Fix docs deployment

.github/workflows/deploy_docs.yml

@@ -81,7 +81,9 @@ jobs:
 
       - name: Replace relative links in Doxygen include
         run: |
-          sed -i 's@acquire_zarr_c_api/acquire_zarr_c_api#@#@g' acquire-docs/site/api_reference/c_api/index.html
+          # Remove include statements from output files
+          sed -i '/<ul>/{N;N;/<ul>\n<li><code>#include \"zarr.types.h\"/d;}' acquire-docs/site/acquire_zarr_c_api/acquire_8zarr_8h/index.html
+          sed -i '/<ul>/{N;N;N;N;/<ul>\n<li><code>#include/d;}' acquire-docs/site/acquire_zarr_c_api/zarr_8types_8h/index.html
 
       - name: Deploy docs
         uses: peaceiris/actions-gh-pages@v3

docs/api_reference/Doxyfile

@@ -1,6 +1,6 @@
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "acquire_zarr_c_api"
-OUTPUT_DIRECTORY       = acquire_zarr_c_api
+OUTPUT_DIRECTORY       = docs/api_reference/acquire_zarr_c_api
 CREATE_SUBDIRS         = NO
 BRIEF_MEMBER_DESC      = YES
 REPEAT_BRIEF           = YES
@@ -10,7 +10,7 @@ FULL_PATH_NAMES        = YES
 SHORT_NAMES            = NO
 PYTHON_DOCSTRING       = YES
 INHERIT_DOCS           = YES
-SEPARATE_MEMBER_PAGES  = NO
+SEPARATE_MEMBER_PAGES  = YES
 MARKDOWN_SUPPORT       = YES
 TOC_INCLUDE_HEADINGS   = 6
 MARKDOWN_ID_STYLE      = DOXYGEN
@@ -41,7 +41,7 @@ SHOW_NAMESPACES        = YES
 QUIET                  = NO
 WARNINGS               = YES
 WARN_AS_ERROR          = NO
-INPUT                  = "../../acquire-zarr/include"
+INPUT                  = "../acquire-zarr/include"
 FILE_PATTERNS          = *.h
 RECURSIVE              = NO
 EXCLUDE_SYMLINKS       = NO
@@ -50,7 +50,7 @@ FILTER_SOURCE_FILES    = NO
 IMPLICIT_DIR_DOCS      = YES
 INLINE_SOURCES         = NO
 STRIP_CODE_COMMENTS    = YES
-GENERATE_HTML          = YES
+GENERATE_HTML          = NO
 HTML_OUTPUT            = html
 HTML_FILE_EXTENSION    = .html
 HTML_DYNAMIC_MENUS     = YES

docs/api_reference/c_api/index.md

@@ -0,0 +1,15 @@
+# Zarr Streaming C API Reference
+
+Information on the `acquire_zarr` C implementation and how to use it. Check
+https://github.com/acquire-project/acquire-zarr for more information.
+
+<div class="cards">
+    <div class="card">
+        <h4><pre>acquire.zarr.h</pre></h4>
+        <a href="../../acquire_zarr_c_api/acquire_8zarr_8h" class="button">acquire.zarr.h</a>
+    </div>
+    <div class="card">
+        <h4><pre>zarr.types.h</pre></h4>
+        <a href="../../acquire_zarr_c_api/zarr_8types_8h" class="button">zarr.types.h</a>
+    </div>
+</div>

docs/for_contributors/codebase.md

@@ -0,0 +1,7 @@
+# Contribute to codebase
+
+To contribute to the latest development version, build the libraries from source
+[following these instructions](https://github.com/acquire-project/acquire-zarr/blob/main/README.md#building) to enable
+adding and testing changes locally before making a
+[PR to the `acquire-zarr` repo](https://github.com/acquire-project/acquire-zarr). We especially welcome contributions of
+bug fixes, new features, and bindings in languages relevant to microscopy such as MATLAB and Julia.

mkdocs.yml

@@ -42,7 +42,10 @@ nav:
   - API Reference:
     - api_reference/index.md
     - api_reference/zarr_api.md
-    - api_reference/c_api.md
+    - Zarr Streaming C API Reference:
+      - api_reference/c_api/index.md
+      - acquire_zarr_c_api/acquire_8zarr_8h.md
+      - acquire_zarr_c_api/zarr_8types_8h.md
   # - Acquire Imaging:
   #   - acquire-imaging/index.md
   #   - Get Started: acquire-imaging/get_started.md
@@ -141,7 +144,7 @@ plugins:
       projects:
         acquire_zarr_c_api: # name of project must be alphanumeric + numbers (without spaces)
           src-dirs: ../acquire-zarr/include # path to source code (support multiple paths separated by space) => INPUT
-          full-doc: True # if you want to generate full documentation
+          full-doc: True # if you want to generate full documentation; i.e. root pages with all objects for a .h file
           doxy-cfg-file: docs/api_reference/Doxyfile
       save-api: docs/api_reference