2 Time-stamp: <2012-10-08 15:44:30 tony>
4 * Current Status: COMPLETELY BROKEN
6 but we are rebuilding it.
12 (This held for the version before we removed liblispstat and plplot
13 and some other "crutches" which had a bit too much bitrot).
15 We assume that you have a lisp installed and that you have a
16 passing acquaintence with the unix shell.
18 1. The first point that you should note that is that these
19 instructions are written with the assumption of the availibility
22 If you do not have quicklisp , please go to www.quicklisp.org and
25 2. The second point to note is that you will need the "git" utility
26 installed on your machine.
28 for mac osx sudo port install git
29 for linux (eg debian) sudo apt-get install git
31 3. Once that is done execute the following shell commands
34 cd ~/quicklisp/local-projects
35 git clone git://github.com/blindglobe/common-lisp-stat.git
40 These commands copy the the source from the repository and all
41 the associated libraries. It will live as a quicklisp project in
42 the local-projects directory. I find it convenient to
43 symbolically link the quicklisp direct to ~/lisp for easy access
46 ln ~/quicklisp/local-projects ~/lisp
49 4. Configure the locations of the BLAS and LINPACK libraries
51 Currently this is a manual operation, which will change in a
54 Edit the file external/cl-blapack/load-blapack-libs.lisp
56 Search for the following 3 parameters *gfortran-lib* *blas-lib*
59 For OS X: change the parameters as suggested in the file. Both
60 BLAS and LAPACK are pre installed on Mac OSX.
62 For linux, make sure you have the neccessary libraries installed,
63 through apt, yum or otherwise
67 sudo apt-get install libblas
68 sudo apt-get install liblapack
71 5. For visualization we are currently using plplot and the
72 cl-plplot interface. this requires the installation of the
75 for MAC OSX you can use macports or homebrew
77 5.1 sudo port install xquartz (or download from the xquartz home site)
79 5.2 sudo port install plplot
81 and on linux your favourite package manager of course.
83 For windows, we recommend you use cygwin to get straightforward
84 access. I'll document the steps if there is a demand.
86 6. You need to check that your dynamic library path has been
87 properly set up in the shell. In your .bashrc (or equivalent
93 DYLD_FALLBACK-LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:/opt/local/lib
99 LD_LIBRARY_PATH=$LD_LIBRARY_PATH:????
102 If you get this wrong the load process will not be able to find
103 the libraries and will prompt you.
105 5. Once the pre prequisites have been done, start your favourite lisp
109 (ql:register-local-projects)
113 Retire for a well earned coffee and upon your return you should
114 find the package completely installed.Obviously, potential
115 errors can creep in with spelling the filenames correctly, so be
120 You probably did (preferred)
122 #+name: LoadWithGitClone
124 git clone git://github.com/blindglobe/common-lisp-stat.git
127 (or maybe using the repo.or.cz git repository archive), or (coming
128 soon!) from within a Lisp instance:
130 #+name: LoadWithQuickLisp
135 At one point, I planned a pure git-delivery via cloning and
136 submodules, but this proved to be a bit more complex than needed,
137 thanks to the creation of quicklisp. It's also a stupid idea if
138 one plans to have users who are not hackers or developers, and
139 eventually we want users.
141 Despite quicklisp, there will need to be a version for delivering a
142 system development-oriented CLS environment and this will consist of
143 git repositories, possibly through submodules, but this (submodules)
146 There are quite a few libraries that are needed, and right now we
147 are working on simplifying the whole thing. Once you get past
148 this step, then you should:
150 1. run a common lisp (SBCL, CMUCL, CLISP, CLOZURE-CL) starting in
151 the current directory. You will need ASDF at a minimum,
152 QUICKLISP preferred. And you should have QUICKLISP.
154 2. (on Debian or similar systems: can use CLC (Common Lisp
155 Controller) or SBCL approaches, i.e. ~/.clc/systems or
156 ~/.sbcl/systems should contain softlinks to the cls and other
157 required ASDF files (i.e. cls.asd, cffi.asd, and lift.asd).
159 There are example sessions and scripts for data analysis, some real,
160 some proposed, in the file:examples/ directory. Also see
161 file:TODO.org for snippets of code that work or fail to work.
163 ** Example Usage steps [2/7]
165 *** DONE Start and Load
174 *** DONE Setup a place to work
176 In Common Lisp, you need to select and setup namespace to store data
177 and functions. There is a scratch user-package, or sandbox, for
178 CLS, *cls-user* , which you can select via:
180 #+BEGIN_SRC lisp -n :tangle "readme-example.lisp"
181 (in-package :cls-user)
184 and this has some basic modules from CLS instantiated (dataframes,
185 probability calculus, numerical linear algebra, basic summaries
186 (numerical and visual displays).
188 However, it can be better is to create a package to work in, which
189 pulls in only desired functionality:
192 #+BEGIN_SRC lisp +n :tangle "readme-example.lisp"
194 (defpackage :my-package-user
195 (:documentation "demo of how to put serious work should be placed in
196 a similar package elsewhere for reproducibility. This hints as to
197 what needs to be done for a user- or analysis-package.")
198 (:nicknames :my-clswork-user)
199 (:use :common-lisp ; always needed for user playgrounds!
200 :lisp-matrix ; we only need the packages that we need...
201 :common-lisp-statistics
203 :lisp-stat-data-examples) ;; this ensures access to a data package
204 (:shadowing-import-from :lisp-stat
205 ;; This is needed temporarily until we resolve the dependency and call structure.
206 call-method call-next-method
208 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
209 asin acos atan sinh cosh tanh asinh acosh atanh float random
210 truncate floor ceiling round minusp zerop plusp evenp oddp
211 < <= = /= >= > > ;; complex
212 conjugate realpart imagpart phase
213 min max logand logior logxor lognot ffloor fceiling
214 ftruncate fround signum cis
218 (:export summarize-data summarize-results this-data this-report))
220 (in-package :my-clswork-user) ;; or :my-package-user
227 We need to pull in the packages with data or functions that we need;
228 just because the data/function is pulled in by another package, in
229 that package's namespace, does NOT mean it is available in this name
230 space. However, the *common-lisp-statistics* package will ensure
231 that fundamental objects and functions are always available.
234 *** TODO Get to work [0/3]
236 **** TODO Pull in or create data
238 **** TODO Summarize results
240 **** TODO Save work and results for knowledge building and reuse
242 One can build a package, or save an image (CL implementation
245 *** TODO Inform moi of problems or successes
247 NEED TO SETUP A MAILING LIST!!
249 mailto:blindglobe@gmail.com if there is anything wrong, or
250 even if something happens to work.
253 - SBCL is target platform. CCL and CMUCL should be similar.
254 - CLISP is finicky regarding the problems that we have with CFFI
255 conversation. In particular that we can not really do typing
256 that we need to take care of. I think this is my (Tony's)
257 problem, not someone elses, and specifically, not CLISP's
262 See files in file:Doc/ for history, design considerations, and
263 random, sometimes false and misleading, musings.
265 * Local modifications, Development, Contributions
267 Since this project is
270 # git clone git://repo.or.cz/CommonLispStat.git
271 git clone git://github.com/blindglobe/common-lisp-stat.git
273 # git submodules init
274 # git submodules update
277 will pull the whole repository, and create a "master" branch to
278 work on. If you are making edits, which I'd like, you don't want
279 to use the master branch, but more to use a topic-centric branch,
283 git checkout -b myTopicBranch
286 and then work on myTopicBranch, pulling back to the master branch when
291 git pull . myTopicBranch
296 git rebase myTopicBranch
300 BETTER DOCUMENTATION EXAMPLES EXIST ON-LINE!! PLEASE READ THEM, THE
301 ABOVE IS SPARSE AND MIGHT BE OUTDATED!
304 ** Contributing through GitHub
306 Alternatively, one can work on the github repositories as well.
307 They are a bit differently organized, and require one to get a
308 github account and work from there.
310 basically, clone the repository on github on the WWW interface,
311 then make a branch (as below), push back the branch to github, and
312 notify the main repository that there is something to be pulled.
313 And we'll pull it back in.
315 ** Commiting with the MOB on repo.or.cz
317 of course, perhaps you want to contribute to the mob branch. For
318 that, after cloning the repository as above, you would:
321 git checkout -b mob remotes/origin/mob
324 (work, work, work... through a cycle of
328 git add <files just edited>
329 git commit -m "what I just did"
332 ad-nauseum. When ready to commit, then just:
335 git push git+ssh://mob@repo.or.cz/srv/git/CommonLispStat.git mob:mob
340 and it'll be put on the mob branch, as a proposal for merging.
342 Another approach would be to pull from the topic branch into the mob
343 branch before uploading. Will work on a formal example soon.
345 (the basic principle is that instead of the edit cycle on mob, do
350 git pull . myTopicBranch
351 git push git+ssh://mob@repo.or.cz/srv/git/CommonLispStat.git mob:mob
358 Licensing will be important. Next decade. But do think through
359 what you intend with your contributions. Should we become famous
360 (Ha!) make sure that you've communicated your expectations...
364 [fn:1] I´m not including instructions for Emacs or git, as the former
365 is dealt with other places and the latter was required for you to get
366 this. Since disk space is cheap, I´m intentionally forcing git to be
367 part of this system. Sorry if you hate it. Org-mode, org-babel, and
368 org-babel-lisp, and hypo are useful for making this file a literate
369 and interactively executable piece of work.