Add Aqua; CODECOV_TOKEN; cut stale dependencies; badges (#134)

* Add Aqua

* Cut stale dependencies; compat for libs

* Add badges

* Add CODECOV_TOKEN

* Fix typo

* Improve codecov

.github/workflows/ci.yml

@@ -27,16 +27,34 @@ jobs:
         os: [ubuntu-latest, windows-latest, macOS-latest]
     steps:
       - uses: actions/checkout@v4
+
 #     - name: "Set up Julia"
       - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.version }}
+
+      - name: Cache artifacts
+        uses: actions/cache@v4
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+
 #     - name: "Unit Test"
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
+
 #     - name: "Cover"
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v4
         if: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }}
         with:
           file: lcov.info
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

Project.toml

@@ -8,9 +8,7 @@ AVSfldIO = "b6189060-daf9-4c28-845a-cc0984b81781"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
-ImageTransformations = "02fcd773-0e25-5acc-982a-7f6622650795"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LazyGrids = "7031d0ef-c40d-4431-b2f8-61a8d2f650db"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -24,15 +22,18 @@ Wavelets = "29a6e085-ba6d-5f35-a997-948ac2efa89a"
 
 [compat]
 AVSfldIO = "0.2"
+Distributed = "1"
 FFTW = "1"
 FileIO = "1"
-FillArrays = "1"
 ImageFiltering = "0.7"
-ImageTransformations = "0.10"
 Interpolations = "0.15"
 LazyGrids = "1"
+LinearAlgebra = "1"
 LinearMapsAA = "0.12"
 NFFT = "0.13"
+Random = "1"
+SharedArrays = "1"
+SparseArrays = "1"
 SpecialFunctions = "2"
 Wavelets = "0.10"
 julia = "1.10"

README.md

@@ -6,6 +6,9 @@
 [![docs stable][docs-stable-img]][docs-stable-url]
 [![docs dev][docs-dev-img]][docs-dev-url]
 [![license][license-img]][license-url]
+[![deps](https://juliahub.com/docs/MIRT/deps.svg)](https://juliahub.com/ui/Packages/MIRT)
+[![version](https://juliahub.com/docs/MIRT/version.svg)](https://juliahub.com/ui/Packages/MIRT)
+[![pkgeval](https://juliahub.com/docs/MIRT/pkgeval.svg)](https://juliahub.com/ui/Packages/MIRT)
 <img src="deps/mirt-logo.svg" alt="MIRTlogo" width="150"/>
 
 https://github.com/JeffFessler/MIRT.jl
@@ -64,7 +67,7 @@ This package includes some tools from
 https://gitlab.eecs.umich.edu/michigan-fast-optimization
 
 For additional reproducible research code, see
-http://web.eecs.umich.edu/~fessler/irt/reproduce/
+http://web.eecs.umich.edu/~fessler/irt/reproduce
 
 
 ## Compatibility
@@ -117,7 +120,7 @@ As of `v0.15`, the following functions are deprecated:
 
 
 <!-- URLs -->
-[action-img]: https://github.com/JeffFessler/MIRT.jl/workflows/Unit%20test/badge.svg
+[action-img]: https://github.com/JeffFessler/MIRT.jl/workflows/CI/badge.svg
 [action-url]: https://github.com/JeffFessler/MIRT.jl/actions
 [build-img]: https://github.com/JeffFessler/MIRT.jl/workflows/CI/badge.svg?branch=main
 [build-url]: https://github.com/JeffFessler/MIRT.jl/actions?query=workflow%3ACI+branch%3Amain

_typos.toml

@@ -5,5 +5,6 @@ extend-ignore-identifiers-re = [
     "Nd",
     "iy",
     "pn",
+    "FOVx",
     "MIRTio",
 ]

src/io/ir_dump.jl

@@ -46,7 +46,6 @@ function ir_dump(y::Any ; io::IO = stdout, ntuplemax::Int = 3)
         end
     end
     println(io)
-    nothing
 end
 
 

test/Project.toml

@@ -1,6 +1,5 @@
 [deps]
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 ImageGeoms = "9ee76f2b-840d-4475-b6d6-e485c9297852"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"

test/aqua.jl

@@ -0,0 +1,7 @@
+using MIRT: MIRT
+import Aqua
+using Test: @testset
+
+@testset "aqua" begin
+    Aqua.test_all(MIRT; stale_deps = (ignore = [:AVSfldIO],))
+end