Issue-259: Add simple functions with doc test examples (#261)

* Issue-259: Add simple functions with doc test examples

Initial port

Try to debug new bindings

Ensure errors are reported

Try to work around issue

Fix swig bug

Most tests fixed

Fix all tests

Cherry pick over fixes

* Fix bug

* Fix warning and unit test

* Fix doctest again

docs/Doxyfile.in

@@ -793,7 +793,7 @@ INPUT_ENCODING         = UTF-8
 # *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd,
 # *.vhdl, *.ucf, *.qsf, *.as and *.js.
 
-FILE_PATTERNS          = *.h *.cpp *.md *.cs
+FILE_PATTERNS          = *.h *.cpp *.md *.cs *.py
 # TODO: *.py
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
@@ -825,7 +825,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = cmake-build-*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the

docs/src/changes.md

@@ -1,5 +1,12 @@
 # Changes                                               {#changes}
 
+## v1.1.22
+
+Date       | Description
+---------- | -----------
+2021-03-24 | Issue-259: Add simple functions with doc test examples
+
+
 ## v1.1.21
 
 Date       | Description

docs/src/python_binding.md

@@ -30,6 +30,14 @@ If you see this error:
 
 Then upgrade numpy and try again.
 
+## New simplified interface
+
+      from interop import *
+      ar = imaging("path/to/run_folder")
+
+See new [interop.core](namespacecore.html) wrapper for the simplified interface
+
+
 ## Tips & Tricks
 
 1. To see which methods/fields are available:

interop/logic/plot/plot_sample_qc.h

@@ -27,7 +27,7 @@ namespace illumina { namespace interop { namespace logic { namespace plot
     void plot_sample_qc(model::metrics::run_metrics &metrics,
                         const size_t lane,
                         model::plot::plot_data <model::plot::bar_point> &data)
-    INTEROP_THROW_SPEC((model::index_out_of_bounds_exception));
+    INTEROP_THROW_SPEC((model::index_out_of_bounds_exception, std::bad_alloc));
 
 
 }}}}

interop/model/metrics/corrected_intensity_metric.h

@@ -213,26 +213,52 @@ namespace illumina { namespace interop { namespace model { namespace metrics
             INTEROP_ASSERT(m_corrected_int_called.size() == constants::NUM_OF_BASES);
             INTEROP_ASSERT(m_called_counts.size() == constants::NUM_OF_BASES_AND_NC);
         }
+
+        /** Constructor
+         *
+         * @note Version 4
+         * @param lane lane number
+         * @param tile tile number
+         * @param cycle cycle number
+         * @param called_count_vec number of clusters called per base
+         */
+        corrected_intensity_metric(const uint_t lane,
+                                   const uint_t tile,
+                                   const uint_t cycle,
+                                   const uint_array_t& called_count) :
+                metric_base::base_cycle_metric(lane, tile, cycle),
+                m_average_cycle_intensity(std::numeric_limits<ushort_t>::max()),
+                m_corrected_int_all(constants::NUM_OF_BASES, std::numeric_limits<ushort_t>::max()),
+                m_corrected_int_called(constants::NUM_OF_BASES, std::numeric_limits<float>::quiet_NaN()),
+                m_called_counts(called_count),
+                m_signal_to_noise(std::numeric_limits<float>::quiet_NaN())
+        {
+            INTEROP_ASSERT(called_count.size() == static_cast<size_t>(constants::NUM_OF_BASES_AND_NC));
+        }
         /** Constructor
          *
          * @note Version 4
          * @param lane lane number
          * @param tile tile number
          * @param cycle cycle number
          * @param called_counts number of clusters called per base
+         * @param num_of_counts number of bases
          */
         corrected_intensity_metric(const uint_t lane,
                                    const uint_t tile,
                                    const uint_t cycle,
-                                   const uint_array_t& called_counts) :
+                                   const ::uint32_t* called_counts,
+                                   const size_t num_of_counts,
+                                   const size_t /*dummy*/, /* dummy parameters work around swig bug */
+                                   const size_t /*dummy*/) :
                 metric_base::base_cycle_metric(lane, tile, cycle),
                 m_average_cycle_intensity(std::numeric_limits<ushort_t>::max()),
                 m_corrected_int_all(constants::NUM_OF_BASES, std::numeric_limits<ushort_t>::max()),
                 m_corrected_int_called(constants::NUM_OF_BASES, std::numeric_limits<float>::quiet_NaN()),
-                m_called_counts(called_counts),
+                m_called_counts(called_counts, called_counts + std::min(num_of_counts, static_cast<size_t>(constants::NUM_OF_BASES_AND_NC))),
                 m_signal_to_noise(std::numeric_limits<float>::quiet_NaN())
         {
-            INTEROP_ASSERT(called_counts.size() == constants::NUM_OF_BASES_AND_NC);
+            INTEROP_ASSERT(num_of_counts== static_cast<size_t>(constants::NUM_OF_BASES_AND_NC));
         }
 
     public:

interop/model/metrics/extraction_metric.h

@@ -262,6 +262,33 @@ namespace illumina { namespace interop { namespace model { namespace metrics
         {
         }
 
+        /** Constructor
+         *
+         * @note Version 3
+         * @param lane lane number
+         * @param tile tile number
+         * @param cycle cycle number
+         * @param intensity_values 90th percentile of intensities for the given channel
+         * @param intensity_count number of channels
+         * @param focus_scores focus score for the given channel
+         * @param focus_count number of channels
+         */
+        extraction_metric(const uint_t lane,
+                          const uint_t tile,
+                          const uint_t cycle,
+                          const ::uint16_t* intensity_values,
+                          const size_t intensity_count,
+                          const float* focus_scores,
+                          const size_t focus_count,
+                          const size_t /*dummy*/) :
+                metric_base::base_cycle_metric(lane, tile, cycle),
+                m_date_time_csharp(0),
+                m_date_time(0),
+                m_max_intensity_values(intensity_values, intensity_values+intensity_count),
+                m_focus_scores(focus_scores, focus_scores+focus_count)
+        {
+        }
+
     public:
         /** Setter
          *

interop/model/metrics/index_metric.h

@@ -358,6 +358,36 @@ namespace illumina { namespace interop { namespace model { namespace metrics
         static const char *prefix()
         { return "Index"; }
 
+        /** Percentage of PF clusters on the tile that have been demultiplexed
+         *
+         * Dependent on tile_metric
+         *
+         * @return percent of demultiplexed PF clusters
+         */
+        float percent_demultiplexed(const std::string& sample_id) const
+        {
+            uint64_t total_demultiplexed_clusters = 0;
+            if (sample_id.empty())
+            {
+                for (size_t index_array_counter = 0; index_array_counter < m_indices.size(); ++index_array_counter)
+                {
+                    total_demultiplexed_clusters += m_indices[index_array_counter].cluster_count();
+                }
+            }
+            else
+            {
+                for (size_t index_array_counter = 0; index_array_counter < m_indices.size(); ++index_array_counter)
+                {
+                    if(m_indices[index_array_counter].sample_id() == sample_id)
+                    {
+                        total_demultiplexed_clusters = m_indices[index_array_counter].cluster_count();
+                        break;
+                    }
+                }
+            }
+            return static_cast<float>(total_demultiplexed_clusters)/m_cluster_count_pf * 100;
+        }
+
     private:
         index_array_t m_indices;
         float m_cluster_count; // Derived from tile metric

src/ext/python/CMakeLists.txt

@@ -146,7 +146,7 @@ string(REPLACE ";" "','" PY_GEN_LIST "${py_gens}")
 set(INTEROP_VERSION ${VERSION_SHORT}${VERSION_DEV})
 configure_file(__init__.py.in interop/__init__.py @ONLY)
 configure_file(__main__.py.in interop/__main__.py @ONLY)
-file(COPY ${CMAKE_SOURCE_DIR}/src/tests/python/CoreTests.py DESTINATION interop)
+
 
 add_custom_command( TARGET python_lib POST_BUILD
         COMMAND ${CMAKE_COMMAND}
@@ -155,8 +155,21 @@ add_custom_command( TARGET python_lib POST_BUILD
         -DCONFIG_INPUT_FILE=${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in
         -DCONFIG_OUTPUT_FILE=${CMAKE_CURRENT_BINARY_DIR}/setup.py
         -P ${CMAKE_SOURCE_DIR}/cmake/ConfigureFile.cmake
+        COMMAND ${CMAKE_COMMAND}
+        -DINTEROP_VERSION=${VERSION_SHORT}${VERSION_DEV}
+        -DINTEROP_LIB_LIST="${PY_GEN_LIST}"
+        -DCONFIG_INPUT_FILE=${CMAKE_CURRENT_SOURCE_DIR}/__main__.py.in
+        -DCONFIG_OUTPUT_FILE=${CMAKE_CURRENT_BINARY_DIR}/__main__.py
+        -P ${CMAKE_SOURCE_DIR}/cmake/ConfigureFile.cmake
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
+        ${CMAKE_CURRENT_SOURCE_DIR}/core.py
+        ${CMAKE_CURRENT_BINARY_DIR}/interop/core.py
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
+        ${CMAKE_SOURCE_DIR}/src/tests/python/CoreTests.py
+        ${CMAKE_CURRENT_BINARY_DIR}/interop/CoreTests.py
 )
 
+
 install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
         DESTINATION share/illumina/interop/src
         FILES_MATCHING
@@ -173,7 +186,7 @@ set(SWIG_GEN_PYTHON_SOURCE_FILES ${py_files} CACHE INTERNAL "Python scripts gene
 
 
 if(NOT PYTHONINTERP_FOUND)
-    message(WARNING "Cannot find Python Interpretor, cannot create wheel package")
+    message(WARNING "Cannot find Python Interpreter, cannot create wheel package")
     return()
 endif()
 
@@ -193,4 +206,4 @@ if(NOT SKIP_PACKAGE_ALL_WHEEL)
 endif()
 
 
-set(PYTHON_BUILD_AVAILABLE "Python ${PYTHON_VERSION_STRING}" CACHE INTERNAL "All dependencies are satisfied for the Java Build" FORCE)
+set(PYTHON_BUILD_AVAILABLE "Python ${PYTHON_VERSION_STRING}" CACHE INTERNAL "All dependencies are satisfied for the Java Build" FORCE)

src/ext/python/__init__.py.in

@@ -7,3 +7,6 @@ __doc_url__ = "http://illumina.github.io/interop/index.html"
 __version__ = "@INTEROP_VERSION@"
 __maintainer__ = "Illumina, inc."
 __contact__ = "https://github.com/Illumina/interop/issues"
+
+from interop.core import *
+

src/ext/python/__main__.py.in

@@ -1,4 +1,5 @@
 import interop
+import interop.core
 import unittest
 import argparse
 from interop import @PY_MOD_NAME_LIST@
@@ -16,6 +17,7 @@ def execute_from_commandline():
     if param.test:
         testsuite = unittest.makeSuite(CoreTests)
         unittest.TextTestRunner(verbosity=1).run(testsuite)
+        interop.core._run_doctests()
 
 if __name__ == "__main__":
     execute_from_commandline();