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Commit 39b7e0a2 authored by François LAURENT's avatar François LAURENT
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slight bootstrap speed improvement

parent 0f850692
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Pipeline #83093 passed
Stage: test
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recipes/Dockerfile
+ 10
− 4
View file @ 39b7e0a2
......@@ -7,15 +7,20 @@ RUN apt-get update && apt-get install -y \
&& rm -rf /var/lib/apt/lists/* \
&& git clone --depth 1 --single-branch -b $BRANCH https://gitlab.pasteur.fr/nyx/larvatagger.jl $DIRNAME \
&& julia --project=$DIRNAME -e 'using Pkg; Pkg.instantiate()' \
&& ln -s /$DIRNAME/scripts/larvatagger.jl /bin
&& ln -s /$DIRNAME/scripts/larvatagger.jl /bin \
&& rm -f $DIRNAME/test/precompile* \
&& rm -f $DIRNAME/scripts/larvatagger.jl
COPY test/precompile.* test/data_sample* $DIRNAME/test/
COPY scripts/larvatagger.jl $DIRNAME/scripts/
COPY test/precompile* test/data_sample* $DIRNAME/test/
COPY src/cli.jl $DIRNAME/src/
ARG TIMEZONE=UTC
RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime \
&& echo $TIMEZONE > /etc/timezone \
&& $DIRNAME/test/precompile.sh --shallow \
&& rm -f test/data_sample*
&& mv larvatagger.so /lib/ \
&& rm -f $DIRNAME/test/data_sample*
COPY external $DIRNAME/
......@@ -30,7 +35,8 @@ RUN if [ "$BACKEND" = "MaggotUBA/20220418" ]; then \
&& python3 -m poetry remove structured-temporal-convolution \
&& python3 -m poetry add ../structured-temporal-convolution \
&& python3 -m poetry install \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*; \
fi
ENTRYPOINT ["larvatagger.jl"]
ENTRYPOINT ["larvatagger.jl", "--sysimage", "/lib/larvatagger.so"]
scripts/larvatagger.jl
+ 6
− 89
View file @ 39b7e0a2
#!/bin/bash
#=
PROJECT_DIR=$(dirname $(dirname $(realpath "${BASH_SOURCE[0]}")))
if [ "$1" == "open" ]; then FLAGS="-iq "; fi
FLAGS=
if [ "$1" == "--sysimage" ]; then FLAGS="--sysimage $2 "; shift 2; fi
if [ "$1" == "open" ]; then FLAGS="$FLAGS -iq "; fi
exec julia --project="$PROJECT_DIR" --color=yes --startup-file=no $FLAGS\
"${BASH_SOURCE[0]}" "$@"
=#
using DocOpt
using PlanarLarvae.Datasets, PlanarLarvae.Formats
using LarvaTagger
using JSServe: JSServe, Server
projectdir = dirname(Base.active_project())
include(joinpath(projectdir, "src/cli.jl")) # defines `main`
usage = """Larva Tagger.
Usage:
larvatagger.jl import <input-path> [<output-file>] [--id=<id>] [--framerate=<fps>]
larvatagger.jl open <input-path> [--backends=<path>] [--port=<number>] [--quiet]
larvatagger.jl open <input-path> [--viewer] [--browser]
larvatagger.jl train <backend-path> <data-repository> [--instance=<name>]
larvatagger.jl -h | --help
Options:
-h --help Show this screen.
-q --quiet Do not show instructions.
--id=<id> Run ID, e.g. `date_time`.
--framerate=<fps> Camera frame rate, in frames per second.
--backends=<path> Path to backend repository.
--port=<number> Port number the server listens to.
--viewer Disable editing capabilities.
--browser Automatically open a browser tab at the served location.
--instance=<name> Name of the trained model.
"""
function main()
parsed_args = docopt(usage)
if parsed_args["import"]
infile = parsed_args["<input-path>"]
if !isfile(infile)
@error "File not found" infile
return
end
outfile = parsed_args["<output-file>"]
kwargs = Dict{Symbol, Any}()
framerate = parsed_args["--framerate"]
if !isnothing(framerate)
kwargs[:framerate] = parse(Float64, framerate)
end
file = load(infile; kwargs...)
runid = parsed_args["--id"]
run = Run(isnothing(runid) ? file.run.id : runid, Track[];
file.run.attributes[:metadata]...)
run.attributes[:labels] = String[]
Datasets.pushdependency!(run, infile)
if isnothing(outfile)
Datasets.write_json(stdout, run)
else
outfile = joinpath(dirname(infile), outfile)
Datasets.to_json_file(outfile, run)
end
elseif parsed_args["open"]
verbose = !parsed_args["--quiet"]
infile = parsed_args["<input-path>"]
if !isfile(infile)
@error "File not found" infile
return
end
if parsed_args["--viewer"]
app = larvaviewer(infile)
else
kwargs = Dict{Symbol, Any}()
backends = parsed_args["--backends"]
if !isnothing(backends)
kwargs[:backend_directory] = backends
end
app = larvaeditor(infile; kwargs...)
end
#
port = parsed_args["--port"]
port = isnothing(port) ? 9284 : parse(Int, port)
server = Server(app, "0.0.0.0", port)
if parsed_args["--browser"]
JSServe.openurl("http://127.0.0.1:$(port)")
#display(JSServe.BrowserDisplay(), app)
elseif verbose
@info "The server is listening to http://127.0.0.1:$(port)"
end
if verbose
@info "Press Ctrl+D to kill the server"
end
elseif parsed_args["train"]
@error "Not implemented yet"
end
end
main()
main();
src/cli.jl 0 → 100644
+ 88
− 0
View file @ 39b7e0a2
using DocOpt
using PlanarLarvae.Datasets, PlanarLarvae.Formats
using LarvaTagger
using JSServe: JSServe, Server
usage = """Larva Tagger.
Usage:
larvatagger.jl import <input-path> [<output-file>] [--id=<id>] [--framerate=<fps>]
larvatagger.jl open <input-path> [--backends=<path>] [--port=<number>] [--quiet]
larvatagger.jl open <input-path> [--viewer] [--browser]
larvatagger.jl train <backend-path> <data-repository> [--instance=<name>]
larvatagger.jl -h | --help
Options:
-h --help Show this screen.
-q --quiet Do not show instructions.
--id=<id> Run ID, e.g. `date_time`.
--framerate=<fps> Camera frame rate, in frames per second.
--backends=<path> Path to backend repository.
--port=<number> Port number the server listens to.
--viewer Disable editing capabilities.
--browser Automatically open a browser tab at the served location.
--instance=<name> Name of the trained model.
"""
function main(args=ARGS)
parsed_args = docopt(usage, args isa String ? split(args) : args)
if parsed_args["import"]
infile = parsed_args["<input-path>"]
if !isfile(infile)
@error "File not found" infile
return
end
outfile = parsed_args["<output-file>"]
kwargs = Dict{Symbol, Any}()
framerate = parsed_args["--framerate"]
if !isnothing(framerate)
kwargs[:framerate] = parse(Float64, framerate)
end
file = load(infile; kwargs...)
runid = parsed_args["--id"]
run = Run(isnothing(runid) ? file.run.id : runid, Track[];
file.run.attributes[:metadata]...)
run.attributes[:labels] = String[]
Datasets.pushdependency!(run, infile)
if isnothing(outfile)
Datasets.write_json(stdout, run)
else
outfile = joinpath(dirname(infile), outfile)
Datasets.to_json_file(outfile, run)
end
elseif parsed_args["open"]
verbose = !parsed_args["--quiet"]
infile = parsed_args["<input-path>"]
if !isfile(infile)
@error "File not found" infile
return
end
if parsed_args["--viewer"]
app = larvaviewer(infile)
else
kwargs = Dict{Symbol, Any}()
backends = parsed_args["--backends"]
if !isnothing(backends)
kwargs[:backend_directory] = backends
end
app = larvaeditor(infile; kwargs...)
end
#
port = parsed_args["--port"]
port = isnothing(port) ? 9284 : parse(Int, port)
server = Server(app, "0.0.0.0", port)
if parsed_args["--browser"]
JSServe.openurl("http://127.0.0.1:$(port)")
#display(JSServe.BrowserDisplay(), app)
elseif verbose
@info "The server is listening to http://127.0.0.1:$(port)"
end
if verbose
@info "Press Ctrl+D to kill the server"
end
return server
elseif parsed_args["train"]
@error "Not implemented yet"
end
end
test/precompile-common.jl 0 → 100644
+ 7
− 0
View file @ 39b7e0a2
datafile = joinpath(@__DIR__, "data_sample")
ispath(datafile) || exit()
projectdir = dirname(Base.active_project())
include(joinpath(projectdir, "src/cli.jl"))
srv = main(["open", datafile])
test/precompile-electron.jl 0 → 100644
+ 9
− 0
View file @ 39b7e0a2
using Blink
include(joinpath(@__DIR__, "precompile-common.jl")) # defines `srv`
win = Window(async=false)
loadurl(win, "http://127.0.0.1:9284")
close(win)
close(srv)
test/precompile.jl
+ 3
− 20
View file @ 39b7e0a2
using LarvaTagger
using JSServe: Server
using HTTP
datafile = joinpath(@__DIR__, "data_sample")
ispath(datafile) || exit()
include(joinpath(@__DIR__, "precompile-common.jl")) # defines `srv`
app = larvaeditor(datafile)
srv = Server(app, "0.0.0.0", 9284)
if isempty(ARGS)
using HTTP
HTTP.request(:GET, "http://127.0.0.1:9284")
elseif ARGS == ["--electron"]
using Blink
win = Window(async=false)
loadurl(win, "http://127.0.0.1:9284")
close(win)
end
HTTP.request(:GET, "http://127.0.0.1:9284")
close(srv)
test/precompile.sh
+ 25
− 18
View file @ 39b7e0a2
#!/bin/sh
root=$(dirname $(dirname $0))
if [ "$1" = "--shallow" ]; then
shift
echo "Project root: $root"
julia --project=$root -e 'using Pkg; Pkg.add("HTTP")'
echo "[$(date +%T)] Further precompiling..."
julia --project=$root $root/test/precompile.jl
echo "[$(date +%T)] Precompilation done"
julia --project=$root -e 'using Pkg; Pkg.rm("HTTP")'
client=HTTP
julia="julia"
script="$root/test/precompile.jl"
packages="g++"
else
packages="unzip xvfb libgtk-3-0 libnss3 libxss1 libasound2"
client=Blink
julia="xvfb-run julia"
script="$root/test/precompile-electron.jl"
# dependencies on Debian Bullseye and Ubuntu Focal
packages="unzip xvfb libgtk-3-0 libnss3 libxss1 libasound2 g++"
fi
apt-get update
apt-get install -y $packages
echo "Project root: $root"
julia --project=$root -e 'using Pkg; Pkg.add("Blink")'
# to find out missing dependencies:
# electron=$(julia --project=$root -e 'using Blink; println(Blink.AtomShell.electron())')
# echo $electron
# $electron
echo "[$(date +%T)] Further precompiling..."
xvfb-run julia --project=$root $root/test/precompile.jl --electron
echo "[$(date +%T)] Precompilation done"
julia --project=$root -e 'using Pkg; Pkg.rm("Blink")'
$julia --project=$root -e "
using Pkg
Pkg.add([\"$client\",\"PackageCompiler\"])
using PackageCompiler
println(\"🢃 🢃 🢃 Includes logs from coverage script. Please ignore 🢃 🢃 🢃\")
create_sysimage(String[], sysimage_path=\"larvatagger.so\", precompile_execution_file=\"$script\")
println(\"🢁 🢁 🢁 Includes logs from coverage script. Please ignore 🢁 🢁 🢁\")
#Pkg.rm([\"PackageCompiler\",\"$client\"])"
apt-get autoremove -y $packages
apt-get clean
rm -rf /var/lib/apt/lists/*
fi
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