Add static_link and aqua verifications.

Makefile

@@ -21,7 +21,14 @@ deps/.format: */*.jl deps/format.sh deps/format.jl
 	@touch deps/.format
 
 .PHONY: check
-check: jet untested_lines
+check: static_analysis jet aqua untested_lines
+
+.PHONY: static_analysis
+static_analysis: deps/.static_analysis
+
+deps/.static_analysis: *.toml src/*.jl test/*.toml test/*.jl deps/static_analysis.sh deps/static_analysis.jl
+	deps/static_analysis.sh
+	@touch deps/.static_analysis
 
 .PHONY: jet
 jet: deps/.jet
@@ -30,6 +37,13 @@ deps/.jet: *.toml src/*.jl test/*.toml test/*.jl deps/jet.sh deps/jet.jl deps/je
 	deps/jet.sh
 	@touch deps/.jet
 
+.PHONY: aqua
+aqua: deps/.aqua
+
+deps/.aqua: *.toml src/*.jl test/*.toml test/*.jl deps/aqua.sh deps/aqua.jl
+	deps/aqua.sh
+	@touch deps/.aqua
+
 .PHONY: test
 test: tracefile.info
 

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.2"
 manifest_format = "2.0"
-project_hash = "59e7df362cbccf9b3489ca11436d43634605ed35"
+project_hash = "8e03bb75bf6f51f8955793f4a225b42fdf673d0d"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
@@ -118,11 +118,6 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 version = "1.6.0"
 
-[[deps.EnumX]]
-git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237"
-uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
-version = "1.0.4"
-
 [[deps.ExprTools]]
 git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec"
 uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
@@ -148,9 +143,9 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[deps.HDF5]]
 deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"]
-git-tree-sha1 = "26407bd1c60129062cec9da63dc7d08251544d53"
+git-tree-sha1 = "e856eef26cf5bf2b0f95f8f4fc37553c72c8641c"
 uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-version = "0.17.1"
+version = "0.17.2"
 
     [deps.HDF5.extensions]
     MPIExt = "MPI"
@@ -160,9 +155,9 @@ version = "0.17.1"
 
 [[deps.HDF5_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
-git-tree-sha1 = "e4591176488495bf44d7456bd73179d87d5e6eab"
+git-tree-sha1 = "6384c847ff5056c5624e30e75b3ca48902cae0ac"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.14.3+1"
+version = "1.14.3+2"
 
 [[deps.Hwloc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -266,12 +261,6 @@ version = "0.3.27"
 [[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
-[[deps.LoggingExtras]]
-deps = ["Dates", "Logging"]
-git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075"
-uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
-version = "1.0.3"
-
 [[deps.MPICH_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
 git-tree-sha1 = "656036b9ed6f942d35e536e249600bc31d0f9df8"
@@ -459,9 +448,9 @@ version = "1.7.0"
 
 [[deps.StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf"
+git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.34.2"
+version = "0.34.3"
 
 [[deps.StringManipulation]]
 deps = ["PrecompileTools"]

Project.toml

@@ -10,13 +10,11 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-EnumX = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
 ExprTools = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
-LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
 Muon = "446846d7-b4ce-489d-bf74-72da18fe3629"
 NamedArrays = "86f7a689-2022-50b4-a561-43c23ac3c673"

deps/add_pkgs.jl

@@ -1,6 +1,18 @@
 using Pkg
 
-for pkg in ("Coverage", "Documenter", "JET", "JuliaFormatter", "Logging", "LoggingExtras", "SnoopCompile")
+for pkg in (
+    "Aqua",
+    "Coverage",
+    "Documenter",
+    "JET",
+    "JuliaFormatter",
+    "LanguageServer",
+    "Logging",
+    "LoggingExtras",
+    "SnoopCompile",
+    "StaticLint",
+    "SymbolServer",
+)
     println("Adding $(pkg):")
     Pkg.add(pkg)
 end

deps/aqua.jl

@@ -0,0 +1,6 @@
+push!(LOAD_PATH, ".")
+
+using Aqua
+using Daf
+Aqua.test_ambiguities([Daf])
+Aqua.test_all(Daf; ambiguities = false, unbound_args = false, deps_compat = false)

deps/aqua.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+julia deps/aqua.jl

deps/static_analysis.jl

@@ -0,0 +1,74 @@
+using LanguageServer
+using StaticLint
+using SymbolServer
+
+language_server = LanguageServerInstance(Pipe(), stdout, ".")
+_, symbols = SymbolServer.getstore(language_server.symbol_server, ".")
+language_server.global_env.symbols = symbols
+language_server.global_env.extended_methods = SymbolServer.collect_extended_methods(language_server.global_env.symbols)
+language_server.global_env.project_deps = collect(keys(language_server.global_env.symbols))
+
+file = StaticLint.loadfile(language_server, abspath("src/Daf.jl"))
+StaticLint.semantic_pass(LanguageServer.getroot(file))
+
+global errors = 0
+global skipped = 0
+global unused = 0
+for doc in LanguageServer.getdocuments_value(language_server)
+    StaticLint.check_all(
+        LanguageServer.getcst(doc),
+        language_server.lint_options,
+        LanguageServer.getenv(doc, language_server),
+    )
+    LanguageServer.mark_errors(doc, doc.diagnostics)
+    no_lint_lines = Set{Int}()
+    unused_no_lint_lines = Set{Int}()
+    for (line_number, line_text) in enumerate(readlines(doc._path))
+        if contains(line_text, "NOLINT")
+            push!(no_lint_lines, line_number)
+            push!(unused_no_lint_lines, line_number)
+        end
+    end
+    for diagnostic in doc.diagnostics
+        line_number = diagnostic.range.start.line + 1
+        character_number = diagnostic.range.start.character + 1
+        if line_number in no_lint_lines
+            delete!(unused_no_lint_lines, line_number)
+            global skipped
+            skipped += 1
+        else
+            println("$(doc._path):$(line_number):$(character_number): $(diagnostic.message)")
+            global errors
+            errors += 1
+        end
+    end
+    for line_number in sort(collect(unused_no_lint_lines))
+        global unused
+        unused += 1
+        println("$(doc._path):$(line_number): unused NOLINT directive)")
+    end
+end
+
+message = "StaticLint:"
+separator = ""
+if errors > 0
+    message *= " $(errors) errors"
+    separator = ","
+end
+if skipped > 0
+    message *= "$(separator) $(skipped) skipped"
+    separator = ","
+end
+if unused > 0
+    message *= "$(separator) $(unused) unused"
+end
+
+if errors + skipped + unused > 0
+    println(message)
+else
+    println("StaticLint: clean!")
+end
+
+if errors + unused > 0
+    exit(1)
+end

deps/static_analysis.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+set -e -o pipefail
+julia deps/static_analysis.jl

docs/v0.1.0/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-04-04T20:19:23","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-04-06T13:17:46","documenter_version":"1.3.0"}}

src/adapters.jl

@@ -117,7 +117,7 @@ function adapter(
 end
 
 function get_adapter_capture_name(view::Union{DafWriter, DafReadOnly}; name::Maybe{AbstractString})::AbstractString
-    _base, prefix = get_base(view, name)
+    _, prefix = get_base(view, name)
     return prefix * ".capture"
 end
 
@@ -126,7 +126,7 @@ function get_adapter_input(
     name::Maybe{AbstractString},
     writer::DafWriter,
 )::DafWriter
-    _base, prefix = get_base(view, name)
+    _, prefix = get_base(view, name)
     return chain_writer([view, writer]; name = "$(prefix).adapted")
 end
 
@@ -153,7 +153,7 @@ function get_base(view::Union{DafWriter, DafReadOnly}, name::Maybe{AbstractStrin
         @assert base isa DafWriter
     end
 
-    if name == nothing
+    if name === nothing
         prefix = base.name
     else
         prefix = name  # untested

src/anndata_format.jl

@@ -160,9 +160,9 @@ function by_annotation(
     name::AbstractString,
     default::AbstractString,
 )::AbstractString
-    if value == nothing
+    if value === nothing
         value = get(adata.uns, name, default)
-        @assert value != nothing
+        @assert value !== nothing
     end
     return value
 end
@@ -218,7 +218,7 @@ function verify_is_supported_type(
     unsupported_handler::AbnormalHandler,
 )::Nothing
     if value isa StorageMatrix &&
-       major_axis(value) == nothing &&
+       major_axis(value) === nothing &&
        !(value isa Muon.TransposedDataset) &&
        !(value isa Muon.SparseDataset)
         report_unsupported(  # untested
@@ -332,11 +332,11 @@ function copy_supported_matrices(
 end
 
 function copy_supported_matrix(  # untested
-    matrix::Any,
-    memory::MemoryDaf,
-    rows_axis::AbstractString,
-    columns_axis::AbstractString,
-    name::AbstractString,
+    ::Any,
+    ::MemoryDaf,
+    ::AbstractString,
+    ::AbstractString,
+    ::AbstractString,
 )::Nothing
     return nothing
 end
@@ -380,7 +380,7 @@ function copy_supported_matrix(
         matrix = transpose(matrix)
         rows_axis, columns_axis = columns_axis, rows_axis
     end
-    if matrix_major_axis != nothing
+    if matrix_major_axis !== nothing
         set_matrix!(memory, rows_axis, columns_axis, name, matrix; relayout = false)
     end
 end
@@ -459,7 +459,7 @@ function daf_as_anndata(
 
     copy_matrices(daf, obs_is, var_is, X_is, adata.layers)
 
-    if h5ad != nothing
+    if h5ad !== nothing
         writeh5ad(h5ad, adata; compress = UInt8(0))  # NOJET
     end
 
@@ -472,9 +472,9 @@ function by_scalar(
     name::AbstractString,
     default::AbstractString,
 )::AbstractString
-    if value == nothing
+    if value === nothing
         value = get_scalar(daf, name; default = default)
-        @assert value != nothing
+        @assert value !== nothing
     end
     return value
 end