refactor: update Dockerfile for IFTPipeline.jl

.github/workflows/test.yml

@@ -25,28 +25,18 @@ jobs:
             arch: x64
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: update pip
-        run: python -m pip install -U pip
-      - name: install python deps
-        run: python -m pip install -U -r requirements.txt
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
+      - run: julia --project=PythonSetupForIFTPipeline.jl PythonSetupForIFTPipeline.jl/setup.jl
       - uses: julia-actions/julia-buildpkg@v1
         with:
           project: IFTPipeline.jl
-        env:
-          PYTHON: python
       - uses: julia-actions/julia-runtest@v1
         with:
           project: IFTPipeline.jl
-        env:
-          PYTHON: python
       - uses: julia-actions/julia-processcoverage@v1
         with:
           directories: IFTPipeline.jl/src

Dockerfile

@@ -1,27 +1,23 @@
-FROM julia:1.9-bookworm
-ENV TERM=xterm
-ENV JULIA_PROJECT=/opt/ice-floe-tracker-pipeline
-ENV JULIA_DEPOT_PATH=/opt/julia
-ENV JULIA_PKGDIR=/opt/julia
-ENV JULIA_BUILD='ENV["PYTHON"]=""; using Pkg; Pkg.build()'
-ENV IFTPIPELINE_REPO='https://github.com/WilhelmusLab/ice-floe-tracker-pipeline.git'
-ENV LOCAL_PATH_TO_IFT_CLI='/usr/local/bin/ice-floe-tracker.jl'
-
-WORKDIR /opt
+FROM julia:1.11-bookworm
 
 # DEPENDENCIES
 #===========================================
-RUN apt-get -y update && \
-    apt-get install -y git python3.10 && \
-    rm -rf /var/lib/apt/list/* 
+ENV TERM=xterm
 
-# Julia package build
+# Python environment build
 #===========================================
+COPY ./PythonSetupForIFTPipeline.jl /opt/PythonSetupForIFTPipeline.jl
+RUN julia --project="/opt/PythonSetupForIFTPipeline.jl" "/opt/PythonSetupForIFTPipeline.jl/setup.jl"
 
-RUN git clone --single-branch --branch main --depth 1 ${IFTPIPELINE_REPO}
-RUN /usr/local/julia/bin/julia --project=${JULIA_PROJECT} -e ${JULIA_BUILD}
-RUN /usr/local/julia/bin/julia --project=${JULIA_PROJECT} -e 'using Pkg; Pkg.instantiate()'
-COPY workflow/scripts/ice-floe-tracker.jl ${LOCAL_PATH_TO_IFT_CLI}
-RUN chmod a+x ${LOCAL_PATH_TO_IFT_CLI}
-ENV JULIA_DEPOT_PATH="/usr/local/bin/julia:$JULIA_DEPOT_PATH"
-CMD [ "/bin/bash", "-c" ]
+# IFT Pipeline package build
+#===========================================
+COPY ./IFTPipeline.jl /opt/IFTPipeline.jl
+RUN julia --project="/opt/IFTPipeline.jl" -e 'using Pkg; Pkg.rm("IceFloeTracker"); Pkg.add(url="https://github.com/WilhelmusLab/IceFloeTracker.jl", rev="main"); Pkg.instantiate()'
+
+# Test the package
+RUN julia --project="/opt/IFTPipeline.jl" -e 'using Pkg; Pkg.test();'
+
+# CLI setup
+#===========================================
+SHELL ["/bin/bash", "-c"]
+ENTRYPOINT ["julia", "--project=/opt/IFTPipeline.jl", "/opt/IFTPipeline.jl/src/cli.jl" ]

IFTPipeline.jl/Project.toml

@@ -12,6 +12,7 @@ Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
 [compat]

IFTPipeline.jl/src/IFTPipeline.jl

@@ -13,7 +13,7 @@ using Folds
 using HDF5
 using TOML: parsefile
 using Pkg
-include("cli-config.jl")
+include("cli.jl")
 include("soit-parser.jl")
 include("landmask.jl")
 include("preprocess.jl")

IFTPipeline.jl/src/cli-config.jl → IFTPipeline.jl/src/cli.jl

@@ -1,3 +1,11 @@
+#!/usr/bin/env julia
+
+using ArgParse
+using LoggingExtras
+using IceFloeTracker
+using IFTPipeline
+using Serialization
+
 function mkclipreprocess!(settings)
     @add_arg_table! settings["preprocess"] begin
         "--truedir", "-t"
@@ -218,3 +226,88 @@ function mkcli!(settings, common_args)
     end
     return nothing
 end
+
+
+"""
+    setuplogger(option::Int64, path::String)
+
+Setup logger for the ice floe tracker. If `option` is 0, log to file only. If `option` is 1, log to file and terminal.
+"""
+function setuplogger(option::Int64, command::Symbol)
+    output = joinpath(@__DIR__, "..", "report")
+    cmd = string(command)
+
+    filelogger = FileLogger(joinpath(output, "$cmd-logfile.log")) # add command prefix to logfile name
+
+    # filter out debug messages
+    filtlogger = EarlyFilteredLogger(filelogger) do args
+        r = Logging.Info <= args.level <= Logging.Warn && args._module === IFTPipeline
+        return r
+    end
+
+    if option == 0
+        return TeeLogger(filtlogger,
+        )
+    elseif option == 1
+        return TeeLogger(
+            global_logger(),
+            filtlogger
+        )
+    end
+end
+
+function main()
+
+    settings = ArgParseSettings(; autofix_names=true)
+
+    @add_arg_table! settings begin
+        "landmask"
+        help = "Generate land mask images"
+        action = :command
+
+        "preprocess"
+        help = "Preprocess truecolor/falsecolor images"
+        action = :command
+
+        "extractfeatures"
+        help = "Extract ice floe features from segmented floe image"
+        action = :command
+
+        "makeh5files"
+        help = "Make HDF5 files from extracted floe features"
+        action = :command
+
+        "track"
+        help = "Pair ice floes in day k with ice floes in day k+1"
+        action = :command
+    end
+
+    command_common_args = [
+        "--log",
+        Dict(:help => "Show log on terminal; either 1 or 0", :required => false, :arg_type => Int,
+            :default => 0, :range_tester => (x -> x == 0 || x == 1)
+        )]
+
+    mkcli!(settings, command_common_args)
+
+    parsed_args = parse_args(settings; as_symbols=true)
+
+    command = parsed_args[:_COMMAND_]
+    command_args = parsed_args[command]
+    command_func = getfield(IFTPipeline, Symbol(command))
+    logoption = command_args[:log]
+
+    # delete log option from command_args so it doesn't get passed to command_func
+    delete!(command_args, :log)
+
+    logger = setuplogger(logoption, command)
+
+    with_logger(logger) do
+        @time command_func(; command_args...)
+    end
+    return nothing
+end
+
+if abspath(PROGRAM_FILE) == @__FILE__
+    main()
+end