[med-svn] [Git][med-team/simrisc][debian/latest] 3 commits: Ready for simrisc 16.02.00-1
Frank B. Brokken (@fbb-guest)
gitlab at salsa.debian.org
Sun Sep 1 10:43:34 BST 2024
Frank B. Brokken pushed to branch debian/latest at Debian Med / simrisc
Commits:
d99fe622 by Frank B. Brokken at 2024-09-01T11:42:59+02:00
Ready for simrisc 16.02.00-1
- - - - -
a4405bca by Frank B. Brokken at 2024-09-01T11:43:01+02:00
New upstream version 16.02.00
- - - - -
cba815ca by Frank B. Brokken at 2024-09-01T11:43:04+02:00
Update upstream source from tag 'upstream/16.02.00'
Update to upstream version '16.02.00'
with Debian dir bdcd16e2c244a51275bd80849cf717b463f3d221
- - - - -
15 changed files:
- VERSION
- changelog
- debian/changelog
- debian/rules
- debian/tests/simrisc-test1.expected.gz
- debian/tests/simrisc-test2.expected.gz
- documentation/manual/simrisc.yo
- loop/gencases.cc
- loop/leaving.cc
- loop/loop.h
- loop/postscreen.cc
- loop/writedata.cc
- + tumor/checkdeath.cc
- tumor/tumor.h
- tumor/writedata.cc
Changes:
=====================================
VERSION
=====================================
@@ -1,3 +1,3 @@
#define AUTHOR "Frank B. Brokken (f.b.brokken at rug.nl)";
-#define VERSION "16.01.00"
+#define VERSION "16.02.00"
#define YEARS "2020-2024"
=====================================
changelog
=====================================
@@ -1,3 +1,12 @@
+simrisc (16.02.00)
+
+ * Natural deaths occurring before tumor onsets are no longer using
+ 'UNDETECTED_XXX' exit codes but 'NATURAL_XXX' exit codes.
+
+ * In those cases 'Yes' status flags are changed to 'No'
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Thu, 15 Jun 2024 11:33:25 +0200
+
simrisc (16.01.00)
* The lung cancer survival parameters (i.e., table S4) received an e
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+simrisc (16.02.00-1) unstable; urgency=medium
+
+ * New upstream version
+ - Natural deaths occurring before tumor onsets are no longer using
+ 'UNDETECTED_XXX' exit codes but 'NATURAL_XXX' exit codes.
+ * debian/tests/expected* files were updated.
+ * debian/rules updated the used C++ standard version to c++26.
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Sun, 01 Sep 2024 11:24:30 +0200
+
simrisc (16.01.00-1) unstable; urgency=medium
* New upstream version
=====================================
debian/rules
=====================================
@@ -21,13 +21,13 @@ export FORCE_SOURCE_DATE=1
export DEB_BUILD_HARDENING = 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-export ICMAKE_CPPSTD = --std=c++23
+export ICMAKE_CPPSTD = --std=c++26
export CPPFLAGS = $(shell dpkg-buildflags --get CXXFLAGS)
export CXXFLAGS += ${ICMAKE_CPPSTD} -Wall -D_FORTIFY_SOURCE=2
# export ICMAKE_CPPSTD = $(shell dpkg-buildflags --get CPPSTD)
-# export ICMAKE_CPPSTD += --std=c++23 -Wall -Werror -D_FORTIFY_SOURCE=2
+# export ICMAKE_CPPSTD += --std=c++26 -Wall -Werror -D_FORTIFY_SOURCE=2
export LDFLAGS = $(shell dpkg-buildflags --get LDFLAGS) -Wl,-z,now
=====================================
debian/tests/simrisc-test1.expected.gz
=====================================
Binary files a/debian/tests/simrisc-test1.expected.gz and b/debian/tests/simrisc-test1.expected.gz differ
=====================================
debian/tests/simrisc-test2.expected.gz
=====================================
Binary files a/debian/tests/simrisc-test2.expected.gz and b/debian/tests/simrisc-test2.expected.gz differ
=====================================
documentation/manual/simrisc.yo
=====================================
@@ -33,7 +33,7 @@ includefile(abstract.yo)
affiliation(University of Groningen)
-report(Simrisc Manual)(Frank B. Brokken)(June 05, 2024)())
+report(Simrisc Manual)(Frank B. Brokken)(September 01, 2024)())
chapter(Introduction)
includefile(intro/intro.yo)
=====================================
loop/gencases.cc
=====================================
@@ -26,7 +26,10 @@ void Loop::genCases(size_t iter, size_t nCases)
d_totalCost += d_caseCost;
if (dataTable.stream() and (showAll or caseIdx + 1 == nCases))
+ {
+ d_tumor.checkDeath(d_naturalDeathAge);
writeData(dataTable, caseIdx);
+ }
}
dataTable << hline();
=====================================
loop/leaving.cc
=====================================
@@ -25,7 +25,12 @@ bool Loop::leaving(double screeningAge)
{
d_tumor.characteristicsAt(d_naturalDeathAge);
d_deathAge = d_naturalDeathAge;
- return left(before1stRound ? UNDETECTED_PRE : UNDETECTED_DURING,
+ bool died = d_naturalDeathAge < d_tumor.onset();
+ return left(
+ before1stRound ?
+ died ? NATURAL_PRE : UNDETECTED_PRE
+ :
+ died ? NATURAL_DURING : UNDETECTED_DURING,
d_naturalDeathAge);
}
=====================================
loop/loop.h
=====================================
@@ -23,18 +23,9 @@ namespace FBB
class Loop: public Globals
{
-// Previous enum Status values:
-// PRESENT, // 0
-// LEFT_PRE, // 1 left the pre, during, post screening
-// LEFT_DURING, // 2 (natural death, no tumor)
-// LEFT_POST, // 3
-// TUMOR_PRE, // 4 tumor
-// TUMOR_DURING, // 5 interval cancer after a screening round
-// TUMOR_POST, // 6
-// UNDETECTED_PRE, // 7 undetected tumor, nat. death before 1st scr.
-// UNDETECTED_DURING, // 8 same, between screening rounds
-// UNDETECTED_POST, // 9 same, after the last screening round
-
+//
+// 2 -> 1, 5 -> 4, 9 -> 8 if the natural death is before the tumor's onset.
+//
enum Status // labels in data.cc
{
PRESENT, // 0
=====================================
loop/postscreen.cc
=====================================
@@ -25,8 +25,12 @@ void Loop::postScreen()
d_deathAge = min(d_naturalDeathAge, d_tumor.deathAge());
- left(d_tumor.selfDetectBefore(d_naturalDeathAge) ?
- SELF_POST : UNDETECTED_POST,
+ left(
+ d_tumor.selfDetectBefore(d_naturalDeathAge) ?
+ SELF_POST :
+ d_naturalDeathAge < d_tumor.onset() ?
+ NATURAL_POST :
+ UNDETECTED_POST,
d_deathAge);
// d_tumor.selfDetectAge());
}
=====================================
loop/writedata.cc
=====================================
@@ -10,6 +10,7 @@ void Loop::writeData(CSVTable &tab, size_t idx) const
(d_deathAge == d_naturalDeathAge ? "Natural"
: "Tumor") << // 2
d_deathAge << d_naturalDeathAge << d_status; // 3 - 5
+
d_tumor.writeData(tab); // 6 - 14
ostringstream out;
=====================================
tumor/checkdeath.cc
=====================================
@@ -0,0 +1,12 @@
+//#define XERR
+#include "tumor.ih"
+
+void Tumor::checkDeath(double naturalDeathAge)
+{
+ if (naturalDeathAge < d_onset) // death before tumor
+ {
+ d_present = false;
+ d_found = false;
+ d_interval = false;
+ }
+}
=====================================
tumor/tumor.h
=====================================
@@ -104,6 +104,7 @@ class Tumor: public Globals
void setDeathAge(); // wrt d_selfDetectAge // .f
void setDeathAge(double refAge); // wrt reference age
+ void checkDeath(double naturalDeathAge);
void writeData(FBB::CSVTable &tab) const;
RowCol const &rowCol() const; // .f
=====================================
tumor/writedata.cc
=====================================
@@ -4,7 +4,7 @@
void Tumor::writeData(CSVTable &tab) const
{
tab.more() << s_noYes[d_present] << // 6
- s_noYes[d_found] << // 7
+ s_noYes[d_found] << // 7
s_noYes[d_interval]; // 8
// see modifications (8)
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/compare/f3841df0de6a93ce306edf130ec53a71ab30a80c...cba815caf9394b15758bc750fce0abc3752a78d0
--
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/compare/f3841df0de6a93ce306edf130ec53a71ab30a80c...cba815caf9394b15758bc750fce0abc3752a78d0
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240901/e4272a3d/attachment-0001.htm>
More information about the debian-med-commit
mailing list