diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml index f19c8cc..f14e385 100644 --- a/.github/workflows/Documenter.yml +++ b/.github/workflows/Documenter.yml @@ -1,25 +1,30 @@ -name: Documenter +name: Documentation + on: push: - branches: [master] - tags: [v*] + branches: + - master # update to match your development branch (master, main, dev, trunk, ...) + tags: '*' pull_request: -defaults: - run: - shell: bash - jobs: - Documenter: - name: Documentation + build: + permissions: + actions: write + contents: write + pull-requests: read + statuses: write runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: julia-actions/setup-julia@latest + - uses: actions/checkout@v4 + - uses: julia-actions/setup-julia@v2 with: - version: 1 - - uses: julia-actions/julia-buildpkg@latest - - uses: julia-actions/julia-docdeploy@releases/v1 + version: '1.10' + - uses: julia-actions/cache@v1 + - name: Install dependencies + run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' + - name: Build and deploy env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token + DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key + run: julia --project=docs/ docs/make.jl \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1444ca5..bd4bd34 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,9 +13,7 @@ jobs: fail-fast: false matrix: version: - - '1.0' - - '1' - - 'nightly' + - '1.10' os: - ubuntu-latest - macOS-latest @@ -24,7 +22,7 @@ jobs: - x64 steps: - uses: actions/checkout@v2 - - uses: julia-actions/setup-julia@v1 + - uses: julia-actions/setup-julia@v2 with: version: ${{ matrix.version }} arch: ${{ matrix.arch }} diff --git a/.gitignore b/.gitignore index 20fe29d..aabab04 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ *.jl.mem /Manifest.toml /docs/build/ +/docs/Manifest.toml diff --git a/Project.toml b/Project.toml index 279dd4d..7244125 100644 --- a/Project.toml +++ b/Project.toml @@ -1,16 +1,16 @@ name = "PubChemCrawler" uuid = "30e472fa-2b12-4c0b-9705-07d174b7a4e1" authors = ["Tim Holy and contributors"] -version = "1.1.0" +version = "1.2.0" [deps] HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3" LightXML = "9c8b4983-aa76-5018-a973-4c85ecc9e179" [compat] -HTTP = "0.8, 0.9" +HTTP = "1" LightXML = "0.8, 0.9" -julia = "1" +julia = "1.10" [extras] BrokenRecord = "bdd55f5b-6e67-4da1-a080-6086e55655a0" diff --git a/docs/Project.toml b/docs/Project.toml index 940b375..4410de2 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -3,4 +3,4 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" PubChemCrawler = "30e472fa-2b12-4c0b-9705-07d174b7a4e1" [compat] -Documenter = "0.25" +Documenter = "1" diff --git a/docs/make.jl b/docs/make.jl index 7c530f8..301f934 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -4,10 +4,8 @@ using Documenter makedocs(; modules=[PubChemCrawler], authors="Tim Holy and contributors", - repo="https://github.com/JuliaHealth/PubChemCrawler.jl/blob/{commit}{path}#L{line}", sitename="PubChemCrawler.jl", format=Documenter.HTML(; - prettyurls=get(ENV, "CI", "false") == "true", canonical="https://JuliaHealth.github.io/PubChemCrawler.jl", assets=String[], ), diff --git a/src/utils.jl b/src/utils.jl index 82b71d1..54ef886 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -34,7 +34,7 @@ Parse `str` as a chemical formula, return a list of `atom=>multiplicity` pairs. ```jldoctest; setup=(using PubChemCrawler) julia> parse_formula("C2CaH2O6") -4-element Array{Pair{String,$Int},1}: +4-element Vector{Pair{String, $Int}}: "C" => 2 "Ca" => 1 "H" => 2 diff --git a/test/http_record/CAS_as_json.bson b/test/http_record/CAS_as_json.bson index eb55386..9dc6a50 100644 Binary files a/test/http_record/CAS_as_json.bson and b/test/http_record/CAS_as_json.bson differ diff --git a/test/http_record/CAS_as_txt.bson b/test/http_record/CAS_as_txt.bson index 7eabc74..22ea517 100644 Binary files a/test/http_record/CAS_as_txt.bson and b/test/http_record/CAS_as_txt.bson differ diff --git a/test/http_record/aspirin_cid_from_name.bson b/test/http_record/aspirin_cid_from_name.bson index f53172f..2730c2d 100644 Binary files a/test/http_record/aspirin_cid_from_name.bson and b/test/http_record/aspirin_cid_from_name.bson differ diff --git a/test/http_record/aspirin_cid_from_smiles.bson b/test/http_record/aspirin_cid_from_smiles.bson index 12e1569..27430f5 100644 Binary files a/test/http_record/aspirin_cid_from_smiles.bson and b/test/http_record/aspirin_cid_from_smiles.bson differ diff --git a/test/http_record/aspirin_smiles_from_cid.bson b/test/http_record/aspirin_smiles_from_cid.bson index 236226d..ef080f4 100644 Binary files a/test/http_record/aspirin_smiles_from_cid.bson and b/test/http_record/aspirin_smiles_from_cid.bson differ diff --git a/test/http_record/asprin_sdf_3d.bson b/test/http_record/asprin_sdf_3d.bson index 9058646..ae37c9e 100644 Binary files a/test/http_record/asprin_sdf_3d.bson and b/test/http_record/asprin_sdf_3d.bson differ diff --git a/test/http_record/cGMP_cid.bson b/test/http_record/cGMP_cid.bson index 4e5b847..1f91adb 100644 Binary files a/test/http_record/cGMP_cid.bson and b/test/http_record/cGMP_cid.bson differ diff --git a/test/http_record/estriol_cid.bson b/test/http_record/estriol_cid.bson index 4a6aa24..a4076da 100644 Binary files a/test/http_record/estriol_cid.bson and b/test/http_record/estriol_cid.bson differ diff --git a/test/http_record/estriol_substructure.bson b/test/http_record/estriol_substructure.bson index ce90d9a..5cae7e9 100644 Binary files a/test/http_record/estriol_substructure.bson and b/test/http_record/estriol_substructure.bson differ diff --git a/test/http_record/estriol_substructure_formulas.bson b/test/http_record/estriol_substructure_formulas.bson index 5aa606f..f1432f7 100644 Binary files a/test/http_record/estriol_substructure_formulas.bson and b/test/http_record/estriol_substructure_formulas.bson differ diff --git a/test/http_record/smarts.bson b/test/http_record/smarts.bson index 0febfb5..90a75d9 100644 Binary files a/test/http_record/smarts.bson and b/test/http_record/smarts.bson differ diff --git a/test/http_record/smarts_pug.bson b/test/http_record/smarts_pug.bson index f0defdb..6d8feaf 100644 Binary files a/test/http_record/smarts_pug.bson and b/test/http_record/smarts_pug.bson differ diff --git a/test/http_record/sodium_acetate_parent.bson b/test/http_record/sodium_acetate_parent.bson index 610f16f..22c639c 100644 Binary files a/test/http_record/sodium_acetate_parent.bson and b/test/http_record/sodium_acetate_parent.bson differ