add docs

.github/workflows/CI.yml

@@ -17,7 +17,7 @@ jobs:
         os:
           - ubuntu-latest
           - macOS-latest
-          - windows-latest
+          # - windows-latest
         arch:
           - x64
     steps:

.github/workflows/temp/docs.yml → .github/workflows/Documenter.yml

@@ -1,10 +1,10 @@
 name: Documenter
 on:
   push:
-    branches: [master]
+    branches: [master, main]
     tags: [v*]
   pull_request:
-
+    branches: [master, main]
 jobs:
   Documenter:
     name: Documentation
@@ -14,5 +14,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-docdeploy@latest
         env:
+          RASTERDATASOURCES_PATH: ".."
+          GKSwstype: "100"
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

docs/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -0,0 +1,29 @@
+using Documenter, Ipaper
+
+CI = get(ENV, "CI", nothing) == "true"
+
+# Logging.disable_logging(Logging.Warn)
+
+# Make the docs, without running the tests again
+# We need to explicitly add all the extensions here
+makedocs(
+  modules=[
+    Ipaper
+  ],
+  format=Documenter.HTML(
+    prettyurls=CI,
+  ),
+  pages=[
+    "Introduction" => "index.md"
+  ],
+  sitename="Ipaper.jl",
+  strict=false,
+  clean=false,
+)
+
+# Enable logging to console again
+# Logging.disable_logging(Logging.BelowMinLevel)
+
+deploydocs(
+  repo="github.com/jl-spatial/Ipaper.jl.git",
+)

docs/src/index.md

@@ -0,0 +1,94 @@
+## Thresholds
+
+```@docs
+cal_anomaly_quantile
+cal_anomaly_clim
+cal_threshold
+```
+
+```@docs
+_cal_anomaly_3d
+```
+
+```@docs
+cal_mTRS_base
+cal_mTRS_full
+
+cal_climatology_base
+cal_climatology_full
+```
+
+
+```@docs
+cal_mTRS_base!
+cal_mTRS_base3!
+NanQuantile_low
+```
+
+
+```@docs
+cal_yearly_Tair
+cal_warming_level
+```
+
+## Quantile
+
+```@docs
+NanQuantile_3d!
+
+movmean
+linreg_simple
+linreg_fast
+```
+
+
+## Statistics
+
+```@docs
+apply
+```
+
+## Strings
+
+```@docs
+str_extract
+str_extract_all
+str_replace
+grepl
+```
+
+## Plots
+
+```@docs
+merge_pdf
+show_pdf
+```
+
+## cmd
+
+```@docs
+dir
+path_mnt
+writelines
+```
+
+## R base
+
+```@docs
+duplicated
+list
+match2
+```
+
+### Missing
+
+```@docs
+drop_missing
+to_missing
+```
+
+## Parallel
+
+```@docs
+isCurrentWorker
+```

src/Climate/anomaly.jl

@@ -61,9 +61,11 @@ Calculate the anomaly of a 3D array of temperature data.
 
 - `A`      : the 3D array of temperature data
 - `dates`    : an array of dates corresponding to the temperature data
-- `parallel` : whether to use parallel processing (default `false`)
-- `use_mov`  : whether to use a moving window to calculate the threshold (default `true`)
-- `method`   : the method to use for calculating the threshold, one of `["full", "season", "base"]` (default `"full"`)
+- `parallel` : whether to use parallel processing (default `true`)
+- `use_mov`  : whether to use a moving window to calculate the threshold
+  (default `true`)
+- `method`   : the method to use for calculating the threshold, one of `["full",
+  "season", "base"]` (default `"full"`)
 - `probs`    : default `[0.5]`
 - `p1`       : the start year for the reference period (default `1981`)
 - `p2`       : the end year for the reference period (default `2010`)
@@ -76,14 +78,14 @@ An array of the same shape as `A` containing the temperature anomaly.
 # References
 
 1. Vogel, M. M., Zscheischler, J., Fischer, E. M., & Seneviratne, S. I. (2020).
-  Development of Future Heatwaves for Different Hazard Thresholds. Journal of
-  Geophysical Research: Atmospheres, 125(9).
-  https://doi.org/10.1029/2019JD032070
+   Development of Future Heatwaves for Different Hazard Thresholds. Journal of
+   Geophysical Research: Atmospheres, 125(9).
+   <https://doi.org/10.1029/2019JD032070>
 
 """
 function cal_anomaly_quantile(
   A::AbstractArray{T}, dates;
-  parallel::Bool=false,
+  parallel::Bool=true,
   use_mov=true, na_rm=true,
   method="full",
   p1=1981, p2=2010,
@@ -109,14 +111,16 @@ end
 
 
 """
+$(TYPEDSIGNATURES)
+
 Calculate the anomaly of an array relative to its climatology.
 
 # Arguments
 
 - `A::AbstractArray{T}`: The input array to calculate the anomaly of.
 - `dates`: The dates corresponding to the input array.
 
-- `parallel::Bool=false`: Whether to use parallel processing.
+- `parallel::Bool=true`: Whether to use parallel processing.
 - `use_mov=true`: Whether to use a moving window to calculate the climatology.
 - `method="full"`: The method to use for calculating the climatology. Can be "base", "season", or "full".
 - `p1=1981`: The start year for the period to use for calculating the climatology.
@@ -142,7 +146,7 @@ anom = cal_anomaly_clim(A, dates; method="base")
 function cal_anomaly_clim(
   A::AbstractArray{T},
   dates;
-  parallel::Bool=false,
+  parallel::Bool=true,
   use_mov=true,
   method="full",
   p1=1981, p2=2010,
@@ -168,15 +172,7 @@ end
 
 
 """
-  cal_threshold(
-    A::AbstractArray{T}, dates;
-    parallel::Bool=false,
-    use_mov=true, na_rm=true,
-    method="full",
-    p1=1981, p2=2010,
-    probs::Vector=[0.90, 0.95, 0.99, 0.999, 0.9999],
-    options...
-  )
+$(TYPEDSIGNATURES)
 
 Calculate the threshold value for a given dataset `A` and dates. The threshold value is calculated based on the specified method.