer_model.rst b/docs/api/developer/augur.titer_model.rst
index 404e917ab..405093084 100644
--- a/docs/api/developer/augur.titer_model.rst
+++ b/docs/api/developer/augur.titer_model.rst
@@ -1,5 +1,5 @@
-augur.titer\_model
-==================
+augur.titer\_model module
+=========================
 
 .. automodule:: augur.titer_model
    :members:
diff --git a/docs/api/developer/augur.titers.rst b/docs/api/developer/augur.titers.rst
index fcb8dc534..a2d0bbedf 100644
--- a/docs/api/developer/augur.titers.rst
+++ b/docs/api/developer/augur.titers.rst
@@ -1,5 +1,5 @@
-augur.titers
-============
+augur.titers module
+===================
 
 .. automodule:: augur.titers
    :members:
diff --git a/docs/api/developer/augur.traits.rst b/docs/api/developer/augur.traits.rst
index ddc2cd024..912997a4d 100644
--- a/docs/api/developer/augur.traits.rst
+++ b/docs/api/developer/augur.traits.rst
@@ -1,5 +1,5 @@
-augur.traits
-============
+augur.traits module
+===================
 
 .. automodule:: augur.traits
    :members:
diff --git a/docs/api/developer/augur.translate.rst b/docs/api/developer/augur.translate.rst
index af5f0d647..8303ece8a 100644
--- a/docs/api/developer/augur.translate.rst
+++ b/docs/api/developer/augur.translate.rst
@@ -1,5 +1,5 @@
-augur.translate
-===============
+augur.translate module
+======================
 
 .. automodule:: augur.translate
    :members:
diff --git a/docs/api/developer/augur.tree.rst b/docs/api/developer/augur.tree.rst
index 6611ca145..59db44a14 100644
--- a/docs/api/developer/augur.tree.rst
+++ b/docs/api/developer/augur.tree.rst
@@ -1,5 +1,5 @@
-augur.tree
-==========
+augur.tree module
+=================
 
 .. automodule:: augur.tree
    :members:
diff --git a/docs/api/developer/augur.types.rst b/docs/api/developer/augur.types.rst
index d37872b71..c64003bdd 100644
--- a/docs/api/developer/augur.types.rst
+++ b/docs/api/developer/augur.types.rst
@@ -1,5 +1,5 @@
-augur.types
-===========
+augur.types module
+==================
 
 .. automodule:: augur.types
    :members:
diff --git a/docs/api/developer/augur.util_support.color_parser.rst b/docs/api/developer/augur.util_support.color_parser.rst
index 9f93912fd..89a47b1af 100644
--- a/docs/api/developer/augur.util_support.color_parser.rst
+++ b/docs/api/developer/augur.util_support.color_parser.rst
@@ -1,5 +1,5 @@
-augur.util\_support.color\_parser
-=================================
+augur.util\_support.color\_parser module
+========================================
 
 .. automodule:: augur.util_support.color_parser
    :members:
diff --git a/docs/api/developer/augur.util_support.color_parser_line.rst b/docs/api/developer/augur.util_support.color_parser_line.rst
index 737977f0b..264fe69d3 100644
--- a/docs/api/developer/augur.util_support.color_parser_line.rst
+++ b/docs/api/developer/augur.util_support.color_parser_line.rst
@@ -1,5 +1,5 @@
-augur.util\_support.color\_parser\_line
-=======================================
+augur.util\_support.color\_parser\_line module
+==============================================
 
 .. automodule:: augur.util_support.color_parser_line
    :members:
diff --git a/docs/api/developer/augur.util_support.node_data.rst b/docs/api/developer/augur.util_support.node_data.rst
index 017478b8a..69b4368ab 100644
--- a/docs/api/developer/augur.util_support.node_data.rst
+++ b/docs/api/developer/augur.util_support.node_data.rst
@@ -1,5 +1,5 @@
-augur.util\_support.node\_data
-==============================
+augur.util\_support.node\_data module
+=====================================
 
 .. automodule:: augur.util_support.node_data
    :members:
diff --git a/docs/api/developer/augur.util_support.node_data_file.rst b/docs/api/developer/augur.util_support.node_data_file.rst
index c4f59e1c2..568e9b885 100644
--- a/docs/api/developer/augur.util_support.node_data_file.rst
+++ b/docs/api/developer/augur.util_support.node_data_file.rst
@@ -1,5 +1,5 @@
-augur.util\_support.node\_data\_file
-====================================
+augur.util\_support.node\_data\_file module
+===========================================
 
 .. automodule:: augur.util_support.node_data_file
    :members:
diff --git a/docs/api/developer/augur.util_support.node_data_reader.rst b/docs/api/developer/augur.util_support.node_data_reader.rst
index 5c2c4df19..ce85ee592 100644
--- a/docs/api/developer/augur.util_support.node_data_reader.rst
+++ b/docs/api/developer/augur.util_support.node_data_reader.rst
@@ -1,5 +1,5 @@
-augur.util\_support.node\_data\_reader
-======================================
+augur.util\_support.node\_data\_reader module
+=============================================
 
 .. automodule:: augur.util_support.node_data_reader
    :members:
diff --git a/docs/api/developer/augur.util_support.rst b/docs/api/developer/augur.util_support.rst
index 0c20d9f1e..3eaf5bd77 100644
--- a/docs/api/developer/augur.util_support.rst
+++ b/docs/api/developer/augur.util_support.rst
@@ -1,12 +1,16 @@
-augur.util\_support
-===================
+augur.util\_support package
+===========================
 
 .. automodule:: augur.util_support
    :members:
    :undoc-members:
    :show-inheritance:
 
+Submodules
+----------
+
 .. toctree::
+   :maxdepth: 4
 
    augur.util_support.color_parser
    augur.util_support.color_parser_line
diff --git a/docs/api/developer/augur.utils.rst b/docs/api/developer/augur.utils.rst
index 4c6e363ad..fc0e6b8c4 100644
--- a/docs/api/developer/augur.utils.rst
+++ b/docs/api/developer/augur.utils.rst
@@ -1,5 +1,5 @@
-augur.utils
-===========
+augur.utils module
+==================
 
 .. automodule:: augur.utils
    :members:
diff --git a/docs/api/developer/augur.validate.rst b/docs/api/developer/augur.validate.rst
index 7a299f64b..9bace5148 100644
--- a/docs/api/developer/augur.validate.rst
+++ b/docs/api/developer/augur.validate.rst
@@ -1,5 +1,5 @@
-augur.validate
-==============
+augur.validate module
+=====================
 
 .. automodule:: augur.validate
    :members:
diff --git a/docs/api/developer/augur.validate_export.rst b/docs/api/developer/augur.validate_export.rst
index 33e225e6d..5cc90837b 100644
--- a/docs/api/developer/augur.validate_export.rst
+++ b/docs/api/developer/augur.validate_export.rst
@@ -1,5 +1,5 @@
-augur.validate\_export
-======================
+augur.validate\_export module
+=============================
 
 .. automodule:: augur.validate_export
    :members:
diff --git a/docs/api/developer/augur.version.rst b/docs/api/developer/augur.version.rst
index 7ee6db25b..f9e59e43a 100644
--- a/docs/api/developer/augur.version.rst
+++ b/docs/api/developer/augur.version.rst
@@ -1,5 +1,5 @@
-augur.version
-=============
+augur.version module
+====================
 
 .. automodule:: augur.version
    :members:
diff --git a/docs/api/public/augur.io.rst b/docs/api/public/augur.io.rst
index 4b9b6880f..36d0fcf8c 100644
--- a/docs/api/public/augur.io.rst
+++ b/docs/api/public/augur.io.rst
@@ -8,3 +8,4 @@ augur.io
    :imported-members:
    :undoc-members:
    :show-inheritance:
+   :noindex:
diff --git a/docs/conf.py b/docs/conf.py
index b072803fc..1a97a5d65 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -131,6 +131,10 @@ def prose_list(items):
      # resolved by intersphinx for a proper link.
      ("py:class", "json.decoder.JSONDecodeError"),
      ("py:class", "json.encoder.JSONEncoder"),
+
+     # This class can't be referenced.
+     # <https://github.com/python/cpython/issues/101503>
+     ("py:class", "argparse._SubParsersAction"),
 ]
 
 # -- Cross-project references ------------------------------------------------
diff --git a/docs/contribute/DEV_DOCS.md b/docs/contribute/DEV_DOCS.md
index 0564058c1..4fc9598ec 100644
--- a/docs/contribute/DEV_DOCS.md
+++ b/docs/contribute/DEV_DOCS.md
@@ -357,11 +357,11 @@ Sphinx can build other formats, such as epub. To see other available formats, ru
 make -C docs help
 ```
 
-To update the API documentation after adding or removing an augur submodule,
+To update the developer API documentation after adding or removing an augur submodule,
 autogenerate a new API file as follows.
 
 ```bash
-sphinx-apidoc -T -f -MeT -o docs/api augur
+./devel/generate-developer-api-docs
 ```
 
 To make doc rebuilds faster, Sphinx caches built documentation by default,