Creating documentation for httomolibgpu

.github/workflows/doc_conda.yml

@@ -0,0 +1,43 @@
+name: HTTomolibGPU doc test
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+        - name: Checkout repository code
+          uses: actions/checkout@v3
+
+        - name: Setup Python 3.10
+          uses: actions/setup-python@v3
+          with:
+            python-version: "3.10"
+
+        - name: httomolibgpu
+          uses: conda-incubator/setup-miniconda@v2
+          with:
+            auto-update-conda: false
+            activate-environment: httomolibgpu
+            environment-file: ./docs/source/doc-conda-requirements.yml
+
+        - name: Build api docs
+          run: sphinx-apidoc -feT -t=./docs/source/_templates -o ./docs/source/api ./httomolibgpu
+
+        - name: Build html
+          run: sphinx-build -a -E -b html ./docs/source/ ./docs/build/
+
+        - name: Run ghp-import
+          run: ghp-import -n -p -f ./docs/build
+          env:
+            GITHUB_TOKEN: ${{ github.token }}

README.rst

@@ -4,14 +4,15 @@ HTTomolibGPU is a library of GPU accelerated methods for tomography
 **HTTomolibGPU** is a collection of image processing methods in Python for computed tomography.
 The methods are GPU-accelerated with the open-source Python library `CuPy <https://cupy.dev/>`_. Most of the 
 methods migrated from `TomoPy <https://tomopy.readthedocs.io/en/stable/>`_ and `Savu <https://savu.readthedocs.io/en/latest/>`_ software packages.
-They have been optimised to ensure higher computational efficiency.
+Some of the methods also have been optimised to ensure higher computational efficiency, before ported to CuPy.
 
-Purpose of HTTomolibGPU
-=======================
+The purpose of HTTomolibGPU
+===========================
 
-**HTTomolibGPU** can be used as a stand-alone library, but it has been specifically developed to 
-work together with the `HTTomo <https://diamondlightsource.github.io/httomo/>`_ package.
-HTTomo is a user interface (UI) written in Python for fast big data processing using MPI protocols. 
+**HTTomolibGPU** can be used as a stand-alone library, see Examples section in `Documentation <https://diamondlightsource.github.io/httomolibgpu/>`_. 
+However, it has been specifically developed to work together with the `HTTomo <https://diamondlightsource.github.io/httomo/>`_ package as 
+its backend for data processing. HTTomo is a user interface (UI) written in Python for fast big tomographic data processing using 
+MPI protocols. 
 
 Install HTTomolibGPU as a pre-built conda Python package
 =========================================================
@@ -40,7 +41,3 @@ Build HTTomolibGPU as a conda Python package
 
    $ conda build conda/recipe/ -c conda-forge -c httomo -c astra-toolbox -c rapidsai
 
-Examples
-=========
-
-There are series of Jupyter Notebooks located in :code:`examples/*` to demonstrate how some of the functions can be used.

docs/source/_templates/module.rst_t

@@ -0,0 +1,7 @@
+{%- if show_headings %}:mod:`{{ basename }}`
+============================================
+{%- endif %}
+.. automodule:: {{ qualname }}
+{%- for option in automodule_options %}
+   :{{ option }}:
+{%- endfor %}

docs/source/api/httomolibgpu.cuda_kernels.rst

@@ -0,0 +1,10 @@
+httomolibgpu.cuda\_kernels package
+==================================
+
+Module contents
+---------------
+
+.. automodule:: httomolibgpu.cuda_kernels
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.cupywrapper.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.cupywrapper`
+============================================
+.. automodule:: httomolibgpu.cupywrapper
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.misc.corr.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.misc.corr`
+============================================
+.. automodule:: httomolibgpu.misc.corr
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.misc.morph.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.misc.morph`
+============================================
+.. automodule:: httomolibgpu.misc.morph
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.misc.rescale.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.misc.rescale`
+============================================
+.. automodule:: httomolibgpu.misc.rescale
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.misc.rst

@@ -0,0 +1,20 @@
+httomolibgpu.misc package
+=========================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   httomolibgpu.misc.corr
+   httomolibgpu.misc.morph
+   httomolibgpu.misc.rescale
+
+Module contents
+---------------
+
+.. automodule:: httomolibgpu.misc
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.prep.alignment.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.prep.alignment`
+============================================
+.. automodule:: httomolibgpu.prep.alignment
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.prep.normalize.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.prep.normalize`
+============================================
+.. automodule:: httomolibgpu.prep.normalize
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.prep.phase.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.prep.phase`
+============================================
+.. automodule:: httomolibgpu.prep.phase
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.prep.rst

@@ -0,0 +1,21 @@
+httomolibgpu.prep package
+=========================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   httomolibgpu.prep.alignment
+   httomolibgpu.prep.normalize
+   httomolibgpu.prep.phase
+   httomolibgpu.prep.stripe
+
+Module contents
+---------------
+
+.. automodule:: httomolibgpu.prep
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.prep.stripe.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.prep.stripe`
+============================================
+.. automodule:: httomolibgpu.prep.stripe
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.recon.algorithm.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.recon.algorithm`
+============================================
+.. automodule:: httomolibgpu.recon.algorithm
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.recon.rotation.rst

@@ -0,0 +1,6 @@
+:mod:`httomolibgpu.recon.rotation`
+============================================
+.. automodule:: httomolibgpu.recon.rotation
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.recon.rst

@@ -0,0 +1,19 @@
+httomolibgpu.recon package
+==========================
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   httomolibgpu.recon.algorithm
+   httomolibgpu.recon.rotation
+
+Module contents
+---------------
+
+.. automodule:: httomolibgpu.recon
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/api/httomolibgpu.rst

@@ -0,0 +1,29 @@
+httomolibgpu package
+====================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   httomolibgpu.cuda_kernels
+   httomolibgpu.misc
+   httomolibgpu.prep
+   httomolibgpu.recon
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   httomolibgpu.cupywrapper
+
+Module contents
+---------------
+
+.. automodule:: httomolibgpu
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/bibliography/biblio.rst

@@ -0,0 +1,8 @@
+.. only:: html
+
+    ************
+    Bibliography
+    ************
+
+.. bibliography:: references.bib
+   :style: plain