Merge pull request #497 from DiamondLightSource/various-docs-fixes

Various small docs fixes

docs/source/conf.py

@@ -44,6 +44,7 @@
 # ------------------------------------------------------------------------------
 
 project = "HTTomo"
+author = "the Imaging Team"
 copyright = f"{date.today().year}, Diamond Light Source"
 
 # Specify a base language to help assistive technology
@@ -72,9 +73,8 @@
     "sphinx_copybutton",
     # use jupyter notebooks
     "nbsphinx",
-    #'IPython.sphinxext.ipython_console_highlighting',
-    "sphinx.ext.githubpages",
     # Generate .nojekyll file for git pages build
+    "sphinx.ext.githubpages",
 ]
 
 autosummary_generate = True
@@ -109,7 +109,3 @@
     "github_version": "main",
     "doc_path": "docs",
 }
-
-
-def setup(app):
-    app.add_css_file("css/general.css")

docs/source/howto/process_lists/process_list_configure.rst

@@ -47,7 +47,7 @@ The pattern of any supported method can be found in :ref:`pl_library`.
 Library files
 -------------
 
-Here is the list of :ref:`pl_library` for backends where patterns and other fixed arguments for methods are specified. When HTTomo operates
+Here is the list of library files for backends where patterns and other fixed arguments for methods are specified. When HTTomo operates
 with a certain method it always refers to its library file in order get the specific requirements for that method.
 
 .. dropdown:: TomoPy's library file

docs/source/howto/run_httomo.rst

@@ -239,8 +239,6 @@ The :code:`run` command has 13 options/flags:
 - :code:`--syslog-port`
 - :code:`--frames-per-chunk`
 
-.. _httomo-saving:
-
 :code:`--output-folder-name`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -253,6 +251,8 @@ For example, if the :code:`OUT_DIR` path provided was :code:`/home/myuser`, and
 :code:`--output-folder-name=test-1` was given, then the absolute path of the output directory
 created by HTTomo would be :code:`/home/myuser/test-1/`.
 
+.. _httomo-saving:
+
 :code:`--save-all`
 ~~~~~~~~~~~~~~~~~~
 

docs/source/pipelines/yaml.rst

@@ -14,14 +14,17 @@ CPU Pipeline templates
 .. dropdown:: Basic TomoPy's (CPU-only) pipeline for the classical 180-degrees scan
 
     .. literalinclude:: ../../../tests/samples/pipeline_template_examples/pipeline_cpu1.yaml
+        :language: yaml
 
 .. dropdown:: TomoPy's pipeline where :ref:`previewing` is demonstrated
 
     .. literalinclude:: ../../../tests/samples/pipeline_template_examples/pipeline_cpu2.yaml
+        :language: yaml
 
 .. dropdown:: This pipeline shows how "calculate_stats" module extracts global statistics in order to be passed to "save_to_images" function which uses it to rescale data for saving images
 
     .. literalinclude:: ../../../tests/samples/pipeline_template_examples/pipeline_cpu3.yaml
+        :language: yaml
 
 .. _tutorials_pl_templates_gpu:
 
@@ -31,6 +34,7 @@ GPU Pipeline templates
 .. dropdown:: Basic GPU pipeline which uses functions from the httomolibgpu library.
 
     .. literalinclude:: ../../../tests/samples/pipeline_template_examples/pipeline_gpu1.yaml
+        :language: yaml
 
 
 .. _tutorials_pl_templates_dls:
@@ -41,14 +45,17 @@ DLS Specific templates
 .. dropdown:: GPU-based pipeline using httomolibgpu methods for DIAD (k11) data. Global statistics and referencing is used.
 
     .. literalinclude:: ../../../tests/samples/pipeline_template_examples/DLS/01_diad_pipeline_gpu.yaml
+        :language: yaml
 
 .. dropdown:: GPU-driven pipeline for the 360-degrees data which estimates the CoR value and the overlap. The 180-degrees sinogram is obtained by stitching using the overlap value. The pipeline shows the extensive use of side_outputs and refrencing.
 
     .. literalinclude:: ../../../tests/samples/pipeline_template_examples/pipeline_360deg_gpu2.yaml
+        :language: yaml
 
 .. dropdown:: More advanced GPU pipeline for the 360-degrees data. Here we preview the section and then reconstruct it iteratively, the result then downsampled before saving smaller images.
 
     .. literalinclude:: ../../../tests/samples/pipeline_template_examples/pipeline_360deg_iterative_gpu3.yaml
+        :language: yaml
 
 .. _tutorials_pl_templates_sweeps:
 

docs/sphinx-build.sh

@@ -12,7 +12,7 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 # show-inheritance displays a list of base classes below the class signature
 
 # Remove directory for api so that there are no obsolete files
-rm -rf $DIR/source/generated/
+rm -rf $DIR/source/developers/generated/
 rm -rf $DIR/build/
 
 # sphinx-build [options] <sourcedir> <outputdir> [filenames]