Merge pull request #19 from EcoJulia/feature-queries

[WIP] Use pairs instead of a dictionary for queries

.github/workflows/CI.yml

@@ -0,0 +1,45 @@
+name: CI
+on:
+  - push
+  - pull_request
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        version:
+          - '1.3'
+          - '1.4'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-runtest@latest
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.4'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/TagBot.yml

@@ -0,0 +1,11 @@
+name: TagBot
+on:
+  schedule:
+    - cron: 0 * * * *
+jobs:
+  TagBot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -6,3 +6,4 @@ deps/deps.jl
 docs/build
 docs/site
 tags
+Manifest.toml

Manifest.toml

@@ -1,35 +1,21 @@
+# This file is machine-generated - editing it directly is not advised
+
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
-[[BinaryProvider]]
-deps = ["Libdl", "Pkg", "SHA", "Test"]
-git-tree-sha1 = "2883bc1b389e3d57a134796c39c788db3f298cef"
-uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.4.0"
-
-[[Compat]]
-deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "277d3807440d9793421354b6680911fc95d91a84"
-uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "1.0.1"
-
 [[Dates]]
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[DelimitedFiles]]
-deps = ["Mmap"]
-uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-
 [[Distributed]]
-deps = ["LinearAlgebra", "Random", "Serialization", "Sockets"]
+deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[HTTP]]
-deps = ["Base64", "Dates", "Distributed", "IniFile", "MbedTLS", "Sockets", "Test"]
-git-tree-sha1 = "8a0f75e8b09df01d9f1ba9ad3fbf8b4983595d20"
+deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"]
+git-tree-sha1 = "cd60d9a575d3b70c026d7e714212fd4ecf86b4bb"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "0.6.14"
+version = "0.8.13"
 
 [[IniFile]]
 deps = ["Test"]
@@ -38,25 +24,22 @@ uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f"
 version = "0.5.0"
 
 [[InteractiveUtils]]
-deps = ["LinearAlgebra", "Markdown"]
+deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[JSON]]
-deps = ["Dates", "Distributed", "Mmap", "Pkg", "Sockets", "Test", "Unicode"]
-git-tree-sha1 = "fec8e4d433072731466d37ed0061b3ba7f70eeb9"
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-version = "0.19.0"
+version = "0.21.0"
 
 [[LibGit2]]
+deps = ["Printf"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LinearAlgebra]]
-deps = ["Libdl"]
-uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
@@ -65,16 +48,28 @@ deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[MbedTLS]]
-deps = ["BinaryProvider", "Compat", "Libdl", "Pkg", "Sockets"]
-git-tree-sha1 = "17d5a81dbb1e682d4ff707c01f0afe5948068fa6"
+deps = ["Dates", "MbedTLS_jll", "Random", "Sockets"]
+git-tree-sha1 = "a9e2221f06b42f56052f43ad7edecb01d0ef5ab4"
 uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
-version = "0.6.0"
+version = "1.0.1"
+
+[[MbedTLS_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "066a4467008745eed36dad973ceb66405785a621"
+uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.16.0+1"
 
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
+[[Parsers]]
+deps = ["Dates", "Test"]
+git-tree-sha1 = "0c16b3179190d3046c073440d94172cfc3bb0553"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "0.3.12"
+
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Printf]]
@@ -95,27 +90,15 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
-[[SharedArrays]]
-deps = ["Distributed", "Mmap", "Random", "Serialization"]
-uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
-
 [[Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
-[[SparseArrays]]
-deps = ["LinearAlgebra", "Random"]
-uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-
-[[Statistics]]
-deps = ["LinearAlgebra", "SparseArrays"]
-uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-
 [[Test]]
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[UUIDs]]
-deps = ["Random"]
+deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]

Project.toml

@@ -1,10 +1,20 @@
 name = "GBIF"
 uuid = "ee291a33-5a6c-5552-a3c8-0f29a1181037"
 authors = ["Timothée Poisot <timothee.poisot@umontreal.ca>"]
-version = "0.1.4"
+version = "0.2.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+
+[compat]
+julia = "1.3"
+HTTP = "0.8"
+JSON = "0.21"
+
+[extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

README.md

@@ -21,8 +21,8 @@ Pkg.add("GBIF")
 
 - get a single occurrence (`occurrence`)
 - look for multiple occurrences (`occurrences`)
-- paging function (`next!`, `restart!`, `complete!`)
-- quality control (`qualitycontrol!`) and arbitrary filters
+- paging function to get the next batch of occurrences (`occurrences!`)
+- quality control (`filter!`) and arbitrary filters
 - species and taxon lookup (`species`)
 
 ## How to contribute

docs/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -3,19 +3,20 @@ push!(LOAD_PATH, "../src/")
 using Documenter, GBIF
 
 makedocs(
-    sitename = "GBIF wrapper in Julia",
+    sitename = "GBIF occurrences API wrapper in Julia",
     authors = "Timothée Poisot",
     modules = [GBIF],
     pages = [
         "Home" => "index.md",
         "Manual" => [
             "Getting data" => "data.md",
-            "Filtering records" => "qaqc.md"
+            "Filtering records" => "filter.md"
         ],
         "Types" => "types.md"
     ]
 )
 
 deploydocs(
-    repo = "github.com/EcoJulia/GBIF.jl.git"
+    repo = "github.com/EcoJulia/GBIF.jl.git",
+    push_preview = true
 )

docs/src/data.md

@@ -47,13 +47,12 @@ end
 ### Query parameters
 
 ```@docs
-occurrences(q::Dict)
-occurrences(t::GBIFTaxon, q::Dict)
+occurrences(query::Pair...)
+occurrences(t::GBIFTaxon, query::Pair...)
 ```
 
 ### Batch-download of occurrences
 
 ```@docs
-next!
-complete!
+occurrences!
 ```

src/GBIF.jl

@@ -84,6 +84,15 @@ const gbifenums = Dict(
   ]
  )
 
+#=
+HACK this is required because some GBIF strings fail to parse, and I do not know
+why.
+=#
+import Base: convert
+function convert(::Type{AbstractString}, t::T) where {T <: Nothing}
+  return "<nothing>"
+end
+
 # package code goes here
 include("query.jl")
 
@@ -100,10 +109,9 @@ include("taxon.jl")
 export taxon
 
 include("occurrence.jl")
-export occurrence, occurrences
-
 include("paging.jl")
-export next!, complete!
+export occurrence, occurrences
+export occurrences!
 
 include("filter.jl")
 export have_both_coordinates, have_neither_zero_coordinates,