diff --git a/recipes/Dockerfile b/recipes/Dockerfile
index e4f2cdffd4d3bc1a801a57fb7b30620b28480023..2310a136a835831a6a6865b2438311ebde6278d0 100644
--- a/recipes/Dockerfile
+++ b/recipes/Dockerfile
@@ -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"]
diff --git a/scripts/larvatagger.jl b/scripts/larvatagger.jl
index ec839916cd9f96161c3b0f5a072bac9ca78b6666..609459d89d4c15f5951674920deada1dcfe72f34 100755
--- a/scripts/larvatagger.jl
+++ b/scripts/larvatagger.jl
@@ -1,97 +1,14 @@
#!/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();
diff --git a/src/cli.jl b/src/cli.jl
new file mode 100644
index 0000000000000000000000000000000000000000..13b6829914215ee0f0ea48396991e419f365bd0d
--- /dev/null
+++ b/src/cli.jl
@@ -0,0 +1,88 @@
+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
diff --git a/test/precompile-common.jl b/test/precompile-common.jl
new file mode 100644
index 0000000000000000000000000000000000000000..4843e0259907da6f12813418eb27203f840487d2
--- /dev/null
+++ b/test/precompile-common.jl
@@ -0,0 +1,7 @@
+datafile = joinpath(@__DIR__, "data_sample")
+ispath(datafile) || exit()
+
+projectdir = dirname(Base.active_project())
+include(joinpath(projectdir, "src/cli.jl"))
+
+srv = main(["open", datafile])
diff --git a/test/precompile-electron.jl b/test/precompile-electron.jl
new file mode 100644
index 0000000000000000000000000000000000000000..42a0cc2a6543b84a64b2762c6e2814d3983f0e28
--- /dev/null
+++ b/test/precompile-electron.jl
@@ -0,0 +1,9 @@
+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)
diff --git a/test/precompile.jl b/test/precompile.jl
index 00f22103b040bac3057e735a3243dbeb5e81a5dd..75f5b7c71eb42106b31a4255ce65f6564f4f83bf 100644
--- a/test/precompile.jl
+++ b/test/precompile.jl
@@ -1,24 +1,7 @@
-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)
diff --git a/test/precompile.sh b/test/precompile.sh
index 4bda55d90a36c4c16fc0a0f0333f1ea86ca4f38b..970dfa413aab5a0eda86f6151c9202fb7a618d53 100755
--- a/test/precompile.sh
+++ b/test/precompile.sh
@@ -1,27 +1,34 @@
#!/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=\"$script\")
+println(\"🢠🢠🢠Includes logs from coverage script. Please ignore 🢠🢠ðŸ¢\")
+#Pkg.rm([\"PackageCompiler\",\"$client\"])"
+
apt-get autoremove -y $packages
+apt-get clean
rm -rf /var/lib/apt/lists/*
-fi