Bump HTTP, update HTTP records (#22)

* Bump HTTP, update HTTP records * Test only on Julia 1.10 due to BrokenRecord limitations * Make Julia 1.10 the minimum * Update docs build and CI Closes #19, closes #21 Co-authored-by: Filipe Chichorro <[email protected]>
JuliaHealth · Aug 30, 2024 · e0a2100 · e0a2100 · timholy · Aug 30, 2024
1 parent c10a088
commit e0a2100
Show file tree

Hide file tree

Showing 20 changed files with 29 additions and 27 deletions.
diff --git 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
diff --git 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
@@ -3,3 +3,4 @@
 *.jl.mem
 /Manifest.toml
 /docs/build/
+/docs/Manifest.toml
diff --git a/Project.toml b/Project.toml
@@ -1,16 +1,16 @@
 name = "PubChemCrawler"
 uuid = "30e472fa-2b12-4c0b-9705-07d174b7a4e1"
 authors = ["Tim Holy <[email protected]> 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
@@ -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
@@ -4,10 +4,8 @@ using Documenter
 makedocs(;
     modules=[PubChemCrawler],
     authors="Tim Holy <[email protected]> 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
@@ -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
diff --git a/test/http_record/CAS_as_txt.bson b/test/http_record/CAS_as_txt.bson
diff --git a/test/http_record/aspirin_cid_from_name.bson b/test/http_record/aspirin_cid_from_name.bson
diff --git a/test/http_record/aspirin_cid_from_smiles.bson b/test/http_record/aspirin_cid_from_smiles.bson
diff --git a/test/http_record/aspirin_smiles_from_cid.bson b/test/http_record/aspirin_smiles_from_cid.bson
diff --git a/test/http_record/asprin_sdf_3d.bson b/test/http_record/asprin_sdf_3d.bson
diff --git a/test/http_record/cGMP_cid.bson b/test/http_record/cGMP_cid.bson
diff --git a/test/http_record/estriol_cid.bson b/test/http_record/estriol_cid.bson
diff --git a/test/http_record/estriol_substructure.bson b/test/http_record/estriol_substructure.bson
diff --git a/test/http_record/estriol_substructure_formulas.bson b/test/http_record/estriol_substructure_formulas.bson
diff --git a/test/http_record/smarts.bson b/test/http_record/smarts.bson
diff --git a/test/http_record/smarts_pug.bson b/test/http_record/smarts_pug.bson
diff --git a/test/http_record/sodium_acetate_parent.bson b/test/http_record/sodium_acetate_parent.bson