diff --git a/docs/source/conf.py b/docs/source/conf.py index e7cb07a6e..ff5f607bc 100644 --- a/docs/source/conf.py +++ b/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") diff --git a/docs/source/howto/process_lists/process_list_configure.rst b/docs/source/howto/process_lists/process_list_configure.rst index 3d93974f0..62ce4284f 100644 --- a/docs/source/howto/process_lists/process_list_configure.rst +++ b/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 diff --git a/docs/source/howto/run_httomo.rst b/docs/source/howto/run_httomo.rst index 1e297dadf..3e4017669 100644 --- a/docs/source/howto/run_httomo.rst +++ b/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` ~~~~~~~~~~~~~~~~~~ diff --git a/docs/source/pipelines/yaml.rst b/docs/source/pipelines/yaml.rst index 5a74296ed..2708436a3 100644 --- a/docs/source/pipelines/yaml.rst +++ b/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: diff --git a/docs/sphinx-build.sh b/docs/sphinx-build.sh index 051ea1a2f..c7b0361dd 100644 --- a/docs/sphinx-build.sh +++ b/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] [filenames]