diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index e55e004..2782578 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -19,7 +19,6 @@ jobs: version: - '1' - '1.6' - #- '^1.7.0-0' os: - ubuntu-latest arch: diff --git a/.gitignore b/.gitignore index cb7d064..668fce5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,8 @@ *.jl.*.cov *.jl.cov *.jl.mem -/Manifest.toml +/Manifest*.toml /docs/build/ /tmp -docs/Manifest.toml -test/Manifest.toml +docs/Manifest*.toml +test/Manifest*.toml diff --git a/.typos.toml b/.typos.toml index 209fa8e..438e694 100644 --- a/.typos.toml +++ b/.typos.toml @@ -4,4 +4,6 @@ SOM = "SOM" som = "som" tha = "tha" Tha = "Tha" +Gam = "Gam" + diff --git a/Project.toml b/Project.toml index ab4a5cf..cd2fc31 100644 --- a/Project.toml +++ b/Project.toml @@ -41,8 +41,5 @@ Tables = "1.6.0" TimeZones = "1.6.1" julia = "1.6" -[extras] -Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[targets] -test = ["Test"] +[workspace] +projects = ["test", "docs"] diff --git a/inst/walkthrough_todo.jmd b/inst/walkthrough_todo.jmd index 1651301..ec0359d 100644 --- a/inst/walkthrough_todo.jmd +++ b/inst/walkthrough_todo.jmd @@ -270,7 +270,7 @@ g1_USO = stomatal_slope(thaf,model="USO",g0=0,robust_nls=true) g1_USO ``` -In this case, we have estimated $g_1$ from the USO (optimal stomatal optimization) model as described in Medlyn et al. 2011. The output is a model object that prints the model formulat that is used to estimate $g_1$, the estimated parameter value(s), as well as the weighted residual sum-of-squares. Further information on this model object can be obtained using the `summary` function. +In this case, we have estimated $g_1$ from the USO (optimal stomatal optimization) model as described in Medlyn et al. 2011. The output is a model object that prints the model formula that is used to estimate $g_1$, the estimated parameter value(s), as well as the weighted residual sum-of-squares. Further information on this model object can be obtained using the `summary` function. In this case we have fixed the model intercept $g_0$ to 0 (this could also be any other value). We can also try to estimate $g_1$ and $g_0$ simultaneously (if we add `fitg0=true` to the function call above), but note that the two parameters are usually correlated, and that the values of $g_0$ are not straightforward to interpret (especially at ecosystem level). The option `robust_nls=true` specifies that $g_1$ is determined by a robust non-linear regression routine (from the `robustbase` package). We recommend to use this option since otherwise the parameter estimates are sensitive to outliers in $G_s$, which often occur even in filtered EC datasets. By default, the model takes VPD and atmospheric CO$_2$ concentration as measured at the tower as input. We can also calculate $g_1$ by taking the surface conditions, which are probably more relevant for plant physiological processes than those measured a certain distance above the canopy: diff --git a/test/runtests.jl b/test/runtests.jl index 5242839..055b47d 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -29,6 +29,8 @@ const GROUP = get(ENV, "GROUP", "All") # defined in in CI.yml @time @safetestset "surface_conductance Tests" include("surface_conductance_test.jl") #@safetestset "Tests" include("test/evapotranspiration_test.jl") @time @safetestset "evapotranspiration Tests" include("evapotranspiration_test.jl") + #@safetestset "Tests" include("test/undoc_test.jl") + @time @safetestset "undocumented objects" include("undoc_test.jl") end end diff --git a/test/undoc_test.jl b/test/undoc_test.jl new file mode 100644 index 0000000..b5edefa --- /dev/null +++ b/test/undoc_test.jl @@ -0,0 +1,12 @@ +using Bigleaf +using Test + +@testset "Docstrings" begin + if VERSION >= v"1.11" + @test_broken isempty(Docs.undocumented_names(Bigleaf)) + end + #undoc = Docs.undocumented_names(Bigleaf) + #@test_broken undoc == [] + #@test undoc = [:bar, :baz] + #@test undoc = [] +end