Fix docs and CI

.gitlab-ci.yml

@@ -36,11 +36,11 @@ build:doc:
     entrypoint: [""]
   script:
     - cd ${DOCS_DIRECTORY}
-    - sphinx-apidoc -o source/src ../src
-    - sphinx-apidoc -o source/tests/heat ../tests/heat
-    - sphinx-apidoc -o source/tests/stress ../tests/stress
-    - sphinx-apidoc -o source/tests/r13 ../tests/r13
-    - sphinx-apidoc -o source/examples ../examples
+    - sphinx-apidoc -f -o source/fenicsR13 ../fenicsR13
+    - sphinx-apidoc -f -o source/tests/heat ../tests/heat
+    - sphinx-apidoc -f -o source/tests/stress ../tests/stress
+    - sphinx-apidoc -f -o source/tests/r13 ../tests/r13
+    - sphinx-apidoc -f -o source/examples ../examples
     - make html
     - make latex
   artifacts:

docs/conf.py

@@ -12,7 +12,7 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../src'))
+sys.path.insert(0, os.path.abspath('..'))
 sys.path.insert(0, os.path.abspath('../tests/heat'))
 sys.path.insert(0, os.path.abspath('../tests/stress'))
 sys.path.insert(0, os.path.abspath('../tests/r13'))

docs/index.rst

@@ -17,8 +17,8 @@ Contents
 .. toctree::
     :glob:
 
-    source/src/modules.rst
+    source/fenicsR13/modules.rst
     source/tests/heat/modules.rst
     source/tests/stress/modules.rst
     source/tests/r13/modules.rst
-    source/examples/modules.rst
\ No newline at end of file
+    source/examples/modules.rst

docs/source/fenicsR13/fenicsR13.rst

+fenicsR13 package
+=================
+
+Submodules
+----------
+
+fenicsR13.fenicsR13 module
+--------------------------
+
+.. automodule:: fenicsR13.fenicsR13
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fenicsR13.geoToH5 module
+------------------------
+
+.. automodule:: fenicsR13.geoToH5
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fenicsR13.input module
+----------------------
+
+.. automodule:: fenicsR13.input
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fenicsR13.meshes module
+-----------------------
+
+.. automodule:: fenicsR13.meshes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fenicsR13.postprocessor module
+------------------------------
+
+.. automodule:: fenicsR13.postprocessor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fenicsR13.solver module
+-----------------------
+
+.. automodule:: fenicsR13.solver
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fenicsR13.tensoroperations module
+---------------------------------
+
+.. automodule:: fenicsR13.tensoroperations
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: fenicsR13
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/src/modules.rst → docs/source/fenicsR13/modules.rst

-src
-===
+fenicsR13
+=========
 
 .. toctree::
    :maxdepth: 4
 
    fenicsR13
-   input
-   meshes
-   postprocessor
-   solver
-   tensoroperations
-   geoToH5

docs/source/src/fenicsR13.rst

-fenicsR13 module
-================
-
-.. automodule:: fenicsR13
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/src/geoToH5.rst

-geoToH5 module
-==============
-
-.. automodule:: geoToH5
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/src/input.rst

-input module
-============
-
-.. automodule:: input
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/src/meshes.rst

-meshes module
-=============
-
-.. automodule:: meshes
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/src/postprocessor.rst

-postprocessor module
-====================
-
-.. automodule:: postprocessor
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/src/solver.rst

-solver module
-=============
-
-.. automodule:: solver
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/src/tensoroperations.rst

-tensoroperations module
-=======================
-
-.. automodule:: tensoroperations
-   :members:
-   :undoc-members:
-   :show-inheritance:

fenicsR13/geoToH5.py

@@ -7,7 +7,7 @@ Converter from geo-format to a mesh in h5-format.
 
 Installation:
 
-.. coe-block:: bash
+.. code-block:: bash
 
     pip install .