[med-svn] [Git][med-team/aevol][master] 5 commits: automake.patch: always apply subdir-objects option

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Fri Nov 5 21:43:26 GMT 2021 


Étienne Mollier pushed to branch master at Debian Med / aevol


Commits:
347cd6a4 by Étienne Mollier at 2021-11-05T22:04:15+01:00
automake.patch: always apply subdir-objects option

Closes: #998479

- - - - -
59100012 by Étienne Mollier at 2021-11-05T22:13:15+01:00
Add groff-message.patch

This is to fix typos in the comment symbols of some manual pages.

- - - - -
53161c12 by Étienne Mollier at 2021-11-05T22:23:24+01:00
Remove now unneeded maintainer manual pages

- - - - -
960eabe5 by Étienne Mollier at 2021-11-05T22:28:20+01:00
Adjust groff-message.patch to all upstream manpages

- - - - -
a1bf3a15 by Étienne Mollier at 2021-11-05T22:41:39+01:00
ready changelog to upload to unstable

- - - - -


18 changed files:

- − debian/aevol.manpages
- − debian/aevol_create.1
- − debian/aevol_misc_ancstats.1
- − debian/aevol_misc_compute_pop_stats.1
- − debian/aevol_misc_create_eps.1
- − debian/aevol_misc_extract.1
- − debian/aevol_misc_fixed_mutations.1
- − debian/aevol_misc_gene_families.1
- − debian/aevol_misc_lineage.1
- − debian/aevol_misc_robustness.1
- − debian/aevol_misc_view_generation.1
- − debian/aevol_modify.1
- − debian/aevol_propagate.1
- − debian/aevol_run.1
- debian/changelog
- debian/patches/automake.patch
- + debian/patches/groff-message.patch
- debian/patches/series


Changes:

=====================================
debian/aevol.manpages deleted
=====================================
@@ -1,13 +0,0 @@
-debian/aevol_create.1
-debian/aevol_run.1
-debian/aevol_modify.1
-debian/aevol_propagate.1
-debian/aevol_misc_ancstats.1
-debian/aevol_misc_compute_pop_stats.1
-debian/aevol_misc_create_eps.1
-debian/aevol_misc_extract.1
-debian/aevol_misc_fixed_mutations.1
-debian/aevol_misc_gene_families.1
-debian/aevol_misc_lineage.1
-debian/aevol_misc_robustness.1
-debian/aevol_misc_view_generation.1


=====================================
debian/aevol_create.1 deleted
=====================================
@@ -1,50 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_create \-h
-or
-.B \-\-help
-.br
-.B aevol_create \-V
-or
-.B \-\-version
-.br
-.B aevol_create \fR[\fB\-v\fR] \fR[\fB\-f\fI PARAM_FILE\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-c\fI CFILE\fR] \fR[\fB\-p\fI PFILE\fR]
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_create
-create an experiment with setup as specified in
-.I param_file
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-f, \-\-file
-.I PARAM_FILE
-.br
-specify parameter file (default: param.in)
-.HP
-.B \-o, \-\-out
-.I OUTDIR
-.br
-specify output directory (default "./")
-.HP
-.B \-c, \-\-chromosome
-.I CFILE
-.br
-load chromosome from given text file instead of generating it
-.HP
-.B \-p, \-\-plasmid
-.I PFILE
-.br
-load plasmid from given text file instead of generating it (params must allow plasmids)
-.SH "SEE ALSO"
-.B aevol_run, aevol_modify, aevol_propagate


=====================================
debian/aevol_misc_ancstats.1 deleted
=====================================
@@ -1,34 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_ancstats \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_ancstats \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_ancstats \fB\-f\fI LINEAGE_FILE
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_ancstats
-issues statistics for the line of descent of a given individual.
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-f, \-\-file
-.I  LINEAGE_FILE
-.br
-specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
-.SH "SEE ALSO"
-.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_misc_compute_pop_stats.1 deleted
=====================================
@@ -1,49 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_compute_pop_stats \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_compute_pop_stats \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_compute_pop_stats \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_compute_pop_stats
-issues population and replication statistics for each available backup from GENER1 to GENER2. These statistics are written in files global_pop_stats.out and stats/pop_stats/*.
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-i, \-\-index
-.I  INDEX
-.br
-specify the index (ID in current generation) of the individual whose replication statistics should be outputted
-.HP
-.B \-r, \-\-rank
-.I  RANK
-.br
-specify the rank of the individual whose replication statistics should be outputted
-.HP
-.B \-b, \-\-begin
-.I  GENER
-.br
-specify the first generation for which the statistics should be computed
-.HP
-.B \-e, \-\-end
-.I  GENER
-.br
-specify the last generation for which the statistics should be computed
-.SH "SEE ALSO"
-.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_misc_create_eps.1 deleted
=====================================
@@ -1,44 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_create_eps \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_create_eps \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_create_eps \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fB\-g\fI GENER
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_create_eps
-produces several eps files describing an individual of this population
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-i, \-\-index
-.I  INDEX
-.br
-specify the index (ID in current generation) of the individual
-.HP
-.B \-r, \-\-rank
-.I  RANK
-.br
-specify the rank of the individual
-.HP
-.B \-g, \-\-gener
-.I  GENER
-.br
-specify the generation of the individual
-.SH "SEE ALSO"
-.B aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_misc_extract.1 deleted
=====================================
@@ -1,58 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_extract \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_extract \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_extract \fR[\fB\-r\fI GENER\fR | \fB\-p\fI POP_FILE\fR] \fR[\fB\-t\fI PHEN_FILE\fR] \fR[\fB\-s\fI SEQ_FILE\fR] \fR[\fB\-g\fI NUM_GU\fR] \fR[\fB\-b\fR]
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_extract
-extracts the genotype and/or data about the phenotype of individuals in the provided population and write them into text files easy to parse with e.g. matlab.
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-r
-.I  GENER
-.br
-read generation GENER from a full aevol backup
-.HP
-.B \-p
-.I  POP_FILE
-.br
-read the population saved in population file POP_FILE
-.HP
-.B \-t
-.I  PHEN_FILE
-.br
-extract and save some infos about the phenotypes of the individuals to file PHEN_FILE
-.HP
-.B \-s
-.I  SEQ_FILE
-.br
-extract and save the sequences of the individuals to file SEQ_FILE
-.HP
-.B \-g
-.I  num_gu
-.br
-only treat this genetic unit (by default: treat all genetic units)
-.HP
-.B \-b
-.br
-only treat the best individual
-.SH "SEE ALSO"
-.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_misc_fixed_mutations.1 deleted
=====================================
@@ -1,34 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_fixed_mutations \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_fixed_mutations \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_fixed_mutations \fB\-f\fI LINEAGE_FILE
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_fixed_mutations
-issues the detailed list of mutations that occurred in the lineage of a given individual
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-f, \-\-file
-.I  LINEAGE_FILE
-.br
-specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
-.SH "SEE ALSO"
-.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_misc_gene_families.1 deleted
=====================================
@@ -1,34 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_gene_families \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_gene_families \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_gene_families \fB\-f\fI LINEAGE_FILE
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_gene_families
-issues the detailed history of each gene family on the lineage of a given individual
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-f, \-\-file
-.I  LINEAGE_FILE
-.br
-specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
-.SH "SEE ALSO"
-.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_misc_lineage.1 deleted
=====================================
@@ -1,49 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_lineage \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_lineage \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_lineage \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_lineage
-allows for the reconstruction of the lineage of a given individual. Requires the tree to have been recorded during evolution.
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-i, \-\-index
-.I  INDEX
-.br
-specify the index (ID in current generation) of the individual whose lineage is to be reconstructed
-.HP
-.B \-r, \-\-rank
-.I  RANK
-.br
-specify the rank of the individual whose lineage is to be reconstructed
-.HP
-.B \-b, \-\-begin
-.I  GENER
-.br
-specify the generation up to which the lineage is to be reconstructed
-.HP
-.B \-e, \-\-end
-.I  GENER
-.br
-specify the generation of the individual whose lineage is to be reconstructed
-.SH "SEE ALSO"
-.B aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_misc_robustness.1 deleted
=====================================
@@ -1,51 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_robustness \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_robustness \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_robustness \fR\fB\-g\fI GENER\fR [\fB\-n\fI NBCHILDREN] \fR[\fB\-i\fI INDEX\fR | \fB\-r\fI RANK\fR]
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_robustness
-computes the replication statistics of all the individuals of a given generation, like the proportion of neutral, beneficial, deleterious offsprings. This is done by simulating NBCHILDREN replications for each individual (1000 replications by default), with its mutation, rearrangement and transfer rates. Depending on those rates and genome size, there can be several mutations per replication. Those global statistics are written in stat/robustness_GENER.out, with one line per individual in the specified generation.  The program also outputs detailed statistics for one of the individuals (the best one by default). The detailed statistics for this individual are written in stats/replication_GENER.out, with one line per simulated child of this particular individual.
-
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-g, \-\-gener
-.I  GENER
-.br
-specify the generation number for which the robustness statistics are desired
-.HP
-.B \-n, \-\-nb\-children
-.I  NBCHILDREN
-.br
-specify the number of reproductions to simulate for each individual
-.HP
-.B \-i, \-\-index
-.I  INDEX
-.br
-specify the index (ID in current generation) of the individual for whom detailed reproduction statistics are desired
-.HP
-.B \-r, \-\-rank
-.I  RANK
-.br
-specify the rank of the individual for whom detailed reproduction statistics are desired
-
-.SH "SEE ALSO"
-.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps


=====================================
debian/aevol_misc_view_generation.1 deleted
=====================================
@@ -1,34 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_misc_view_generation \-h
-|
-.B \-\-help
-.br
-.B aevol_misc_view_generation \-V
-|
-.B \-\-version
-.br
-.B aevol_misc_view_generation \fB\-g\fI GENER
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_misc_view_generation
-allows one to visualize a generation using the exact same graphical outputs used in aevol_run.
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-g, \-\-gener
-.I  GENER
-.br
-specify generation to visualize (default 0)
-.SH "SEE ALSO"
-.B aevol_create, aevol_modify, aevol_propagate, aevol_run


=====================================
debian/aevol_modify.1 deleted
=====================================
@@ -1,40 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_modify \-h
-or
-.B \-\-help
-.br
-.B aevol_modify \-V
-or
-.B \-\-version
-.br
-.B aevol_modify \-g\fI GENER \fR[\fB\-f\fI param_file\fR]
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_modify
-modify an experiment as specified in
-.I param_file
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-g, \-\-gener
-.I GENER
-.br
-specify generation number
-.HP
-.B \-f, \-\-file
-.I param_file
-.br
-specify parameter file (default: param.in)
-.SH "SEE ALSO"
-.B aevol_create, aevol_run, aevol_propagate


=====================================
debian/aevol_propagate.1 deleted
=====================================
@@ -1,80 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_propagate \-h
-or
-.B \-\-help
-.br
-.B aevol_propagate \-V
-or
-.B \-\-version
-.br
-.B aevol_propagate \fR[\fB\-v\fR]  \fR[\fB\-g\fI GENER\fR]  \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-S\fI GENERALSEED\fR]
-.br
-.B aevol_propagate \fR[\fB\-v\fR]  \fR[\fB\-g\fI GENER\fR]  \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-s\fI SELSEED\fR]   \fR[\fB\-m\fI MUTSEED\fR]   \fR[\fB\-t\fI STOCHSEED\fR]   \fR[\fB\-e\fI ENVVARSEED\fR]   \fR[\fB\-n\fI ENVNOISESEED\fR]
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_propagate
-creates a fresh copy of the experiment as it was at the given generation. The generation number of the copy will be reset to 0. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different seed for each simulation, otherwise all simulations will yield exactly the same results. You can use the option \-S to do so. In this case, the random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). Alternatively, to change the random drawings for specific random processes only, do not use \-S but the options \-m, \-s, \-t, \-e, \-n (see below).
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.TP
-.B \-v, \-\-verbose
-be verbose
-.HP
-.B \-g, \-\-gener
-.I GENER
-.br
-specify generation number
-(default: that contained in file last_gener.txt, if any)
-.HP
-.B \-i, \-\-in
-.I INDIR
-.br
-specify input directory (default ".")
-.HP
-.B \-o, \-\-out
-.I OUTDIR
-.br
-specify output directory (default "./output")
-.HP
-.B \-S, \-\-general\-seed
-.I GENERALSEED
-.br
-specify an integer to be used as a seed for random numbers. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different	seed for each simulation, otherwise all simulations will yield exactly the same results. If you specify this general seed, random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). To change the random drawings for a specific random process only, do not use \-S but the options below.
-.HP
-.B \-s, \-\-sel\-seed
-.I SELSEED
-.br
-specify an integer as a seed for random numbers needed for selection and migration (if spatial structure is enabled).
-.HP
-.B \-m, \-\-mut\-seed
-.I MUTSEED
-.br
-specify an integer as a seed for random numbers needed for mutations.
-.HP
-.B \-t, \-\-stoch\-seed
-.I STOCHSEED
-.br
-specify an integer as a seed for random numbers needed for stochastic gene expression.
-.HP
-.B \-e, \-\-env\-var\-seed
-.I ENVVARSEED
-.br
-specify an integer as a seed for random numbers needed for environmental variation.
-.HP
-.B \-n, \-\-env\-noise\-seed
-.I ENVNOISESEED
-.br
-specify an integer as a seed for random numbers needed for environmental noise.
-.SH "SEE ALSO"
-.B aevol_create, aevol_run, aevol_modify


=====================================
debian/aevol_run.1 deleted
=====================================
@@ -1,53 +0,0 @@
-/#test with man \-l <file>
-.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
-.SH NAME
-aevol \- an in silico experimental evolution platform
-.SH SYNOPSIS
-.B aevol_run \-h
-|
-.B \-\-help
-.br
-.B aevol_run \-V
-|
-.B \-\-version
-.br
-.B aevol_run \fR[\fB\-r\fI GENER\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR]
-.SH DESCRIPTION
-.B Aevol
-is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
-.TP
-.B aevol_run
-run an aevol simulation.
-.SH OPTIONS
-.TP
-.B \-h, \-\-help
-print help, then exit
-.TP
-.B \-V, \-\-version
-print version number, then exit
-.HP
-.B \-r, \-\-resume
-.I  GENER
-.br
-specify generation to resume simulation at (default 0)
-.HP
-.B \-n, \-\-nbgener
-.I NB_GENER
-.br
-specify number of generations to be run (default 1000)
-.TP
-.B \-t, \-\-text
-use text files instead of binary files when possible
-.TP
-.B \-v, \-\-verbose
-be verbose
-.TP
-.B \-w, \-\-wait
-pause after loading
-.TP
-.B \-x, \-\-noX
-don't display X outputs upon start
-.br
-send SIGUSR1 to switch X output on/off
-.SH "SEE ALSO"
-.B aevol_create, aevol_modify, aevol_propagate


=====================================
debian/changelog
=====================================
@@ -1,11 +1,16 @@
-aevol (5.0+ds-3) UNRELEASED; urgency=medium
+aevol (5.0+ds-3) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * Team upload.
   * Do not call AM_INIT_AUTOMAKE twice
     Closes: #998479
   * Standards-Version: 4.6.0 (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Fri, 05 Nov 2021 08:00:27 +0100
+  [ Étienne Mollier ]
+  * Remove now unneeded maintainer manual pages.
+  * Add groff-message.patch to fix multiple typos in the comment marker '.\"'.
+
+ -- Étienne Mollier <emollier at debian.org>  Fri, 05 Nov 2021 22:39:02 +0100
 
 aevol (5.0+ds-2) unstable; urgency=medium
 


=====================================
debian/patches/automake.patch
=====================================
@@ -1,25 +1,24 @@
 Description: Do not call AM_INIT_AUTOMAKE twice
 Bug-Debian: https://bugs.debian.org/998479
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 05 Nov 2021 08:00:27 +0100
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -20,7 +20,7 @@ fi
+Last-Update: Fri, 05 Nov 2021 22:03:24 +0100
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+--- aevol.orig/configure.ac
++++ aevol/configure.ac
+@@ -20,7 +20,7 @@
  AC_CONFIG_MACRO_DIR([m4])
  
  # We want to use automake
 -AM_INIT_AUTOMAKE
-+# AM_INIT_AUTOMAKE
++AM_INIT_AUTOMAKE([subdir-objects])
  
  # Select compiler
  AC_PROG_CXX([clang-omp++ clang++ g++ icc])
-@@ -299,6 +299,8 @@ AM_CONDITIONAL(WITH_RAEVOL, test x"$raev
+@@ -298,7 +298,6 @@
+ AM_CONDITIONAL(WITH_RAEVOL, test x"$raevol" != xno)
  if test "x$raevol" = "xyes" ; then
     AC_DEFINE(__REGUL)
-    AM_INIT_AUTOMAKE([subdir-objects])
-+else
-+   AM_INIT_AUTOMAKE
+-   AM_INIT_AUTOMAKE([subdir-objects])
  fi
  
  #  ************************* --with-blas option *******************************


=====================================
debian/patches/groff-message.patch
=====================================
@@ -0,0 +1,102 @@
+Description: fix groff-message caused by typos in comment symbol
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2021-11-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- aevol.orig/doc/aevol_misc_ancestor_stats.1
++++ aevol/doc/aevol_misc_ancestor_stats.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_misc_view.1
++++ aevol/doc/aevol_misc_view.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_create.1
++++ aevol/doc/aevol_create.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_misc_compute_pop_stats.1
++++ aevol/doc/aevol_misc_compute_pop_stats.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_misc_create_eps.1
++++ aevol/doc/aevol_misc_create_eps.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_misc_extract.1
++++ aevol/doc/aevol_misc_extract.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_misc_gene_families.1
++++ aevol/doc/aevol_misc_gene_families.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_misc_lineage.1
++++ aevol/doc/aevol_misc_lineage.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_misc_robustness.1
++++ aevol/doc/aevol_misc_robustness.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_modify.1
++++ aevol/doc/aevol_modify.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_propagate.1
++++ aevol/doc/aevol_propagate.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform
+--- aevol.orig/doc/aevol_run.1
++++ aevol/doc/aevol_run.1
+@@ -1,4 +1,4 @@
+-./"test with man -l <file>
++.\"test with man -l <file>
+ .TH AEVOL "1" "July 2016" "aevol 5.0" "User Manual"
+ .SH NAME
+ Aevol \- an in silico experimental evolution platform


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 automake.patch
+groff-message.patch



View it on GitLab: https://salsa.debian.org/med-team/aevol/-/compare/2aaf2303cdfeee1941ba8e13fd95feba8183ee6f...a1bf3a15ea9b03d2b44028779c400aaec4b63e64

-- 
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