Merge pull request #386 from pjotrp/odgi-master

Added python tests, documentation and moved tests to CMakeLists.txt.

.gitignore

@@ -9,3 +9,4 @@ include/
 docs/sphinx_build
 docs/sphinx_build_man
 docs/_build
+Testing/

CMakeLists.txt

@@ -101,10 +101,10 @@ endif()
 # Function to invoke doctests
 function(add_pydoctest TEST_FILE)
   add_test(
-    NAME ${TEST_FILE}
+    NAME pydoctest_${TEST_FILE}
     COMMAND python3 -m doctest -o NORMALIZE_WHITESPACE -o REPORT_UDIFF python/${TEST_FILE}.md
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test)
-  set_tests_properties(${TEST_FILE} PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_SOURCE_DIR}/lib;LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};LD_PRELOAD=${PRELOAD}")
+  set_tests_properties(pydoctest_${TEST_FILE} PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_SOURCE_DIR}/lib;LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};LD_PRELOAD=${PRELOAD}")
 endfunction()
 
 if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") # untested
@@ -820,6 +820,7 @@ else (NOT PIC)
   set_target_properties(odgi_ffi PROPERTIES OUTPUT_NAME "odgi_ffi")
   install(TARGETS odgi_ffi LIBRARY DESTINATION lib)
   add_pydoctest(odgi_ffi)
+  add_pydoctest(odgi_performance)
 
   # Build original Python module
   pybind11_add_module(odgi_pybind11 "${CMAKE_SOURCE_DIR}/src/pythonmodule.cpp")
@@ -828,6 +829,11 @@ else (NOT PIC)
   target_link_libraries(odgi_pybind11 PRIVATE "${CMAKE_SOURCE_DIR}/lib/libodgi.a" "${odgi_LIBS}")
   set_target_properties(odgi_pybind11 PROPERTIES OUTPUT_NAME "odgi")
   install(TARGETS odgi_pybind11 LIBRARY DESTINATION lib)
+  add_test(
+    NAME pythonmodule
+    COMMAND python3 -c "import odgi; g = odgi.graph()"
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test)
+  set_tests_properties(pythonmodule PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_SOURCE_DIR}/lib;LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};LD_PRELOAD=${PRELOAD}")
 
 endif (NOT PIC)
 

guix.scm

@@ -6,16 +6,16 @@
 ;;
 ;;   guix build -f guix.scm --target=aarch64-linux
 ;;
-;; To get a development container (emacs shell will work)
+;; To get a development container (inside emacs shell will work)
 ;;
-;;   guix shell -C -D -f guix.scm
+;;   guix shell -C -D -f guix.scm -- bash --init-file <(echo "ln -s /bin/sh /bin/bash")
 ;;
 ;; and build
 ;;
 ;;   find -name CMakeCache.txt|xargs rm -v
 ;;   cd build
 ;;   cmake -DCMAKE_BUILD_TYPE=Debug ..
-;;   cmake --build . --verbose
+;;   cmake --build . --verbose -- -j 14 && ctest . --verbose
 ;;
 ;; For the tests you may need /usr/bin/env. In a container create it with
 ;;
@@ -89,8 +89,8 @@
        ; ("lodepng" ,lodepng) later!
        ("openmpi" ,openmpi)
        ("python" ,python)
-       ; ("sdsl-lite" ,sdsl-lite)
-       ; ("libdivsufsort" ,libdivsufsort)
+       ("sdsl-lite" ,sdsl-lite)
+       ("libdivsufsort" ,libdivsufsort)
        ))
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -99,6 +99,10 @@
       `(#:phases
         (modify-phases
          %standard-phases
+         (add-after 'unpack 'symlink-bash
+           (lambda _
+             (symlinklink "/bin/bash" "/bin/sh")
+             #t))
          ;; This stashes our build version in the executable
          (add-after 'unpack 'set-version
            (lambda _

scripts/test_binary.sh

@@ -44,4 +44,4 @@ if [[ $ret -eq 0 ]]; then
 else
     echo "[binary_tester] FAILED: At least one binary test for odgi untangle failed."
     exit 1
-fi
+fi

test/python/odgi_ffi.md

@@ -4,6 +4,7 @@
 
 The odgi toolkit for pangenomics comes with a simple "C" foreign function interface (FFI) that can be used from any computer language.
 The header file for the C-API can be found [here](https://github.com/pjotrp/odgi/blob/master/src/odgi-api.h).
+This C-API is covered by the `odgi-ffi` module.
 In this document we walk through the low-level API using the Python `odgi_ffi` module that comes with odgi.
 
 Note that odgi also has an older high-level Python API `import odgi` that is somewhat obsolete. Instead you should probably use below `import odgi_ffi` lower level API to construct your own library.

test/python/odgi_performance.md

@@ -0,0 +1,61 @@
+% -*- coding: utf-8 -*-
+
+# ODGI Python performance
+
+Here we showcase the new `odgi_ffi` module that is faster than the original `odgi` python module. Both are shipped with odgi now.
+
+Python bindings will always be slower than C++, or Rust, because much low level copying is going on and python keeps track of typing. Still python can be useful as a tool for exploring graphs. With the newer `odgi_ffi` module we using values instead of implicit C references.
+
+Let's time loading a graph and traversing it 100 times
+
+```python
+>>> import time
+>>> from odgi_ffi import *
+
+>>> graph = odgi_load_graph("DRB1-3123_sorted.og")
+
+>>> odgi_get_node_count(graph)
+3214
+
+>>> res = []
+>>> tic = time.perf_counter()
+>>> for x in range(1, 100):
+...    res.append(odgi_for_each_handle(graph, lambda h: odgi_get_sequence(graph,h) and True))
+
+>>> toc = time.perf_counter()
+>>> print(f"{toc - tic:0.4f} seconds")  # doctest: +SKIP
+0.7916 seconds
+
+```
+
+This is twice as fast as the older `odgi` module. That would look like
+
+```python
+from odgi import *
+import time
+
+gr = graph()
+
+gr.load("DRB1-3123_sorted.og")
+
+gr.get_node_count()
+
+tic = time.perf_counter()
+for x in range(1, 100):
+    gr.for_each_handle(lambda h: gr.get_sequence(h) and True)
+toc = time.perf_counter()
+print(f"{toc - tic:0.4f} seconds")
+
+```
+
+Run that in the odgi built source repository with something like
+
+```sh
+cd test
+env LD_PRELOAD=libjemalloc.so.2 \
+  LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib:../lib \
+  PYTHONPATH=../lib python3 performance2.py
+1.4674 seconds
+```
+
+For more see the [odgi_ffi interface](odgi_ffi.md).