-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #198 from WilhelmusLab/merge-attempt-1
feat: add Buckley's preprocessing to the pipeline
- Loading branch information
Showing
112 changed files
with
3,983 additions
and
1,525 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| style = "blue" | ||
| indent = 4 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| FROM mcr.microsoft.com/devcontainers/base:debian | ||
|
|
||
| RUN apt-get update | ||
| RUN apt-get install -y software-properties-common | ||
| RUN apt-get install -y gdal-bin libgdal-dev libgtk-3-dev graphviz |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| { | ||
| "name": "Ice Floe Tracker Pipeline", | ||
|
|
||
| "build": { | ||
| "dockerfile": "Dockerfile" | ||
| }, | ||
|
|
||
| "features": { | ||
| "ghcr.io/julialang/devcontainer-features/julia:1": { | ||
| "channel": "lts" | ||
| }, | ||
| "ghcr.io/devcontainers/features/python:1": { | ||
| "installTools": true, | ||
| "version": "3.11" | ||
| }, | ||
| "ghcr.io/devcontainers-contrib/features/pipx-package:1": { | ||
| "includeDeps": true, | ||
| "package": "cylc-rose", | ||
| "interpreter": "python3.11" | ||
| }, | ||
| "ghcr.io/devcontainers/features/docker-in-docker:2": {} | ||
|
|
||
| }, | ||
|
|
||
| "customizations": { | ||
| "vscode": { | ||
| "extensions": [ | ||
| "ms-azuretools.vscode-docker", | ||
| "github.vscode-github-actions", | ||
| "mechatroner.rainbow-csv", | ||
| "analytic-signal.preview-tiff", | ||
| "cylc.vscode-cylc" | ||
| ] | ||
| } | ||
| }, | ||
|
|
||
| "postCreateCommand": "" | ||
| } |
Empty file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| # Development Guide | ||
|
|
||
| We have found VSCode to be a good IDE for development. You can use the [devcontainer](https://code.visualstudio.com/docs/devcontainers/containers) configuration to initialize a virtual machine with the Julia, Python and the geospatial dependencies for this project. | ||
|
|
||
| Before running any Julia code for the first time, follow the instructions in | ||
| [PythonSetupForIFTPipeline.jl](./PythonSetupForIFTPipeline.jl/README.md) | ||
| to initialize a working Conda environment. | ||
|
|
||
| Follow the instructions in [IFTPipeline.jl](./IFTPipeline.jl/) to run the tests of the pipeline. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,27 +1,28 @@ | ||
| 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' | ||
| FROM --platform=$BUILDPLATFORM julia:1.11-bookworm | ||
| ARG TARGETARCH | ||
| ARG JULIA_CPU_TARGET="generic" | ||
| ENV JULIA_CPU_TARGET=${JULIA_CPU_TARGET} | ||
|
|
||
| WORKDIR /opt | ||
| # Dependencies | ||
| #=========================================== | ||
| ENV TERM=xterm | ||
|
|
||
| # DEPENDENCIES | ||
| # Python environment build | ||
| #=========================================== | ||
| RUN apt-get -y update && \ | ||
| apt-get install -y git python3.10 && \ | ||
| rm -rf /var/lib/apt/list/* | ||
| ENV CONDA_JL_HOME=/opt/conda | ||
| ENV JULIA_DEPOT_PATH=/opt/julia | ||
| COPY ./PythonSetupForIFTPipeline.jl /opt/PythonSetupForIFTPipeline.jl | ||
| RUN julia --project="/opt/PythonSetupForIFTPipeline.jl" "/opt/PythonSetupForIFTPipeline.jl/setup.jl" | ||
|
|
||
| # Julia package build | ||
| # IFT Pipeline package build | ||
| #=========================================== | ||
| COPY ./IFTPipeline.jl /opt/IFTPipeline.jl | ||
| RUN julia --project="/opt/IFTPipeline.jl" -e "using Pkg; Pkg.instantiate(); Pkg.precompile();" | ||
|
|
||
| # Test the package | ||
| # RUN julia --project="/opt/IFTPipeline.jl" -e "using Pkg; Pkg.test();" | ||
|
|
||
| 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" ] | ||
| # CLI setup | ||
| #=========================================== | ||
| SHELL ["/bin/bash", "-c"] | ||
| ENTRYPOINT ["julia", "--project=/opt/IFTPipeline.jl", "/opt/IFTPipeline.jl/src/cli.jl" ] |
Oops, something went wrong.