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anil.recoil.org
1opam-version: "2.0"
2authors: "Francois Berenger"
3maintainer: "unixjunkie@sdf.org"
4homepage: "https://github.com/UnixJunkie/linwrap"
5bug-reports: "https://github.com/UnixJunkie/linwrap/issues"
6dev-repo: "git+https://github.com/UnixJunkie/linwrap.git"
7license: "BSD-3-Clause"
8build: ["dune" "build" "-p" name "-j" jobs]
9install: ["cp" "bin/ecfp6.py" "%{bin}%/linwrap_ecfp6.py"]
10depends: [
11 "base-unix"
12 "batteries"
13 "conf-liblinear-tools"
14 "cpm" {>= "10.2.1"}
15 "dokeysto_camltc"
16 "dolog" {>= "4.0.0" & < "5.0.0"}
17 "dune" {>= "1.10"}
18 "minicli" {>= "5.0.0"}
19 "parany" {>= "11.0.0"}
20]
21# the package can compile and install without the depopts.
22# however, some tools and options will not work anymore at run-time
23depopts: [
24 "conf-gnuplot"
25 "conf-python-3"
26 "conf-rdkit"
27]
28synopsis: "Wrapper around liblinear-tools"
29description: """
30For classification, only L2-regularized logistic regression is supported.
31For regression, only linear SVR.
32When doing classification with bagging, each model is trained on balanced
33bootstraps from the training set (one bootstrap for the positive class,
34one for the negative class). The size of the bootstrap is the size of the
35smallest (under-represented) class.
36
37usage: linwrap
38 -i <filename>: training set or DB to screen
39 [-o <filename>]: predictions output file
40 [-np <int>]: ncores
41 [-c <float>]: fix C
42 [-e <float>]: fix epsilon (for SVR);
43 (0 <= epsilon <= max_i(|y_i|))
44 [-w <float>]: fix w1
45 [--no-plot]: no gnuplot
46 [-k <int>]: number of bags for bagging (default=off)
47 [{-n|--NxCV} <int>]: folds of cross validation
48 [--mcc-scan]: MCC scan for a trained model (requires n>1)
49 also requires (c, w, k) to be known
50 [--seed <int>]: fix random seed
51 [-p <float>]: training set portion (in [0.0:1.0])
52 [--pairs]: read from .AP files (atom pairs; will offset feat. indexes by 1)
53 [--train <train.liblin>]: training set (overrides -p)
54 [--valid <valid.liblin>]: validation set (overrides -p)
55 [--test <test.liblin>]: test set (overrides -p)
56 [{-l|--load} <filename>]: prod. mode; use trained models
57 [{-s|--save} <filename>]: train. mode; save trained models
58 [-f]: force overwriting existing model file
59 [--scan-c]: scan for best C
60 [--scan-e <int>]: epsilon scan #steps for SVR
61 [--regr]: regression (SVR); also, implied by -e and --scan-e
62 [--scan-w]: scan weight to counter class imbalance
63 [--w-range <float>:<int>:<float>]: specific range for w
64 (semantic=start:nsteps:stop)
65 [--c-range <float,float,...>] explicit scan range for C
66 (example='0.01,0.02,0.03')
67 [--k-range <int,int,...>] explicit scan range for k
68 (example='1,2,3,5,10')
69 [--scan-k]: scan number of bags (advice: optim. k rather than w)
70"""
71url {
72 src: "https://github.com/UnixJunkie/linwrap/archive/v8.0.3.tar.gz"
73 checksum: [
74 "sha256=ca038c8bdf5965c974ab1daa2c4167be86af9c2985aab825febf5bd70a7461f5"
75 "md5=b49ebc3f67f2a143b426f9c3309bf3a6"
76 ]
77}