feat: lean package for testing build

.github/workflows/CI.yml

@@ -25,11 +25,11 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: update pip
         run: python -m pip install -U pip
       - name: install python deps
-        run: python -m pip install -U numpy==1.23 scikit-image==0.20.0 pyproj==3.6.0 rasterio==1.3.7 requests==2.31.0 skyfield==1.45.0 pandas==2 jinja2==3.1
+        run: python -m pip install -U -r requirements.txt
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}

requirements.txt

@@ -0,0 +1,8 @@
+numpy==1.23.2
+scikit-image==0.20.0
+pyproj==3.6.0
+rasterio==1.3.7
+requests==2.31.0
+skyfield==1.45.0
+pandas==2.1
+jinja2==3.1

src/IceFloeTracker.jl

@@ -49,24 +49,6 @@ export DataFrames, DataFrame, nrow, Not, select!
 export Dates, Time, Date, DateTime, @dateformat_str
 export addlatlon!, getlatlon, convertcentroid!, converttounits!, dropcols!
 
-include("utils.jl")
-include("persist.jl")
-include("landmask.jl")
-include("cloudmask.jl")
-include("normalization.jl")
-include("ice-water-discrimination.jl")
-include("anisotropic_image_diffusion.jl")
-include("bwtraceboundary.jl")
-include("resample-boundary.jl")
-include("psi-s.jl")
-include("crosscorr.jl")
-include("register-mismatch.jl")
-include("bwareamaxfilt.jl")
-include("hbreak.jl")
-include("bridge.jl")
-include("branch.jl")
-include("special_strels.jl")
-
 const sk_measure = PyNULL()
 const getlatlon = PyNULL()
 
@@ -90,90 +72,7 @@ function __init__()
 end
 
 include("regionprops.jl")
-include("segmentation_a_direct.jl")
-include("segmentation_b.jl")
-include("segmentation_watershed.jl")
-include("bwperim.jl")
-include("find_ice_labels.jl")
-include("segmentation_f.jl")
-include("tracker/tracker-funcs.jl")
-include("tracker/matchcorr.jl")
-include("tracker/tracker.jl")
-
-"""
-    MorphSE
-
-Module for morphological operations with structuring element functionality adapted from ImageMorphology v0.4.3.
-
-This module is temporary until v0.5 of ImageMorphology is released.
-
-Main functionality is `dilate(img, se)` for landmask computations.
-
-# Example
-
-```jldoctest; setup = :(using IceFloeTracker)
-julia> a = zeros(Int, 11, 11); a[6, 6] = 1;
-
-julia> a
-11×11 Matrix{Int64}:
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  1  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
-
-julia> se = trues(5,5);
-
-julia> IceFloeTracker.MorphSE.dilate(a, se)
-11×11 Matrix{Int64}:
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  1  1  1  1  1  0  0  0
- 0  0  0  1  1  1  1  1  0  0  0
- 0  0  0  1  1  1  1  1  0  0  0
- 0  0  0  1  1  1  1  1  0  0  0
- 0  0  0  1  1  1  1  1  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
- 0  0  0  0  0  0  0  0  0  0  0
-```
-"""
-module MorphSE
-using ImageCore
-using ColorTypes
-using LoopVectorization
-using OffsetArrays
-using TiledIteration: EdgeIterator
-using DataStructures
-include("morphSE/StructuringElements.jl")
-using .StructuringElements
-include("morphSE/extreme_filter.jl")
-include("morphSE/utils.jl")
-include("morphSE/dilate.jl")
-include("morphSE/erode.jl")
-include("morphSE/opening.jl")
-include("morphSE/closing.jl")
-include("morphSE/bothat.jl")
-include("morphSE/mreconstruct.jl")
-include("morphSE/fill_holes.jl")
-end
-
-module Register
-include("Register/CenterIndexedArrays.jl-0.2.0/CenterIndexedArrays.jl")
-include("Register/RegisterCore.jl-0.2.4/src/RegisterCore.jl")
-include("Register/RegisterMismatchCommon.jl-master/RegisterMismatchCommon.jl")
-include("Register/RegisterUtilities.jl-master/RegisterUtilities.jl")
-include("Register/RFFT.jl-master/RFFT.jl")
-include("Register/RegisterDeformation.jl-0.4.4/RegisterDeformation.jl")
-include("Register/QuadDIRECT.jl-master/QuadDIRECT.jl")
-include("Register/RegisterQD.jl-0.3.1/RegisterQD.jl")
-include("Register/RegisterMismatch.jl-0.4.0/RegisterMismatch.jl")
-end
+include("utils.jl")
+include("persist.jl")
+include("bwareamaxfilt.jl")
 end

test/runtests.jl

@@ -12,19 +12,20 @@ include("config.jl")
 
 # Setting things up (see config.jl)
 
-## Get all test files filenames "test-*" in test folder and their corresponding names/label 
+## Get all test files filenames "test-*" in test folder and their corresponding names/label
 alltests = [f for f in readdir() if startswith(f, "test-")]
 testnames = [n[6:(end - 3)] for n in alltests]
 
 ## Put the filenames to test below
 
-to_test = alltests # uncomment this line to run all tests or add individual files below 
+to_test = #alltests # uncomment this line to run all tests or add individual files below
 [
     # "test-create-landmask.jl",
     # "test-create-cloudmask.jl",
     # "test-normalize-image.jl",
-    # "test-persist.jl",
-    # "test-utils-padding.jl",
+    "test-persist.jl",
+    "test-utils-padding.jl",
+    "test-regionprops.jl",
     # "test-discrim-ice-water.jl",
     # "test-find-ice-labels.jl",
     # "test-segmentation-a.jl",
@@ -33,7 +34,6 @@ to_test = alltests # uncomment this line to run all tests or add individual file
     # "test-segmentation-f.jl",
     # "test-bwtraceboundary.jl",
     # "test-resample-boundary.jl",
-    # "test-regionprops.jl",
     # "test-psi-s.jl",
     # "test-crosscorr.jl"
     # "test-bwperim.jl",