Merge pull request #217 from eendebakpt/dev

Release 2.7.2

.pre-commit-config.yaml

@@ -2,14 +2,14 @@ exclude: 'doc/conf.py'
 
 repos:
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.20.0
+    rev: v2.37.3
     hooks:
     -   id: pyupgrade
         # for now don't force to change from %-operator to {}
         args: [--keep-percent-format, --py37-plus]
 
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.3.0
     hooks:
     -   id: check-ast
     -   id: check-builtin-literals
@@ -22,18 +22,18 @@ repos:
         args: [--remove]
 
 -   repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: 'v1.5.7'
+    rev: 'v1.7.0'
     hooks:
     -   id: autopep8
         args: [--max-line-length=120]
 
 -   repo: https://github.com/PyCQA/isort/
-    rev: 5.9.1
+    rev: 5.10.1
     hooks:
     -   id: isort
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 0.13.1
+  rev: 1.4.0
   hooks:
     - id: nbqa-black
       additional_dependencies: [black==20.8b1]

.travis.yml

@@ -1,11 +1,14 @@
 # C++ build
 language: cpp
-compiler:
-    - gcc
-    - clang
-os:
-- osx
-- linux
+
+jobs:
+   include:
+     - os: linux
+       compiler: gcc
+     - os: linux
+       compiler: clang
+     - os: osx
+       compiler: gcc
 
 #before_install:
 #  - sudo apt-get install cmake
@@ -35,5 +38,3 @@ script:
 
   - ./oaconference -N 12 -k 6 -v 0
   - ./oapareto result-20.2-2-2.oa -f B -o dummy.oa
-
-

CMakeLists.txt

@@ -1,5 +1,5 @@
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.0)
 
 PROJECT(OApackage)
 
@@ -8,9 +8,7 @@ PROJECT(OApackage)
 # ----------------------------------------------------------------------------
 
 if(WIN32)
-	#message(STATUS "Set build type...")
 	set(CMAKE_CONFIGURATION_TYPES Release CACHE TYPE INTERNAL FORCE) # no Debug
-	#set(CMAKE_BUILD_TYPE Release STRING)
 endif()
 
 if (NOT WIN32)
@@ -27,8 +25,6 @@ if(ZLIB_FOUND)
 endif()
 message(STATUS "ZLIB_FOUND: ${ZLIB_FOUND}")
 if(ZLIB_FOUND)
-	#message(STATUS "ZLIB_INCLUDE_DIRS: ${ZLIB_INCLUDE_DIRS}")
-	#message(STATUS "ZLIB_LIBRARIES: ${ZLIB_LIBRARIES}")
 	include_directories(${ZLIB_INCLUDE_DIRS})
 endif()
 
@@ -38,12 +34,13 @@ if (NumPy_FOUND)
   message(STATUS "NumPy was found")
 endif()
 
-# find_package(MPI)	# Needed for legacy code and OpenMP functionality
 
 # ----------------------------------------------------------------------------
 #   Code
 # ----------------------------------------------------------------------------
 
+set (CMAKE_CXX_STANDARD 11)
+
 include_directories(.)
 include_directories(src)
 include_directories(nauty)
@@ -151,10 +148,6 @@ if("$ENV{OADEBUG}" STREQUAL "1")
   set(COPTS "-g -O0 -DOADEBUG" ) # -std=c++0x -Weffc++")
 endif()
 
-if(WIN32)
-else()
-    set(LINKOPTS "${LINKOPTS}") # or use -s option
-endif()
 
 if(WIN32)
   set(COPTS "/MT /wd4018 /wd4996")
@@ -167,7 +160,7 @@ endif()
 
 set(COPTS "${COPTS} -DFULLPACKAGE")
 
-if(ZLIB_FOUND AND 1)
+if(ZLIB_FOUND)
   set(COPTS "${COPTS} -DUSEZLIB")
   include_directories(ZLIB_INCLUDE_DIRS)
 else()
@@ -208,7 +201,7 @@ set(progs oacat oajoin oapareto oasplit oaanalyse oainfo oaunittest oaconvert oa
 set(progsextend )
 
 list(APPEND progs oacheck oastreaming oaranktest oatest oaclustergather)
-list(APPEND progs oa_depth_extend)
+list(APPEND progs oa_depth_extend oa_select_maxj)
 
 if (WIN32)
   add_library(oalib STATIC ${srcsextend} ${headersextend} ${nautysrc} ${graphsrc})
@@ -240,39 +233,6 @@ endif()
   TARGET_LINK_LIBRARIES(oaextendsingle oalib)
   set(extendprogs oaextendsingle )
 
-  if (MPI_FOUND AND NOT WIN32 AND 1)
-    message(STATUS "Found MPI package: adding oaextendmpi")
-    if (VERBOSE)
-	message(STATUS "MPI executable: ${MPIEXEC}, libs ${MPI_LIBRARIES}")
-    endif()
-    #message(STATUS "   libs ${MPI_LIBRARIES}; flags ${MPI_COMPILE_FLAGS}; libs ${MPI_LIBRARIES}")
-    include_directories( ${MPI_INCLUDE_PATH} )
-    include_directories( src/mpitools )
-
-  add_executable(oaextendmpi EXCLUDE_FROM_ALL "utils/oaextend.cpp" ${headersextend} ${srcsextend} "src/mpitools/mpitools.cpp")
-  target_link_libraries(oaextendmpi ${MPI_LIBRARIES})
-  if(MPI_COMPILE_FLAGS)
-    set_target_properties(oaextendmpi PROPERTIES COMPILE_FLAGS "${MPI_COMPILE_FLAGS}")
-  endif()
-  if(MPI_LINK_FLAGS)
-      if (WIN32)
-		set_target_properties(oaextendmpi PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS} /MT")
-		endif()
-    set_target_properties(oaextendmpi PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
-  endif()
-
-  set_target_properties(oaextendmpi PROPERTIES COMPILE_DEFINITIONS "OAEXTEND_MULTICORE;NEWINTERFACE" )
-
-   if (WIN32)
-    if(ZLIB_FOUND)
-      TARGET_LINK_LIBRARIES(oaextendmpi ${ZLIB_LIBRARIES})
-    endif()
-   else()
-      TARGET_LINK_LIBRARIES(oaextendmpi m ${ZLIB_LIBRARIES})
-   endif()
-
-  endif(MPI_FOUND AND NOT WIN32 AND 1)
-
 message(STATUS "Extend progs: ${extendprogs}")
 
 message(STATUS "Progs: ${progs}")

CONTRIBUTORS.md

@@ -3,5 +3,4 @@
 * Pieter Eendebak
 * Eric Schoen
 * Alan Vazquez-Alcocer
-
-
+* Alexandre Bohyn

appveyor.yml

@@ -11,6 +11,10 @@ environment:
 
   matrix:
 
+    - PYTHON: "C:\\Python310-x64"
+      PYTHON_VERSION: "3.10.4"
+      PYTHON_ARCH: "64"
+
     - PYTHON: "C:\\Python39-x64"
       PYTHON_VERSION: "3.9.1"
       PYTHON_ARCH: "64"
@@ -27,10 +31,6 @@ environment:
       PYTHON_VERSION: "3.7.x"
       PYTHON_ARCH: "64"
 
-    - PYTHON: "C:\\Python37"
-      PYTHON_VERSION: "3.7.x"
-      PYTHON_ARCH: "32"
-
 matrix:
       fast_finish: true
 
@@ -100,7 +100,7 @@ install:
   - "%CMD_IN_ENV% pip install mock"
   - "%CMD_IN_ENV% python -c \"import mock\""
 
-  - cinst -y swig --version 4.0.1
+  - cinst -y swig # --version 3.0.12
 
 build: off
 

docs/examples/example_mixed_level_gwlp.ipynb

@@ -11,13 +11,43 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "References [xx]"
+    "This notebook contains example code to compute the type-specific generalized word-length pattern (GWLP) for mixed-level designs, more specifically for regular four-and-two-level designs.\n",
+    "\n",
+    "In four-and-two-level designs, the four-level factors are constructed us the grouping scheme of [Wu & Zhang (1989)](https://doi.org/10.1093/biomet/80.1.203) where the levels of a four-level factor $A$ are based on the levels of three two-level factors $a_1$, $a_2$ and $a_3$, called the pseudo-factors, where $I=a_1a_2a_3$:\n",
+    "$$\n",
+    "\\begin{array}{ccccc}\n",
+    "        a_1 & a_2 & a_3 & & A \\\\\n",
+    "        1 & 1 & 0 & \\rightarrow & 0 \\\\\n",
+    "        1 & 0 & 1 & \\rightarrow & 1 \\\\\n",
+    "        0 & 1 & 1 & \\rightarrow & 2 \\\\\n",
+    "        0 & 0 & 0 & \\rightarrow & 3 \\\\\n",
+    "    \\end{array}\n",
+    "$$\n",
+    "The two-level factors can either be main factors or be entirely aliased with a combination of the main factors. Such aliased factors are called added factors. If one of the main factors, used in an added factor, is also used as pseudo-factor in a four-level factor, then the added factor has type $I$. If it is used as pseudo-factor in two distinct four-level factor, it has type $II$, etc $\\ldots$."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "import oapackage"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create a $4^{1}2^{7}$ four-and-two-level regular design in 32 runs with 1 four-level factor and 7 two-level factors."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -60,16 +90,22 @@
     }
    ],
    "source": [
-    "import numpy as np\n",
-    "\n",
-    "import oapackage\n",
-    "\n",
     "array = oapackage.exampleArray(56, 1)\n",
     "array = array.selectFirstColumns(7)\n",
     "arrayclass = oapackage.arraylink2arraydata(array)\n",
     "array.showarraycompact()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The GWLP for mixed-level designs is computed using the adapted forms of equations (7) and (8) in [Xu and Wu (2001)](https://www.doi.org/10.1214/aos/1009210552).\n",
+    "\n",
+    "## Distance distribution\n",
+    "First, the distance distribution is first computed for all combinations of $(i,j)$ with $i \\in \\{0,1\\}$ and $j=0,\\ldots,7$ and $i\\neq j$. In this example with a $4^12^{7}$ design, that is a $2 \\times 8$ matrix $B$, where $B_{i,j}$ is the number of rows that have $(1-i)$ different elements if their four-level parts and $(7-j)$ different elements in their two-level parts, divided by the number of runs."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,
@@ -79,15 +115,31 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "distance distribution for mixed-level design [[1 0 1 4 1 0 1]\n",
+      "distance distribution for mixed-level design\n",
+      "[[1 0 1 4 1 0 1]\n",
       " [0 2 6 8 6 2 0]]\n"
      ]
     }
    ],
    "source": [
     "Dm = oapackage.distance_distribution_mixed(array, 0)\n",
     "D = np.array(Dm).astype(int)\n",
-    "print(f\"distance distribution for mixed-level design {D}\")"
+    "print(f\"distance distribution for mixed-level design\\n{D}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This is verified since the sum of the matrix is 32 which is equal to $\\binom{32}{2} 32^{-1}$.\n",
+    "\n",
+    "## McWilliams Transforms\n",
+    "\n",
+    "Now, the second step in the computation of the GWLP, is to use the McWilliams Transforms to obtain the GWLP from the distance distribution matrix. The McWilliams Transform will create another $2 \\times 8$ matrix $B^{\\prime}$, obtained using the following formula\n",
+    "$$\n",
+    "B_{j_{1}, j_{2}}^{\\prime}=N^{-1} \\sum_{i_{1}=0}^{m} \\sum_{i_{2}=0}^{n} B_{i_{1}, i_{2}} P_{j_{1}}\\left(i_{1} ; 1, 4\\right) P_{j_{2}}\\left(i_{2} ; 7, 2\\right)\n",
+    "$$\n",
+    "where $P_j(x,n,s)$ is the Krawtchouck polynomials for a total of $n$ factors with $s$ levels."
    ]
   },
   {
@@ -108,17 +160,24 @@
    "source": [
     "N = array.n_rows\n",
     "factor_levels_for_groups = arrayclass.factor_levels_column_groups()\n",
-    "\n",
-    "Bprime = oapackage.macwilliams_transform_mixed(\n",
-    "    Dm, N, factor_levels_for_groups=arrayclass.factor_levels_column_groups(), verbose=0\n",
-    ")\n",
+    "Bprime = oapackage.macwilliams_transform_mixed(Dm, N, factor_levels_for_groups, verbose=0)\n",
     "print(f\"MacWilliams transform:\")\n",
-    "print(np.array(Bprime))"
+    "print(np.array(Bprime).astype(int))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This matrix is equivalent to the type specific generalized word-length pattern, where the row index indicates the type of words (0 to 1) and the column index indicates the length of the words (0 to 7).\n",
+    "\n",
+    "The generalized word-length pattern ($A$) can be obtained by summing the rows of the $B^{\\prime}$ matrix anti-diagonally. That is:\n",
+    "$$A_j(D) = \\sum_{i^{\\prime}+j^{\\prime}=j} B^{\\prime}_{i^{\\prime},j^{\\prime}}$$"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -136,6 +195,9 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "3a893c4079a4533c9db639b850e04910700d284bba4afe56b82dceecf522f906"
+  },
   "kernelspec": {
    "display_name": "Python 3 (ipykernel)",
    "language": "python",

oalib.i

@@ -516,6 +516,13 @@ public:
     }
 }
 
+%extend jstructconference_t {
+public:
+    std::string __repr__() {
+      return $self->showstr();
+    }
+}
+
 #ifdef SWIGPYTHON
 // Add module docstring
 %pythoncode

oapackage/oahelper.py

@@ -578,6 +578,15 @@ def write_text_arrayfile(filename: str, designs: List[Any], comment: str = None)
     afile.append_arrays(designs)
     afile.closefile()
 
+def arrayfile_generator(afile):
+    """ Return generator to read all files in the array file """
+    af = oapackage.arrayfile_t(afile)
+
+    na=af.narrays
+    for ii in range(na):
+        yield af.readnext()
+    af.closefile()
+
 
 def runcommand(cmd: str, dryrun=0, idstr: Optional[None] = None, verbose: int = 1, logfile: Optional[str] = None, shell: bool = True):
     """ Run specified command in external environment