Init julia package (#7)

* Files generated by PkgTemplates

PkgTemplates version: 0.7.52

* Add files from open-call-use-case-pangeo-julia

* Add funding note

* Add citation to README

* Update README.md

* Add dependencies

* Fix dependencies and compat close #1 #2 #3 #4 #5 #6

* Fix julia compat

* Remove arch x86

* Update documentation CI

* Add debug shell to Documenter CI

* Remove debug shell to Documenter CI

* Fix github org

* Fix documentation links in README.md

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CI.yml

@@ -0,0 +1,46 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+    tags: ["*"]
+  pull_request:
+  workflow_dispatch:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - "1"
+          - "lts"
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/Documenter.yml

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+# Sample workflow for building and deploying a VitePress site to GitHub Pages
+#
+name: Documenter
+
+on:
+  # Runs on pushes targeting the `main` branch. Change this to `master` if you're
+  # using the `master` branch as the default branch.
+  push:
+    branches:
+      - main
+    tags: ["*"]
+  pull_request:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+  statuses: write
+
+# Cancel previous runs if a new one is triggered (by push on PR)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+      - name: Pull Julia cache
+        uses: julia-actions/cache@v2
+      - name: Install documentation dependencies
+        run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev libcairo2-dev libfreetype6-dev libffi-dev libjpeg-dev libpng-dev libz-dev
+      - name: Install custom documentation dependencies
+        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs -e 'using Pkg; pkg"dev ."; Pkg.instantiate(); Pkg.precompile(); Pkg.status()'
+      #- name: Creating new mds from src
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          GKSwstype: "100"
+          JULIA_DEBUG: "Documenter"
+          DATADEPS_ALWAYS_ACCEPT: true
+        run: |
+          DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ --color=yes docs/make.jl

.github/workflows/TagBot.yml

@@ -0,0 +1,31 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -0,0 +1,6 @@
+*.jl.*.cov
+*.jl.cov
+*.jl.mem
+/docs/Manifest.toml
+/docs/build/
+Manifest.toml

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Daniel Loos <[email protected]> and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Project.toml

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+name = "RQADeforestation"
+uuid = "3f1d9318-18cc-4ffd-9937-04025ce33b74"
+authors = ["Felix Cremer <[email protected]>, Daniel Loos <[email protected]> and contributors"]
+version = "1.0.0-DEV"
+
+[deps]
+ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+DiskArrayEngine = "2d4b2e14-ccd6-4284-b8b0-2378ace7c126"
+DiskArrayTools = "fcd2136c-9f69-4db6-97e5-f31981721d63"
+DiskArrays = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+Extents = "411431e0-e8b7-467b-b5e0-f676ba4f2910"
+FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
+GDAL = "add2ef01-049f-52c4-9ee2-e494f65e021a"
+GeoFormatTypes = "68eda718-8dee-11e9-39e7-89f7f65f511f"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+KML = "1284bf3a-1e3d-4f4e-a7a9-b9d235a28f35"
+LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
+Missings = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
+NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
+Proj = "c94c279d-25a6-4763-9509-64d165bea63e"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
+RecurrenceAnalysis = "639c3291-70d9-5ea2-8c5b-839eba1ee399"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+TimeseriesSurrogates = "c804724b-8c18-5caa-8579-6025a0767c70"
+UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
+YAXArrayBase = "90b8fcef-0c2d-428d-9c56-5f86629e9d14"
+YAXArrays = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c"
+Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"
+
+[compat]
+julia = "1.10"
+YAXArrayBase = "=0.6"
+Glob = "1"
+NetCDF="0.12"
+Zarr = "0.9"
+ArchGDAL = "0.10"
+YAXArrays = "0.5"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

README.md

@@ -0,0 +1,20 @@
+# RQADeforestation
+
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://earthyscience.github.io/RQADeforestation.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://earthyscience.github.io/RQADeforestation.jl/dev/)
+[![Build Status](https://github.com/EarthyScience/RQADeforestation.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/EarthyScience/RQADeforestation.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/EarthyScience/RQADeforestation.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/EarthyScience/RQADeforestation.jl)
+
+This is the Julia package developed within the [FAIRSenDD project](https://github.com/EarthyScience/FAIRSenDD).
+
+## Citation
+
+F. Cremer, M. Urbazaev, J. Cortés, J. Truckenbrodt, C. Schmullius and C. Thiel, "Potential of Recurrence Metrics from Sentinel-1 Time Series for Deforestation Mapping," in IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, vol. 13, pp. 5233-5240, 2020, doi: [10.1109/JSTARS.2020.3019333](https://dx.doi.org/10.1109/JSTARS.2020.3019333).
+
+## Funding
+
+<img src="https://raw.githubusercontent.com/EarthyScience/FAIRSenDD/refs/heads/main/assets/ESA_logo.svg" align="left" height="50px"/>
+<img src="https://raw.githubusercontent.com/EarthyScience/FAIRSenDD/refs/heads/main/assets/ESA_NoR_logo.svg" align="left" height="50px" style="filter: contrast(0);"/>
+
+This project was funded by the European Space Agency in the Science Result Long-Term Availability & Reusability Demonstrator Initiative.
+In addition, this project was supported by the ESA Network of Resources.

docs/Project.toml

@@ -0,0 +1,3 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+RQADeforestation = "3f1d9318-18cc-4ffd-9937-04025ce33b74"

docs/make.jl

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+using RQADeforestation
+using Documenter
+
+DocMeta.setdocmeta!(RQADeforestation, :DocTestSetup, :(using RQADeforestation); recursive=true)
+
+makedocs(;
+    modules=[RQADeforestation],
+    authors="Daniel Loos <[email protected]> and contributors",
+    sitename="RQADeforestation.jl",
+    format=Documenter.HTML(;
+        canonical="https://danlooo.github.io/RQADeforestation.jl",
+        edit_link="main",
+        assets=String[],
+    ),
+    pages=[
+        "Home" => "index.md",
+    ],
+)
+
+deploydocs(;
+    repo="github.com/EarthyScience/RQADeforestation.jl",
+    devbranch="main",
+)

docs/src/index.md

@@ -0,0 +1,14 @@
+```@meta
+CurrentModule = RQADeforestation
+```
+
+# RQADeforestation
+
+Documentation for [RQADeforestation](https://github.com/EarthyScience/RQADeforestation.jl).
+
+```@index
+```
+
+```@autodocs
+Modules = [RQADeforestation]
+```

src/RQADeforestation.jl

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+module RQADeforestation
+__precompile__(false)
+using Dates
+using ArchGDAL: ArchGDAL as AG
+using Glob
+using YAXArrays
+using Zarr
+using Distributed: myid
+using NetCDF
+
+export gdalcube
+
+include("auxil.jl")
+include("analysis.jl")
+include("timestats.jl")
+end