Add detrending methods

.github/workflows/CompatHelper.yml

@@ -1,45 +1,24 @@
 name: CompatHelper
+
 on:
   schedule:
-    - cron: 0 0 * * *
-  workflow_dispatch:
-permissions:
-  contents: write
-  pull-requests: write
+    - cron: '00 * * * *'
+
 jobs:
   CompatHelper:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
     steps:
-      - name: Check if Julia is already available in the PATH
-        id: julia_in_path
-        run: which julia
-        continue-on-error: true
-      - name: Install Julia, but only if it is not already available in the PATH
-        uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
-          version: '1'
-          arch: ${{ runner.arch }}
-        if: steps.julia_in_path.outcome != 'success'
-      - name: "Add the General registry via Git"
-        run: |
-          import Pkg
-          ENV["JULIA_PKG_SERVER"] = ""
-          Pkg.Registry.add("General")
-        shell: julia --color=yes {0}
-      - name: "Install CompatHelper"
-        run: |
-          import Pkg
-          name = "CompatHelper"
-          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
-          version = "3"
-          Pkg.add(; name, uuid, version)
-        shell: julia --color=yes {0}
-      - name: "Run CompatHelper"
-        run: |
-          import CompatHelper
-          CompatHelper.main()
-        shell: julia --color=yes {0}
+          version: ${{ matrix.julia-version }}
+      - 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 }}
-          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -12,4 +12,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -2,10 +2,11 @@ name: CI
 on:
   pull_request:
     branches:
-      - master
+      - main
+      - '**' # matches every branch
   push:
     branches:
-      - master
+      - main
     tags: '*'
 jobs:
   test:
@@ -15,17 +16,25 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
-        os:  [ubuntu-latest]
+          - '1'
+        os:  [ubuntu-latest] # adjust according to need, e.g. os: [ubuntu-latest] if testing only on linux
         arch:
           - x64
     steps:
+      # Cancel ongoing CI test runs if pushing to branch again before the previous tests
+      # have finished
+      - name: Cancel ongoing test runs for previous commits
+        uses: styfle/cancel-workflow-action@0.6.0
+        with:
+          access_token: ${{ github.token }}
+
+      # Do tests
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -36,24 +45,9 @@ jobs:
             ${{ runner.os }}-test-
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
+
       - uses: julia-actions/julia-runtest@v1
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
         with:
-          version: '1'
-      - name: Instantiate and install dependencies
-        run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - name: Generate documentation and deploy
-        env: # needed for pushing to gh-pages branch
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-        run:
-          julia --project=docs docs/make.jl
+          file: lcov.info

.github/workflows/doccleanup.yml

@@ -0,0 +1,26 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "documenter@juliadocs.github.io"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.github/workflows/documentation.yml

@@ -0,0 +1,26 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

.gitignore

@@ -9,6 +9,7 @@ videos
 plots
 notebooks
 _research
+docs/build_docs_with_style.jl
 
 ################################################################################
 #                                    Julia                                     #

CHANGELOG.md

@@ -0,0 +1,12 @@
+*changelog kept with respect to version 1.0*
+
+# v1.2
+
+- Add new functionality for the package: detrending
+- Add new functionality for the package: smoothing
+- Add new `Decompositions`: `PolynomialDetrending, NoDecomposition, MovingAverageSmoothing, LoessSmoothing, HodrickPrescott`.
+- Package is now part of DynamicalSystems.jl as well under the category "Nonlinear Timeseries Analysis".
+
+# v1.1
+
+Update to Julia 1.9, and bump dependency compatibility versions to those of Julia 1.9+.

Project.toml

@@ -1,7 +1,7 @@
 name = "SignalDecomposition"
 uuid = "11a47235-7b84-4c7c-b885-fc3e2a9cf955"
 authors = ["Datseris <datseris.george@gmail.com>"]
-version = "1.1.0"
+version = "1.2.0"
 
 [deps]
 BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
@@ -10,8 +10,11 @@ DelayEmbeddings = "5732040d-69e3-5649-938a-b6b4f237613f"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 LPVSpectral = "26dcc766-85df-5edc-b560-6076d5dbac63"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Loess = "4345ca2d-374a-55d4-8d30-97f9976e7612"
 Neighborhood = "645ca80c-8b79-4109-87ea-e1f58159d116"
+Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
@@ -20,15 +23,10 @@ BandedMatrices = "1"
 DelayEmbeddings = "2"
 FFTW = "1.2"
 LPVSpectral = "0.3"
+Loess = "0.6"
 Neighborhood = "0.2"
+Polynomials = "4"
+SparseArrays = "1.11"
 StaticArrays = "1"
 Statistics = "1"
 julia = "1.9"
-
-[extras]
-DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test", "DelimitedFiles", "DynamicalSystemsBase"]

README.md

@@ -1,9 +1,19 @@
-![SignalDecomposition.jl](https://github.com/JuliaDynamics/JuliaDynamics/blob/master/videos/other/signaldecomposition.gif?raw=true)
+[![docsdev](https://img.shields.io/badge/docs-dev-lightblue.svg)](https://juliadynamics.github.io/DynamicalSystemsDocs.jl/signaldecomposition/dev/)
+[![docsstable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadynamics.github.io/DynamicalSystemsDocs.jl/signaldecomposition/stable/)
+[![CI](https://github.com/JuliaDynamics/SignalDecomposition.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/SignalDecomposition.jl/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/JuliaDynamics/SignalDecomposition.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaDynamics/SignalDecomposition.jl)
 
-| **Documentation**   |  **Tests**     | **Chat** |
-|:--------:|:---------------:|:-----:|
-|[![](https://img.shields.io/badge/docs-online-blue.svg)](https://JuliaDynamics.github.io/SignalDecomposition.jl/dev)| [![CI](https://github.com/juliadynamics/SignalDecomposition.jl/workflows/CI/badge.svg)](https://github.com/JuliaDynamics/SignalDecomposition.jl/actions) | [![Gitter](https://img.shields.io/gitter/room/nwjs/nw.js.svg)](https://gitter.im/JuliaDynamics/Lobby)
+SignalDecomposition.jl is a Julia package providing an interface and dozens of algorithm implementations for signal decomposition.
+Given a signal (or timeseries), the function `decompose` splits it into two components.
+These may be:
 
+- structure and noise (de-noising or smoothing)
+- seasonal and residual (climatologies or anomalies)
+- trend and residual (de-trending)
 
-Decompose a signal/timeseries into structure and noise or seasonal and residual components.
-Further info in the docs!
+It can be used as a standalone package, or as part of
+[DynamicalSystems.jl](https://juliadynamics.github.io/DynamicalSystemsDocs.jl/dynamicalsystems/stable/).
+
+To install it, run `import Pkg; Pkg.add("SignalDecomposition")`.
+
+All further information is provided in the documentation, which you can either find [online](https://juliadynamics.github.io/DynamicalSystemsDocs.jl/signaldecomposition/stable/) or build locally by running the `docs/make.jl` file.

docs/Project.toml

@@ -2,7 +2,10 @@
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
-DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+PredefinedDynamicalSystems = "31e2f376-db9e-427a-b76e-a14f56347a14"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 SignalDecomposition = "11a47235-7b84-4c7c-b885-fc3e2a9cf955"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+
+[compat]
+PredefinedDynamicalSystems = "1.4"

docs/make.jl

@@ -1,49 +1,21 @@
-using Pkg
-Pkg.activate(@__DIR__)
-CI = get(ENV, "CI", nothing) == "true" || get(ENV, "GITHUB_TOKEN", nothing) !== nothing
-CI && Pkg.instantiate()
-CI && (ENV["GKSwstype"] = "100")
+cd(@__DIR__)
+using SignalDecomposition
+decompose = SignalDecomposition.decompose
+using PredefinedDynamicalSystems
 
-using SignalDecomposition, Documenter, DocumenterTools
-using DocumenterTools: Themes
-using Plots
-
-# %%
-# download the themes
-for file in ("juliadynamics-lightdefs.scss", "juliadynamics-darkdefs.scss", "juliadynamics-style.scss")
-    download("https://raw.githubusercontent.com/JuliaDynamics/doctheme/master/$file", joinpath(@__DIR__, file))
-end
-# create the themes
-for w in ("light", "dark")
-    header = read(joinpath(@__DIR__, "juliadynamics-style.scss"), String)
-    theme = read(joinpath(@__DIR__, "juliadynamics-$(w)defs.scss"), String)
-    write(joinpath(@__DIR__, "juliadynamics-$(w).scss"), header*"\n"*theme)
-end
-# compile the themes
-Themes.compile(joinpath(@__DIR__, "juliadynamics-light.scss"), joinpath(@__DIR__, "src/assets/themes/documenter-light.css"))
-Themes.compile(joinpath(@__DIR__, "juliadynamics-dark.scss"), joinpath(@__DIR__, "src/assets/themes/documenter-dark.css"))
-
-makedocs(modules = [SignalDecomposition],
-sitename= "SignalDecomposition.jl",
-authors = "George Datseris and contributors.",
-doctest = false,
-format = Documenter.HTML(
-    prettyurls = CI,
-    assets = [
-        "assets/logo.ico",
-        asset("https://fonts.googleapis.com/css?family=Quicksand|Montserrat|Source+Code+Pro|Lora&display=swap", class=:css),
-        ],
-    ),
 pages = [
-    "Documentation" => "index.md",
-    "Examples" => "examples.md",
-    ],
+    "index.md",
+    "examples.md",
+]
+
+import Downloads
+Downloads.download(
+    "https://raw.githubusercontent.com/JuliaDynamics/doctheme/master/build_docs_with_style.jl",
+    joinpath(@__DIR__, "build_docs_with_style.jl")
 )
+include("build_docs_with_style.jl")
 
-if CI
-    deploydocs(
-        repo = "github.com/JuliaDynamics/SignalDecomposition.jl.git",
-        target = "build",
-        push_preview = true
-    )
-end
+build_docs_with_style(pages, SignalDecomposition;
+    authors = "George Datseris <datseris.george@gmail.com>",
+    expandfirst = ["index.md"], #  this is the first script that loads colorscheme
+)