small clean up of David's section, more to go.

[CommonLispStat.git] / README.org

Time-stamp: <2012-10-08 15:44:30 tony>

* Current Status: COMPLETELY BROKEN

  but we are rebuilding it.

* Fast Start

** Version 2 (David)

   (This held for the version before we removed liblispstat and plplot
   and some other "crutches" which had a bit too much bitrot).

   We assume that you have a lisp installed and that you have a
   passing acquaintence with the unix shell.

   1. The first point that you should note that is that these
      instructions are written with the assumption of the availibility
      of quicklisp.

   If you do not have quicklisp , please go to www.quicklisp.org and
   install it now

   2. The second point to note is that you will need the "git" utility
      installed on your machine.

      for mac osx sudo port install git
      for linux (eg debian) sudo apt-get install git

   3. Once that is done execute the following shell commands

#+begin_src shell
  cd ~/quicklisp/local-projects
  git clone git://github.com/blindglobe/common-lisp-stat.git
  cd comon-list-stat
  git submodules init
#+end_src

      These commands copy the the source from the repository and all
      the associated libraries. It will live as a quicklisp project in
      the local-projects directory. I find it convenient to
      symbolically link the quicklisp direct to ~/lisp for easy access

#+begin_src shell
   ln ~/quicklisp/local-projects ~/lisp
#+end_src

   4. Configure the locations of the BLAS and LINPACK libraries

      Currently this is a manual operation, which will change in a
      later version.

      Edit the file external/cl-blapack/load-blapack-libs.lisp

      Search for the following 3 parameters *gfortran-lib* *blas-lib*
      *lapack-lib*

      For OS X: change the parameters as suggested in the file. Both
      BLAS and LAPACK are pre installed on Mac OSX.

      For linux, make sure you have the neccessary libraries installed,
      through apt, yum or otherwise

      i.e.: 
#+BEGIN_SRC shell
sudo apt-get install libblas
sudo apt-get install liblapack
#+END_SRC

   5. For visualization we are currently using plplot and the
      cl-plplot interface. this requires the installation of the
      plplot library

      for MAC OSX you can use macports or homebrew

      5.1 sudo port install xquartz (or download from the xquartz home site)

      5.2 sudo port install plplot

      and on linux your favourite package manager of course.

      For windows, we recommend you use cygwin to get straightforward
      access. I'll document the steps if there is a demand.

   6. You need to check that your dynamic library path has been
      properly set up in the shell.  In your .bashrc (or equivalent
      shell init file)

      For Mac OSX set 

#+BEGIN_SRC 
DYLD_FALLBACK-LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:/opt/local/lib
#+END_SRC

      For Linux set 

#+BEGIN_SRC 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:????
#+END_SRC

      If you get this wrong the load process will not be able to find
      the libraries and will prompt you.

   5. Once the pre prequisites have been done, start your favourite lisp
      and enter 

#+begin_src lisp
(ql:register-local-projects)
(ql:quickload :cls) 
#+end_src lisp

      Retire for a well earned coffee and upon your return you should
      find the package completely installed.Obviously, potential
      errors can creep in with spelling the filenames correctly, so be
      careful.

** Version 1 (Tony)

  You probably did  (preferred)

#+name: LoadWithGitClone
#+begin_src shell
  git clone git://github.com/blindglobe/common-lisp-stat.git
#+end_src

  (or maybe using the repo.or.cz git repository archive), or (coming
  soon!) from within a Lisp instance:

#+name: LoadWithQuickLisp
#+begin_src lisp
  (ql:quickload :cls)
#+end_src

  At one point, I planned a pure git-delivery via cloning and
  submodules, but this proved to be a bit more complex than needed,
  thanks to the creation of quicklisp.  It's also a stupid idea if
  one plans to have users who are not hackers or developers, and
  eventually we want users.

  Despite quicklisp, there will need to be a version for delivering a
  system development-oriented CLS environment and this will consist of
  git repositories, possibly through submodules, but this (submodules)
  is for discussion.

  There are quite a few libraries that are needed, and right now we
  are working on simplifying the whole thing.   Once you get past
  this step, then you should:

  1. run a common lisp (SBCL, CMUCL, CLISP, CLOZURE-CL) starting in
     the current directory.  You will need ASDF at a minimum,
     QUICKLISP preferred.  And you should have QUICKLISP.

  2. (on Debian or similar systems: can use CLC (Common Lisp
     Controller) or SBCL approaches, i.e.  ~/.clc/systems or
     ~/.sbcl/systems should contain softlinks to the cls and other
     required ASDF files (i.e. cls.asd, cffi.asd, and lift.asd).

  There are example sessions and scripts for data analysis, some real,
  some proposed, in the file:examples/ directory.  Also see
  file:TODO.org for snippets of code that work or fail to work.

** Example Usage steps [2/7]

*** DONE Start and Load 
  
1. start your lisp
2. load CLS

#+BEGIN_SRC lisp
(ql:quickload :cls)
#+END_SRC

*** DONE Setup a place to work

In Common Lisp, you need to select and setup namespace to store data
and functions.  There is a scratch user-package, or sandbox, for
CLS, *cls-user* , which you can select via:

#+BEGIN_SRC lisp -n :tangle "readme-example.lisp"
(in-package :cls-user)
#+END_SRC

and this has some basic modules from CLS instantiated (dataframes,
probability calculus, numerical linear algebra, basic summaries
(numerical and visual displays).  

However, it can be better is to create a package to work in, which
pulls in only desired functionality:


#+BEGIN_SRC lisp +n :tangle "readme-example.lisp"
  (in-package cl-user)
  (defpackage :my-package-user
    (:documentation "demo of how to put serious work should be placed in
      a similar package elsewhere for reproducibility.  This hints as to
      what needs to be done for a user- or analysis-package.")
    (:nicknames :my-clswork-user)
    (:use :common-lisp ; always needed for user playgrounds!
          :lisp-matrix ; we only need the packages that we need...
          :common-lisp-statistics
          :cl-variates
          :lisp-stat-data-examples) ;; this ensures access to a data package
    (:shadowing-import-from :lisp-stat
        ;; This is needed temporarily until we resolve the dependency and call structure. 
        call-method call-next-method
  
        expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
        asin acos atan sinh cosh tanh asinh acosh atanh float random
        truncate floor ceiling round minusp zerop plusp evenp oddp 
        < <= = /= >= > > ;; complex
        conjugate realpart imagpart phase
        min max logand logior logxor lognot ffloor fceiling
        ftruncate fround signum cis
  
        <= float imagpart)
  
    (:export summarize-data summarize-results this-data this-report))
  
  (in-package :my-clswork-user) ;; or :my-package-user
  
  (setf my-data
        (let ((var1 )) ))
  
#+END_SRC

We need to pull in the packages with data or functions that we need;
just because the data/function is pulled in by another package, in
that package's namespace, does NOT mean it is available in this name
space.  However, the *common-lisp-statistics* package will ensure
that fundamental objects and functions are always available. 


*** TODO Get to work [0/3]

**** TODO Pull in or create data

**** TODO Summarize results

**** TODO Save work and results for knowledge building and reuse 

One can build a package, or save an image (CL implementation
dependent) or...
  
*** TODO Inform  moi of problems or successes

    NEED TO SETUP A MAILING LIST!!

    mailto:blindglobe@gmail.com if there is anything wrong, or
    even if something happens to work.

    Current beliefs:
    - SBCL is target platform.   CCL and CMUCL should be similar.
    - CLISP is finicky regarding the problems that we have with CFFI
      conversation.  In particular that we can not really do typing
      that we need to take care of.  I think this is my (Tony's)
      problem, not someone elses, and specifically, not CLISP's
    - Need to test ECL.

* History

   See files in file:Doc/  for history, design considerations, and
   random, sometimes false and misleading, musings.

* Local modifications, Development, Contributions

  Since this project is 

#+begin_src shell
#   git clone git://repo.or.cz/CommonLispStat.git 
   git clone git://github.com/blindglobe/common-lisp-stat.git 
   cd common-lisp-stat
#   git submodules init
#   git submodules update
#+end_src

   will pull the whole repository, and create a "master" branch to
   work on.  If you are making edits, which I'd like, you don't want
   to use the master branch, but more to use a topic-centric branch,
   so you might:

#+begin_src shell
    git checkout -b myTopicBranch
#+end_src

and then work on myTopicBranch, pulling back to the master branch when
needed by

#+begin_src shell
    git checkout master
    git pull . myTopicBranch
#+end_src

(or
#+begin_src shell
    git rebase myTopicBranch
#+end_src
)

BETTER DOCUMENTATION EXAMPLES EXIST ON-LINE!! PLEASE READ THEM, THE
ABOVE IS SPARSE AND MIGHT BE OUTDATED!


** Contributing through GitHub

   Alternatively, one can work on the github repositories as well.
   They are a bit differently organized, and require one to get a
   github account and work from there.

   basically, clone the repository on github on the WWW interface,
   then make a branch (as below), push back the branch to github, and
   notify the main repository that there is something to be pulled.
   And we'll pull it back in.

** Commiting with the MOB on repo.or.cz

of course, perhaps you want to contribute to the mob branch.   For
that, after cloning the repository as above, you would:

#+begin_src shell
    git checkout -b mob remotes/origin/mob
#+end_src

(work, work, work... through a cycle of

#+begin_src shell
         <edit>
         git add <files just edited>
         git commit -m "what I just did"
#+end_src

 ad-nauseum.  When ready to commit, then just:

#+begin_src shell
     git push git+ssh://mob@repo.or.cz/srv/git/CommonLispStat.git mob:mob
#+end_src

)

and it'll be put on the mob branch, as a proposal for merging. 

Another approach would be to pull from the topic branch into the mob
branch before uploading.   Will work on a formal example soon.

(the basic principle is that instead of the edit cycle on mob, do
something like:

#+begin_src shell
  git checkout mob
  git pull . myTopicBranch   
  git push git+ssh://mob@repo.or.cz/srv/git/CommonLispStat.git mob:mob
#+end_src

)

** Licensing

   Licensing will be important.  Next decade.  But do think through
   what you intend with your contributions.  Should we become famous
   (Ha!) make sure that you've communicated your expectations...

* Footnotes

[fn:1] I´m not including instructions for Emacs or git, as the former
is dealt with other places and the latter was required for you to get
this.  Since disk space is cheap, I´m intentionally forcing git to be
part of this system.  Sorry if you hate it.  Org-mode, org-babel, and
org-babel-lisp, and hypo are useful for making this file a literate
and interactively executable piece of work.