Merge branch 'master' into master

.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/Documenter.yml

@@ -10,7 +10,7 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: nightly               # change this to 1.6 once's that's official

.github/workflows/Invalidations.yml

@@ -0,0 +1,40 @@
+name: Invalidations
+
+on:
+  pull_request:
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: always.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  evaluate:
+    # Only run on PRs to the default branch.
+    # In the PR trigger above branches can be specified only explicitly whereas this check should work for master, main, or any other default branch
+    if: github.base_ref == github.event.repository.default_branch
+    runs-on: ubuntu-latest
+    steps:
+    - uses: julia-actions/setup-julia@v1
+      with:
+        version: '1'
+    - uses: actions/checkout@v4
+    - uses: julia-actions/julia-buildpkg@v1
+    - uses: julia-actions/julia-invalidations@v1
+      id: invs_pr
+
+    - uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.repository.default_branch }}
+    - uses: julia-actions/julia-buildpkg@v1
+    - uses: julia-actions/julia-invalidations@v1
+      id: invs_default
+
+    - name: Report invalidation counts
+      run: |
+        echo "Invalidations on default branch: ${{ steps.invs_default.outputs.total }} (${{ steps.invs_default.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
+        echo "This branch: ${{ steps.invs_pr.outputs.total }} (${{ steps.invs_pr.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
+    - name: Check if the PR does increase number of invalidations
+      if: steps.invs_pr.outputs.total > steps.invs_default.outputs.total
+      run: exit 1

.github/workflows/test.yml

@@ -13,12 +13,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ['1.0', '1', 'nightly']
-        julia-arch: [x64, x86]
-        os: [ubuntu-latest, macOS-latest, windows-latest]
+        julia-version: ['1.0', '1.6', '1', 'nightly']
+        julia-arch: [x64, x86, aarch64]
+        os: [ubuntu-latest, windows-latest, macOS-13, macOS-14]
         exclude:
-          - os: macOS-latest
+          - os: ubuntu-latest
+            julia-arch: aarch64
+          - os: windows-latest
+            julia-arch: aarch64
+          - os: macOS-13
             julia-arch: x86
+          - os: macOS-13
+            julia-arch: aarch64
+          - os: macOS-14
+            julia-arch: x86
+          - os: macOS-14
+            julia-arch: x64
+          - os: macOS-14
+            julia-version: '1.6'
+          - os: macOS-14
+            julia-version: '1.0'
 
     steps:
       - name: Set git to use LF (Windows only)
@@ -31,14 +45,15 @@ jobs:
         run: |
           echo "TMP=${USERPROFILE}\AppData\Local\Temp" >> ${GITHUB_ENV}
           echo "TEMP=${USERPROFILE}\AppData\Local\Temp" >> ${GITHUB_ENV}
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.julia-version }}
       - uses: julia-actions/julia-runtest@latest
         env:
           JULIA_NUM_THREADS: 2
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

Project.toml

@@ -1,17 +1,28 @@
 name = "FileIO"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.16.0"
+version = "1.16.2"
 
 [deps]
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [compat]
+Pkg = "<0.0.1, 0.7, 1"
 Requires = "1"
+UUIDs = "<0.0.1, 0.7, 1"
 julia = "0.7, 1"
+Aqua = "0.8"
+CSVFiles = "1"
+CodecZlib = "0.5, 0.6, 0.7"
+ColorTypes = "0.11"
+FilePathsBase = "0.9"
+HTTP = "0.6, 1"
+Random = "<0.0.1, 0.7, 1"
+Test = "<0.0.1, 0.7, 1"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
@@ -21,4 +32,4 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["ColorTypes", "CodecZlib", "CSVFiles", "FilePathsBase", "HTTP", "Random", "Test"]
+test = ["Aqua", "ColorTypes", "CodecZlib", "CSVFiles", "FilePathsBase", "HTTP", "Random", "Test"]

docs/src/index.md

@@ -15,7 +15,7 @@ Install FileIO within Julia via
 ```julia
 julia> using Pkg
 
-julia> Pkg.add("FileIO")`
+julia> Pkg.add("FileIO")
 ```
 
 ## Usage
@@ -48,6 +48,12 @@ Likewise, saving might be as simple as
 save(filename, obj)
 ```
 
+You can also utilize a piping style to save values to files like this
+
+```julia
+obj |> save(filename)
+```
+
 If you just want to inspect a file to determine its format, then
 
 ```julia

src/mimesave.jl

@@ -2,10 +2,14 @@ module MimeWriter
 
 using ..FileIO: File, @format_str
 
-function save(file::File{format"PNG"}, data)
+function save(file::File{format"PNG"}, data; ppi::Union{Nothing,Number}=nothing)
     if showable("image/png", data)
         open(file.filename, "w") do s
-            show(IOContext(s, :full_fidelity=>true), "image/png", data)
+            if ppi === nothing
+                show(IOContext(s, :full_fidelity=>true), "image/png", data)
+            else
+                show(IOContext(s, :full_fidelity=>true, :ppi=>ppi), "image/png", data)
+            end
         end
     else
         throw(ArgumentError("Argument does not support conversion to png."))

src/registry.jl

@@ -7,6 +7,7 @@ const idImageIO = :ImageIO => UUID("82e4d734-157c-48bb-816b-45c225c6df19")
 const idImageMagick = :ImageMagick => UUID("6218d12a-5da1-5696-b52f-db25d2ecc6d1")
 const idMeshIO = :MeshIO => UUID("7269a6da-0436-5bbc-96c2-40638cbb6118")
 const idNetpbm = :Netpbm => UUID("f09324ee-3d7c-5217-9330-fc30815ba969")
+const idOpenCV = :OpenCV => UUID("f878e3a2-a245-4720-8660-60795d644f2a")
 const idQuartzImageIO = :QuartzImageIO => UUID("dca85d43-d64c-5e67-8c65-017450d5d020")
 const idRData = :RData => UUID("df47a6cb-8c03-5eed-afd8-b6050d6c41da")
 const idStatFiles = :StatFiles => UUID("1463e38c-9381-5320-bcd4-4134955f093a")
@@ -116,6 +117,7 @@ add_format(format"AVSfld", "# AVS", [".fld"], [idAVSfldIO])
 add_format(format"CSV", (), [".csv"], [idCSVFiles])
 add_format(format"TSV", (), [".tsv"], [idCSVFiles])
 add_format(format"Feather", "FEA1", [".feather"], [:FeatherFiles => UUID("b675d258-116a-5741-b937-b79f054b0542")])
+add_format(format"Arrow", b"ARROW1\0\0", [".arrow"], [:Arrow => UUID("69666777-d1a9-59fb-9406-91d4454c9d45")])
 add_format(format"Excel", (), [".xls", ".xlsx"], [:ExcelFiles => UUID("89b67f3b-d1aa-5f6f-9ca4-282e8d98620d")])
 add_format(format"Stata", (), [".dta"], [idStatFiles, LOAD])
 add_format(format"SPSS", "\$FL2", [".sav"], [idStatFiles, LOAD])
@@ -148,7 +150,7 @@ add_format(format"EXR", UInt8[0x76,0x2f,0x31,0x01],                     ".exr",
 add_format(format"HDR", UInt8[0x23,0x3f,0x52,0x41,0x44,0x49,0x41,0x4e], ".hdr", [idImageMagick])
 add_format(format"ICO", UInt8[0x00,0x00,0x01,0x00],                     ".ico", [idImageMagick])
 add_format(format"INFO", UInt8[0x7a,0x62,0x65,0x78],                    ".info",[idImageMagick])
-add_format(format"JP2", UInt8[0x00,0x00,0x00,0x0c,0x6a,0x50,0x20,0x20], ".jp2", [idImageMagick])
+add_format(format"JP2", UInt8[0x00,0x00,0x00,0x0c,0x6a,0x50,0x20,0x20], ".jp2", [idImageMagick], [idOpenCV])
 add_format(format"PDB", UInt8[0x73,0x7a,0x65,0x7a],                     ".pdb", [idImageMagick])
 add_format(format"PDF", UInt8[0x25,0x50,0x44,0x46],                     ".pdf", [idImageMagick], [MimeWriter, SAVE])
 add_format(format"PGM", UInt8[0x50,0x35,0x0a],                          ".pgm", [idImageMagick])
@@ -179,6 +181,7 @@ add_format(
     [idImageIO],
     [idQuartzImageIO, OSX],
     [idImageMagick],
+    [idOpenCV],
     [MimeWriter, SAVE]
 )
 add_format(
@@ -188,14 +191,16 @@ add_format(
     [idJpegTurbo],
     [idImageIO],
     [idQuartzImageIO, OSX],
-    [idImageMagick]
+    [idImageMagick],
+    [idOpenCV]
 ) # 0xe1
 add_format(
     format"BMP",
     UInt8[0x42,0x4d],
     ".bmp",
     [idQuartzImageIO, OSX],
-    [idImageMagick]
+    [idImageMagick],
+    [idOpenCV]
 )
 add_format(
     format"PCX",
@@ -384,7 +389,7 @@ function detecttiff(io)
 end
 # normal TIFF
 detect_noometiff(io) = detecttiff(io) && ((:name ∉ propertynames(io)) || !(endswith(io.name, ".ome.tif>") || endswith(io.name, ".ome.tiff>")))
-add_format(format"TIFF", detect_noometiff, [".tiff", ".tif"], [idImageIO], [idQuartzImageIO, OSX], [idImageMagick])
+add_format(format"TIFF", detect_noometiff, [".tiff", ".tif"], [idImageIO], [idQuartzImageIO, OSX], [idImageMagick], [idOpenCV])
 # OME-TIFF
 detect_ometiff(io) = detecttiff(io) && (:name ∈ propertynames(io)) && (endswith(io.name, ".ome.tif>") || endswith(io.name, ".ome.tiff>"))
 add_format(format"OMETIFF", detect_ometiff, [".tif", ".tiff"], [:OMETIFF => UUID("2d0ec36b-e807-5756-994b-45af29551fcf")])

test/runtests.jl

@@ -25,3 +25,6 @@ end
     include("test_mimesave.jl")
     include("integration.jl")
 end
+
+using Aqua
+Aqua.test_all(FileIO)