Merge pull request #43 from lbl-srg/issue42_syslogCheck

Issue42 syslog check

.gitignore

@@ -1,18 +1,17 @@
 # Binaries
-bin/*
-!bin/*.py
+*.py[cod]
 
 # Object files
 *.o
 
 # Tests outputs
 tests/**/*.html
-tests/test_numerics*/*
+tests/test_numerics*/
 
 # Generated by CMake
 DartConfiguration.tcl
-build/*
+build/
 
 # Generated by development tools
-.vscode/*
+.vscode/
 *.pyc

.travis.yml

@@ -2,6 +2,7 @@ language: c
 
 python:
   - "2.7"
+  - "3.6"
 
 notifications:
   email: false
@@ -24,19 +25,22 @@ matrix:
       before_install:
         - choco install python2
         - export PATH="/c/Python27:/c/Python27/Scripts:$PATH"
-        - python -m pip install --upgrade pip wheel
+
+before_install:
+  - python -m pip install --user --upgrade pip
 
 install:
   - pip install --user -r requirements.txt
+  - pip install --user .
 
 before_script:
-  - mkdir build && cd build && cmake .. $ARCH_OPTION
+  - rm -rf build && mkdir build && cd build && cmake .. $ARCH_OPTION
 
 script:
   # Compile, link, install.
   - cmake --build . --target install --config Release
   # Test and clean.
-  - ctest -C Release && python ../tests/test_summary.py ../tests
+  - ctest -C Release
   # Compare.
   - git status tests
   - git diff --exit-code tests

CMakeLists.txt

@@ -18,7 +18,8 @@
 
 cmake_policy(SET CMP0048 NEW)
 cmake_minimum_required(VERSION 3.11.0)
-project(funnel VERSION 0.1.0 LANGUAGES C)
+file(READ "${CMAKE_SOURCE_DIR}/pyfunnel/VERSION" VERSION)
+project(funnel VERSION ${VERSION} LANGUAGES C)
 enable_testing()
 
 # Detect OS.
@@ -35,10 +36,6 @@ else()
     message(WARNING "OS unknown!")
 endif()
 
-# Output build system directories.
-message("CMake source directory is: ${CMAKE_SOURCE_DIR}")
-message("CMake binary directory is: ${CMAKE_BINARY_DIR}")
-
 # Set compiling and linking options.
 # Consider adding -std=c89 -pedantic to gcc options to improve portability.
 set(UNIX_COMPILE_FLAGS "-Wall -Wfloat-equal -o3 -fPIC")
@@ -70,10 +67,14 @@ elseif(MACOSX)
     set(PLATFORM_INSTALL_PREFIX darwin64)
 endif()
 
-set(ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/lib/${PLATFORM_INSTALL_PREFIX}")
-set(LIBRARY_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/lib/${PLATFORM_INSTALL_PREFIX}")
-set(RUNTIME_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/bin")
-set(PUBLIC_INCLUDE_DIRECTORY "${CMAKE_SOURCE_DIR}/include")
+set(ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/pyfunnel/lib/${PLATFORM_INSTALL_PREFIX}")
+set(LIBRARY_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/pyfunnel/lib/${PLATFORM_INSTALL_PREFIX}")
+
+# Print build system directories.
+message("CMake source directory is: ${CMAKE_SOURCE_DIR}")
+message("CMake binary directory is: ${CMAKE_BINARY_DIR}")
+message("CMake archive directory is: ${ARCHIVE_OUTPUT_DIRECTORY}")
+message("CMake library directory is: ${LIBRARY_OUTPUT_DIRECTORY}")
 
 # Manage subdirectories.
 add_subdirectory(src)
@@ -105,30 +106,30 @@ add_test(
 set(TEST_ARGS_0 --reference trended.csv --test simulated.csv --atolx 0.002 --atoly 0.002 --output results)
 add_test(
     NAME test_py_0
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/bin/pyfunnel.py" ${TEST_ARGS_0}
+    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_0}
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 ### Wrong arguments
 set(TEST_ARGS_1 --reference wrong.csv --test simulated.csv --atolx 0.002 --atoly 0.002 --output results)
 add_test(
     NAME test_py_1
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/bin/pyfunnel.py" ${TEST_ARGS_1}
+    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_1}
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 set_tests_properties(test_py_1 PROPERTIES PASS_REGULAR_EXPRESSION "No such file")
 ### Again
 set(TEST_ARGS_2 --reference trended.csv --test simulated.csv --atoly 0.002 --output results)
 add_test(
     NAME test_py_2
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/bin/pyfunnel.py" ${TEST_ARGS_2}
+    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_2}
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 set_tests_properties(test_py_2 PROPERTIES PASS_REGULAR_EXPRESSION "At least one of the two possible tolerance parameters")
 ### Again
 set(TEST_ARGS_3 --reference trended.csv --test simulated.csv --atolx 0.002 --atoly 0.002)
 add_test(
     NAME test_py_3
-    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/bin/pyfunnel.py" ${TEST_ARGS_3}
+    COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_SOURCE_DIR}/pyfunnel/pyfunnel.py" ${TEST_ARGS_3}
     WORKING_DIRECTORY "${CMAKE_TEST_DIR}/test_bin"
 )
 set_tests_properties(test_py_3 PROPERTIES PASS_REGULAR_EXPRESSION "Output directory not specified")
@@ -173,9 +174,15 @@ add_test(
 set_tests_properties(test_plot PROPERTIES FAIL_REGULAR_EXPRESSION "Exception;Error;Traceback")
 
 ## Configure pre/post test.
+set(summary_path "${CMAKE_TEST_DIR}/test_summary.py")
+set(CTEST_CUSTOM_POST_TEST
+    "${PYTHON_EXECUTABLE} ${summary_path} ${CMAKE_TEST_DIR}"
+)
 set(content "# Numerics testing configuration file
     set(CTEST_CUSTOM_PRE_TEST
-        ${CTEST_CUSTOM_PRE_TEST})"
+        ${CTEST_CUSTOM_PRE_TEST})
+    set(CTEST_CUSTOM_POST_TEST
+        \"${CTEST_CUSTOM_POST_TEST}\")"
 )
 file(WRITE
     "${CMAKE_BINARY_DIR}/CTestCustom.cmake"

COPYRIGHT.md

@@ -1,8 +1,8 @@
 # Copyright Notice
 
-"funnel v0.0.1" Copyright (c) 2018, The Regents of the University of California,
+"funnel" Copyright (c) 2018, The Regents of the University of California,
 through Lawrence Berkeley National Laboratory (subject to receipt of any required
-approvals from the U.S. Dept. of Energy).  All rights reserved.
+approvals from the U.S. Dept. of Energy). All rights reserved.
 
 If you have questions about your rights to use or distribute this software, please
 contact Berkeley Lab's Innovation & Partnerships Office at  [email protected].
@@ -12,4 +12,4 @@ Energy and the U.S. Government consequently retains certain rights.  As such,
 the U.S. Government has been granted for itself and others acting on its behalf
 a paid-up, non-exclusive, irrevocable, worldwide license in the Software to
 reproduce, distribute copies to the public, prepare derivative works, and perform
-publicly and display publicly, and to permit others to do so. 
+publicly and display publicly, and to permit others to do so.

LICENSE.md

@@ -1,25 +1,25 @@
 # License Agreement
 
-"funnel v0.0.1" Copyright (c) 2018, The Regents of the University of California,
+"funnel" Copyright (c) 2020, The Regents of the University of California,
 through Lawrence Berkeley National Laboratory (subject to receipt of any required
-approvals from the U.S. Dept. of Energy).  All rights reserved.
+approvals from the U.S. Dept. of Energy). All rights reserved.
 
-Redistribution and use in source and binary forms, with or without modification,
+1. Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:
 
-(1) Redistributions of source code must retain the above copyright notice, this
+   1. Redistributions of source code must retain the above copyright notice, this
 list of conditions and the following disclaimer.
 
-(2) Redistributions in binary form must reproduce the above copyright notice,
+   2. Redistributions in binary form must reproduce the above copyright notice,
 this list of conditions and the following disclaimer in the documentation and/or
 other materials provided with the distribution.
 
-(3) Neither the name of the University of California, Lawrence Berkeley National
+   3. Neither the name of the University of California, Lawrence Berkeley National
 Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used
 to endorse or promote products derived from this software without specific prior
 written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+2. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
 IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
@@ -30,12 +30,12 @@ OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
 EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-You are under no obligation whatsoever to provide any bug fixes, patches, or
+3. You are under no obligation whatsoever to provide any bug fixes, patches, or
 upgrades to the features, functionality or performance of the source code
 ("Enhancements") to anyone; however, if you choose to make your Enhancements
 available either publicly, or directly to Lawrence Berkeley National Laboratory,
 without imposing a separate written license agreement for such Enhancements,
 then you hereby grant the following license: a  non-exclusive, royalty-free
 perpetual license to install, use, modify, prepare derivative works, incorporate
 into other computer software, distribute, and sublicense such enhancements
-or derivative works thereof, in binary and source code form.  
+or derivative works thereof, in binary and source code form.

MANIFEST.in

@@ -0,0 +1,2 @@
+include pyfunnel/VERSION
+recursive-include pyfunnel/templates *

README.md

@@ -4,9 +4,6 @@
 
 A cross-platform C-based software for comparing two `(x, y)` data sets given tolerances in `x` and `y` directions.
 
-Handles: different time (`x`) scales, time events offsets, relative and absolute tolerances
-in `x` and `y` directions.
-
 ## Principles
 
 ### Overall
@@ -54,19 +51,30 @@ By convention, the error is `max(0, y - y_up) - min(0, y - y_low)` and hence it
 
 ### System Requirements
 
-The software has been tested on the following platforms for which a library is provided in `./lib`:
+The software has been tested on the following platforms.
 
   * Linux x64
   * Windows x64
   * Mac OS X
 
-The Python binding has been tested with Python `2.7.*` and `3.7.*`.
-See `requirements.txt` for the required Python packages.
+A Python binding is available to access the library. It is compatible with Python 2 and 3.
+
+### Installing
+
+The Python binding is delivered as a package named `pyfunnel`.
+
+The package is not published on PyPI but can be installed from GitHub with
+
+`pip git+https://github.com/lbl-srg/funnel.git@master`
 
-### Python Binding
+For development, additional dependencies are needed and can be installed with
+
+`pip install -r requirements.txt`
+
+### Main Functions
 
 The software is primarily intended to be used by means of a Python binding.
-The module `./bin/pyfunnel.py` provides the following functions:
+The package `pyfunnel` provides the following functions.
 
   * `compareAndReport`: calls `funnel` binary with list-like objects as `x`, `y` reference and test values.
     Outputs `errors.csv`, `lowerBound.csv`, `upperBound.csv`, `reference.csv`, `test.csv`
@@ -77,7 +85,8 @@ The module `./bin/pyfunnel.py` provides the following functions:
   * `plot_funnel`: plots `funnel` results stored in the directory which path is provided as argument.
     Displays plot in default browser. See function docstring for further details.
 
-The module might also be called directly from terminal:
+The module `pyfunnel.py` might also be called directly from terminal.
+
 ```
 usage: pyfunnel.py [-h] --reference REFERENCE --test TEST [--output OUTPUT]
                    [--atolx ATOLX] [--atoly ATOLY] [--rtolx RTOLX]
@@ -111,23 +120,19 @@ Full documentation at https://github.com/lbl-srg/funnel
 
 ### Example
 
-From a Python shell with `./tests/test_bin` as the current working directory, type
+From a Python shell with `./tests/test_bin` as the current working directory, run
 ```python
->>> import os
->>> import sys
 >>> import pandas as pd
->>> pyfunnel_dir = os.path.join(os.path.pardir, os.path.pardir, 'bin')
->>> sys.path.append(pyfunnel_dir)
 >>> import pyfunnel
 >>> ref = pd.read_csv('trended.csv')
 >>> test = pd.read_csv('simulated.csv')
 >>> pyfunnel.compareAndReport(xReference=ref.iloc(axis=1)[0], yReference=ref.iloc(axis=1)[1],
 ... xTest=test.iloc(axis=1)[0], yTest=test.iloc(axis=1)[1], atolx=0.002, atoly=0.002)
 >>> pyfunnel.plot_funnel('results')
 ```
-Or from a terminal with `./tests/test_bin` as the current working directory, type
+Or from a terminal with `./tests/test_bin` as the current working directory, run
 ```
-$ python ../../bin/pyfunnel.py --reference trended.csv --test simulated.csv --atolx 0.002 --atoly 0.002
+$ python ../../pyfunnel/pyfunnel.py --reference trended.csv --test simulated.csv --atolx 0.002 --atoly 0.002
 ```
 
 ## Build from Source
@@ -141,7 +146,7 @@ The distributed binaries have been built with Microsoft Visual Studio C/C++ comp
 
 ### Procedure
 
-To compile, link and install, from the top-level directory, run the following commands:
+To compile, link and install, from the top-level directory, run the following commands
 
 ```
 mkdir build
@@ -150,10 +155,10 @@ cmake ..                           (add `-A x64` on Windows to compile in 64 bit
 cmake --build . --target install   (add `--config Release` on Windows)
 ```
 
-To run the tests, from `./build` run the following commands:
+To run the tests, from `./build` run
+
 ```
 ctest                               (add `-C Release` on Windows)
-python ../tests/test_summary.py ../tests
 ```
 
 ## License

pyfunnel/VERSION

@@ -0,0 +1 @@
+0.1.0

pyfunnel/__init__.py

@@ -0,0 +1,18 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+    Python binding for funnel library.
+"""
+
+from __future__ import absolute_import
+
+import os
+
+from .core import compareAndReport, MyHTTPServer, CORSRequestHandler, plot_funnel
+
+# Version.
+version_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'VERSION'))
+with open(version_path) as f:
+    __version__ = f.read().strip()
+