Update docs to PyData Sphinx Theme and reorganize tabs

docs/conf.py

@@ -8,7 +8,7 @@
 
 sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../'))
-# sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath('../../'))
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
@@ -48,32 +48,34 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'karma_sphinx_theme'
+html_theme = 'pydata_sphinx_theme'
 html_static_path = ['_static']
 html_domain_indices = True
 html_use_index = True
 html_split_index = False
+html_show_sourcelink = False
+html_show_sphinx = True
 #
-# html_theme_options = {
-#     "icon_links": [
-#         {
-#             "name": "GitHub",
-#             "url": "https://github.com/digital-porous-media/dpm_tools",
-#             "icon": "fab fa-github-square",
-#         },
-#     ],
-#     "external_links": [
-#         {
-#             "name": "Issue Tracker", "url": "https://github.com/digital-porous-media/dpm_tools/issues"
-#         },
-#         {
-#             "name": "Get Help", "url": "https://github.com/digital-porous-media/dpm_tools/discussions"
-#         },
-#     ],
-#     "navigation_with_keys": False,
-#     "show_prev_next": False,
-#     "icon_links_label": "Quick Links",
-#     "use_edit_page_button": False,
-#     "search_bar_position": "sidebar",
-#     "navbar_align": "left",
-# }
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/digital-porous-media/dpm_tools",
+            "icon": "fab fa-github-square",
+        },
+    ],
+    "external_links": [
+        {
+            "name": "Issue Tracker", "url": "https://github.com/digital-porous-media/dpm_tools/issues"
+        },
+        {
+            "name": "Get Help", "url": "https://github.com/digital-porous-media/dpm_tools/discussions"
+        },
+    ],
+    "navigation_with_keys": False,
+    "show_prev_next": False,
+    "icon_links_label": "Quick Links",
+    "use_edit_page_button": False,
+    "search_bar_position": "sidebar",
+    "navbar_align": "left",
+}

docs/index.rst

@@ -3,19 +3,10 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to DPM_Tools's documentation!
+Digital Porous Media Tools
 =====================================
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
-   modules
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   modules/index

docs/modules/generated/dpm_tools.io.io_utils.rst

@@ -0,0 +1,29 @@
+dpm\_tools.io.io\_utils
+=======================
+
+.. automodule:: dpm_tools.io.io_utils
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      convert_filetype
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/modules/generated/dpm_tools.io.read_data.rst

@@ -0,0 +1,37 @@
+dpm\_tools.io.read\_data
+========================
+
+.. automodule:: dpm_tools.io.read_data
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      read_image
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Image
+      ImageFromFile
+      Vector
+
+
+
+
+
+
+
+
+

docs/modules/generated/dpm_tools.io.rst

@@ -0,0 +1,33 @@
+dpm\_tools.io
+=============
+
+.. automodule:: dpm_tools.io
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   dpm_tools.io.io_utils
+   dpm_tools.io.read_data
+   dpm_tools.io.write_data
+

docs/modules/generated/dpm_tools.io.write_data.rst

@@ -0,0 +1,29 @@
+dpm\_tools.io.write\_data
+=========================
+
+.. automodule:: dpm_tools.io.write_data
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      write_image
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/modules/generated/dpm_tools.morphology.features.rst

@@ -0,0 +1,34 @@
+dpm\_tools.morphology.features
+==============================
+
+.. automodule:: dpm_tools.morphology.features
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      chords
+      constriction_factor
+      edt
+      slicewise_edt
+      slicewise_mis
+      tof
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/modules/generated/dpm_tools.morphology.rst

@@ -0,0 +1,31 @@
+dpm\_tools.morphology
+=====================
+
+.. automodule:: dpm_tools.morphology
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   dpm_tools.morphology.features
+

docs/modules/generated/dpm_tools.visualization.plot_2d.rst

@@ -0,0 +1,32 @@
+dpm\_tools.visualization.plot\_2d
+=================================
+
+.. automodule:: dpm_tools.visualization.plot_2d
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      hist
+      make_gif
+      make_thumbnail
+      plot_slice
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/modules/generated/dpm_tools.visualization.plot_3d.rst

@@ -0,0 +1,34 @@
+dpm\_tools.visualization.plot\_3d
+=================================
+
+.. automodule:: dpm_tools.visualization.plot_3d
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      bounding_box
+      orthogonal_slices
+      plot_glyph
+      plot_isosurface
+      plot_scalar_volume
+      plot_streamlines
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/modules/generated/dpm_tools.visualization.rst

@@ -0,0 +1,32 @@
+dpm\_tools.visualization
+========================
+
+.. automodule:: dpm_tools.visualization
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   dpm_tools.visualization.plot_2d
+   dpm_tools.visualization.plot_3d
+