Clean up docs

docs/src/datahandling.md

@@ -1,4 +1,4 @@
-# `DataHandling`
+# [`DataHandling`](@id datahandling_module)
 
 The `DataHandling` module is responsible for reading data from files and
 resampling it onto the simulation grid.
@@ -11,7 +11,7 @@ This is no trivial task. Among the challenges:
 
 The `DataHandling` takes the divide-and-conquer approach: the various core tasks
 and features and split into other independent modules (chiefly
-[`FileReaders`](@ref), and [`Regridders`](@ref)). Such modules can be developed,
+[`FileReaders`](@ref file_reader_module), and [`Regridders`](@ref regridder_module) regridder_module). Such modules can be developed,
 tested, and extended independently (as long as they maintain a consistent
 interface). For instance, if need arises, the `DataHandler` can be used (almost)
 directly to process files with a different format from NetCDF.
@@ -47,7 +47,7 @@ the `NCFileReader`.
 
 > This extension is loaded when loading `ClimaCore` and `NCDatasets` are loaded.
 > In addition to this, a `Regridder` is needed (which might require importing
-> additional packages) - see [`Regridders`](@ref) for more information.
+> additional packages) - see [`Regridders`](@ref regridder_module) for more information.
 
 It is possible to pass down keyword arguments to underlying constructors in
 `DataHandler` with the `regridder_kwargs` and `file_reader_kwargs`. These have
@@ -65,28 +65,28 @@ Note that, if a non-identity pre-processing function is provided as part of
 `file_reader_kwargs`, it will be applied to each input variable before they
 are composed.
 Composing multiple input variables is currently only supported with the
-`InterpolationsRegridder`, not with `TempestRegridder`.
+[`InterpolationsRegridder`](@ref interp_regridder), not with [`TempestRegridder`](@ref tempest_regridder).
 
 Sometimes, the time development of a variable is split across multiple NetCDF
 files. `DataHandler` knows how to combine them and treat multiple files as if
 they were a single one. To use this feature, just pass the list of NetCDF files
 (while the file don't have to be sorted, it is good practice to pass them sorted
-in ascending order by time). 
+in ascending order by time).
 
 #### Heuristics to do-what-you-mean
 
 `DataHandler` tries to interpret the files provided and identify if they are
 split across variables or along the time dimension. The heuristics implement are
 the following:
-- When just a file is passed, it is assumed that it contains everything 
+- When just a file is passed, it is assumed that it contains everything
 - When multiple files are passed, `DataHandler` will assume that the files are
   split along variables if the number of files is the same the number of
   variables, otherwise, it will assume that each file contains all the variables
   for a portion of the total time.
 - When the above assumption is incorrect, you can pass a list of list of files
   that fully specifies variables and times.
 
-For example, 
+For example,
 ```julia
 data_handler = DataHandling.DataHandler(
     ["era1980.nc", "era1981.nc"],
@@ -98,9 +98,9 @@ data_handler = DataHandling.DataHandler(
 
 In this case, `DataHandler` will incorrectly assume that `lai_hv` is contained
 in `era1980.nc`, and `lai_lv` is in `era1980.nc`. Instead, construct the
-`data_handler` by passing a list of lists 
+`data_handler` by passing a list of lists
 ```julia
-files = ["era1980.nc", "era1981.nc"] 
+files = ["era1980.nc", "era1981.nc"]
 data_handler = DataHandling.DataHandler(
     [files, files],
     ["lai_hv", "lai_lv"],
@@ -163,7 +163,7 @@ file path), which knows how to combine them.
 Suppose that the input NetCDF file `era5_example.nc` contains two variables `u`
 and `v`, and we care about their sum `u + v` but not their individual values.
 We can provide a pointwise composing function to perform the sum, along with
-the `InterpolationsRegridder` to produce the data we want, `u + v`.
+the [`InterpolationsRegridder`](@ref interp_regridder) to produce the data we want, `u + v`.
 The `preprocess_func` passed in `file_reader_kwargs` will be applied to `u`
 and to `v` individually, before the composing function is applied. The regridding
 is applied after the composing function. `u` and `v` could also come from separate

docs/src/faqs.md

@@ -2,9 +2,9 @@
 
 ## Is it possible to preprocess the data in `TimeVaryingInput` or `SpaceVaryingInput`, for instance, to remove NaNs or change units?
 
-Yes, [`TimeVaryingInput`](@ref) and [`SpaceVaryingInput`](@ref) support this
-feature. [`TimeVaryingInput`](@ref) and [`SpaceVaryingInput`](@ref) that read
-NetCDF files use [`NCFileReader`](@ref) under the hood. `NCFileReader`s can be
+Yes, [`TimeVaryingInput`](@ref timevaryinginput) and [`SpaceVaryingInput`](@ref spacevaryinginput) support this
+feature. [`TimeVaryingInput`](@ref timevaryinginput) and [`SpaceVaryingInput`](@ref spacevaryinginput) that read
+NetCDF files use [`NCFileReader`](@ref ncfilereaders) under the hood. `NCFileReader`s can be
 constructed with an optional keyword argument `preprocess_func`, a pointwise
 function that transforms the data read into something else. `Input`s can be
 constructed to pass down this keyword argument. Let us have a look at an

docs/src/filereaders.md

@@ -1,4 +1,4 @@
-# `FileReaders`
+# [`FileReaders`](@id file_reader_module)
 
 Reading files is a common need for most scientific projects. This can come with
 a series of problems that have to be solved, from performance (accessing can be
@@ -14,7 +14,7 @@ Future extensions might include:
 - doing chunked reads;
 - async reads.
 
-## `NCFileReaders`
+## [`NCFileReaders`](@id ncfilereaders)
 
 > This extension is loaded when loading `NCDatasets`
 

docs/src/index.md

@@ -38,7 +38,7 @@ is mostly and interface barrier to provide a path for future improvements.
 ### `Regridders`
 
 `ClimaUtilities` comes with two modules to map rectangular grids two (extruded)
-finite spectral elements, `InterpolationsRegridder` and `TempestRegridder`.
+finite spectral elements, `InterpolationsRegridder` and [`TempestRegridder`](@ref tempest_regridder).
 These modules are primarily used to ingest data and resample it onto the
 computational grid.
 

docs/src/inputs.md

@@ -6,7 +6,7 @@ describes the types of plants on the surface of the globe. The
 `SpaceVaringInputs` and `TimeVaryingInputs` modules provide a unified
 infrastructure to handle all these cases.
 
-## `TimeVaryingInputs`
+## [`TimeVaryingInputs`](@id timevaryinginput)
 
 > This extension is loaded when loading `ClimaCore` is loaded. In addition to
 > this, if NetCDF files are used, `NCDatasets` has to be loaded too. Finally, a
@@ -21,9 +21,9 @@ developers to update their `Field`s.
 This example shows that `TimeVaryingInput` can take different types of inputs
 and be used with a single interface (`evaluate!`). In all of this,
 `TimeVaryingInput`s internally handle all the complexity related to reading
-files (using [`FileReaders`](@ref)), dealing with parallelism and GPUs,
-regridding onto the computational domains (using [`Regridders`](@ref) and
-[`DataHandling`](@ref)), and so on.
+files (using [`FileReaders`](@ref file_reader_module)), dealing with parallelism and GPUs,
+regridding onto the computational domains (using [`Regridders`](@ref regridder_module) and
+[`DataHandling`](@ref datahandling_module)), and so on.
 
 `TimeVaryingInputs` support:
 - analytic functions of time;
@@ -53,7 +53,7 @@ All input variables to be composed together must have the same spatial and
 temporal dimensions.
 
 Composing multiple input variables is currently only supported with the
-`InterpolationsRegridder`, not with `TempestRegridder`. The regridding
+[`InterpolationsRegridder`](@ref interp_regridder), not with [`TempestRegridder`](@ref tempest_regridder). The regridding
 is applied after the pre-processing and composing.
 
 Composing multiple input variables in one `Input` is also possible with
@@ -64,7 +64,7 @@ a `SpaceVaryingInput`, and everything mentioned here applies in that case.
 Suppose that the input NetCDF file `era5_example.nc` contains two variables `u`
 and `v`, and we care about their sum `u + v` but not their individual values.
 We can provide a pointwise composing function to perform the sum, along with
-the `InterpolationsRegridder` to produce the data we want, `u + v`.
+the [`InterpolationsRegridder`](@ref interp_regridder) to produce the data we want, `u + v`.
 The `preprocess_func` passed in `file_reader_kwargs` will be applied to `u`
 and to `v` individually, before the composing function is applied. The regridding
 is applied after the composing function. `u` and `v` could also come from separate
@@ -109,7 +109,7 @@ timevaryinginput = TimeVaryingInputs.TimeVaryingInput(["era5_1980.nc", "era5_198
 
 This capability is only available for the `InterpolationsRegridder`.
 
-Read more about this feature in the page about [`DataHandler`](@ref).
+Read more about this feature in the page about [`DataHandler`](@ref datahandling_module).
 
 ### Extrapolation boundary conditions
 
@@ -213,23 +213,24 @@ albedo_tv = TimeVaryingInputs.TimeVaryingInput("cesem_albedo.nc", "alb", target_
 
 !!! note
 
-    In this example we used the [`TempestRegridder`](@ref). This is not the best
-    choice in most cases because the [`TempestRegridder`](@ref) is slower, and
+    In this example we used the [`TempestRegridder`](@ref tempest_regridder).
+    This is not the best
+    choice in most cases because the [`TempestRegridder`](@ref tempest_regridder) is slower, and
     not well-compatible with MPI and GPUs (`ClimaUtilities` implements
     workarounds for this, so the code would still work).
-    [`InterpolationsRegridder`](@ref) should be preferred, unless there is a
-    strict requirement of conservation: while [`TempestRegridder`](@ref) is
-    guaranteed to conserve various properties, [`InterpolationsRegridder`](@ref)
+    [`InterpolationsRegridder`](@ref interp_regridder) should be preferred, unless there is a
+    strict requirement of conservation: while [`TempestRegridder`](@ref tempest_regridder) is
+    guaranteed to conserve various properties, [`InterpolationsRegridder`](@ref interp_regridder)
     is not.
 
-## `SpaceVaryingInputs`
+## [`SpaceVaryingInputs`](@id spacevaryinginput)
 
 > This extension is loaded when loading `ClimaCore` is loaded. In addition to
 > this, if NetCDF files are used, `NCDatasets` has to be loaded too. Finally, a
 > `Regridder` is needed (which might require importing additional packages).
 
 `SpaceVaryingInput`s uses the same building blocks as `TimeVaryingInput`
-(chiefly the [`DataHandling`](@ref) module) to construct a `Field` from
+(chiefly the [`DataHandling`](@ref datahandling_module) datahandling_module) to construct a `Field` from
 different sources.
 
 `SpaceVaryingInputs` support:
@@ -246,7 +247,7 @@ be a named tuple or a dictionary that maps `Symbol`s to values.
 
 `SpaceVaryingInputs` support reading individual input variables from NetCDF files,
 as well as composing multiple input variables into one `SpaceVaryingInput`.
-See the [`TimeVaryingInput`](@ref) "NetCDF file inputs" section for more
+See the [`TimeVaryingInput`](@ref timevaryinginput) "NetCDF file inputs" section for more
 information about this feature.
 
 ### Example
@@ -284,5 +285,6 @@ ClimaUtilities.TimeVaryingInputs.Flat
 ClimaUtilities.TimeVaryingInputs.evaluate!
 ClimaUtilities.TimeVaryingInputs.extrapolation_bc
 Base.in
-Base.close
+Base.close(::ClimaUtilities.TimeVaryingInputs.AbstractTimeVaryingInput)
+
 ```

docs/src/onlinelogging.md

@@ -24,7 +24,7 @@ about current step, simulation time, and average performance. With
 
 `WallTimeInfo` is a struct that holds information about wall time (the time you
 see on your watch, not the simulation time) and that can be used to report
-timing information with [`report_walltime`](@ref).
+timing information with [`report_walltime`](@ref ClimaUtilities.OnlineLogging.report_walltime).
 
 `WallTimeInfo` keeps track and accumulates how much time has elapsed since the
 last time it was updated. In this, `WallTimeInfo` tries to automatically remove

docs/src/regridders.md

@@ -1,4 +1,4 @@
-# Regridders
+# [`Regridders`](@id regridder_module)
 
 Simulations often need to import external data directly onto the computational
 grid. The `Regridders` module implements different schemes to accomplish this
@@ -27,7 +27,7 @@ If a regridder type is not specified by the user, and multiple are available,
 the `InterpolationsRegridder` will be used by default. At least one regridder
 extension must be loaded to be able to use regridding.
 
-## `TempestRegridder`
+## [`TempestRegridder`](@id tempest_regridder)
 
 > This extension is loaded when loading `ClimaCoreTempestRemap`
 
@@ -57,7 +57,7 @@ reg = Regridders.TempestRegridder(target_space, "regrid_output", "u", "era5_exam
 regridded_u = Regridders.regrid(reg, target_date)
 ```
 
-## `InterpolationsRegridder`
+## [`InterpolationsRegridder`](@id interp_regridder)
 
 > This extension is loaded when loading `ClimaCore` and `Interpolations`
 

src/TimeManager.jl

@@ -67,7 +67,11 @@ datetime_to_strdate(datetime::Dates.DateTime) =
     string(lpad(Dates.day(datetime), 2, "0"))
 
 abstract type AbstractFrequency end
+
+"Struct used to dispatch callback that is triggered monthly"
 struct Monthly <: AbstractFrequency end
+
+"Struct used to dispatch callback that is triggered every timestep"
 struct EveryTimestep <: AbstractFrequency end
 
 """