add autoformatting (#73)

* autoformatting * maybe if we push one change the action will fail?? * println debugging * Update .github/workflows/Format.yml Co-authored-by: Phillip Alday <[email protected]> * Update .github/workflows/Format.yml Co-authored-by: Phillip Alday <[email protected]> * Update .github/workflows/Format.yml Co-authored-by: Phillip Alday <[email protected]> * Update .github/workflows/Format.yml Co-authored-by: Phillip Alday <[email protected]> * fix * insert malformed change * Revert "insert malformed change" This reverts commit 4f397e5. * format everything --------- Co-authored-by: Phillip Alday <[email protected]>
beacon-biosignals · Oct 17, 2023 · 2eef49f · 2eef49f
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diff --git a/.github/workflows/Format.yml b/.github/workflows/Format.yml
@@ -0,0 +1,42 @@
+name: Format Check
+on:
+  # because we rely on ReviewDog to trigger failure, there's no reason to run on anything
+  pull_request:
+    paths:
+      - "**/*.jl"
+      - ".github/workflows/FormatCheck.yml"
+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:
+  format-check:
+    if: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        version:
+          - "1.9"
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+        with:
+          cache-name: "${{ github.workflow }}-${{ github.job }}-${{ matrix.pkg.name }}-${{ matrix.version }}-${{ matrix.os }}-${{ matrix.arch }}"
+          cache-compiled: true
+      - name: Instantiate `format` environment and format
+        run: |
+          julia --project=format -e 'using Pkg; Pkg.instantiate()'
+          julia --project=format 'format/run.jl'
+      - uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: JuliaFormatter
+          fail_on_error: true
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,4 @@
 *.DS_Store
 Manifest.toml
 docs/build/
+!format/Manifest.toml
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,9 +1,9 @@
 using Documenter
 using EDF
 
-makedocs(modules=[EDF],
+makedocs(; modules=[EDF],
          sitename="EDF.jl",
          authors="Beacon Biosignals, Inc.",
          pages=["API" => "index.md"])
 
-deploydocs(repo="github.com/beacon-biosignals/EDF.jl.git")
+deploydocs(; repo="github.com/beacon-biosignals/EDF.jl.git")
diff --git a/format/Manifest.toml b/format/Manifest.toml
@@ -0,0 +1,221 @@
+# This file is machine-generated - editing it directly is not advised
+
+julia_version = "1.9.3"
+manifest_format = "2.0"
+project_hash = "30b405be1c677184b7703a9bfb3d2100029ccad0"
+
+[[deps.ArgTools]]
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+version = "1.1.1"
+
+[[deps.Artifacts]]
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+
+[[deps.Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[deps.CSTParser]]
+deps = ["Tokenize"]
+git-tree-sha1 = "3ddd48d200eb8ddf9cb3e0189fc059fd49b97c1f"
+uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f"
+version = "3.3.6"
+
+[[deps.CommonMark]]
+deps = ["Crayons", "JSON", "PrecompileTools", "URIs"]
+git-tree-sha1 = "532c4185d3c9037c0237546d817858b23cf9e071"
+uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
+version = "0.8.12"
+
+[[deps.Compat]]
+deps = ["UUIDs"]
+git-tree-sha1 = "8a62af3e248a8c4bad6b32cbbe663ae02275e32c"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "4.10.0"
+
+    [deps.Compat.extensions]
+    CompatLinearAlgebraExt = "LinearAlgebra"
+
+    [deps.Compat.weakdeps]
+    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[deps.Crayons]]
+git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
+uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
+version = "4.1.1"
+
+[[deps.DataStructures]]
+deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
+git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d"
+uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+version = "0.18.15"
+
+[[deps.Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[deps.Downloads]]
+deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
+uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+version = "1.6.0"
+
+[[deps.FileWatching]]
+uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
+
+[[deps.Glob]]
+git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
+uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
+version = "1.3.1"
+
+[[deps.InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[deps.JSON]]
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.21.4"
+
+[[deps.JuliaFormatter]]
+deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
+git-tree-sha1 = "80031f6e58b09b0de4553bf63d9a36ec5db57967"
+uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+version = "1.0.39"
+
+[[deps.LibCURL]]
+deps = ["LibCURL_jll", "MozillaCACerts_jll"]
+uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+version = "0.6.3"
+
+[[deps.LibCURL_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
+uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+version = "7.84.0+0"
+
+[[deps.LibGit2]]
+deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[deps.LibSSH2_jll]]
+deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
+uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+version = "1.10.2+0"
+
+[[deps.Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[deps.Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[deps.Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[deps.MbedTLS_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.28.2+0"
+
+[[deps.Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[deps.MozillaCACerts_jll]]
+uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+version = "2022.10.11"
+
+[[deps.NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+version = "1.2.0"
+
+[[deps.OrderedCollections]]
+git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3"
+uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+version = "1.6.2"
+
+[[deps.Parsers]]
+deps = ["Dates", "PrecompileTools", "UUIDs"]
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "2.7.2"
+
+[[deps.Pkg]]
+deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+version = "1.9.2"
+
+[[deps.PrecompileTools]]
+deps = ["Preferences"]
+git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f"
+uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+version = "1.2.0"
+
+[[deps.Preferences]]
+deps = ["TOML"]
+git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e"
+uuid = "21216c6a-2e73-6563-6e65-726566657250"
+version = "1.4.1"
+
+[[deps.Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[deps.REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[deps.Random]]
+deps = ["SHA", "Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[deps.SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
+
+[[deps.Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[deps.Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[deps.TOML]]
+deps = ["Dates"]
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+version = "1.0.3"
+
+[[deps.Tar]]
+deps = ["ArgTools", "SHA"]
+uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+version = "1.10.0"
+
+[[deps.Tokenize]]
+git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5"
+uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
+version = "0.5.25"
+
+[[deps.URIs]]
+git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b"
+uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
+version = "1.5.1"
+
+[[deps.UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[deps.Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[deps.Zlib_jll]]
+deps = ["Libdl"]
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.13+0"
+
+[[deps.nghttp2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+version = "1.48.0+0"
+
+[[deps.p7zip_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
+version = "17.4.0+0"
diff --git a/format/Project.toml b/format/Project.toml
@@ -0,0 +1,2 @@
+[deps]
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
diff --git a/format/run.jl b/format/run.jl
@@ -0,0 +1,14 @@
+using JuliaFormatter
+
+function main()
+    perfect = format("."; style=YASStyle(), verbose=true)
+    if perfect
+        @info "Linting complete - no files altered"
+    else
+        @info "Linting complete - files altered"
+        run(`git status`)
+    end
+    return nothing
+end
+
+main()
diff --git a/src/read.jl b/src/read.jl
@@ -81,7 +81,8 @@ function read_file_header(io::IO)
     patient_id = something(tryparse(PatientID, patient_id_raw), String(patient_id_raw))
 
     recording_id_raw = strip(String(Base.read(io, 80)))
-    recording_id = something(tryparse(RecordingID, recording_id_raw), String(recording_id_raw))
+    recording_id = something(tryparse(RecordingID, recording_id_raw),
+                             String(recording_id_raw))
 
     start_raw = Base.read(io, 8)
     push!(start_raw, UInt8(' '))
@@ -108,7 +109,8 @@ function read_file_header(io::IO)
 end
 
 function read_signal_headers(io::IO, signal_count)
-    fields = [String(Base.read(io, size)) for signal in 1:signal_count, (_, size) in SIGNAL_HEADER_FIELDS]
+    fields = [String(Base.read(io, size))
+              for signal in 1:signal_count, (_, size) in SIGNAL_HEADER_FIELDS]
     signal_headers = [SignalHeader(strip(fields[i, 1]), strip(fields[i, 2]),
                                    strip(fields[i, 3]), parse_float(fields[i, 4]),
                                    parse_float(fields[i, 5]), parse_float(fields[i, 6]),
@@ -139,7 +141,7 @@ function read_to!(io::IO, x::AbstractArray{T}) where {T}
 end
 
 function read_signals!(file::File)
-    for record_index in 1:file.header.record_count, signal in file.signals
+    for record_index in 1:(file.header.record_count), signal in file.signals
         read_signal_record!(file, signal, record_index)
     end
     return nothing
@@ -157,7 +159,8 @@ end
 
 function read_signal_record!(file::File, signal::AnnotationsSignal, record_index::Int)
     bytes_per_sample = sizeof(sample_type(file))
-    io_for_record = IOBuffer(Base.read(file.io, bytes_per_sample * signal.samples_per_record))
+    io_for_record = IOBuffer(Base.read(file.io,
+                                       bytes_per_sample * signal.samples_per_record))
     tals_for_record = TimestampedAnnotationList[]
     while !eof(io_for_record) && Base.peek(io_for_record) != 0x00
         push!(tals_for_record, read_tal(io_for_record))
@@ -172,7 +175,8 @@ function read_tal(io::IO)
     timestamp = split(String(bytes), '\x15'; keepempty=false)
     onset_in_seconds = flipsign(parse(Float64, timestamp[1]), sign)
     duration_in_seconds = length(timestamp) == 2 ? parse(Float64, timestamp[2]) : nothing
-    annotations = convert(Vector{String}, split(String(readuntil(io, 0x00)), '\x14'; keepempty=true))
+    annotations = convert(Vector{String},
+                          split(String(readuntil(io, 0x00)), '\x14'; keepempty=true))
     isempty(last(annotations)) && pop!(annotations)
     return TimestampedAnnotationList(onset_in_seconds, duration_in_seconds, annotations)
 end
@@ -182,6 +186,7 @@ function read_tal_onset_sign(io::IO)
     sign === 0x2b && return 1
     sign === 0x2d && return -1
     error("starting byte of a TAL must be '+' or '-'; found $sign")
+    return nothing
 end
 
 #####

diff --git a/src/types.jl b/src/types.jl
@@ -161,7 +161,8 @@ function AnnotationsSignal(records::Vector{Vector{TimestampedAnnotationList}})
     # but cleanly refactoring the package to do this would be a more involved
     # change than is meritted at the moment (since normal signals are already
     # treated similarly, i.e. the `SignalHeader` is overly trusted).
-    max_bytes_per_record = maximum(sum(write_tal(IOBuffer(), tal) for tal in record) for record in records)
+    max_bytes_per_record = maximum(sum(write_tal(IOBuffer(), tal) for tal in record)
+                                   for record in records)
     return AnnotationsSignal(Int16(cld(max_bytes_per_record, 2)), records)
 end
 
@@ -267,7 +268,7 @@ struct File{T<:SUPPORTED_SAMPLE_TYPES,I<:IO}
     signals::Vector{Union{Signal{T},AnnotationsSignal}}
 end
 
-function Base.show(io::IO, edf::File{T}) where T
+function Base.show(io::IO, edf::File{T}) where {T}
     print(io, "EDF.File with ", length(edf.signals), ' ', 8 * sizeof(T),
           "-bit-encoded signals")
     return nothing