[med-svn] [Git][med-team/simrisc][master] 3 commits: Ready for simrisc 14.05.01-1
Frank B. Brokken (@fbb-guest)
gitlab at salsa.debian.org
Sat Sep 17 16:21:47 BST 2022
Frank B. Brokken pushed to branch master at Debian Med / simrisc
Commits:
8bbf596c by Frank B. Brokken at 2022-09-17T17:21:15+02:00
Ready for simrisc 14.05.01-1
- - - - -
512601e1 by Frank B. Brokken at 2022-09-17T17:21:17+02:00
New upstream version 14.05.01
- - - - -
61f9b007 by Frank B. Brokken at 2022-09-17T17:21:19+02:00
Update upstream source from tag 'upstream/14.05.01'
Update to upstream version '14.05.01'
with Debian dir a6893c6a300076c90220bfadc7007f3f8907512f
- - - - -
21 changed files:
- INSTALL.im
- VERSION
- build
- + c++std
- changelog
- debian/changelog
- debian/control
- − debian/patches/gcc12.patch
- debian/patches/series
- debian/rules
- density/density.ih
- documentation/manual/simrisc.yo
- + documentation/simrisc/supplementary.odt
- icmconf.lib
- incidence/incidence.ih
- − parser/test/analysis
- − parser/test/icmconf
- − parser/test/main.cc
- − parser/test/main.ih
- − parser/test/simrisc
- + stdconfig/mrinew
Changes:
=====================================
INSTALL.im
=====================================
@@ -1,3 +1,5 @@
+#include "c++std"
+
// Specify the name of the project:
#define PROGRAM "simrisc"
@@ -5,8 +7,10 @@
#define CXX "g++"
// The compiler options to use:
-#define CXXFLAGS "--std=c++2a -Wall -O2 -fdiagnostics-color=never"
-// #define CXXFLAGS "--std=c++2a -Wall -O2 -pthread -fdiagnostics-color=never"
+#define CXXFLAGS ${CPPSTD} " -Wall -Werror -O2 -fdiagnostics-color=never"
+
+// #define CXXFLAGS ${CPPSTD} " -Wall -Werror -O2 -pthread " \<-- note !!
+// "-fdiagnostics-color=never"
// Flags passed to the linker:
//#define LDFLAGS "-lpthread"
=====================================
VERSION
=====================================
@@ -1,3 +1,3 @@
#define AUTHOR "Frank B. Brokken (f.b.brokken at rug.nl)";
-#define VERSION "14.05.00"
-#define YEARS "2020-2021"
+#define VERSION "14.05.01"
+#define YEARS "2020-2022"
=====================================
build
=====================================
@@ -97,7 +97,7 @@ void main(int argc, list argv)
exit(0);
}
- if (option == "oxref")
+ if (option == "xref")
{
system("icmbuild program");
run("oxref -t main -r oxref/replace -fxs tmp/main.o tmp/lib"
@@ -118,7 +118,7 @@ void main(int argc, list argv)
" pdf - build the pdf manual (requires Yodl)\n"
" program [strip] - build " PROGRAM " (optionally strip the\n"
" executable)\n"
- " oxref [strip] - same a `program', also builds xref file\n"
+ " xref [strip] - same a `program', also builds xref file\n"
" using oxref\n"
" install selection [base] - to install the software in the \n"
" locations defined in the INSTALL.im file,\n"
=====================================
c++std
=====================================
@@ -0,0 +1,2 @@
+#define CPPSTD "--std=c++20"
+
=====================================
changelog
=====================================
@@ -1,3 +1,14 @@
+simrisc (14.05.01)
+
+ * Ready for libbobcat6
+
+ * Added 'c++std' defining the c++ standard to use for
+ compilation. Compilation commands also use -Werror
+
+ * Renamed the 'oxref' option in the 'build' script to 'xref'
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Sat, 17 Sep 2022 16:07:04 +0200
+
simrisc (14.05.00)
* Added option --err (-e) to select the previously used but inorrect
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+simrisc (14.05.01-1) unstable; urgency=medium
+
+ * New upstream version 14.05.01
+ * debian/rules determines the C++ version to use from upstream's 'c++std'
+ file
+ * The patch added by Nilesh was processed in the upstream version and is
+ remoeed from the Debian distribution
+ * Specified Standards-Version: 4.6.1 in 'cotrol'
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Sat, 17 Sep 2022 17:01:14 +0200
+
simrisc (14.05.00-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
texlive-latex-recommended,
texlive-plain-generic,
yodl (>= 4.02.02)
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/simrisc
Vcs-Git: https://salsa.debian.org/med-team/simrisc.git
Homepage: https://fbb-git.gitlab.io/simrisc/
=====================================
debian/patches/gcc12.patch deleted
=====================================
@@ -1,25 +0,0 @@
-Description: Include algorthm in density.ih and incidence.ih
-Author: Nilesh Patra <nilesh at debian.org>
-Last-Update: 2022-07-25
---- a/density/density.ih
-+++ b/density/density.ih
-@@ -1,7 +1,7 @@
- #include "density.h"
- #include "../xerr/xerr.ih"
-
--//#include <algorithm>
-+#include <algorithm>
-
- #include <iomanip>
- #include <istream>
---- a/incidence/incidence.ih
-+++ b/incidence/incidence.ih
-@@ -5,6 +5,8 @@
- #include "../parser/parser.h"
- #include "../random/random.h"
-
-+#include <algorithm>
-+
- using namespace std;
-
- // static
=====================================
debian/patches/series
=====================================
@@ -1 +1 @@
-gcc12.patch
+
=====================================
debian/rules
=====================================
@@ -23,9 +23,15 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export CPPFLAGS = $(shell dpkg-buildflags --get CPPFLAGS)
export CPPFLAGS += -D_FORTIFY_SOURCE=2
-export LDFLAGS = $(shell dpkg-buildflags --get LDFLAGS) -Wl,-z,now
+
export CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
-export CXXFLAGS += -Wall --std=c++2a -D_FORTIFY_SOURCE=2
+export CXXFLAGS += -D_FORTIFY_SOURCE=2
+
+# Define the c++std to use by processing the upstream 'c++std' file
+export CXXFLAGS += $(shell cat c++std|sed -e 's/#define CPPSTD "//' -e 's/"//')
+
+export LDFLAGS = $(shell dpkg-buildflags --get LDFLAGS) -Wl,-z,now
+
export CXX = g++
%:
=====================================
density/density.ih
=====================================
@@ -1,7 +1,7 @@
#include "density.h"
#include "../xerr/xerr.ih"
-//#include <algorithm>
+#include <algorithm>
#include <iomanip>
#include <istream>
=====================================
documentation/manual/simrisc.yo
=====================================
@@ -33,7 +33,7 @@ includefile(abstract.yo)
affiliation(University of Groningen)
-report(Simrisc Manual)(Frank B. Brokken)(April 11, 2021)())
+report(Simrisc Manual)(Frank B. Brokken)(September 17, 2022)())
chapter(Introduction)
includefile(intro/intro.yo)
=====================================
documentation/simrisc/supplementary.odt
=====================================
Binary files /dev/null and b/documentation/simrisc/supplementary.odt differ
=====================================
icmconf.lib
=====================================
@@ -1,3 +1,5 @@
+#include "c++std"
+
#define PRECOMP "-x c++-header"
#define CLS
@@ -7,7 +9,7 @@
#define USE_ECHO ON
#define IH ".ih"
#define CXX "g++"
-#define CXXFLAGS " --std=c++2a -Wall -O2 " \
+#define CXXFLAGS ${CPPSTD} " -Wall -Werror -O2 " \
" -fdiagnostics-color=never "
#define ADD_LIBRARIES "bobcat"
#define ADD_LIBRARY_PATHS ""
=====================================
incidence/incidence.ih
=====================================
@@ -1,6 +1,8 @@
#include "incidence.h"
#include "../xerr/xerr.ih"
+#include <algorithm>
+
#include "../globals/globals.h"
#include "../parser/parser.h"
#include "../random/random.h"
=====================================
parser/test/analysis deleted
=====================================
@@ -1,10 +0,0 @@
-label: first line
-label: second line
-
-simple
-this that
-next: what
-
-Scenario:
- nCases: 1000
-
=====================================
parser/test/icmconf deleted
=====================================
@@ -1,19 +0,0 @@
-#define CLS
-#define MAIN "main.cc"
-#define SOURCES "*.cc"
-#define OBJ_EXT ".o"
-#define TMP_DIR "tmp"
-
-#define USE_ECHO ON
-#define IH ".ih"
-
-#define CXX "g++"
-#define CXXFLAGS " --std=c++2a -Wall -O2 " \
- " -fdiagnostics-color=never "
-#define REFRESH
-#define LDFLAGS "-s"
-
-#define ADD_LIBRARIES "parser configlines err bobcat"
-#define ADD_LIBRARY_PATHS "../../lib"
-
-#define DEFCOM "program"
=====================================
parser/test/main.cc deleted
=====================================
@@ -1,75 +0,0 @@
-//#define XERR
-#include "main.ih"
-
-// needs parser, parserlines and error
-
-int main(int argc, char **argv)
-try
-{
- if (argc == 1)
- throw Exception{} << "arg1: simrisc conf., arg2: one analysis spec\n";
-
- Parser parser;
-
- StringVect labels;
- Parser::OptionsVect options;
-
- ifstream in{ argv[2] };
- parser.load(in, 1, labels, options);
- parser.load(argv[1]);
-
- cout << "Labels:\n";
- for (string const &label: labels)
- cout << " Label: " << label << '\n';
-
- cout << "Options:\n";
- for (auto const &option: options)
- cout << " Option: `" << option.name << "': " <<
- option.value << '\n';
-
-
- cout << "Spread:\n";
- for (auto element: parser.select({"Scenario:", "spread:"}))
- cout << "src: " << element.src << ", nr: " << element.lineNr <<
- ", tail: " << element.tail << '\n';
-
- cout << "nCases:\n";
- for (auto element: parser.select({"Scenario:", "nCases:"}))
- cout << "src: " << element.src << ", nr: " << element.lineNr <<
- ", tail: " << element.tail << '\n';
-
- {
- cout << "Costs:\n";
- LineInfoVect const &lines = Parser::select({ "Costs:" });
-
- if (lines.front().tail.empty())
- Err::msg(Err::UNDEFINED_SPEC) << ": Costs" << endl;
- else
- {
- double refAge;
- double prop;
- uint16_t biop;
-
- std::istringstream in{
- Parser::extract(
- lines[0], refAge, prop, biop
- )
- };
- if (in)
- cout << refAge << ", " << biop << '\n';
- }
- }
-}
-catch(int x)
-{
- return x;
-}
-catch (exception const &exc)
-{
- cerr << exc.what() << '\n';
-}
-catch (...)
-{
- cerr << "unexpected exception\n";
- return 1;
-}
=====================================
parser/test/main.ih deleted
=====================================
@@ -1,12 +0,0 @@
-#include <iostream>
-#include <string>
-#include <fstream>
-#include <sstream>
-
-#include <bobcat/exception>
-
-#include "../parser.h"
-
-using namespace std;
-using namespace FBB;
-
=====================================
parser/test/simrisc deleted
=====================================
@@ -1,121 +0,0 @@
-# supported distribution names are: Normal, LogNormal, Uniform, Exponential
-
-Scenario:
-
- # uncomment to use variable spreading
- #variableSpread: true (or (default if not specified: false))
- spread: false
-
- iterations: 1
-
- # random generator random, fixed, increasing (default: random)
- generator: random
-
- # with fixed, increasing generators: initial seed (default 1)
- seed: 1
-
- # nWomen -> nCases
- nCases: 100000
-
- # discount: pairs of (increasing) begin-diam: cost
- # age proportion biop (first diameter must be 0)
-Costs: 50 .0 176 0: 6438 20: 7128 50: 7701
-
-Screening:
- # round: age (space separated) type(s).
- # Types are Mammo, Tomo, MRI, see below at Modalities.
- round: 50 Mammo
- round: 52 Mammo
- round: 54 Mammo
- round: 56 Mammo
- round: 58 Mammo
- round: 60 Mammo
- round: 62 Mammo
- round: 64 Mammo
- round: 66 Mammo
- round: 68 Mammo
- round: 70 Mammo
- round: 72 Mammo
- round: 74 Mammo
-
- # value distribution:
- systematicError: 0 Normal
- attendanceRate: .8 Normal
-
-BreastDensities:
- # bi-rad classification
- # ----------------------------
- # a b c d
- ageGroup: 0 - 40 .05 .30 .48 .17
- ageGroup: 40 - 50 .06 .34 .47 .13
- ageGroup: 50 - 60 .08 .50 .37 .05
- ageGroup: 60 - 70 .15 .53 .29 .03
- ageGroup: 70 - * .18 .54 .26 .02
-
-
-Modalities:
- Mammo:
- costs: 64
-
-# bi-rad cat: a b c d
- dose: 3 3 3 3
-
-# agegroup
- specificity: 0 - 40: .961 40 - *: .965
-
-# 1 2 3 4 m
- beta: -4.38 Normal .49 Normal -1.34 Normal -7.18 Normal .136 Normal
-
- Tomo:
- costs: 64
-
-# bi-rad cat: a b c d
- dose: 3 3 3 3
- sensitivity: .87 .84 .73 .65
-
-# agegroup
- specificity: 0 - 40: .961 40 - *: .965
-
- MRI:
- costs: 280
- sensitivity: .94
- specificity: .95
-
-Tumor:
- Incidence:
- Normal:
- prob: 1 # value spread dist.
- lifetimeRisk: .226 .0053 Normal
- meanAge: 72.9 .552 Normal
- standardDev: 21.1 .048 Normal
- BRCA1:
- prob: 0
- lifetimeRisk: .96
- meanAge: 53.90
- standardDev: 16.51
- BRCA2:
- prob: 0
- lifetimeRisk: .96
- meanAge: 53.90
- standardDev: 16.51
- Growth: # value spread dist.
- start: 5 0 Normal
- selfDetectMu: 2.92 .084 Normal
- selfDetectSigma: .70 0 Normal
-
- DoublingTime:
- # mean spread dist. stdev spread dist.
- ageGroup: 1 - 50: 4.38 .43 Normal .61 0 Normal
- ageGroup: 50 - 70: 5.06 .17 Normal .26 0 Normal
- ageGroup: 70 - * : 5.24 .23 Normal .45 0 Normal
-
- # b e spread dist.
- Beir7: .51 -2.0 .32 Normal
-
- Survival:
- # value spread dist:
- type: a .00004475 .000004392 Normal
- type: b 1.85867 .0420 Normal
- type: c - .271 .0101 Normal
- type: d 2.0167 .0366 Normal
-
=====================================
stdconfig/mrinew
=====================================
@@ -0,0 +1,182 @@
+# supported distribution names are: Normal, LogNormal, Uniform, Exponential
+# Modalities are: Mammo, Tomo, MRI
+
+Scenario:
+ # use true for variable spreading
+# spread: true
+ spread: false
+
+ iterations: 1
+
+ # random generator behavior:
+ # random, fixed, increasing
+ generator: fixed
+
+ # initial seed unless using generator: random
+ seed: 1
+
+ # n cases to simulate
+ cases: 1000
+
+ # Used for all modalities except for CT:
+ # discount: pairs of (increasing) 'begin-diam: cost'
+ # ref.age proportion biop specs (first diameter must be 0)
+Costs:
+ biop: 176
+ diameters: 0: 6438 20: 7128 50: 7701
+ Discount:
+ age: 50
+ proportion: 0
+ # Lungcancer costs: configured at Modalities: CT: costs:
+
+BreastDensities:
+
+ # bi-rad: a b c d
+ ageGroup: 0 - 40: .05 .30 .48 .17
+ ageGroup: 40 - 50: .06 .34 .47 .13
+ ageGroup: 50 - 60: .08 .50 .37 .05
+ ageGroup: 60 - 70: .15 .53 .29 .03
+ ageGroup: 70 - * : .18 .54 .26 .02
+
+Modalities:
+
+ CT:
+ # screening diagnosis M0 M1 (M0, M1: Table S3)
+ costs: 176 1908 37909 56556
+
+ # diam. value (must be integral 0..100 or -1)
+ sensitivity: 0 - 3: 0
+ sensitivity: 3 - 5: -1 # formula: (.5 * diam - 1.5) * 100
+ sensitivity: 5 - *: 100
+
+ # mean stddev dist
+ specificity: 99.2 .076 Normal
+
+ Mammo:
+ costs: 64
+
+ # bi-rad: a b c d
+ dose: 3 3 3 3
+ m: .136 .136 .136 .136
+
+ # ageGroup
+ specificity: 0 - 40: .961 40 - *: .965
+
+ # 1 2 3 4
+ beta: -4.38 .49 -1.34 -7.18
+
+ systematicError: 0.1
+
+ Tomo:
+ costs: 64
+
+ # bi-rad: a b c d
+ dose: 3 3 3 3
+ sensitivity: .87 .84 .73 .65
+
+ # ageGroup
+ specificity: 0 - 40: .961 40 - *: .965
+
+ MRI:
+ costs: 280
+ sensitivity: .94
+ specificity: .95
+
+Screening:
+
+ # round: age space separated modalities.
+ # subsequent ages must exceed the last age by at least 1
+ # with lung cancer simulations only CT can be specified,
+ # with breast cancer simulations CT cannot be specified,
+ round: 50 MRI
+ round: 52 MRI
+ round: 54 MRI
+ round: 56 MRI
+ round: 58 MRI
+ round: 60 MRI
+ round: 62 MRI
+ round: 64 MRI
+ round: 66 MRI
+ round: 68 MRI
+ round: 70 MRI
+ round: 72 MRI
+ round: 74 MRI
+
+ # proportion:
+ attendanceRate: .8
+
+Tumor:
+
+ # eta beta spread dist.
+ beir7: -2.0 0.51 0.32 Normal
+
+ Growth:
+ start: 5
+ # stdev mean spread dist
+ selfDetect: .70 2.92 .084 Normal
+
+ DoublingTime:
+ # stdev mean spread dist.
+ ageGroup: 1 - 50: .61 4.38 .43 Normal
+ ageGroup: 50 - 70: .26 5.06 .17 Normal
+ ageGroup: 70 - * : .45 5.24 .23 Normal
+
+ Incidence:
+ Normal:
+ probability: 1
+ stdDev: 21.1
+ # value spread distr.
+ lifetimeRisk: .226 .0053 Normal
+ meanAge: 72.9 .552 Normal
+
+ BRCA1:
+ probability: 0
+ stdDev: 16.51
+ # value spread distr.
+ lifetimeRisk: .96
+ meanAge: 53.9
+
+ BRCA2:
+ probability: 0
+ stdDev: 16.51
+ # value spread distr.
+ lifetimeRisk: .96
+ meanAge: 53.9
+
+ Survival:
+ # value spread dist:
+ type: a .00004475 .000004392 Normal
+ type: b 1.85867 .0420 Normal
+ type: c -.271 .0101 Normal
+ type: d 2.0167 .0366 Normal
+
+ # table S4: 4 columns per a..d parameter
+ # lungX: X is table S4's column index
+ lung0: a .00143 .00095 Normal
+ lung0: b 1.84559 .33748 Normal
+ lung0: c -.22794 .07823 Normal
+ lung0: d 1.06799 .16226 Normal
+
+ lung1: a .01530 .00381 Normal
+ lung1: b 1.69434 .10979 Normal
+ lung1: c -.19358 .02105 Normal
+ lung1: d .66690 .03869 Normal
+
+ lung2: a .78600 .29815 Normal
+ lung2: b .69791 .05425 Normal
+ lung2: c .0 .0 Normal
+ lung2: d .0 .0 Normal
+
+ lung3: a 1.25148 .32305 Normal
+ lung3: b .77852 .34149 Normal
+ lung3: c .0 .0 Normal
+ lung3: d .0 .0 Normal
+
+
+ S3:
+ # T-row range N0,M0 N1-3,M0 N1-3,M1a-b N0-3M1c
+ prob: 0 - 21: .8186 .0333 .0832 .0709 // T1a,b
+ prob: 21 - 31: .6626 .0474 .1566 .1334 // T1c
+ prob: 31 - 51: .5077 .0802 .2225 .1896 // T2a,b
+ prob: 51 - 71: .3116 .3116 .3115 .2653 // T3
+ prob: 71 - * : .2203 .2203 .3498 .2980 // T4
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/compare/7c799cabc2b04cc09dc6e5bfee39bb78d2c95386...61f9b007c1369b8d12fb8c535e841abb2a9faae7
--
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/compare/7c799cabc2b04cc09dc6e5bfee39bb78d2c95386...61f9b007c1369b8d12fb8c535e841abb2a9faae7
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