Fixing tests

.github/workflows/CI.yml

@@ -0,0 +1,64 @@
+name: CI
+on:
+  push:
+    branches:
+      - master
+    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 }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+          - '1.9'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      statuses: write
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - name: Configure doc environment
+        run: |
+          julia --project=docs/ -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - run: |
+          julia --project=docs -e '
+            using Documenter: DocMeta, doctest
+            using SeisMain
+            DocMeta.setdocmeta!(SeisMain, :DocTestSetup, :(using SeisMain); recursive=true)
+            doctest(SeisMain)'

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+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()'

Project.toml

@@ -7,13 +7,15 @@ version = "0.1.1"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-julia = "1"
 Documenter = "0.27"
 DocumenterTools = "0.1"
+julia = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

src/Utils/DownloadIfNeeded.jl

@@ -0,0 +1,50 @@
+using Downloads
+using SHA
+
+"""
+    download_if_needed(url::String, output::String, sha256sum::String)
+
+Download the file from `url` to `output` if the file is not already present
+or if its SHA256 checksum does not match the `sha256sum`.
+
+# Arguments
+- `url::String`: The URL from which to download the file.
+- `output::String`: The path where the downloaded file will be saved.
+
+# Keyword arguments
+- `sha256sum::String`: The expected SHA256 checksum of the file to ensure its integrity.
+
+# Output
+- `nothing`: This function returns `nothing`. It performs the side effect of downloading a file and verifying its checksum. If the checksum does not match, the function raises an error and deletes the downloaded file.
+
+*Credits: Átila Saraiva Quintela Soares, 2024*
+"""
+function download_if_needed(url::String, output::String; sha256sum::String)
+    file_exists = isfile(output)
+
+    if file_exists
+        file_sha256 = open(output) do io
+            io |> sha256 |> bytes2hex
+        end
+        if file_sha256 == sha256sum
+            return nothing
+        else
+            @warn("File exists but checksum does not match. Downloading again.")
+        end
+    end
+
+    # Download the file
+    Downloads.download(url, output)
+
+    # Verify checksum of the downloaded file
+    open(output) do io
+        file_sha256 = io |> sha256 |> bytes2hex
+        if file_sha256 != sha256sum
+            rm(output)
+            error("Downloaded file checksum does not match the expected checksum.")
+        end
+    end
+
+    return nothing
+end
+

src/Utils/Utils.jl

@@ -10,7 +10,8 @@ SeisUnPatch,
 SeisWindow,
 SeisWindowHeaders,
 SeisBinData,
-SeisBinHeaders
+SeisBinHeaders,
+download_if_needed
 include("SeisGeometry.jl")
 include("SeisPatch.jl")
 include("SeisWindowPatch.jl")
@@ -24,3 +25,4 @@ include("SeisWindow.jl")
 include("SeisWindowHeaders.jl")
 include("SeisBinData.jl")
 include("SeisBinHeaders.jl")
+include("DownloadIfNeeded.jl")

test/runtests.jl

@@ -1,3 +1,6 @@
+using SeisMain
+using Test
+
 include("test_IO.jl")
 include("test_bin.jl")
 include("test_patch.jl")

test/test_IO.jl

@@ -1,15 +1,23 @@
-using SeisMain
-using Test
-
 #From USGS, National Petroleum Reserve - Alaska Data Archive
 #https://energy.usgs.gov/GeochemistryGeophysics/SeismicDataProcessingInterpretation/NPRASeismicDataArchive.aspx#3862174-data-
 
-download("http://certmapper.cr.usgs.gov/data/NPRA/seismic/1976/125_76/PROCESSED/125_76_PT2_PR.SGY","125_76.SGY")
-
+download_if_needed("https://saigfileserver.physics.ualberta.ca/static/Datasets/Testing/16_81_PT1_PR.SGY", "16_81_PT1_PR.SGY", sha256sum="54791e8626215d36f6ebcecc3039da2fd74f3472518f47d8e8137c81c2ccfc2f")
 
-SegyToSeis("125_76.SGY","125_76")
-d,h,ext = SeisRead("125_76")
+SegyToSeis("16_81_PT1_PR.SGY","16_81_PT1_PR")
+d,h,ext = SeisRead("16_81_PT1_PR")
 imx = SeisMain.ExtractHeader(h,"imx")
 println("size(d)=",size(d))
 println("imx=",imx)
-SeisWrite("125_76_copy",d,h,ext)
+SeisWrite("16_81_PT1_PR_copy",d,h,ext)
+
+for file in (
+             "16_81_PT1_PR",
+             "16_81_PT1_PR.SGY",
+             "16_81_PT1_PR@data@",
+             "16_81_PT1_PR@headers@",
+             "16_81_PT1_PR_copy",
+             "16_81_PT1_PR_copy@data@",
+             "16_81_PT1_PR_copy@headers@",
+            )
+    rm(joinpath(@__DIR__, file))
+end

test/test_bin.jl

@@ -1,14 +1,11 @@
-using SeisMain
-using Test
-
 println("Testing test_bin.jl")
 
-download("http://seismic.physics.ualberta.ca/data/prestack_section.su","section.su");
+download_if_needed("https://saigfileserver.physics.ualberta.ca/static/Datasets/Testing/prestack_section.su", "section.su", sha256sum="8baaf281a36dcd5656e07e728bf97e0c1b513302b12206efbb24c3edb34d9ec8");
 
 SegyToSeis("section.su","section",format="su",input_type="ieee");
 
 param1 = Dict( :dmx=>15, :dmy=>15, :dh=>30, :daz=>45 );
- 
+
 param2 = Dict(:style=>"mxmyhaz", :min_imx=>10,:max_imx=>100, :min_imy=>35, :max_imy=>45,
                :min_ih=>1, :max_ih=>6, :min_iaz=>0, :max_iaz=>7);
 
@@ -22,4 +19,13 @@ db,hb,eb=SeisRead("section_bin");
 
 N =size(db)
 
-@test N == (251, 91, 11, 6, 8)
+@test N == (251, 91, 11, 6, 8)
+
+for file in (
+             "section",
+             "section@data@",
+             "section@headers@",
+             "section.su",
+            )
+    rm(joinpath(@__DIR__, file))
+end

test/test_patch.jl

@@ -1,6 +1,3 @@
-using SeisMain
-using Test
-
 param2 = Dict(:style=>"mxmyhaz", :min_imx=>10,:max_imx=>100, :min_imy=>35, :max_imy=>45,
                :min_ih=>1, :max_ih=>6, :min_iaz=>0, :max_iaz=>7);
 
@@ -20,4 +17,17 @@ df,hf,ef=SeisRead(file_final);
 
 alpha = maximum(db-df)
 
-@test alpha < 0.1
+@test alpha < 0.1
+
+for file in (
+             "section_bin",
+             "section_bin_final",
+             "patch_1",
+             "patch_2",
+             "patch_3",
+             "patch_4",
+            )
+    rm(joinpath(@__DIR__, file))
+    rm(joinpath(@__DIR__, file*"@data@"))
+    rm(joinpath(@__DIR__, file*"@headers@"))
+end