Adds mock modules to sphinx autodoc

doc/source/api/savu.plugins.filters.azimuthal_integrators.rst

@@ -13,5 +13,6 @@ Submodules
 .. toctree::
 
    savu.plugins.filters.azimuthal_integrators.pyfai_azimuthal_integrator
+   savu.plugins.filters.azimuthal_integrators.pyfai_azimuthal_integrator_separate
    savu.plugins.filters.azimuthal_integrators.pyfai_azimuthal_integrator_with_bragg_filter
 

doc/source/api/savu.plugins.loaders.rst

@@ -22,6 +22,7 @@ Submodules
    savu.plugins.loaders.base_multi_modal_loader
    savu.plugins.loaders.i12_tomo_loader
    savu.plugins.loaders.i18loader
+   savu.plugins.loaders.image_loader
    savu.plugins.loaders.mm_loader
    savu.plugins.loaders.nxtomo_loader
    savu.plugins.loaders.projection_tomo_loader

doc/source/api/savu.test.plugin_tests.filter_tests.rst

@@ -25,7 +25,12 @@ Submodules
    savu.test.plugin_tests.filter_tests.median_filter_test
    savu.test.plugin_tests.filter_tests.monitor_correction_test
    savu.test.plugin_tests.filter_tests.paganin_test
-   savu.test.plugin_tests.filter_tests.pyfai_test
+   savu.test.plugin_tests.filter_tests.pyfai_filtered_test_d
+   savu.test.plugin_tests.filter_tests.pyfai_filtered_test_q
+   savu.test.plugin_tests.filter_tests.pyfai_separate_test_d
+   savu.test.plugin_tests.filter_tests.pyfai_separate_test_q
+   savu.test.plugin_tests.filter_tests.pyfai_test_d
+   savu.test.plugin_tests.filter_tests.pyfai_test_q
    savu.test.plugin_tests.filter_tests.raven_filter_test
    savu.test.plugin_tests.filter_tests.ring_artefact_test
    savu.test.plugin_tests.filter_tests.sinogram_alignment_test

doc/source/api/savu.test.process_list_tests.rst

@@ -22,6 +22,7 @@ Submodules
    savu.test.process_list_tests.simple_fit_recon_test
    savu.test.process_list_tests.simple_stxm_tomo_test
    savu.test.process_list_tests.spectra_tomo_chunking_test
+   savu.test.process_list_tests.spectra_tomo_chunking_with_scanned_parameter_test
    savu.test.process_list_tests.spectrum_crop_test
    savu.test.process_list_tests.stats_test
    savu.test.process_list_tests.stxm_tomo_test

doc/source/autosummary.rst

@@ -35,9 +35,9 @@ savu.data
 .. toctree::
    api/savu.data.experiment_collection
    api/savu.data.plugin_list
-   api/savu.data.transport_data
    api/savu.data.chunking
    api/savu.data.meta_data
+   api/savu.data.transport_data
 
 
 savu.data.transport_data
@@ -52,13 +52,13 @@ savu.data.data_structures
 ------------------------------------------------------------
 
 .. toctree::
-   api/savu.data.data_structures.utils
    api/savu.data.data_structures.data
-   api/savu.data.data_structures.plugin_data
+   api/savu.data.data_structures.data_add_ons
    api/savu.data.data_structures.data_create
-   api/savu.data.data_structures.preview
    api/savu.data.data_structures.data_notes
-   api/savu.data.data_structures.data_add_ons
+   api/savu.data.data_structures.plugin_data
+   api/savu.data.data_structures.preview
+   api/savu.data.data_structures.utils
 
 
 savu.plugins
@@ -71,12 +71,12 @@ savu.plugins
    api/savu.plugins.base_saver
    api/savu.plugins.base_filter
    api/savu.plugins.plugin
-   api/savu.plugins.plugin_datasets_notes
+   api/savu.plugins.base_correction
    api/savu.plugins.plugin_datasets
    api/savu.plugins.test_plugin
-   api/savu.plugins.base_correction
-   api/savu.plugins.dimension_adder
+   api/savu.plugins.plugin_datasets_notes
    api/savu.plugins.simple_fit_xrf_bounded
+   api/savu.plugins.dimension_adder
 
 
 savu.plugins.reconstructions
@@ -144,8 +144,8 @@ savu.plugins.filters
    api/savu.plugins.filters.monitor_correction
    api/savu.plugins.filters.histogram
    api/savu.plugins.filters.no_process_plugin
-   api/savu.plugins.filters.base_azimuthal_integrator
    api/savu.plugins.filters.poly_background_estimator
+   api/savu.plugins.filters.base_azimuthal_integrator
 
 
 savu.plugins.filters.component_analysis
@@ -176,6 +176,7 @@ savu.plugins.filters.azimuthal_integrators
 .. toctree::
    api/savu.plugins.filters.azimuthal_integrators
    api/savu.plugins.filters.azimuthal_integrators
+   api/savu.plugins.filters.azimuthal_integrators
 
 
 savu.plugins.loaders
@@ -187,8 +188,9 @@ savu.plugins.loaders
    api/savu.plugins.loaders.nxtomo_loader
    api/savu.plugins.loaders.projection_tomo_loader
    api/savu.plugins.loaders.i12_tomo_loader
-   api/savu.plugins.loaders.savu_loader
    api/savu.plugins.loaders.i18loader
+   api/savu.plugins.loaders.savu_loader
+   api/savu.plugins.loaders.image_loader
 
 
 savu.plugins.loaders.multi_modal_loaders

doc/source/conf.py

@@ -11,9 +11,12 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+
 import sys, os
 from os import path
 
+autodoc_mock_imports = ['numpy', 'mpi4py', 'astra', 'scipy']
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -40,6 +43,7 @@
 sys.path.insert(0, os.path.abspath('../../savu/plugins/loaders/multi_modal_loaders'))
 sys.path.insert(0, os.path.abspath('../../savu/plugins/savers'))
 
+print sys.path
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.

savu/test/plugin_tests/filter_tests/paganin_test.py

@@ -29,10 +29,10 @@
 
 class PaganinTest(unittest.TestCase):
 
-    def test_paganin1(self):
-        options = tu.set_experiment('tomoRaw')
-        plugin = 'savu.plugins.paganin_filter'
-        run_protected_plugin_runner_no_process_list(options, plugin)
+#    def test_paganin1(self):
+#        options = tu.set_experiment('tomoRaw')
+#        plugin = 'savu.plugins.paganin_filter'
+#        run_protected_plugin_runner_no_process_list(options, plugin)
 
     def test_paganin2(self):
         options = tu.set_experiment('tomo')