Update to newer packages (#5)

.github/workflows/CI.yml

@@ -0,0 +1,69 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+  pull_request:
+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:
+          - '1.9'
+          - '1'
+        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
+        env:
+            SSH_AUTH_SOCK: /tmp/ssh_agent.sock
+            HOME: /home/runner
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v3
+        with:
+          files: lcov.info
+  # 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 TaylorRemainders
+  #           DocMeta.setdocmeta!(TaylorRemainders, :DocTestSetup, :(using TaylorRemainders); recursive=true)
+  #           doctest(TaylorRemainders)'

.gitignore

@@ -1,5 +1,8 @@
-*.jl.cov
 *.jl.*.cov
+*.jl.cov
 *.jl.mem
-data
-Manifest.toml
+/Manifest.toml
+/docs/Manifest.toml
+/docs/build/
+/deps/build.log
+/data

Project.toml

@@ -1,16 +1,15 @@
 name = "AllenBrain"
 uuid = "0a79a13e-b89b-5a1e-b6bf-ef7ebeca6040"
 authors = ["Tim Holy <[email protected]>"]
-version = "0.1.0"
+version = "0.2.0"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
-ColorVectorSpace = "c3611d14-8923-5661-9e6a-0046d554d3a4"
 CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
-ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
 ImageTransformations = "02fcd773-0e25-5acc-982a-7f6622650795"
 IndirectArrays = "9b13fd28-a010-5f03-acff-a1bbcff69959"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
@@ -20,31 +19,33 @@ LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 NRRD = "9bb6cfbd-7763-5393-b1b5-1c8e09872146"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
+[weakdeps]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+
+[extensions]
+AllenBrainMakieExt = "Makie"
+
 [compat]
-AxisArrays = "0.3, 0.4"
-ColorVectorSpace = "0.6, 0.8"
-CoordinateTransformations = "0.5"
+AxisArrays = "0.4"
+CoordinateTransformations = "0.6"
 FileIO = "1"
-HTTP = "0.8"
-ImageCore = "0.8.1"
-ImageMagick = "0.7, 1"
-ImageTransformations = "0.7, 0.8"
-IndirectArrays = "0.5"
-Interpolations = "0.11, 0.12"
-IntervalSets = "0.3, 0.4"
+HTTP = "1"
+ImageCore = "0.9, 0.10"
+ImageTransformations = "0.10"
+IndirectArrays = "1"
+Interpolations = "0.14"
+IntervalSets = "0.7"
 JSON = "0.21"
-LightGraphs = "1"
-NRRD = "0.5, 0.6"
-OffsetArrays = "0.11, 1"
+NRRD = "0.6"
+OffsetArrays = "1"
 ProgressMeter = "1"
-Requires = "1"
-StaticArrays = "0.10, 0.11, 0.12"
-Unitful = "0.17, 0.18, 1"
+StaticArrays = "1"
+Unitful = "1"
+julia = "1.9"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

deps/build.jl

@@ -10,7 +10,7 @@ genes = joinpath(mousedir, "genes.json")
 
 if !isfile(sg)
     rq = HTTP.request("GET", "http://api.brain-map.org/api/v2/structure_graph_download/1.json")
-    data = JSON.parse(String(rq.data))
+    data = JSON.parse(String(rq.body))
     hierarchy = data["msg"][1]
 
     open(sg, "w") do io
@@ -19,9 +19,9 @@ if !isfile(sg)
 end
 
 if !isfile(genes)
-    info("Downloading genes database. This will take a while, but only needs to be done once.")
+    @info "Downloading genes database. This will take a while, but only needs to be done once."
     rq = HTTP.request("GET", "http://api.brain-map.org/api/v2/data/Gene/query.json?criteria=products[id\$eq1]"; query=Dict("num_rows"=>19991))
-    data = JSON.parse(String(rq.data))
+    data = JSON.parse(String(rq.body))
     g = data["msg"]
     open(genes, "w") do io
         write(io, JSON.json(g))

ext/AllenBrainMakieExt.jl

@@ -0,0 +1,14 @@
+module AllenBrainMakieExt
+
+using AllenBrain, Makie
+
+# NOTE: this was written against GLVisualize which is deprecated for
+# Makie. The code below likely needs updating.
+function AllenBrain.visualize_volume(volumedata)
+    window = Makie.glscreen()
+    volume = Makie.visualize(volumedata, :absorption)
+    Makie._view(volume, window)
+    @schedule Makie.renderloop(window)
+end
+
+end

src/AllenBrain.jl

@@ -3,11 +3,9 @@ module AllenBrain
 using Statistics
 using JSON, LightGraphs, IndirectArrays, AxisArrays, OffsetArrays
 using StaticArrays, CoordinateTransformations
-using ImageMagick, ImageTransformations, ImageCore, Interpolations
-using ColorVectorSpace
+using ImageTransformations, ImageCore, Interpolations
 using IntervalSets, ProgressMeter, FileIO
 using Unitful: μm
-using Requires
 import HTTP
 
 export #
@@ -42,7 +40,7 @@ function dataset(species, category)
         species == "mouse" && return joinpath(mousedir, "structure_graph.json")
     elseif startswith(category, "annotation") && species == "mouse"
         if !endswith(category, ".nrrd")
-            if !ismatch(r"[0-9]$", category)
+            if match(r"[0-9]$", category) === nothing
                 category = category*"_25"
             end
             category = category*".nrrd"
@@ -70,17 +68,4 @@ include("projections.jl")
 include("genes.jl")
 include("visualize.jl")
 
-function __init__()
-    # NOTE: this was written against GLVisualize which is deprecated for
-    # Makie. The code below likely needs updating.
-    @require Makie="ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" begin
-        function visualize_volume(volumedata)
-            window = Makie.glscreen()
-            volume = Makie.visualize(volumedata, :absorption)
-            Makie._view(volume, window)
-            @schedule Makie.renderloop(window)
-        end
-    end
-end
-
 end # module

src/genes.jl

@@ -6,7 +6,7 @@ const planedict = Dict("coronal"=>1, "sagittal"=>2)
 
 function query_insitu(key::AbstractString; plane="coronal", fieldname="acronym")
     rq = HTTP.request("GET", "http://api.brain-map.org/api/v2/data/SectionDataSet/query.json?criteria=products[id\$eq1],genes[$fieldname\$eq'$key']&include=section_images,alignment3d,section_images(alignment2d)")
-    data = JSON.parse(String(rq.data))
+    data = JSON.parse(String(rq.body))
     planeid = planedict[plane]
     for sectiondataset in data["msg"]
         if sectiondataset["plane_of_section_id"] == planeid
@@ -66,23 +66,6 @@ function download_insitu_images(sectiondataset::Dict, bb::BoundingBox, dirname;
                      "boundingbox"=>bb))
 end
 
-    # showall(filenames)
-    # showall(slicepos)
-    # sz = imagesize(joinpath(dirname, filenames[1]))
-    # for i = 2:length(filenames)
-    #     sz = map(max, sz, imagesize(joinpath(dirname, filenames[i])))
-    # end
-    # img2d = load(joinpath(dirname, first(filenames)))
-    # img = similar(img2d, sz[2], sz[1], length(filenames))
-    # fill!(img, zero(eltype(img)))
-    # for i = 1:length(filenames)
-    #     fn = joinpath(dirname, filenames[i])
-    #     if imagesize(fn) == sz
-    #         img[:,:,i] = load(fn)
-    #     end
-    # end
-    # resp = median(diff(slicepos))
-    # FileIO.save(joinpath(dirname, "merged.nrrd"), AxisArray(img, (:P, :I, :R), (resp, res, res)))
 
 # function download_insitu_images(genekey::AbstractString, x, y, dirname=genekey; plane="coronal", fieldname="acronym", downsample=0)
 #     if !isdir(dirname)

src/images.jl

@@ -11,7 +11,7 @@ function query_reference2image(sectiondataset::Dict, x, y, z)
     xr, yr, zr = inmicrons(x), inmicrons(y), inmicrons(z)
     str = "http://api.brain-map.org/api/v2/reference_to_image/$refspace.json?x=$xr&y=$yr&z=$zr&section_data_set_ids=$id"
     rq = HTTP.request("GET", str)
-    data = JSON.parse(String(rq.data))
+    data = JSON.parse(String(rq.body))
     data["msg"][1]["image_sync"]
 end
 
@@ -24,7 +24,7 @@ return the posterior, inferior, right coordinates `p`, `i`, `r` in microns.
 function query_image2reference(sectionimageid::Integer, x, y)
     str = "http://api.brain-map.org/api/v2/image_to_reference/$sectionimageid.json?x=$x&y=$y"
     rq = HTTP.request("GET", str)
-    data = JSON.parse(String(rq.data))
+    data = JSON.parse(String(rq.body))
     ret = data["msg"]["image_to_reference"]
     ret["x"], ret["y"], ret["z"]
 end
@@ -159,9 +159,3 @@ function isinrange(idx, pos, x, Δx)
     1 <= idx <= length(pos) || return false
     abs(pos[idx] - x) <= Δx
 end
-
-function imagesize(filename)
-    wand = ImageMagick.MagickWand()
-    ImageMagick.readimage(wand, filename)
-    size(wand)
-end

src/ontology.jl

@@ -16,7 +16,7 @@ end
 Return the structure graph `g` and list `vertexlist` of metadata for nodes.
 """
 function ontology(filename)
-    str = readstring(dataset(filename, "ontology"))
+    str = read(dataset(filename, "ontology"), String)
     hierarchy = JSON.parse(str)
     g = DiGraph()
     add_vertex!(g)  # for the root node
@@ -49,9 +49,9 @@ function annotation(resolution=50; species="mouse")
     return AxisArray(anno.data, (:P, :I, :R), (r, r, r))
 end
 
-function download_annotation(resolution=50)
+function download_annotation(resolution=50; species="mouse", year=2016)
     dest = joinpath(mousedir, "annotation_$resolution.nrrd")
-    download("http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2016/annotation_$resolution.nrrd", dest)
+    download("http://download.alleninstitute.org/informatics-archive/current-release/$(species)_ccf/annotation/ccf_$year/annotation_$resolution.nrrd", dest)
 end
 
 """

src/projections.jl

@@ -1,6 +1,6 @@
 function query_projection(id)
     rq = HTTP.request("GET", "http://api.brain-map.org/api/v2/data/WellKnownFile/query.json?criteria=well_known_file_type[name\$eq'ImagesResampledTo25MicronARA'][attachable_id\$eq$id]")
-    data = JSON.parse(String(rq.data))
+    data = JSON.parse(String(rq.body))
     data["msg"][1]
 end