March 2021 Commit Log

Number of Commits:
282
Number of Active Developers:
5
nfijg 2021-03-31 15:43 Rev.: 10972

fixed fear,hunger,Fsize,Flight,Fothers,Fmort,Hstomach,Hsize,Hfood in SRdecision for behavfiles

59 lines of code changed in 3 files:

aru047 2021-03-31 11:48 Rev.: 10971

some results

9895 lines of code changed in 1 file:

aru047 2021-03-31 11:43 Rev.: 10970

stats

0 lines of code changed in 1 file:

hje044 2021-03-31 11:19 Rev.: 10969

Fisheries mortality implemented. Calculated for Trawl, Gillnet and Unselective. R script now generates plots for population dynamics by year.

45 lines of code changed in 2 files:

nfijg 2021-03-30 21:58 Rev.: 10968

corrected gene-data for behavfiles

402 lines of code changed in 3 files:

aru047 2021-03-30 20:38 Rev.: 10967

additional output

32 lines of code changed in 1 file:

sbu062 2021-03-30 14:20 Rev.: 10966

dollar sign needs escaping

1 lines of code changed in 1 file:

sbu062 2021-03-30 12:37 Rev.: 10965

report script revision in weekly check

1 lines of code changed in 1 file:

sbu062 2021-03-30 12:26 Rev.: 10964

include last log piece in warning message

2 lines of code changed in 1 file:

sbu062 2021-03-30 10:52 Rev.: 10963

must use set command in check

1 lines of code changed in 1 file:

sbu062 2021-03-30 10:51 Rev.: 10962

weekly xmpp report check

8 lines of code changed in 1 file:

sbu062 2021-03-30 10:06 Rev.: 10961

check log file only if model is running, ignore otherwise

7 lines of code changed in 1 file:

sbu062 2021-03-30 09:55 Rev.: 10960

log hash should be checked only if model is running to avoid hassle

3 lines of code changed in 1 file:

sbu062 2021-03-30 09:41 Rev.: 10959

need force to overwrite existing script

1 lines of code changed in 1 file:

sbu062 2021-03-30 09:39 Rev.: 10958

added keywords

2 lines of code changed in 1 file:

sbu062 2021-03-30 09:36 Rev.: 10957

warning messages must be consustent

2 lines of code changed in 1 file:

sbu062 2021-03-30 09:34 Rev.: 10956

check for model hung by comparing md5 hashes of tails of model log

18 lines of code changed in 1 file:

nfijg 2021-03-28 21:15

nothing

6 lines of code changed in 2 files:

sbu062 2021-03-28 16:14 Rev.: 10953

disallow message is fixed string

13 lines of code changed in 1 file:

sbu062 2021-03-28 15:01 Rev.: 10952

use asynchronous `subprocess.call` for long execution commands that have their own reporting

6 lines of code changed in 1 file:

sbu062 2021-03-28 14:43 Rev.: 10951

use subprocess.call with process return code reporting

3 lines of code changed in 1 file:

sbu062 2021-03-28 12:52 Rev.: 10950

fox: needed the reverse condition

1 lines of code changed in 1 file:

sbu062 2021-03-28 12:45 Rev.: 10949

add encrypt type in re pattern for reliability
but note that it works only with `-B` bcrypt algo

1 lines of code changed in 1 file:

sbu062 2021-03-28 11:29 Rev.: 10948

backup and sync require physical protected user

12 lines of code changed in 1 file:

sbu062 2021-03-28 11:22 Rev.: 10947

fix: the reverse condition must hold

1 lines of code changed in 1 file:

sbu062 2021-03-28 11:14 Rev.: 10946

fix non-ascii symbols

2 lines of code changed in 1 file:

sbu062 2021-03-28 11:12 Rev.: 10945

only protected physical users can manage xmpp and reset password

8 lines of code changed in 1 file:

sbu062 2021-03-28 10:49 Rev.: 10944

use (is_in_svn_auth_file) to check protected users

1 lines of code changed in 1 file:

sbu062 2021-03-28 10:40 Rev.: 10943

use global vars for PASSWORD_USER_FILE ALLOWED_DOMAINS TEGSVN_DOMAIN everywhere

5 lines of code changed in 1 file:

sbu062 2021-03-28 10:26 Rev.: 10942

try using global vars for allowde_domain and password_user_file

7 lines of code changed in 1 file:

sbu062 2021-03-28 10:11 Rev.: 10941

shorter separator without encrypt type

2 lines of code changed in 1 file:

sbu062 2021-03-28 10:09 Rev.: 10940

fix user, referred to undefined

1 lines of code changed in 1 file:

sbu062 2021-03-28 10:05 Rev.: 10939

password check file is function for reuse

20 lines of code changed in 1 file:

sbu062 2021-03-27 19:51 Rev.: 10938

renamed main bot resource

2 lines of code changed in 1 file:

sbu062 2021-03-27 16:22 Rev.: 10937

strip whitespace, extra spaces in commands can cause mess

6 lines of code changed in 1 file:

sbu062 2021-03-27 14:01 Rev.: 10936

install and start info

5 lines of code changed in 1 file:

sbu062 2021-03-27 13:53 Rev.: 10935

added security check for bot

83 lines of code changed in 1 file:

sbu062 2021-03-26 18:09 Rev.: 10934

need larger generation limit for long target string

1 lines of code changed in 1 file:

sbu062 2021-03-26 17:38 Rev.: 10933

long GA_TARGET string

0 lines of code changed in 2 files:

sbu062 2021-03-26 13:47 Rev.: 10931

show log on standard output, screen

1 lines of code changed in 1 file:

sbu062 2021-03-26 13:46 Rev.: 10930

merged fixes to LOGGER from the latest branch

35 lines of code changed in 1 file:

sbu062 2021-03-26 13:31 Rev.: 10929

renamed main code file for clarity

548 lines of code changed in 2 files:

sbu062 2021-03-26 13:29 Rev.: 10928

added keywords

0 lines of code changed in 2 files:

sbu062 2021-03-26 13:27 Rev.: 10927

combined an early OO code r513 with include files for Intel compiler without need in make, code can work as a project in Visual Studio

5894 lines of code changed in 7 files:

tla051 2021-03-26 12:31 Rev.: 10926

first commit with changed folder structure

10917 lines of code changed in 9 files:

aru047 2021-03-26 11:43 Rev.: 10925

3 age classes for each breeding seasons

9 lines of code changed in 1 file:

tla051 2021-03-26 11:00 Rev.: 10924

0 lines of code changed in 10 files:

tla051 2021-03-26 10:57

visual foraging model implemented for barent sea

10917 lines of code changed in 9 files:

tla051 2021-03-26 10:53 Rev.: 10914

test

0 lines of code changed in 10 files:

tla051 2021-03-26 10:51

theoretical foraging model

10917 lines of code changed in 9 files:

sbu062 2021-03-25 21:53 Rev.: 10904

more info message, less confusing

1 lines of code changed in 1 file:

sbu062 2021-03-25 21:47 Rev.: 10903

small changes

2 lines of code changed in 1 file:

sbu062 2021-03-25 21:40 Rev.: 10902

security check for XMPP domain

10 lines of code changed in 1 file:

sbu062 2021-03-25 18:42 Rev.: 10901

disable security report

2 lines of code changed in 1 file:

sbu062 2021-03-25 18:29 Rev.: 10900

check password security with craklib

4 lines of code changed in 1 file:

sbu062 2021-03-25 18:17 Rev.: 10899

a clear indication of success

1 lines of code changed in 1 file:

sbu062 2021-03-25 18:14 Rev.: 10898

sudo must be under htpasswd

1 lines of code changed in 1 file:

sbu062 2021-03-25 18:02 Rev.: 10897

some typos

2 lines of code changed in 1 file:

sbu062 2021-03-25 17:51 Rev.: 10896

utf chars not supported

1 lines of code changed in 1 file:

sbu062 2021-03-25 17:46 Rev.: 10895

good to check password length

3 lines of code changed in 1 file:

sbu062 2021-03-25 17:43 Rev.: 10894

reset password command

41 lines of code changed in 1 file:

sbu062 2021-03-25 17:01 Rev.: 10893

shorter is better

1 lines of code changed in 1 file:

sbu062 2021-03-25 16:50 Rev.: 10892

shorter is better

2 lines of code changed in 1 file:

sbu062 2021-03-25 16:47 Rev.: 10891

only one password

4 lines of code changed in 1 file:

sbu062 2021-03-25 16:45 Rev.: 10890

need to check arguments

6 lines of code changed in 1 file:

sbu062 2021-03-25 16:40 Rev.: 10889

suggest random secure password

11 lines of code changed in 1 file:

sbu062 2021-03-25 16:24 Rev.: 10888

allow all users on tegsvn to use the bot, security list check for user is disabled

1 lines of code changed in 1 file:

sbu062 2021-03-25 16:18 Rev.: 10887

xmpp_user is a better name, more intuitive

7 lines of code changed in 1 file:

sbu062 2021-03-25 16:12 Rev.: 10886

disallow message as getter

22 lines of code changed in 1 file:

sbu062 2021-03-25 16:01 Rev.: 10885

security lists with both username and domain

4 lines of code changed in 1 file:

sbu062 2021-03-25 14:39 Rev.: 10884

basic security check for commands, check if the user is from TEGsvn domain

74 lines of code changed in 1 file:

sbu062 2021-03-25 13:55 Rev.: 10883

need group info in help

1 lines of code changed in 1 file:

sbu062 2021-03-25 13:52 Rev.: 10882

swap user and server parameters to actually add bot user to the who user group on roster

2 lines of code changed in 1 file:

sbu062 2021-03-25 13:24 Rev.: 10881

typo

1 lines of code changed in 1 file:

nfijg 2021-03-25 13:23 Rev.: 10880

removed zdominant

48 lines of code changed in 3 files:

sbu062 2021-03-25 13:23 Rev.: 10879

fix help text

1 lines of code changed in 1 file:

sbu062 2021-03-25 13:18 Rev.: 10878

fix helper

1 lines of code changed in 1 file:

sbu062 2021-03-25 13:15 Rev.: 10877

comments fix

4 lines of code changed in 1 file:

sbu062 2021-03-25 13:12 Rev.: 10876

more info on usage

3 lines of code changed in 1 file:

sbu062 2021-03-25 13:01 Rev.: 10875

fix typo in string

2 lines of code changed in 1 file:

sbu062 2021-03-25 12:59 Rev.: 10874

one-liner build string should work for subprocess.call, not array

6 lines of code changed in 1 file:

sbu062 2021-03-25 12:33 Rev.: 10873

xmpp_bot: command to manage temporary bots

75 lines of code changed in 1 file:

sbu062 2021-03-25 09:37 Rev.: 10872

add headurl to allow easy deploy on ahafarm server, via `svn export`

1 lines of code changed in 1 file:

sbu062 2021-03-25 09:34 Rev.: 10871

disable debugging
`lock-2` was used for testing on ahafarm server without interruption of the simulation

1 lines of code changed in 1 file:

nfijg 2021-03-25 09:34 Rev.: 10870

commented out calc and print to file o009-cooccurence.txt in SRfecundity

93 lines of code changed in 2 files:

sbu062 2021-03-25 09:30 Rev.: 10869

need some help to unhalt model

2 lines of code changed in 1 file:

sbu062 2021-03-25 09:25 Rev.: 10868

fix bug in (report)

1 lines of code changed in 1 file:

sbu062 2021-03-25 09:12 Rev.: 10867

check errors in abstract file

5 lines of code changed in 1 file:

sbu062 2021-03-25 09:08 Rev.: 10866

check stop for errors; if nonexistent

6 lines of code changed in 1 file:

sbu062 2021-03-25 08:53 Rev.: 10865

typo fix, os import

2 lines of code changed in 1 file:

sbu062 2021-03-25 08:47 Rev.: 10864

model halt and unhalt / disable command

16 lines of code changed in 1 file:

sbu062 2021-03-25 08:34 Rev.: 10863

better formatting for abstract

1 lines of code changed in 1 file:

sbu062 2021-03-25 08:30 Rev.: 10862

added model abstract to output

5 lines of code changed in 1 file:

sbu062 2021-03-25 08:17 Rev.: 10861

initial version of model bot

49 lines of code changed in 1 file:

sbu062 2021-03-25 07:33 Rev.: 10860

sys: copied server bot for model watchdog

140 lines of code changed in 1 file:

sbu062 2021-03-24 17:40 Rev.: 10859

web: need full logging of all commands for security

20 lines of code changed in 1 file:

nfijg 2021-03-24 17:37 Rev.: 10858

corrected many errors in GOS()

56 lines of code changed in 1 file:

sbu062 2021-03-24 15:41 Rev.: 10857

web: apache server log command

8 lines of code changed in 1 file:

sbu062 2021-03-24 15:29 Rev.: 10856

web: better begin from new line if there are several dirs

1 lines of code changed in 1 file:

sbu062 2021-03-24 15:28 Rev.: 10855

web: fix wrong revision, was latest

1 lines of code changed in 1 file:

sbu062 2021-03-24 15:24 Rev.: 10854

web: added directory changed

4 lines of code changed in 1 file:

sbu062 2021-03-24 15:14 Rev.: 10853

web: uptime command

6 lines of code changed in 1 file:

sbu062 2021-03-24 15:09 Rev.: 10852

web: check and parse revision

10 lines of code changed in 1 file:

nfijg 2021-03-24 14:04 Rev.: 10851

corrected prints to SRcorrplots files (110-144)

237 lines of code changed in 2 files:

sbu062 2021-03-24 13:56 Rev.: 10850

web: doc note on apt package

1 lines of code changed in 1 file:

sbu062 2021-03-24 13:35 Rev.: 10849

web: use consistnt help messages

4 lines of code changed in 1 file:

sbu062 2021-03-24 13:01 Rev.: 10848

version command and revision keyword

9 lines of code changed in 1 file:

sbu062 2021-03-24 12:30 Rev.: 10847

web: forgot `-r`

1 lines of code changed in 1 file:

sbu062 2021-03-24 12:27 Rev.: 10846

web: commit info function

7 lines of code changed in 1 file:

hje044 2021-03-24 12:03 Rev.: 10845

Finally figured out how to properly set ignore for subfolders for all unversioned files.

16 lines of code changed in 2 files:

sbu062 2021-03-24 12:01 Rev.: 10844

web: better server info

3 lines of code changed in 1 file:

hje044 2021-03-24 11:49 Rev.: 10843

Remove output folder, all generated when running scripts

0 lines of code changed in 1 file:

hje044 2021-03-24 11:47 Rev.: 10842

Attempting to clean up files and ignores

262 lines of code changed in 8 files:

sbu062 2021-03-24 11:37 Rev.: 10841

added svn server xmpp bot

88 lines of code changed in 1 file:

hje044 2021-03-24 11:17 Rev.: 10840

Starting out using svn properly, hopefully

406 lines of code changed in 2 files:

sbu062 2021-03-23 08:43 Rev.: 10839

gnuplot works better with auto syntax highlighters

6 lines of code changed in 2 files:

sbu062 2021-03-23 07:40 Rev.: 10838

added templates from BIO

0 lines of code changed in 2 files:

sbu062 2021-03-22 13:32 Rev.: 10837

more informative comment on `FFA_MODEL_OUTPUT_TAG_CONFIG_REV`

3 lines of code changed in 1 file:

sbu062 2021-03-21 08:35 Rev.: 10836

added only title page seminar number

5783 lines of code changed in 1 file:

nfijg 2021-03-20 15:36 Rev.: 10835

moved the calls to SRchrom?create to SRinitfishmodel so that ChromNumber() is made only once. Now recombination works for NR-genes.

81 lines of code changed in 1 file:

nfijg 2021-03-20 09:31 Rev.: 10834

removed chrom(ind,g) and eggchrom(). NumChrom(g) does the job.

230 lines of code changed in 1 file:

sbu062 2021-03-19 18:02 Rev.: 10833

doc. fix typo

1 lines of code changed in 1 file:

sbu062 2021-03-19 17:56 Rev.: 10832

doc: a couple of typos fixed

4 lines of code changed in 2 files:

sbu062 2021-03-19 17:26 Rev.: 10831

small resize for boxes

748 lines of code changed in 1 file:

aru047 2021-03-19 14:08 Rev.: 10830

Shuffling new male and female parents before breeding, simulations march

91 lines of code changed in 5 files:

sbu062 2021-03-19 12:14 Rev.: 10829

point to revision keyword

577 lines of code changed in 1 file:

sbu062 2021-03-19 10:50 Rev.: 10828

`configuration_version` added prefix

16 lines of code changed in 4 files:

sbu062 2021-03-19 10:48 Rev.: 10827

done slides: keywords, branshing

2939 lines of code changed in 1 file:

sbu062 2021-03-19 08:57 Rev.: 10826

documnent `FFA_MODEL_OUTPUT_TAG_CONFIG_REV` environment variable and `configuration_version` parameter

41 lines of code changed in 3 files:

sbu062 2021-03-19 08:20 Rev.: 10825

environment variable `FFA_MODEL_OUTPUT_TAG_CONFIG_REV` sets model tag from svn revision string defined as `svn_version_string` in the model configuration parameters file

69 lines of code changed in 2 files:

sbu062 2021-03-19 07:30 Rev.: 10824

configuration revision tag

4 lines of code changed in 1 file:

sbu062 2021-03-19 07:28 Rev.: 10823

added revision tag to file

1 lines of code changed in 1 file:

sbu062 2021-03-19 07:27 Rev.: 10822

no need and difficult to maintain numbering

26 lines of code changed in 1 file:

sbu062 2021-03-19 07:23 Rev.: 10821

keywords only

1 lines of code changed in 1 file:

sbu062 2021-03-19 06:59 Rev.: 10820

todays seminar slides

13362 lines of code changed in 1 file:

sbu062 2021-03-19 06:56 Rev.: 10819

moved sapience workshop presentation to dedicated dir

77543 lines of code changed in 4 files:

nfijg 2021-03-18 14:22 Rev.: 10818

new array genes()

85 lines of code changed in 1 file:

aru047 2021-03-18 14:20 Rev.: 10817

Mixing new male and female parents

11 lines of code changed in 1 file:

nfijg 2021-03-18 13:28 Rev.: 10816

added parameter CHROMOSOMES

29 lines of code changed in 1 file:

nfijg 2021-03-18 12:58 Rev.: 10815

if (random < recomb) then a recombination occurs !changed from > to < 18.03.21

16 lines of code changed in 1 file:

sbu062 2021-03-18 12:41 Rev.: 10814

added general statistics show to main menu in GUI mode

2 lines of code changed in 1 file:

sbu062 2021-03-18 12:29 Rev.: 10813

fix format for longer runs

2 lines of code changed in 1 file:

sbu062 2021-03-18 12:18 Rev.: 10812

cleaner GUI with general stats above

4 lines of code changed in 1 file:

nfijg 2021-03-18 12:17 Rev.: 10811

now also SRchrom4create

60 lines of code changed in 2 files:

sbu062 2021-03-18 12:09 Rev.: 10810

doc: added general stats command to model docs

1 lines of code changed in 1 file:

sbu062 2021-03-18 12:00 Rev.: 10809

code to show general model statistics in GUI mode
TODO: need to refactor for show global parameters with a similar universal backend function callable from GUI and CMD

26 lines of code changed in 1 file:

sbu062 2021-03-18 11:40 Rev.: 10808

added entries for help screens on `show statistics`

2 lines of code changed in 1 file:

sbu062 2021-03-18 11:34 Rev.: 10807

added `show statistics`command to CMD interface

13 lines of code changed in 2 files:

nfijg 2021-03-18 11:31 Rev.: 10806

created SRchrom3create for chromarr == 3

54 lines of code changed in 2 files:

sbu062 2021-03-18 11:19 Rev.: 10805

better labels

3 lines of code changed in 1 file:

sbu062 2021-03-18 11:09 Rev.: 10804

(model_output_stats_txt) produces general model output statistics
Need to call it in both GUI and CMD

35 lines of code changed in 1 file:

sbu062 2021-03-18 09:29 Rev.: 10803

case and line length must fit coding style

33 lines of code changed in 1 file:

sbu062 2021-03-18 09:19 Rev.: 10802

short date look better

1 lines of code changed in 1 file:

sbu062 2021-03-18 09:18 Rev.: 10801

info tags for svn

4 lines of code changed in 1 file:

sbu062 2021-03-18 09:12 Rev.: 10800

better name

4 lines of code changed in 1 file:

sbu062 2021-03-18 09:04 Rev.: 10799

got rid of magical numbers, use constant parameters

31 lines of code changed in 1 file:

sbu062 2021-03-18 08:30 Rev.: 10798

case changed according to code style, PARSETEXT uppercase as external library

93 lines of code changed in 2 files:

sbu062 2021-03-18 08:05 Rev.: 10797

check and explicitly define `pure` or `impure` for functions and procedures
Note that HEDTOOLS procedures untouched because they are synced with main module but main module must support older F95 and F2003 compilers such as Oracle f95

41 lines of code changed in 6 files:

nfijg 2021-03-17 18:39 Rev.: 10796

removed new calculation of genelocation on chroms in SRdiploideggs14 (all inds equal)

163 lines of code changed in 1 file:

nfijg 2021-03-17 14:59 Rev.: 10795

new SRchrom1create for locating genes for chromarr == 1

176 lines of code changed in 2 files:

sbu062 2021-03-17 12:29 Rev.: 10794

doc: added short description to `daytime_hours` to docs

6 lines of code changed in 1 file:

sbu062 2021-03-17 12:24 Rev.: 10793

typo in comment delimiter

1 lines of code changed in 1 file:

sbu062 2021-03-17 12:22 Rev.: 10792

GUI table widget for `daytime_hours` parameter, needed adaptation of other table widget rows IDs (+1) and linked adaptation in (do_update_params_table_edited)

86 lines of code changed in 1 file:

sbu062 2021-03-17 11:16 Rev.: 10791

CMD interface commands to set and show `daytime_hours` parameter

12 lines of code changed in 1 file:

sbu062 2021-03-17 11:03 Rev.: 10790

parameter `Global_Hours_Daytime_Feeding` with parameter file `daytime_hours` defines day:night pattern

21 lines of code changed in 4 files:

sbu062 2021-03-16 21:56 Rev.: 10789

implement diurnal pattern within the main loop, no need in `where`

6 lines of code changed in 1 file:

sbu062 2021-03-16 14:35 Rev.: 10788

need only one diurnal parameter

4 lines of code changed in 1 file:

sbu062 2021-03-16 13:28 Rev.: 10787

(schedule_2_int) is used to impose the diel pattern of food provisioning, testing with 12:12 regime, needs additional global parameter

8 lines of code changed in 1 file:

nfijg 2021-03-16 12:20 Rev.: 10786

corrected scaling and EFFgenes for alleleconv = 4

49 lines of code changed in 3 files:

sbu062 2021-03-16 10:46 Rev.: 10785

`food_volume_absorb_mean_midgut` is not informative and has not been used for debug or test, deleted

10 lines of code changed in 1 file:

sbu062 2021-03-16 10:45 Rev.: 10784

(history_update) is public interface for (midgut_fish_history_update)
now can be used outside of (mg_step), e.g. in `SIMULATE`

4 lines of code changed in 1 file:

sbu062 2021-03-16 08:50 Rev.: 10783

temporary work branch for refactoring deleted

0 lines of code changed in 3 files:

sbu062 2021-03-16 08:47 Rev.: 10782

refactor: global output arrays not used in `THE_FISH`, instead, individual-fish specific history stack arrays are used
merged bransh `STOMACH_globalarrays` r10766 through r10781

233 lines of code changed in 3 files:

sbu062 2021-03-16 08:39 Rev.: 10781

debug print code deleted, reverted to r10766 not touching added output arrays definitions

0 lines of code changed in 1 file:

sbu062 2021-03-16 08:14 Rev.: 10780

move definition of global output arrays back to `SIMULATE` module, no reference to globals is needed in `THE_FISH`. This reverts r10677

41 lines of code changed in 2 files:

sbu062 2021-03-16 07:52 Rev.: 10779

only comment on cumulative versus instantaneous absorption use to calculate cumulative absorption

4 lines of code changed in 1 file:

sbu062 2021-03-16 07:41 Rev.: 10778

debug: only debug print code

30 lines of code changed in 1 file:

sbu062 2021-03-16 07:40 Rev.: 10777

iadded current instantaneous absorption to history stack array, so it is now possible to correctly calculate absorption rate without requiring global output arrays in `THE_FISH` module; call (midgut_fish_history_update) moved below (check_disappear) call, fixes wrong cumulative absorption history update before checking for disappearing item

41 lines of code changed in 1 file:

sbu062 2021-03-15 17:19 Rev.: 10776

(fish_midgut_update_from_stomach) is declared *impure* but could be converted to `pure` if `write` statements are deleted

1 lines of code changed in 1 file:

sbu062 2021-03-15 17:15 Rev.: 10775

block `UPDATE_HISTORY_ABSORP` isolated to subroutine (midgut_fish_history_update)

38 lines of code changed in 1 file:

aru047 2021-03-15 15:07 Rev.: 10774

older individuals have guaranteed nest sites, new cumulative plots for demography

194 lines of code changed in 5 files:

nfijg 2021-03-15 14:54 Rev.: 10773

fixed file names of 170-177 and headings in files 160-177

36 lines of code changed in 2 files:

sbu062 2021-03-15 13:42 Rev.: 10772

block UPDATE_HISTORY_ABSORP updates history stack array for cimulative absorption

37 lines of code changed in 1 file:

sbu062 2021-03-15 13:41 Rev.: 10771

debug: debug code only

0 lines of code changed in 2 files:

sbu062 2021-03-15 12:02 Rev.: 10770

added history array subcomponent to FISH_SKEL, this will include history arrays, done and init cumulative absorption so far

24 lines of code changed in 1 file:

sbu062 2021-03-15 12:00 Rev.: 10769

got back output arrays to COMMONDATA because it is difficult to implement FISH class component transfer to IF_CMD and IF_GUI without `this` argument, need smaller history arrays subcomponent in FISH class; history array management code copied from AHA: (add_to_history)

132 lines of code changed in 1 file:

nfijg 2021-03-15 11:34 Rev.: 10768

small changes after converting to integer gene values

1 lines of code changed in 1 file:

sbu062 2021-03-15 08:38 Rev.: 10767

definitions of output arrays moved to THE_FISH module to integrate with FISH class

0 lines of code changed in 4 files:

sbu062 2021-03-14 14:13 Rev.: 10765

fix keyword

8 lines of code changed in 1 file:

sbu062 2021-03-14 14:12 Rev.: 10764

keywords added to doc properties

8 lines of code changed in 1 file:

sbu062 2021-03-14 14:10 Rev.: 10763

added archival JORH paper v1.0 21/09/20 at 08:17:53

589 lines of code changed in 1 file:

sbu062 2021-03-14 14:09 Rev.: 10762

added archival JORH paper v0.2c 18/09/20 at 18:53:34

525 lines of code changed in 1 file:

sbu062 2021-03-14 14:05

added archival JORH paper v0.2b 18/09/20 at 11:03:15

627 lines of code changed in 2 files:

sbu062 2021-03-14 14:04 Rev.: 10759

added archival JORH paper v0.2a 15/09/20 at 15:02:41

233 lines of code changed in 1 file:

sbu062 2021-03-14 14:02 Rev.: 10758

added archival v 0.2 JORH paper, 15/09/20 at 12:33:26

572 lines of code changed in 1 file:

sbu062 2021-03-14 14:01 Rev.: 10757

added archival paper COVID for JORH v0.1 14/09/20 at 17:26:37

1826 lines of code changed in 1 file:

nfijg 2021-03-14 12:15 Rev.: 10756

converted both NR-genes and MOD-genes to INTEGER, no error messaged in building.

52 lines of code changed in 1 file:

sbu062 2021-03-14 00:09 Rev.: 10755

viewvc is long obsolete

0 lines of code changed in 1 file:

sbu062 2021-03-14 00:06 Rev.: 10754

deleted obsolete auth group for zed014

0 lines of code changed in 1 file:

nfijg 2021-03-13 15:50 Rev.: 10753

integer values of genomeNR

261 lines of code changed in 3 files:

nfijg 2021-03-13 11:25 Rev.: 10752

added fish parameters file

105 lines of code changed in 1 file:

nfijg 2021-03-13 08:32 Rev.: 10751

Added option alleleconv = 4 for a x^2 relationship between gene value and effective gene value

58 lines of code changed in 2 files:

aru047 2021-03-12 23:41 Rev.: 10750

Extrapair mating main code, first version with longevity

638 lines of code changed in 1 file:

aru047 2021-03-12 23:37 Rev.: 10749

Initial commit

2600 lines of code changed in 4 files:

nfijg 2021-03-12 15:17 Rev.: 10748

assigned chromosomes to genes for chromarr 1-4. not finished because first remove SQUIRREL from model

111 lines of code changed in 1 file:

tla051 2021-03-12 13:47 Rev.: 10747

initial upload

0 lines of code changed in 1 file:

tla051 2021-03-12 13:42 Rev.: 10746

in master_grd average changed mean to median

1 lines of code changed in 1 file:

tla051 2021-03-12 13:36 Rev.: 10745

Rmarkdown code and documentation of the analysis

212 lines of code changed in 1 file:

tla051 2021-03-12 13:21 Rev.: 10744

removed because archived under https://tegsvn.uib.no/svn/tegsvn/branches/tom_langbehn/archive

0 lines of code changed in 689 files:

tla051 2021-03-12 13:19 Rev.: 10742

removed here because archived under https://tegsvn.uib.no/svn/tegsvn/branches/tom_langbehn/archive

0 lines of code changed in 18 files:

tla051 2021-03-12 13:19 Rev.: 10741

removed because archived under https://tegsvn.uib.no/svn/tegsvn/branches/tom_langbehn/archive

0 lines of code changed in 16 files:

tla051 2021-03-12 13:12 Rev.: 10738

remove because archived under https://tegsvn.uib.no/svn/tegsvn/branches/tom_langbehn/archive

0 lines of code changed in 29 files:

sbu062 2021-03-12 10:22 Rev.: 10731

obsolete file, can be autogenerated

0 lines of code changed in 1 file:

sbu062 2021-03-12 10:21 Rev.: 10730

proved to be unneeded, empty

0 lines of code changed in 2 files:

sbu062 2021-03-12 10:20 Rev.: 10729

obsolete directory, project moved to `tags` directory, with updated code

0 lines of code changed in 5 files:

nfijg 2021-03-12 08:34 Rev.: 10728

prevented exceeding boundary of o101slig(x) etc in SRdecision.

79 lines of code changed in 1 file:

sbu062 2021-03-12 08:32 Rev.: 10727

warning sign

5663 lines of code changed in 1 file:

sbu062 2021-03-11 22:01 Rev.: 10726

big rule applies to wc

210 lines of code changed in 1 file:

sbu062 2021-03-11 21:57 Rev.: 10725

main svn concepts red

5516 lines of code changed in 1 file:

sbu062 2021-03-11 21:55 Rev.: 10724

describe working copy

234 lines of code changed in 1 file:

sbu062 2021-03-11 21:40 Rev.: 10723

describe testing repository

285 lines of code changed in 1 file:

sbu062 2021-03-11 21:01 Rev.: 10722

make forkflow more visible

312 lines of code changed in 1 file:

sbu062 2021-03-11 20:58 Rev.: 10721

need to checkout after import

5584 lines of code changed in 1 file:

nfijg 2021-03-11 20:56 Rev.: 10720

found new error in finfo(9) exceeding boundary

8 lines of code changed in 1 file:

sbu062 2021-03-11 20:26 Rev.: 10719

added title in document properties

5562 lines of code changed in 1 file:

sbu062 2021-03-11 20:25 Rev.: 10718

document properties and info email

5558 lines of code changed in 1 file:

nfijg 2021-03-11 19:11 Rev.: 10717

converted from totAFlight etc to totXYpairs (based on genome(NR) in SRallelefrequency.

90 lines of code changed in 1 file:

sbu062 2021-03-11 15:21 Rev.: 10716

only dirs in tree

56 lines of code changed in 1 file:

sbu062 2021-03-11 15:20 Rev.: 10715

need working copy concept

92 lines of code changed in 1 file:

sbu062 2021-03-11 15:17 Rev.: 10714

wider box needed

14 lines of code changed in 1 file:

sbu062 2021-03-11 15:16 Rev.: 10713

need bigger box

5593 lines of code changed in 1 file:

sbu062 2021-03-11 15:15 Rev.: 10712

added some on commit message

8361 lines of code changed in 1 file:

sbu062 2021-03-11 14:36 Rev.: 10711

first version of svn basic usage presentation

27323 lines of code changed in 1 file:

nfijg 2021-03-11 14:06 Rev.: 10710

150 lines of code changed in 1 file:

sbu062 2021-03-11 09:43 Rev.: 10709

higher `midgut_michaelis_r_max` results in earlier full absorption, fitting within 24 h

2 lines of code changed in 2 files:

sbu062 2021-03-11 09:04 Rev.: 10708

added hour indicators for x axis

7 lines of code changed in 1 file:

sbu062 2021-03-11 08:50 Rev.: 10707

fix legends, add cumulative absorption plot

5 lines of code changed in 1 file:

sbu062 2021-03-11 08:41 Rev.: 10706

save instantaneous absorption rate to the output arrays, update plot utils

27 lines of code changed in 4 files:

nfijg 2021-03-10 14:41 Rev.: 10705

5 lines of code changed in 1 file:

nfijg 2021-03-10 14:22 Rev.: 10704

HED26 created from Hed24 9Oct15.f90 (file date 09 Oct 2015) at R:\Modellering\FishEmotion\FORTRAN HED23\HED24\working 09102015

69 lines of code changed in 1 file:

nfijg 2021-03-10 14:20 Rev.: 10703

5744 lines of code changed in 1 file:

nfijg 2021-03-10 14:15 Rev.: 10702

13830 lines of code changed in 2 files:

nfijg 2021-03-10 14:13 Rev.: 10701

created from HED23, but fortran file thereafter swapped with HED24 of R:\Modellering\FishEmotion\FORTRAN HED23\HED24\working 09102015

264 lines of code changed in 4 files:

nfijg 2021-03-10 14:09

4 lines of code changed in 9 files:

nfijg 2021-03-10 13:36 Rev.: 10698

found arrays that exceeded upper bounds. Found that CHROM() is never initiated.

31 lines of code changed in 3 files:

sbu062 2021-03-10 13:23 Rev.: 10697

doc: added class diagram to manual

18 lines of code changed in 1 file:

sbu062 2021-03-10 13:11 Rev.: 10696

added class diagram for THE_FISH module
Note: produced with ForUML, based on m_fish.f90 and m_env.f90 sources

0 lines of code changed in 1 file:

nfijg 2021-03-10 11:39 Rev.: 10695

just made new HEd25 from HED23

13830 lines of code changed in 2 files:

sbu062 2021-03-10 09:59 Rev.: 10693

fix save plot function for absorption rate plot in GUI mode; need using `PLOT_OUT_ABSORP_RATE`

5 lines of code changed in 1 file:

sbu062 2021-03-10 09:48 Rev.: 10692

doc: added fish inheritance diagram using `@dot`

12 lines of code changed in 1 file:

sbu062 2021-03-09 23:22 Rev.: 10691

fix units in rate plots, use TeX notation

19 lines of code changed in 3 files:

sbu062 2021-03-09 22:55 Rev.: 10690

fix interpolation grid borders in if conditions

6 lines of code changed in 1 file:

sbu062 2021-03-09 22:42 Rev.: 10689

implemented instantaneous absorption rate function (absorption_rate) and appetite factor based on instantaneous absorption rate (absorption_factor)

73 lines of code changed in 1 file:

sbu062 2021-03-09 11:39 Rev.: 10688

rate plots scale per minute

9 lines of code changed in 2 files:

sbu062 2021-03-09 11:20 Rev.: 10687

doc: document `save command`

7 lines of code changed in 1 file:

sbu062 2021-03-09 11:07 Rev.: 10686

implemented save rate data, with GUI and CMD interface bindings and file error trapping

183 lines of code changed in 4 files:

sbu062 2021-03-09 07:40 Rev.: 10685

absorption rate plot axis name

2 lines of code changed in 2 files:

sbu062 2021-03-08 22:02 Rev.: 10684

doc: fix (cum2rate) comments

2 lines of code changed in 2 files:

sbu062 2021-03-08 21:58 Rev.: 10683

implemented absorption rate plot in GUI

43 lines of code changed in 1 file:

sbu062 2021-03-08 21:48 Rev.: 10682

command `plot absorption` is now primary, other are aliases

5 lines of code changed in 2 files:

sbu062 2021-03-08 18:40 Rev.: 10681

doc: plot command

19 lines of code changed in 1 file:

sbu062 2021-03-08 17:14 Rev.: 10680

implemented plotting absorption rate (command `plot absorption_rate`)

64 lines of code changed in 1 file:

sbu062 2021-03-08 14:03 Rev.: 10679

implemented generic (cum2rate) function and interface, adding `real` version

56 lines of code changed in 3 files:

sbu062 2021-03-08 13:27 Rev.: 10678

reorganize: introduced umbrella class FISH extending MID_GUT for the whole fish organism

10 lines of code changed in 2 files:

sbu062 2021-03-08 12:58 Rev.: 10677

move definition of `Output_Arrays` to COMMONDATA
This is needed to make it possible to use absorption rate in THE_FISH,
if appetite is affected by absorption rate

41 lines of code changed in 2 files:

sbu062 2021-03-04 12:28 Rev.: 10676

doc: more on digestion and absorption

38 lines of code changed in 1 file:

sbu062 2021-03-04 10:46 Rev.: 10675

doc: digestion delay described

15 lines of code changed in 1 file:

nfijg 2021-03-03 13:19 Rev.: 10674

264 lines of code changed in 7 files:

nfijg 2021-03-03 09:04 Rev.: 10673

1 lines of code changed in 1 file:

nfijg 2021-03-03 08:53 Rev.: 10672

1 lines of code changed in 1 file:

sbu062 2021-03-02 19:54 Rev.: 10671

docs are for all non-code docs

0 lines of code changed in 1 file:

sbu062 2021-03-02 14:33 Rev.: 10670

specific version is not important

1 lines of code changed in 1 file:

sbu062 2021-03-02 13:45 Rev.: 10669

updated script for Intel Visual Studio 2020

2 lines of code changed in 1 file:

nfijg 2021-03-02 11:37 Rev.: 10668

deleted files placed by mistake

0 lines of code changed in 4 files:

nfijg 2021-03-02 11:31

14094 lines of code changed in 8 files:

sbu062 2021-03-02 07:34 Rev.: 10665

reverted r8435 wrongly committed temporary change
poisson code is not well tested, not much needed for SIMGUT
`vn merge -r HEAD:8435 BASE_RANDOM.f90`

0 lines of code changed in 1 file:

sbu062 2021-03-02 07:28 Rev.: 10664

better name

59 lines of code changed in 46 files:

sbu062 2021-03-01 21:59 Rev.: 10663

web: fix rev number

2 lines of code changed in 1 file:

sbu062 2021-03-01 21:49 Rev.: 10662

web: new src link to hedtools

2 lines of code changed in 1 file:

sbu062 2021-03-01 14:09 Rev.: 10661

implicit loop breaks and crash on Windows Intel Fortran 19 (19.1.3.311 Build 20201010_000000)
{{{
forrtl: severe (170): Program Exception - stack overflow
Image PC Routine Line Source
simgut.exe 00007FF7B68434D8 Unknown Unknown Unknown
simgut.exe 00007FF7B668AF5E ENVIRON_mp_FOOD_P 144 m_env.f90
simgut.exe 00007FF7B66A2D31 SIMULATE_mp_TEST_ 517 m_simulate.f90
simgut.exe 00007FF7B66D0737 IF_GUI_mp_DO_RUN_ 713 m_ifgui.f90
simgut.exe 00007FF7B66F1379 Unknown Unknown Unknown
simgut.exe 00007FF7B6703205 Unknown Unknown Unknown
USER32.dll 00007FFE00275C1D Unknown Unknown Unknown
USER32.dll 00007FFE0027522C Unknown Unknown Unknown
USER32.dll 00007FFE00274F98 Unknown Unknown Unknown
USER32.dll 00007FFE002961A5 Unknown Unknown Unknown
USER32.dll 00007FFE0029E52A Unknown Unknown Unknown
USER32.dll 00007FFE0027ABE7 Unknown Unknown Unknown
USER32.dll 00007FFE00275C1D Unknown Unknown Unknown
USER32.dll 00007FFE002758EE Unknown Unknown Unknown
simgut.exe 00007FF7B66F55B9 Unknown Unknown Unknown
USER32.dll 00007FFE00275C1D Unknown Unknown Unknown
USER32.dll 00007FFE00275612 Unknown Unknown Unknown
simgut.exe 00007FF7B66F2AE6 Unknown Unknown Unknown
simgut.exe 00007FF7B66CCD23 IF_GUI_mp_GUI_CRE 416 m_ifgui.f90
simgut.exe 00007FF7B66EC34B RUNTIME_mp_SYSTEM 186 m_runtime.f90
simgut.exe 00007FF7B66EF342 MAIN__ 11 main.f90
simgut.exe 00007FF7B6842D3E Unknown Unknown Unknown
simgut.exe 00007FF7B68436E4 Unknown Unknown Unknown
KERNEL32.DLL 00007FFE00417C24 Unknown Unknown Unknown
ntdll.dll 00007FFE0198D721 Unknown Unknown Unknown
}}}

5 lines of code changed in 1 file:

sbu062 2021-03-01 13:55 Rev.: 10660

web: updated binary build of HEDTOOLS to latest Intel Fortran 19

3 lines of code changed in 1 file:

sbu062 2021-03-01 08:55 Rev.: 10659

web: added biopages for SB

7013 lines of code changed in 5 files:

February 2021 »

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