Mercurial > pytave
changeset 33:1d7bab3bc745 task
Documentation
| author | David Grundberg <individ@acc.umu.se> |
|---|---|
| date | Tue, 05 May 2009 20:57:54 +0200 |
| parents | def8098ddb9e |
| children | 24e1734d26b0 |
| files | ChangeLog INSTALL NEWS README |
| diffstat | 4 files changed, 295 insertions(+), 331 deletions(-) [+] |
line wrap: on
line diff
--- a/ChangeLog Tue May 05 20:57:24 2009 +0200 +++ b/ChangeLog Tue May 05 20:57:54 2009 +0200 @@ -1,3 +1,12 @@ +2009-05-05 David Grundberg <individ@acc.umu.se> + + * python_to_octave.cc: Function pydict_to_octmap modified. + * m4/ax_octave.m4, m4/ax_python_devel.m4: New files. + * m4/ax_python.m4: Removed. + * m4/ax_boost_python.m4, README, INSTALL: Rewritten. + * configure.ac, setup.py.in, Jamfile.in, Makefile.am: Adjusted to + new Autoconf macros. + 2008-11-17 Håkan Fors Nilsson <c04hfn@cs.umu.se> * octave_to_python.cc: Added functions octcell_to_pyobject and @@ -39,6 +48,6 @@ Local Variables: coding: utf-8 -fillcolumn: 72 +fill-column: 74 End: -vim: set textwidth=72 noexpandtab : +vim: set textwidth=74 noexpandtab :
--- a/INSTALL Tue May 05 20:57:24 2009 +0200 +++ b/INSTALL Tue May 05 20:57:54 2009 +0200 @@ -1,237 +1,145 @@ -Installation Instructions -************************* - -Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005 Free -Software Foundation, Inc. - -This file is free documentation; the Free Software Foundation gives -unlimited permission to copy, distribute and modify it. - -Basic Installation -================== - -These are generic installation instructions. See README for pytave -instructions. - - The `configure' shell script attempts to guess correct values for -various system-dependent variables used during compilation. It uses -those values to create a `Makefile' in each directory of the package. -It may also create one or more `.h' files containing system-dependent -definitions. Finally, it creates a shell script `config.status' that -you can run in the future to recreate the current configuration, and a -file `config.log' containing compiler output (useful mainly for -debugging `configure'). - - It can also use an optional file (typically called `config.cache' -and enabled with `--cache-file=config.cache' or simply `-C') that saves -the results of its tests to speed up reconfiguring. (Caching is -disabled by default to prevent problems with accidental use of stale -cache files.) - - If you need to do unusual things to compile the package, please try -to figure out how `configure' could check whether to do them, and mail -diffs or instructions to the address given in the `README' so they can -be considered for the next release. If you are using the cache, and at -some point `config.cache' contains results you don't want to keep, you -may remove or edit it. - - The file `configure.ac' (or `configure.in') is used to create -`configure' by a program called `autoconf'. You only need -`configure.ac' if you want to change it or regenerate `configure' using -a newer version of `autoconf'. - -The simplest way to compile this package is: - - 1. `cd' to the directory containing the package's source code and type - `./configure' to configure the package for your system. If you're - using `csh' on an old version of System V, you might need to type - `sh ./configure' instead to prevent `csh' from trying to execute - `configure' itself. - - Running `configure' takes awhile. While running, it prints some - messages telling which features it is checking for. - - 2. Type `make' to compile the package. - - 3. Optionally, type `make check' to run any self-tests that come with - the package. - - 4. Type `make install' to install the programs and any data files and - documentation. - - 5. You can remove the program binaries and object files from the - source code directory by typing `make clean'. To also remove the - files that `configure' created (so you can compile the package for - a different kind of computer), type `make distclean'. There is - also a `make maintainer-clean' target, but that is intended mainly - for the package's developers. If you use it, you may have to get - all sorts of other programs in order to regenerate files that came - with the distribution. - -Compilers and Options +Building instructions ===================== -Some systems require unusual options for compilation or linking that the -`configure' script does not know about. Run `./configure --help' for -details on some of the pertinent environment variables. +You can use either Python distutils, GNU Automake or Boost BJam to +build pytave. The configure script outputs files for all these build +systems. Autoconf's VPATH is supported on all build systems. + + Use the configure script to set up Octave and Boost::Python +paths. Run `./configure --help' for more info. + +Dependencies +============ + +Configuring: + an sh shell capable of running `configure' - You can give `configure' initial values for configuration parameters -by setting variables in the command line or in the environment. Here -is an example: +Building: + Python's distutils or + make or + BJam - ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix +Linked and tested with: + Python 2.4 + Boost::Python 1.33 + Octave 3.0.2 - *Note Defining Variables::, for more details. +Bootstraping from Bazaar trunk +============================== -Compiling For Multiple Architectures -==================================== + 1. `bzr branch lp:pytave' + + 2. `autoreconf --install' + + 3. `./configure' -You can compile the package for more than one kind of computer at the -same time, by placing the object files for each architecture in their -own directory. To do this, you must use a version of `make' that -supports the `VPATH' variable, such as GNU `make'. `cd' to the -directory where you want the object files and executables to go and run -the `configure' script. `configure' automatically checks for the -source code in the directory that `configure' is in and in `..'. +Autotools +========= + +The Autotools build system need not be installed to build the +module. You need `make' and all library dependencies though. + + 1. Create the `Makefile' by typing: + `./configure --prefix=/directory/where/you/want/the/module/file' + + 2. Type `make' to build the extention module. + + 3. To copy the pytave dynamic library to the prefix, type + `make install' - If you have to use a `make' that does not support the `VPATH' -variable, you have to compile the package for one architecture at a -time in the source code directory. After you have installed the -package for one architecture, use `make distclean' before reconfiguring -for another architecture. +BJam +==== + +BJam must be installed in order to build the module. You also need a +proper `user-config.jam' file in your home directory. + + 1. Create `Jamfile' and `project-root.jam' by typing `./configure' -Installation Names -================== + 2. Use your `bjam' command to build the extention module. + +user-config.jam +=============== + +For your convenience, here the content of a typical ~/user-config.jam +on a GNU/Linux system: + +using gcc ; +using python : 2.5 ; -By default, `make install' installs the package's commands under -`/usr/local/bin', include files under `/usr/local/include', etc. You -can specify an installation prefix other than `/usr/local' by giving -`configure' the option `--prefix=PREFIX'. +Distutils +========= + + 1. Create the `setup.py' file by typing `./configure' + + 2. Run `python setup.py build' to build and package the extention + module together with the pure Python files. + +Running from build directory +============================ - You can specify separate installation prefixes for -architecture-specific files and architecture-independent files. If you -pass the option `--exec-prefix=PREFIX' to `configure', the package uses -PREFIX as the prefix for installing programs and libraries. -Documentation and other data files still use the regular prefix. +Pytave is made up of three parts. The `pytave' package, the +`pytave/pytave' module and the `pytave/_pytave' extention. When the +user uses `import pytave', the pytave package __init__ script loads +both the module and the extention. It is important that they both can +be found. + + 1. Follow the Distutils build instructions. A complete Python + package directory called `pytave' is created in + `build/lib.something' - In addition, if you use an unusual directory layout you can give -options like `--bindir=DIR' to specify different values for particular -kinds of files. Run `configure --help' for a list of the directories -you can set and what kinds of files go in them. + 2. Start the Python interactive interpreter with + `PYTHONPATH=build/lib.linux-i686-2.4/ python' (with appropiate + changes for your system.) + + 3. In the interpreter you can now access Octave through Python: + +import pytave +import Numeric +pytave.feval(1, "cos", 0) +b = pytave.addpath(".") +pytave.feval(1, "testfile", 42) - If the package supports it, you can cause programs to be installed -with an extra prefix or suffix on their names by giving `configure' the -option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. + (Observe that there is a testfile.m file in the distribution.) + + Using BJam or Automake instead of Distutils, you load the +`pytave/pytave' module and the extention instead of the whole +package. Using `import pytave' now calls the module directly, but the +difference is transparent to the user. -Optional Features -================= + Basically all you want to do is load Python with shared library +for the pytave extention (called `pytave/_pytave') and the native +`pytave/pytave' module. BJam creates shared library in the +`bin/something/something' directory, while Autotools hide a working +shared library in the `.libs' directory. The contents of the `pytave' +package is stored in the directory `package' of the source +package. This is an example for an Autotools build. + + 1. Follow the Autotools build instructions. -Some packages pay attention to `--enable-FEATURE' options to -`configure', where FEATURE indicates an optional part of the package. -They may also pay attention to `--with-PACKAGE' options, where PACKAGE -is something like `gnu-as' or `x' (for the X Window System). The -`README' should mention any `--enable-' and `--with-' options that the -package recognizes. + 2. Start the Python interpreter with a Python path set to a path + containing `_pytave.so' and the `package' directory. A common way + to do this with the bash shell is to execute this command: + `PYTHONPATH=.libs:package python'. + +Installing with distutils +========================= - For packages that use the X Window System, `configure' can usually -find the X include and library files automatically, but if it doesn't, -you can use the `configure' options `--x-includes=DIR' and -`--x-libraries=DIR' to specify their locations. + 1. Run `python setup.py install' -Specifying the System Type +Creating a source dist +====================== + + 1. Run `make distcheck' + +Hint about foreign systems ========================== -There may be some features `configure' cannot figure out automatically, -but needs to determine by the type of machine the package will run on. -Usually, assuming the package is built to be run on the _same_ -architectures, `configure' can figure that out, but if it prints a -message saying it cannot guess the machine type, give it the -`--build=TYPE' option. TYPE can either be a short name for the system -type, such as `sun4', or a canonical name which has the form: - - CPU-COMPANY-SYSTEM - -where SYSTEM can have one of these forms: - - OS KERNEL-OS - - See the file `config.sub' for the possible values of each field. If -`config.sub' isn't included in this package, then this package doesn't -need to know the machine type. - - If you are _building_ compiler tools for cross-compiling, you should -use the option `--target=TYPE' to select the type of system they will -produce code for. - - If you want to _use_ a cross compiler, that generates code for a -platform different from the build platform, you should specify the -"host" platform (i.e., that on which the generated programs will -eventually be run) with `--host=TYPE'. - -Sharing Defaults -================ - -If you want to set default values for `configure' scripts to share, you -can create a site shell script called `config.site' that gives default -values for variables like `CC', `cache_file', and `prefix'. -`configure' looks for `PREFIX/share/config.site' if it exists, then -`PREFIX/etc/config.site' if it exists. Or, you can set the -`CONFIG_SITE' environment variable to the location of the site script. -A warning: not all `configure' scripts look for a site script. - -Defining Variables -================== - -Variables not defined in a site shell script can be set in the -environment passed to `configure'. However, some packages may run -configure again during the build, and the customized values of these -variables may be lost. In order to avoid this problem, you should set -them in the `configure' command line, using `VAR=value'. For example: +If you are running on a system incapable of executing the configure +scripts (e.g. a Microsoft Windows system), you may want to try +installing the `MinGW' and `MSYS' packages, and build everything +inside that environment. This isn't for the faint of hearted though, +since you need/want to build Octave too. It is probably easier than +trying to build without configure scripts, that's all. There are no +guarentees that it will build at all, it has not been tested. - ./configure CC=/usr/local2/bin/gcc - -causes the specified `gcc' to be used as the C compiler (unless it is -overridden in the site shell script). Here is a another example: - - /bin/bash ./configure CONFIG_SHELL=/bin/bash - -Here the `CONFIG_SHELL=/bin/bash' operand causes subsequent -configuration-related scripts to be executed by `/bin/bash'. - -`configure' Invocation -====================== - -`configure' recognizes the following options to control how it operates. - -`--help' -`-h' - Print a summary of the options to `configure', and exit. - -`--version' -`-V' - Print the version of Autoconf used to generate the `configure' - script, and exit. - -`--cache-file=FILE' - Enable the cache: use and save the results of the tests in FILE, - traditionally `config.cache'. FILE defaults to `/dev/null' to - disable caching. - -`--config-cache' -`-C' - Alias for `--cache-file=config.cache'. - -`--quiet' -`--silent' -`-q' - Do not print messages saying which checks are being made. To - suppress all normal output, redirect it to `/dev/null' (any error - messages will still be shown). - -`--srcdir=DIR' - Look for the package's source code in directory DIR. Usually - `configure' can determine that directory automatically. - -`configure' also accepts some other, not widely useful, options. Run -`configure --help' for more details. - +EOF. \ No newline at end of file
--- a/NEWS Tue May 05 20:57:24 2009 +0200 +++ b/NEWS Tue May 05 20:57:54 2009 +0200 @@ -1,9 +1,8 @@ Version 0.1-bzr -* Added functionality for one dimensional cell arrays. Python list represents -a one dimensional cell array. Pytave will throw an exception if a cell array -has higher dimensions. +* Added functionality for one-row cell arrays. The Python list is + converted to a one-row cell array and vice versa. -* Added functionality for structs, a Octave struct is represented by a Python -dictionary. The implementation tries to be as true as possible to Octave's -struct constructor. +* Added functionality for structs. The Python distionary is converted + to a Octave struct and vice versa. The implementation tries to be + as true as possible to Octave's struct constructor.
--- a/README Tue May 05 20:57:24 2009 +0200 +++ b/README Tue May 05 20:57:54 2009 +0200 @@ -1,148 +1,196 @@ -pytave README -************* +-*- coding:utf-8 -*- -Building instructions -===================== +Pytave README + +For installation instructions specific for Pytave, please see the +INSTALL file. -You can use either Python distutils, GNU Automake or Boost BJam to -build pytave. The configure script outputs files for all these build -systems. Autoconf's VPATH is supported on all build systems. +Contents of this document +========================= - Use the configure script to set up Octave and Boost::Python -paths. Run `./configure --help' for more info. +1. What is Pytave? +2. Gotchas +3. Pytave and multi-threading +4. Python/Octave cheat sheet -Dependencies -============ - -Configuring: - an sh shell capable of running `configure' +What is Pytave? +*************** -Building: - Python's distutils or - make or - BJam +Pytave enables Python scripts to use existing m-files (Octave/Matlab +scripts) for numerical calculations. The Octave language interpreter +is embedded as a module to Python. + +Example use +=========== + +Calling Octave code in the interactive Python interpreter: -Linked and tested with: - Python 2.4 - Boost::Python 1.33 - Octave 3.0.2 +>>> import pytave +>>> pytave.feval(1, "cos", 0) +(1.0,) + +Goals +===== -Bootstraping from Bazaar trunk -============================== +Pytave strives to uphold these points - 1. `bzr branch lp:pytave' + * Good out of the box experience - 2. `autoreconf --install' - - 3. `./configure' + * Good-natured implicit type conversions, no strange PyApple -> + octave_orange -> PyBanana chains -Autotools -========= +Features +======== -The Autotools build system need not be installed to build the -module. You need `make' and all library dependencies though. +A short list of what Pytave is capable of - 1. Create the `Makefile' by typing: - `./configure --prefix=/directory/where/you/want/the/module/file' + * Implicit type conversions between Python and Octave. Supports all + Numeric integer, real double (and possibly real float) matrices - 2. Type `make' to build the extention module. + * Architecture independent - no assumption on endian type or integer + sizes - 3. To copy the pytave dynamic library to the prefix, type - `make install' + * Supports cell <-> list and struct <-> dict conversions. -BJam -==== +Project homepage +================ -BJam must be installed in order to build the module. You also need a -proper `user-config.jam' file in your home directory. +https://launchpad.net/pytave + +Using/hacking +============= - 1. Create `Jamfile' and `project-root.jam' by typing `./configure' +You need the Bazaar version control software (bzr). Branch from trunk +with: - 2. Use your `bjam' command to build the extention module. + $ bzr branch lp:pytave -user-config.jam -=============== + You will now have a directory called `pytave' with source code for +the module. Read the INSTALL file for building instructions. -For your convenience, here the content of a typical ~/user-config.jam -on a GNU/Linux system: +Gotchas +******* -using gcc ; -using python : 2.5 ; +Unfortunately, the implicit conversion is not bijective (there is not +a one-to-one relation between Octave and Python values). Pytave users +should be aware of the following cases. -Distutils -========= +Numeric row vectors to Octave matrices +====================================== - 1. Create the `setup.py' file by typing `./configure' +Numeric row vectors are converted to Octave 1xN matrices; returned 1xN +matrices will become 1xN numerical arrays, not row vectors. As an +example, a Numeric array with shape == (3,) will become (1, 3) when +converted back and forth. - 2. Run `python setup.py build' to build and package the extention - module together with the pure Python files. - -Running from build directory +Octave cells to Python lists ============================ -Pytave is made up of three parts. The `pytave' package, the -`pytave/pytave' module and the `pytave/_pytave' extention. When the -user uses `import pytave', the pytave package __init__ script loads -both the module and the extention. It is important that they both can -be found. +Only row cell arrays can be converted to Python lists. + +Python dictionaries to Octave structures +======================================== + +Dictionaries converted to structures must only have string keys. This +is because Octave structures only allow string keys. Keys must also +be valid Octave identifiers. + + As Octave structures are built using cells, simple variables are +upgraded to cells when a dictionary is converted. A dictionary - 1. Follow the Distutils build instructions. A complete Python - package directory called `pytave' is created in - `build/lib.something' +{"name": "Pytave"} + +thus will become - 2. Start the Python interactive interpreter with - `PYTHONPATH=build/lib.linux-i686-2.4/ python' (with appropiate - changes for your system.) +ans = +{ + name = Pytave +} + +in Octave. In this listing, Octave is hiding the fact that the value +is wrapped in a cell. Converted back, cells are converted to Python +lists. The re-converted Python dictionary will read - 3. In the interpreter you can now access Octave through Python: +{"name": ["Pytave"]} + +which is natural effect because of the way Octave handles structures. + + The list values in dictionaries to be converted must be of equal +length. All restrictions demanded by the Octave `struct' built-in +applies. + +Pytave and multi-threading +************************** -import pytave -import Numeric -pytave.feval(1, "cos", 0) -b = pytave.addpath(".") -pytave.feval(1, "testfile", 42) +Pytave does not handle reentrant calls. It is not thread-safe, and +you cannot make several Pytave calls in parallel. There are no safety +harnesses in Pytave (unlike e.g. PySqlite), and Pytave will not stop +you if you try to make concurrent calls. The behavior is undefined. +It is not possible to run several calculations in parallel. - (Observe that there is a testfile.m file in the distribution.) + That being said, it is possible to do other things while one Pytave +call is running. Pytave is aware of the Global Interpreter Lock. The +lock will be released while the Octave interpreter is running, +allowing you to have other Python threads to run in parallel with the +one Octave call. - Using BJam or Automake instead of Distutils, you load the -`pytave/pytave' module and the extention instead of the whole -package. Using `import pytave' now calls the module directly, but the -difference is transparent to the user. +Python/Octave cheat sheet +************************* - Basically all you want to do is load Python with shared library -for the pytave extention (called `pytave/_pytave') and the native -`pytave/pytave' module. BJam creates shared library in the -`bin/something/something' directory, while Autotools hide a working -shared library in the `.libs' directory. The contents of the `pytave' -package is stored in the directory `package' of the source -package. This is an example for an Autotools build. +Octave and Python share some syntax elements, which unfortunately +makes it harder to distinguish between the languages. Here are some +examples in both languages, showing how to build related constructs. + +Create a 2x3 matrix +=================== + +octave:1> [1, 1, 1; 2, 2, 2] +python>>> array([[1, 1, 1], [2, 2, 2]]) + +Create a 3x2 matrix +=================== - 1. Follow the Autotools build instructions. +octave:1> [1, 1; 2, 2; 3, 3] +python>>> array([[1, 1], [2, 2], [3, 3]]) + +Create a 1x3 matrix +=================== - 2. Start the Python interpreter with a Python path set to a path - containing `_pytave.so' and the `package' directory. A common way - to do this with the bash shell is to execute this command: - `PYTHONPATH=.libs:package python'. +octave:1> [1, 1, 1] +python>>> array([[1, 1, 1]]) -Installing with distutils -========================= +Create a row vector +=================== + +Not applicable to Octave. +python>>> array([1, 1, 1]) - 1. Run `python setup.py install' +Note: Python row vectors will be converted to Octave 1xN matrices. -Creating a source dist -====================== +Create a 3x1 matrix +=================== - 1. Run `make distcheck' +octave:1> [1; 2; 3] +python>>> array([[1], [2], [3]]) -Hint about foreign systems -========================== +Create a 1x1 structure/dictionary +================================= + +octave:1> struct("x", 1, "y", 2) +python>>> {"x": 1, "y": 2} -If you are running on a system incapable of executing the configure -scripts (e.g. a Microsoft Windows system), you may want to try -installing the `MinGW' and `MSYS' packages, and build everything -inside that environment. This isn't for the faint of hearted though, -since you need/want to build Octave too. It is probably easier than -trying to build without configure scripts, that's all. There are no -guarentees that it will build at all, it has not been tested. +Create a 1x2 structure array/dictionary containing lists of length 2 +==================================================================== + +octave:1> struct("firstname", {"David", "Håkan"}, ... + "lastname", {"Grundberg", "Fors Nilsson"}) +python>>> {"firstname": ["David", "Håkan"], \ + "lastname": ["Grundberg", "Fors Nilsson"]} -EOF. \ No newline at end of file +Create a 1x3 cell array/list +============================ + +octave:1> {"foo", "bar", "baz"} +python>>> ["foo", "bar", "baz"] + +EOF.