From b97c2f404c6b7851a103ab1cdc6a02916cb0f915 Mon Sep 17 00:00:00 2001
From: Martijn Visser <mgvisser@gmail.com>
Date: Thu, 18 Nov 2021 17:09:01 +0100
Subject: [PATCH] add support for dir_input and dir_output

---
 docs/src/changelog.md     |  6 ++++++
 docs/src/config.md        | 20 ++++++++++--------
 src/hbv_model.jl          |  6 ++----
 src/io.jl                 | 43 +++++++++++++++++++++++++++------------
 src/reservoir_lake.jl     |  5 ++++-
 src/sbm_gwf_model.jl      |  6 ++----
 src/sbm_model.jl          |  6 ++----
 src/sediment_model.jl     |  5 ++---
 test/hbv_config.toml      | 12 +++++------
 test/io.jl                | 16 +++++++++++++--
 test/reservoir_lake.jl    |  6 +++---
 test/runtests.jl          |  5 +++--
 test/sbm_config.toml      | 16 ++++++++-------
 test/sbm_gw.toml          | 16 ++++++++-------
 test/sbm_gwf_config.toml  | 14 +++++++------
 test/sbm_simple.toml      |  8 +++++---
 test/sediment_config.toml | 14 +++++++------
 17 files changed, 124 insertions(+), 80 deletions(-)

diff --git a/docs/src/changelog.md b/docs/src/changelog.md
index ca152c9e6..ca97e89f9 100644
--- a/docs/src/changelog.md
+++ b/docs/src/changelog.md
@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Added
+- Optional `dir_input` and `dir_output` keys in the TOML, which can be used to quickly
+  change the path for all input or output files that are given as a relative path.
+
 ## v0.5.0 - 2021-11-12
 
 ### Changed
diff --git a/docs/src/config.md b/docs/src/config.md
index 0a2954c3a..5da906c84 100644
--- a/docs/src/config.md
+++ b/docs/src/config.md
@@ -2,7 +2,7 @@
 
 [TOML](https://github.com/toml-lang/toml) is used as the configuration format for models
 available in wflow. File paths included in the configuration TOML file are relative to the
-TOML file location.
+TOML file location, or to `dir_input` and `dir_output` if they are given.
 
 ## General time info
 Time information is optional. When left out, each time step in the forcing NetCDF will be
@@ -21,6 +21,8 @@ endtime = 2000-02-01T00:00:00                   # optional, default from forcing
 starttime = 2000-01-01T00:00:00                 # optional, default from forcing NetCDF
 time_units = "days since 1900-01-01 00:00:00"   # optional, this is default value
 timestepsecs = 86400                            # optional, default from forcing NetCDF
+dir_input = "data/input"                        # optional, default is the path of the TOML
+dir_output = "data/output"                      # optional, default is the path of the TOML
 ```
 
 ## Model section
@@ -53,8 +55,8 @@ the entire `state` section can be left out.
 
 ```toml
 [state]
-path_input = "data/instates-moselle.nc" 
-path_output = "data/outstates-moselle.nc"
+path_input = "instates-moselle.nc" 
+path_output = "outstates-moselle.nc"
 
 [state.vertical]
 satwaterdepth = "satwaterdepth"
@@ -95,9 +97,9 @@ mapped a default value will be used if available.
 
 ```toml
 [input]
-# use "data/forcing-year-*.nc" if forcing files are split in time
-path_forcing = "data/forcing-moselle.nc"
-path_static = "data/staticmaps-moselle.nc"
+# use "forcing-year-*.nc" if forcing files are split in time
+path_forcing = "forcing-moselle.nc"
+path_static = "staticmaps-moselle.nc"
 
 # these are not directly part of the model
 gauges = "wflow_gauges"
@@ -180,7 +182,7 @@ netCDF variables.
 
 ```toml
 [output]
-path = "data/output_moselle.nc"
+path = "output_moselle.nc"
 
 [output.vertical]
 satwaterdepth = "satwaterdepth"
@@ -220,7 +222,7 @@ Delft-FEWS can ingest this data format directly.
 
 ```toml
 [netcdf]
-path = "data/output_scalar_moselle.nc"
+path = "output_scalar_moselle.nc"
 
 [[netcdf.variable]]
 name = "Q"
@@ -268,7 +270,7 @@ list. You may specify as many entries as you wish.
 
 ```toml
 [csv]
-path = "data/output_moselle.csv"
+path = "output_moselle.csv"
 
 [[csv.column]]
 header = "Q"
diff --git a/src/hbv_model.jl b/src/hbv_model.jl
index af23097dc..4e5fbe5c1 100644
--- a/src/hbv_model.jl
+++ b/src/hbv_model.jl
@@ -6,8 +6,7 @@ Config object. Will return a Model that is ready to run.
 """
 function initialize_hbv_model(config::Config)
     # unpack the paths to the NetCDF files
-    tomldir = dirname(config)
-    static_path = joinpath(tomldir, config.input.path_static)
+    static_path = input_path(config, config.input.path_static)
 
     reader = prepare_reader(config)
     clock = Clock(config, reader)
@@ -357,7 +356,6 @@ function initialize_hbv_model(config::Config)
     if do_lakes
         lakes, lakeindex, lake, pits = initialize_natural_lake(
             config,
-            static_path,
             nc,
             inds_riv,
             nriv,
@@ -560,7 +558,7 @@ function initialize_hbv_model(config::Config)
 
     # read and set states in model object if reinit=true
     if reinit == false
-        instate_path = joinpath(tomldir, config.state.path_input)
+        instate_path = input_path(config, config.state.path_input)
         state_ncnames = ncnames(config.state)
         set_states(instate_path, model, state_ncnames; type = Float)
         # update kinematic wave volume for river and land domain
diff --git a/src/io.jl b/src/io.jl
index 167c24abb..89f8506d8 100644
--- a/src/io.jl
+++ b/src/io.jl
@@ -81,6 +81,23 @@ Base.dirname(config::Config) = dirname(pathof(config))
 Base.iterate(config::Config) = iterate(Dict(config))
 Base.iterate(config::Config, state) = iterate(Dict(config), state)
 
+function combined_path(config::Config, dir::AbstractString, path::AbstractString)
+    tomldir = dirname(config)
+    return normpath(tomldir, dir, path)
+end
+
+"Construct a path relative to both the TOML directory and the optional `dir_input`"
+function input_path(config::Config, path::AbstractString)
+    dir = get(config, "dir_input", ".")
+    return combined_path(config, dir, path)
+end
+
+"Construct a path relative to both the TOML directory and the optional `dir_output`"
+function output_path(config::Config, path::AbstractString)
+    dir = get(config, "dir_output", ".")
+    return combined_path(config, dir, path)
+end
+
 "Extract NetCDF variable name `ncname` from `var` (type `String` or `Config`). If `var` has 
 type `Config`, either `scale` and `offset` are expected (with `ncname`) or a `value` (uniform
 value), these are stored as part of `NamedTuple` `modifier`"
@@ -336,13 +353,13 @@ end
 
 "prepare an output dataset for scalar data"
 function setup_scalar_netcdf(
-    output_path,
+    path,
     ncvars,
     calendar,
     time_units,
     float_type = Float32,
 )
-    ds = create_tracked_netcdf(output_path)
+    ds = create_tracked_netcdf(path)
     defDim(ds, "time", Inf)  # unlimited
     defVar(
         ds,
@@ -374,7 +391,7 @@ end
 
 "prepare an output dataset for grid data"
 function setup_grid_netcdf(
-    output_path,
+    path,
     ncx,
     ncy,
     parameters,
@@ -385,7 +402,7 @@ function setup_grid_netcdf(
     float_type = Float32,
 )
 
-    ds = create_tracked_netcdf(output_path)
+    ds = create_tracked_netcdf(path)
     defDim(ds, "time", Inf)  # unlimited
     if sizeinmetres
         defVar(
@@ -537,18 +554,19 @@ struct Writer
 end
 
 function prepare_reader(config)
-    tomldir = dirname(config)
     path_forcing = config.input.path_forcing
-    cyclic_path = joinpath(tomldir, config.input.path_static)
+    cyclic_path = input_path(config, config.input.path_static)
 
     # absolute paths are not supported, see Glob.jl#2
     if isabspath(path_forcing)
         parts = splitpath(path_forcing)
         # use the root/drive as the dir, to support * in directory names as well
         glob_dir = parts[1]
-        glob_path = joinpath(parts[2:end])
+        glob_path = normpath(parts[2:end])
     else
-        glob_dir = tomldir
+        tomldir = dirname(config)
+        dir_input = get(config, "dir_input", ".")
+        glob_dir = normpath(tomldir, dir_input)
         glob_path = path_forcing
     end
 
@@ -773,7 +791,6 @@ function prepare_writer(
     nc_static;
     maxlayers = nothing,
 )
-    tomldir = dirname(config)
     sizeinmetres = get(config.model, "sizeinmetres", false)::Bool
 
     calendar = get(config, "calendar", "standard")::String
@@ -782,7 +799,7 @@ function prepare_writer(
     # create an output NetCDF that will hold all timesteps of selected parameters for grid
     # data but only if config.output.path has been set
     if haskey(config, "output") && haskey(config.output, "path")
-        nc_path = joinpath(tomldir, config.output.path)
+        nc_path = output_path(config, config.output.path)
         # create a flat mapping from internal parameter locations to NetCDF variable names
         output_ncnames = ncnames(config.output)
         # fill the output_map by mapping parameter NetCDF names to arrays
@@ -808,7 +825,7 @@ function prepare_writer(
     if haskey(config, "state") && haskey(config.state, "path_output")
         state_ncnames = ncnames(config.state)
         state_map = out_map(state_ncnames, modelmap)
-        nc_state_path = joinpath(tomldir, config.state.path_output)
+        nc_state_path = output_path(config, config.state.path_output)
         ds_outstate = setup_grid_netcdf(
             nc_state_path,
             x_nc,
@@ -829,7 +846,7 @@ function prepare_writer(
     # create an output NetCDF that will hold all timesteps of selected parameters for scalar
     # data, but only if config.netcdf.variable has been set. 
     if haskey(config, "netcdf") && haskey(config.netcdf, "variable")
-        nc_scalar_path = joinpath(tomldir, config.netcdf.path)
+        nc_scalar_path = output_path(config, config.netcdf.path)
         # get NetCDF info for scalar data (variable name, locationset (dim) and 
         # location ids)
         ncvars_dims = nc_variables_dims(config.netcdf.variable, nc_static, config)
@@ -851,7 +868,7 @@ function prepare_writer(
 
     if haskey(config, "csv") && haskey(config.csv, "column")
         # open CSV file and write header
-        csv_path = joinpath(tomldir, config.csv.path)
+        csv_path = output_path(config, config.csv.path)
         # create directory if needed
         mkpath(dirname(csv_path))
         csv_io = open(csv_path, "w")
diff --git a/src/reservoir_lake.jl b/src/reservoir_lake.jl
index cde38c6b4..b10705512 100644
--- a/src/reservoir_lake.jl
+++ b/src/reservoir_lake.jl
@@ -211,7 +211,7 @@ end
     end
 end
 
-function initialize_natural_lake(config, path, nc, inds_riv, nriv, pits, Δt)
+function initialize_natural_lake(config, nc, inds_riv, nriv, pits, Δt)
     # read only lake data if lakes true
     # allow lakes only in river cells
     # note that these locations are only the lake outlet pixels
@@ -318,6 +318,9 @@ function initialize_natural_lake(config, path, nc, inds_riv, nriv, pits, Δt)
     sh = Vector{Union{SH,Missing}}(missing, n_lakes)
     hq = Vector{Union{HQ,Missing}}(missing, n_lakes)
     lowerlake_ind = fill(0, n_lakes)
+    # lake CSV parameter files are expected in the same directory as path_static
+    path = dirname(input_path(config, config.input.path_static))
+
     for i = 1:n_lakes
         lakeloc = lakelocs[i]
         if linked_lakelocs[i] > 0
diff --git a/src/sbm_gwf_model.jl b/src/sbm_gwf_model.jl
index ea4e3b5ef..71ca114ac 100644
--- a/src/sbm_gwf_model.jl
+++ b/src/sbm_gwf_model.jl
@@ -16,8 +16,7 @@ Will return a Model that is ready to run.
 function initialize_sbm_gwf_model(config::Config)
 
     # unpack the paths to the NetCDF files
-    tomldir = dirname(config)
-    static_path = joinpath(tomldir, config.input.path_static)
+    static_path = input_path(config, config.input.path_static)
 
     reader = prepare_reader(config)
     clock = Clock(config, reader)
@@ -80,7 +79,6 @@ function initialize_sbm_gwf_model(config::Config)
     if do_lakes
         lakes, lakeindex, lake, pits = initialize_natural_lake(
             config,
-            dirname(static_path),
             nc,
             inds_riv,
             nriv,
@@ -443,7 +441,7 @@ function initialize_sbm_gwf_model(config::Config)
 
     # read and set states in model object if reinit=false
     if reinit == false
-        instate_path = joinpath(tomldir, config.state.path_input)
+        instate_path = input_path(config, config.state.path_input)
         state_ncnames = ncnames(config.state)
         set_states(instate_path, model, state_ncnames, type = Float)
         # update kinematic wave volume for river and land domain
diff --git a/src/sbm_model.jl b/src/sbm_model.jl
index e45cbedec..6b10bf3bb 100644
--- a/src/sbm_model.jl
+++ b/src/sbm_model.jl
@@ -7,8 +7,7 @@ Config object. Will return a Model that is ready to run.
 function initialize_sbm_model(config::Config)
 
     # unpack the paths to the NetCDF files
-    tomldir = dirname(config)
-    static_path = joinpath(tomldir, config.input.path_static)
+    static_path = input_path(config, config.input.path_static)
 
     reader = prepare_reader(config)
     clock = Clock(config, reader)
@@ -68,7 +67,6 @@ function initialize_sbm_model(config::Config)
     if do_lakes
         lakes, lakeindex, lake, pits = initialize_natural_lake(
             config,
-            dirname(static_path),
             nc,
             inds_riv,
             nriv,
@@ -332,7 +330,7 @@ function initialize_sbm_model(config::Config)
 
     # read and set states in model object if reinit=false
     if reinit == false
-        instate_path = joinpath(tomldir, config.state.path_input)
+        instate_path = input_path(config, config.state.path_input)
         state_ncnames = ncnames(config.state)
         set_states(instate_path, model, state_ncnames; type = Float)
         @unpack lateral, vertical = model
diff --git a/src/sediment_model.jl b/src/sediment_model.jl
index 745c797df..89c829cfa 100644
--- a/src/sediment_model.jl
+++ b/src/sediment_model.jl
@@ -7,8 +7,7 @@ Config object. Will return a Model that is ready to run.
 function initialize_sediment_model(config::Config)
 
     # unpack the paths to the NetCDF files
-    tomldir = dirname(config)
-    static_path = joinpath(tomldir, config.input.path_static)
+    static_path = input_path(config, config.input.path_static)
 
     reader = prepare_reader(config)
     clock = Clock(config, reader)
@@ -143,7 +142,7 @@ function initialize_sediment_model(config::Config)
 
     # read and set states in model object if reinit=false
     if reinit == false
-        instate_path = joinpath(tomldir, config.state.path_input)
+        instate_path = input_path(config, config.state.path_input)
         state_ncnames = ncnames(config.state)
         set_states(instate_path, model, state_ncnames; type = Float)
     end
diff --git a/test/hbv_config.toml b/test/hbv_config.toml
index a60e10198..7edece2dd 100644
--- a/test/hbv_config.toml
+++ b/test/hbv_config.toml
@@ -10,8 +10,8 @@ time_units = "days since 1900-01-01 00:00:00"
 timestepsecs = 86400
 
 [state]
-path_input = "data/instates-lahn.nc"
-path_output = "data/outstates-lahn.nc"
+path_input = "data/input/instates-lahn.nc"
+path_output = "data/output/outstates-lahn.nc"
 
 # if listed, the variable must be present in the NetCDF or error
 # if not listed, the variable can get a default value if it has one
@@ -33,8 +33,8 @@ h = "h_land"
 q = "q_land"
 
 [input]
-path_forcing = "data/forcing-lahn.nc"
-path_static = "data/staticmaps-lahn.nc"
+path_forcing = "data/input/forcing-lahn.nc"
+path_static = "data/input/staticmaps-lahn.nc"
 
 # these are not directly part of the model
 gauges = "wflow_gauges"
@@ -93,7 +93,7 @@ snow = true
 type = "hbv"
 
 [output]
-path = "data/output_lahn.nc"
+path = "data/output/output_lahn.nc"
 
 [output.vertical]
 lowerzonestorage = "lowerzonestorage"
@@ -106,7 +106,7 @@ upperzonestorage = "upperzonestorage"
 q = "q"
 
 [csv]
-path = "data/output_lahn.csv"
+path = "data/output/output_lahn.csv"
 
 [[csv.column]]
 header = "Q"
diff --git a/test/io.jl b/test/io.jl
index cfc3c81ea..aae8d2826 100644
--- a/test/io.jl
+++ b/test/io.jl
@@ -19,7 +19,7 @@ config = Wflow.Config(tomlpath)
     # test if the values are parsed as expected
     @test config.starttime === DateTime(2000)
     @test config.endtime === DateTime(2000, 2)
-    @test config.output.path == "data/output_moselle.nc"
+    @test config.output.path == "output_moselle.nc"
     @test config.output isa Wflow.Config
     @test collect(keys(config.output)) == ["lateral", "vertical", "path"]
 
@@ -37,13 +37,25 @@ config = Wflow.Config(tomlpath)
     @test modifier.scale == 1.0
     @test modifier.offset == 0.0
     @test modifier.value === nothing
+
+    # test the optional "dir_input" and "dir_output" keys
+    @test haskey(config, "dir_input")
+    @test haskey(config, "dir_output")
+    @test Wflow.input_path(config, config.state.path_input) == joinpath(@__DIR__, "data", "input", "instates-moselle.nc")
+    @test Wflow.output_path(config, config.state.path_output) == joinpath(@__DIR__, "data", "output", "outstates-moselle.nc")
+    # hbv_config doesn't use dir_input and dir_output
+    hbv_config = Wflow.Config(joinpath(@__DIR__, "hbv_config.toml"))
+    @test !haskey(hbv_config, "dir_input")
+    @test !haskey(hbv_config, "dir_output")
+    @test Wflow.input_path(hbv_config, hbv_config.state.path_input) == joinpath(@__DIR__, "data", "input", "instates-lahn.nc")
+    @test Wflow.output_path(hbv_config, hbv_config.state.path_output) == joinpath(@__DIR__, "data", "output", "outstates-lahn.nc")
 end
 
 @testset "Clock constructor" begin
     config = Wflow.Config(tomlpath)
 
     # mock a NCReader object
-    ncpath = joinpath(dirname(pathof(config)), config.input.path_forcing)
+    ncpath = Wflow.input_path(config, config.input.path_forcing)
     ds = NCDataset(ncpath)
     reader = (; dataset = ds)
 
diff --git a/test/reservoir_lake.jl b/test/reservoir_lake.jl
index 103141f51..9087b5b0b 100644
--- a/test/reservoir_lake.jl
+++ b/test/reservoir_lake.jl
@@ -59,8 +59,8 @@ end
 
 datadir = joinpath(@__DIR__, "data")
 sh = [
-    Wflow.read_sh_csv(joinpath(datadir, "lake_sh_1.csv")),
-    Wflow.read_sh_csv(joinpath(datadir, "lake_sh_2.csv")),
+    Wflow.read_sh_csv(joinpath(datadir, "input", "lake_sh_1.csv")),
+    Wflow.read_sh_csv(joinpath(datadir, "input", "lake_sh_2.csv")),
 ]
 @testset "linked lakes (HBV)" begin
     @test keys(sh[1]) == (:H, :S)
@@ -78,7 +78,7 @@ sh = [
         b = [140.0, 0.0],
         e = [1.5, 1.5],
         sh = sh,
-        hq = [missing, Wflow.read_hq_csv(joinpath(datadir, "lake_hq_2.csv"))],
+        hq = [missing, Wflow.read_hq_csv(joinpath(datadir, "input", "lake_hq_2.csv"))],
         waterlevel = [395.03027, 394.87833],
         precipitation = [10.0, 10.0],
         evaporation = [2.0, 2.0],
diff --git a/test/runtests.jl b/test/runtests.jl
index 7343a1484..e6746dc72 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -21,11 +21,12 @@ const Float = Wflow.Float
 # ensure test data is present
 testdir = @__DIR__
 datadir = joinpath(testdir, "data")
-isdir(datadir) || mkdir(datadir)
+inputdir = joinpath(datadir, "input")
+isdir(inputdir) || mkpath(inputdir)
 
 "Download a test data file if it does not already exist"
 function testdata(version, source_filename, target_filename)
-    target_path = joinpath(datadir, target_filename)
+    target_path = joinpath(inputdir, target_filename)
     base_url = "https://github.com/visr/wflow-artifacts/releases/download"
     url = string(base_url, '/', string('v', version), '/', source_filename)
     isfile(target_path) || Downloads.download(url, target_path)
diff --git a/test/sbm_config.toml b/test/sbm_config.toml
index 9007c52eb..7e776dc90 100644
--- a/test/sbm_config.toml
+++ b/test/sbm_config.toml
@@ -8,10 +8,12 @@ endtime = 2000-02-01T00:00:00
 starttime = 2000-01-01T00:00:00
 time_units = "days since 1900-01-01 00:00:00"
 timestepsecs = 86400
+dir_input = "data/input"
+dir_output = "data/output"
 
 [state]
-path_input = "data/instates-moselle.nc"
-path_output = "data/outstates-moselle.nc"
+path_input = "instates-moselle.nc"
+path_output = "outstates-moselle.nc"
 
 # if listed, the variable must be present in the NetCDF or error
 # if not listed, the variable can get a default value if it has one
@@ -41,8 +43,8 @@ h_av = "h_av_land"
 q = "q_land"
 
 [input]
-path_forcing = "data/forcing-moselle.nc"
-path_static = "data/staticmaps-moselle.nc"
+path_forcing = "forcing-moselle.nc"
+path_static = "staticmaps-moselle.nc"
 
 # these are not directly part of the model
 gauges = "wflow_gauges"
@@ -127,7 +129,7 @@ type = "sbm"
 min_streamorder = 3
 
 [output]
-path = "data/output_moselle.nc"
+path = "output_moselle.nc"
 
 [output.vertical]
 canopystorage = "canopystorage"
@@ -152,7 +154,7 @@ h = "h_land"
 q = "q_land"
 
 [netcdf]
-path = "data/output_scalar_moselle.nc"
+path = "output_scalar_moselle.nc"
 
 [[netcdf.variable]]
 name = "Q"
@@ -174,7 +176,7 @@ index.y = 264
 parameter = "vertical.temperature"
 
 [csv]
-path = "data/output_moselle.csv"
+path = "output_moselle.csv"
 
 [[csv.column]]
 header = "Q"
diff --git a/test/sbm_gw.toml b/test/sbm_gw.toml
index 861a0a66a..da4c7b56e 100644
--- a/test/sbm_gw.toml
+++ b/test/sbm_gw.toml
@@ -8,10 +8,12 @@ endtime = 2000-02-01T00:00:00
 starttime = 2000-01-01T00:00:00
 time_units = "days since 1900-01-01 00:00:00"
 timestepsecs = 86400
+dir_input = "data/input"
+dir_output = "data/output"
 
 [state]
-path_input = "data/instates-moselle.nc"
-path_output = "data/outstates-moselle.nc"
+path_input = "instates-moselle.nc"
+path_output = "outstates-moselle.nc"
 
 # if listed, the variable must be present in the NetCDF or error
 # if not listed, the variable can get a default value if it has one
@@ -38,8 +40,8 @@ h_av = "h_av_land"
 q = "q_land"
 
 [input]
-path_forcing = "data/forcing-moselle.nc"
-path_static = "data/staticmaps-moselle.nc"
+path_forcing = "forcing-moselle.nc"
+path_static = "staticmaps-moselle.nc"
 
 # these are not directly part of the model
 gauges = "wflow_gauges"
@@ -116,7 +118,7 @@ thicknesslayers = [100, 300, 800]
 type = "sbm"
 
 [output]
-path = "data/output_moselle.nc"
+path = "output_moselle.nc"
 
 [output.vertical]
 canopystorage = "canopystorage"
@@ -138,7 +140,7 @@ h = "h_land"
 q = "q_land"
 
 [netcdf]
-path = "data/output_scalar_moselle.nc"
+path = "output_scalar_moselle.nc"
 
 [[netcdf.variable]]
 name = "Q"
@@ -160,7 +162,7 @@ index.y = 264
 parameter = "vertical.temperature"
 
 [csv]
-path = "data/output_moselle.csv"
+path = "output_moselle.csv"
 
 [[csv.column]]
 header = "Q"
diff --git a/test/sbm_gwf_config.toml b/test/sbm_gwf_config.toml
index 94726d38e..f7b2155aa 100644
--- a/test/sbm_gwf_config.toml
+++ b/test/sbm_gwf_config.toml
@@ -8,10 +8,12 @@ endtime = 2000-06-30T00:00:00
 starttime = 2000-06-01T00:00:00
 time_units = "days since 1900-01-01 00:00:00"
 timestepsecs = 86400
+dir_input = "data/input"
+dir_output = "data/output"
 
 [state]
-path_input = "data/instates-example-sbm-gwf.nc"
-path_output = "data/outstates-example-sbm-gwf.nc"
+path_input = "instates-example-sbm-gwf.nc"
+path_output = "outstates-example-sbm-gwf.nc"
 
 # if listed, the variable must be present in the NetCDF or error
 # if not listed, the variable can get a default value if it has one
@@ -33,8 +35,8 @@ q = "q_land"
 head = "head"
 
 [input]
-path_forcing = "data/forcing-sbm-groundwater-part*.nc"
-path_static = "data/staticmaps-sbm-groundwater.nc"
+path_forcing = "forcing-sbm-groundwater-part*.nc"
+path_static = "staticmaps-sbm-groundwater.nc"
 
 # these are not directly part of the model
 ldd = "wflow_ldd"
@@ -96,7 +98,7 @@ thicknesslayers = [100, 300, 800]
 type = "sbm_gwf"
 
 [output]
-path = "data/output_example-sbm-gwf.nc"
+path = "output_example-sbm-gwf.nc"
 
 [output.vertical]
 canopystorage = "canopystorage"
@@ -120,7 +122,7 @@ flux = "drain_flux"
 flux = "flux"
 
 [csv]
-path = "data/output_example-sbm-gwf.csv"
+path = "output_example-sbm-gwf.csv"
 
 [[csv.column]]
 header = "Q_av"
diff --git a/test/sbm_simple.toml b/test/sbm_simple.toml
index 60d30bb45..33170cda5 100644
--- a/test/sbm_simple.toml
+++ b/test/sbm_simple.toml
@@ -4,10 +4,12 @@
 # TOML documentation: https://github.com/toml-lang/toml
 
 endtime = 2000-01-10T00:00:00
+dir_input = "data/input"
+dir_output = "data/output"
 
 [input]
-path_forcing = "data/forcing-moselle.nc"
-path_static = "data/staticmaps-moselle.nc"
+path_forcing = "forcing-moselle.nc"
+path_static = "staticmaps-moselle.nc"
 
 # these are not directly part of the model
 ldd = "wflow_ldd"
@@ -84,7 +86,7 @@ thicknesslayers = [100, 300, 800]
 type = "sbm"
 
 [csv]
-path = "data/output_moselle_simple.csv"
+path = "output_moselle_simple.csv"
 
 [[csv.column]]
 coordinate.x = 7.378
diff --git a/test/sediment_config.toml b/test/sediment_config.toml
index 8c2f10e3c..18e2920b8 100644
--- a/test/sediment_config.toml
+++ b/test/sediment_config.toml
@@ -8,10 +8,12 @@ endtime = 2000-01-03T00:00:00
 starttime = 2000-01-01T00:00:00
 time_units = "days since 1900-01-01 00:00:00"
 timestepsecs = 86400
+dir_input = "data/input"
+dir_output = "data/output"
 
 [state]
-path_input = "data/instates-moselle-sed.nc"
-path_output = "data/outstates-moselle-sed.nc"
+path_input = "instates-moselle-sed.nc"
+path_output = "outstates-moselle-sed.nc"
 
 # if listed, the variable must be present in the NetCDF or error
 # if not listed, the variable can get a default value if it has one
@@ -37,8 +39,8 @@ siltload = "siltload"
 siltstore = "siltstore"
 
 [input]
-path_forcing = "data/forcing-moselle-sed.nc"
-path_static = "data/staticmaps-moselle-sed.nc"
+path_forcing = "forcing-moselle-sed.nc"
+path_static = "staticmaps-moselle-sed.nc"
 
 # these are not directly part of the model
 gauges = "wflow_gauges"
@@ -123,7 +125,7 @@ runrivermodel = true
 type = "sediment" 
 
 [output]
-path = "data/output-moselle-sed.nc"
+path = "output-moselle-sed.nc"
 
 [output.vertical]
 TCclay = "TCclay"
@@ -152,7 +154,7 @@ outclay = "outclay"
 width = "widthriv"
 
 [csv]
-path = "data/output-moselle-sediment.csv"
+path = "output-moselle-sediment.csv"
 
 [[csv.column]]
 coordinate.x = 6.931