Merge pull request #15 from eWaterCycle/julia-tests

Add tests for RemoteBmi.jl

RemoteBMI.jl/.github/workflows/ReusableTest.yml → .github/workflows/JuliaReusableTest.yml

@@ -23,9 +23,9 @@ on:
         required: false
         type: boolean
         default: false
-    secrets:
-      codecov_token:
-        required: true
+
+permissions:
+  id-token: write # This is required for requesting the JWT
 
 jobs:
   test:
@@ -39,14 +39,21 @@ jobs:
         with:
           version: ${{ inputs.version }}
           arch: ${{ inputs.arch }}
+          project: './RemoteBMI.jl'
       - name: Use Julia cache
         uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
+        with:
+          project: './RemoteBMI.jl'
       - uses: julia-actions/julia-runtest@v1
+        with:
+          project: './RemoteBMI.jl'
       - uses: julia-actions/julia-processcoverage@v1
-        if: ${{ inputs.run_codecov }}
+        if: ${{ inputs.run_codecov }}      
+        with:
+          directories: "RemoteBMI.jl/src"
       - uses: codecov/codecov-action@v4
         if: ${{ inputs.run_codecov }}
         with:
           file: lcov.info
-          token: ${{ secrets.codecov_token }}
+          use_oidc: true

RemoteBMI.jl/.github/workflows/TestOnPRs.yml → .github/workflows/julia-test-on-prs.yml

@@ -1,13 +1,13 @@
-name: Test on PRs
+name: Julia test on PRs
 
 on:
   pull_request:
-    branches:
-      - main
+    # branches:
+    #   - main
     paths:
-      - "src/**"
-      - "test/**"
-      - "*.toml"
+      - "RemoteBMI.jl/src/**"
+      - "RemoteBMI.jl/test/**"
+      - "RemoteBMI.jl/*.toml"
     types: [opened, synchronize, reopened]
 
 concurrency:
@@ -18,12 +18,10 @@ concurrency:
 
 jobs:
   test:
-    uses: ./.github/workflows/ReusableTest.yml
+    uses: ./.github/workflows/JuliaReusableTest.yml
     with:
       os: ubuntu-latest
       version: "1"
       arch: x64
       allow_failure: false
       run_codecov: true
-    secrets:
-      codecov_token: ${{ secrets.CODECOV_TOKEN }}

RemoteBMI.jl/.github/workflows/Test.yml → .github/workflows/julia-test.yml

@@ -1,35 +1,32 @@
-name: Test
+name: Julia test
 
 on:
   push:
     branches:
       - main
     tags: ["*"]
-
+    paths:
+        - "RemoteBMI.jl/**"
+        - .github/workflows/julia-test.yml
   workflow_dispatch:
 
 jobs:
   test:
-    uses: ./.github/workflows/ReusableTest.yml
+    uses: ./.github/workflows/JuliaReusableTest.yml
     with:
       os: ${{ matrix.os }}
       version: ${{ matrix.version }}
       arch: ${{ matrix.arch }}
       allow_failure: ${{ matrix.allow_failure }}
       run_codecov: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }}
-    secrets:
-      codecov_token: ${{ secrets.CODECOV_TOKEN }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - "1.6"
+          - "lts"
           - "1"
         os:
           - ubuntu-latest
-          #- macOS-latest
-          #- windows-latest
         arch:
           - x64
         allow_failure: [false]
-

README.md

@@ -1,5 +1,6 @@
 # Remote BMI
 
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
 [![Codecov test coverage](https://codecov.io/gh/eWaterCycle/remotebmi/graph/badge.svg)](https://app.codecov.io/gh/eWaterCycle/remotebmi)
 
 The [Basic Model Interface (BMI)](https://bmi.readthedocs.io/en/stable/) is a standard interface for models. 
@@ -21,6 +22,12 @@ The [REST API specification](openapi.yaml) is in the [OpenAPI](https://swagger.i
 
 [OpenAPI reference documentation](https://redocly.github.io/redoc/?url=https://github.com/eWaterCycle/remotebmi/raw/main/openapi.yaml)
 
+## Structure
+
+This repository is a monorepo containing packages for different languages.
+1. Python client and server, in [./python/](./python) directory
+2. Julia server, in [./RemoteBMI.jl/](./RemoteBMI.jl/) directory
+
 ### Python consumer
 
 Installation
@@ -94,10 +101,19 @@ Given you have a model class called `MyModel` and a BMI called `BMI` inside the
 
 ```julia
 using MyPackage
-using RemoteBMI
+import RemoteBMI.Server: run_bmi_server
 
 port = parse(Int, get(ENV, "BMI_PORT", "50051"))
-RemoteBMI.run(MyPackage.Model, "0.0.0.0", port)
+run_bmi_server(MyPackage.Model, "0.0.0.0", port)
+```
+
+### Julia consumer
+
+```julia
+import RemoteBMI.Client: BMIClient
+import BasicModelInterface as BMI
+model = BMIClient("http://localhost:50555")
+BMI.get_component_name(m)
 ```
 
 ### R provider

RemoteBMI.jl/.editorconfig

@@ -5,6 +5,14 @@ root = true
 end_of_line = lf
 insert_final_newline = true
 charset = utf-8
-indent_size = 2
 indent_style = space
 trim_trailing_whitespace = true
+
+[*.jl]
+indent_size = 4
+
+[*.md]
+indent_size = 2
+
+[*.{yml,toml,json}]
+indent_size = 2

RemoteBMI.jl/.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 <!--
 Thanks for making a pull request to RemoteBMI.jl.
 We have added this PR template to help you help us.
-Make sure to read the contributing guidelines and abide to the code of conduct.
+Make sure to read the contributing guidelines and abide by the code of conduct.
 See the comments below, fill the required fields, and check the items.
 -->
 

RemoteBMI.jl/.github/workflows/Docs.yml

@@ -35,19 +35,23 @@ jobs:
           version: "1"
       - name: Use Julia cache
         uses: julia-actions/cache@v2
-      - run: |
+      - name: Instantiate environment with development version of the package
+        run: |
           julia --project=docs -e '
             using Pkg
             Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
-      - run: |
+      - name: Run doctest
+        run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
             using RemoteBMI
             DocMeta.setdocmeta!(RemoteBMI, :DocTestSetup, :(using RemoteBMI); recursive=true)
             doctest(RemoteBMI)'
-      - run: julia --project=docs docs/make.jl
+      - name: Generate and deploy documentation
+        run: julia --project=docs docs/make.jl
         env:
           JULIA_PKG_SERVER: ""
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988

RemoteBMI.jl/.gitignore

@@ -1,7 +1,12 @@
 *.jl.*.cov
 *.jl.cov
 *.jl.mem
+*.rej
+.DS_Store
+.benchmarkci
 Manifest.toml
+benchmark/*.json
+coverage
 docs/build/
-*.rej
+env
 node_modules

RemoteBMI.jl/CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at
+reported to the community leaders responsible for enforcement:
 `[email protected]`.
 All complaints will be reviewed and investigated promptly and fairly.
 

RemoteBMI.jl/Project.toml

@@ -7,9 +7,11 @@ version = "0.1.0"
 BasicModelInterface = "59605e27-edc0-445a-b93d-c09a3a50b330"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 OpenAPI = "d5e62ea6-ddf3-4d43-8e4c-ad5e6c8bfd7d"
 TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
 URIs = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
 
 [compat]
-julia = "1.6"
+JSON = "0.21.4"
+julia = "1.10"

RemoteBMI.jl/README.md

@@ -1,15 +1,14 @@
 # RemoteBMI
 
-[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://eWaterCycle.github.io/RemoteBMI.jl/stable)
-[![In development documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://eWaterCycle.github.io/RemoteBMI.jl/dev)
-[![Build Status](https://github.com/eWaterCycle/RemoteBMI.jl/workflows/Test/badge.svg)](https://github.com/eWaterCycle/RemoteBMI.jl/actions)
-[![Test workflow status](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Test.yml?query=branch%3Amain)
-[![Lint workflow Status](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Lint.yml/badge.svg?branch=main)](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Lint.yml?query=branch%3Amain)
-[![Docs workflow Status](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Docs.yml/badge.svg?branch=main)](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Docs.yml?query=branch%3Amain)
+<!-- [![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://eWaterCycle.github.io/RemoteBMI.jl/stable) -->
+<!-- [![In development documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://eWaterCycle.github.io/RemoteBMI.jl/dev) -->
+[![Build Status](https://github.com/eWaterCycle/RemoteBMI.jl/workflows/Julia%20test/badge.svg)](https://github.com/eWaterCycle/RemoteBMI/actions)
+[![Test workflow status](https://github.com/eWaterCycle/RemoteBMI/actions/workflows/julia-test.yml/badge.svg?branch=main)](https://github.com/eWaterCycle/RemoteBMI/actions/workflows/julia-test.yml?query=branch%3Amain)
+<!-- [![Docs workflow Status](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Docs.yml/badge.svg?branch=main)](https://github.com/eWaterCycle/RemoteBMI.jl/actions/workflows/Docs.yml?query=branch%3Amain) -->
 
-[![Coverage](https://codecov.io/gh/eWaterCycle/RemoteBMI.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/eWaterCycle/RemoteBMI.jl)
-[![DOI](https://zenodo.org/badge/DOI/FIXME)](https://doi.org/FIXME)
-[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
+<!-- TODO filter on Julia component
+[![Coverage](https://codecov.io/gh/eWaterCycle/RemoteBMI/branch/main/graph/badge.svg)](https://codecov.io/gh/eWaterCycle/RemoteBMI)
+-->
 
 ## Usage
 
@@ -35,7 +34,8 @@ BestieTemplate.generate("RemoteBMI.jl")
 The openapi server stubs where generated using the following command:
 
 ```shell
-wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.8.0/openapi-generator-cli-7.8.0.jar -O openapi-generator-cli.jar
+wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.9.0/openapi-generator-cli-7.9.0.jar -O openapi-generator-cli.jar
 java -jar ./openapi-generator-cli.jar  generate -i ./openapi.yaml  -g julia-server -o julia-server --additional-properties=packageName=BmiServer --additional-properties=exportModels=true
+java -jar ./openapi-generator-cli.jar  generate -i ./openapi.yaml  -g julia-client -o julia-client --additional-properties=packageName=BmiClient --additional-properties=exportModels=true
 # Copy the generated files to RemoteBMI.jl/src/
 ```

RemoteBMI.jl/docs/make.jl

@@ -4,34 +4,18 @@ using Documenter
 DocMeta.setdocmeta!(RemoteBMI, :DocTestSetup, :(using RemoteBMI); recursive = true)
 
 const page_rename = Dict("developer.md" => "Developer docs") # Without the numbers
-
-function nice_name(file)
-  file = replace(file, r"^[0-9]*-" => "")
-  if haskey(page_rename, file)
-    return page_rename[file]
-  end
-  return splitext(file)[1] |> x -> replace(x, "-" => " ") |> titlecase
-end
+const numbered_pages = [
+  file for
+  file in readdir(joinpath(@__DIR__, "src")) if file != "index.md" && splitext(file)[2] == ".md"
+]
 
 makedocs(;
   modules = [RemoteBMI],
-  doctest = true,
-  linkcheck = false, # Rely on Lint.yml/lychee for the links
-  authors = "Stefan Verhoeven <[email protected]> and contributors",
+  authors = "",
   repo = "https://github.com/eWaterCycle/RemoteBMI.jl/blob/{commit}{path}#{line}",
   sitename = "RemoteBMI.jl",
-  format = Documenter.HTML(;
-    prettyurls = true,
-    canonical = "https://eWaterCycle.github.io/RemoteBMI.jl",
-    assets = ["assets/style.css"],
-  ),
-  pages = [
-    "Home" => "index.md"
-    [
-      nice_name(file) => file for
-      file in readdir(joinpath(@__DIR__, "src")) if file != "index.md" && splitext(file)[2] == ".md"
-    ]
-  ],
+  format = Documenter.HTML(; canonical = "https://eWaterCycle.github.io/RemoteBMI.jl"),
+  pages = ["index.md"; numbered_pages],
 )
 
-deploydocs(; repo = "github.com/eWaterCycle/RemoteBMI.jl", push_preview = true)
+deploydocs(; repo = "github.com/eWaterCycle/RemoteBMI.jl")

RemoteBMI.jl/docs/src/91-developer.md

@@ -40,6 +40,10 @@ pkg> activate .
 pkg> test
 ```
 
+```shell
+julia -e 'using Pkg; Pkg.activate("."); Pkg.test()'
+```
+
 ## Working on a new issue
 
 We try to keep a linear history in this repo, so it is important to keep your branches up-to-date.
@@ -86,7 +90,6 @@ We try to keep a linear history in this repo, so it is important to keep your br
     Try to create "atomic git commits" (recommended reading: [The Utopic Git History](https://blog.esciencecenter.nl/the-utopic-git-history-d44b81c09593)).
 
 - Make sure the tests pass.
-
 - Fetch any `main` updates from upstream and rebase your branch, if necessary:
 
   ```bash

RemoteBMI.jl/docs/src/index.md

@@ -6,4 +6,3 @@ CurrentModule = RemoteBMI
 
 Documentation for [RemoteBMI](https://github.com/eWaterCycle/RemoteBMI.jl).
 
-

RemoteBMI.jl/example/README.md

@@ -44,12 +44,32 @@ client.get_var_grid('plate_surface__temperature')
 0
 client.get_grid_type(0)
 'uniform_rectilinear'
+client.get_grid_shape(0)
 dest = reserve_values(client, 'plate_surface__temperature')
 r = client.get_value('plate_surface__temperature', dest)
 r
 client.finalize()
 ```
 
+Interact using the Julia client.
+
+```julia
+# julia --project=$PWD/..
+import RemoteBMI.Client: BMIClient
+import BasicModelInterface as BMI
+model = BMIClient("http://localhost:50555")
+m = BMI.initialize(model, joinpath(pwd(), "heat.toml"))
+BMI.get_component_name(m)
+# "The 2D Heat Equation"
+BMI.get_grid_type(m, 0)
+# "uniform_rectilinear"
+BMI.get_grid_shape(m, 0)
+# {}
+BMI.get_grid_rank(m, 0)
+# 2
+BMI.get_grid_x(m, 0, [0.0, 0.0])
+```
+
 # Run Wflow.jl
 
 ```shell
@@ -81,9 +101,9 @@ download(toml_url, toml_path)
 
 # Run server
 using Wflow
-import RemoteBMI
+import RemoteBMI.Server: run_bmi_server
 port = parse(Int, get(ENV, "BMI_PORT", "50051"))
-RemoteBMI.run(Wflow.Model, "0.0.0.0", port)
+run_bmi_server(Wflow.Model, "0.0.0.0", port)
 ```
 
 Interact with it using the Python client.

RemoteBMI.jl/example/heat_bmi_server.jl

@@ -2,7 +2,7 @@
 # TODO include https://github.com/csdms/bmi-example-julia as test dependency 
 using Heat
 
-import RemoteBMI 
+import RemoteBMI.Server: run_bmi_server
 
 port = parse(Int, get(ENV, "BMI_PORT", "50051"))
-RemoteBMI.run(Heat.Model, "0.0.0.0", port)
+run_bmi_server(Heat.Model, "0.0.0.0", port)