Fix more links

docs/src/defining_sequence.md

@@ -80,7 +80,7 @@ Here the coherence [`Pathway`](@ref) sets out what a specific set of spins might
 In this case the sequence experiences two RF pulses and is excited by the first pulse and flipped by the second (`[90, 180]`).
 It is then observed during the first readout (`1`). 
 For such a [`Pathway`](@ref) we can compute:
-- the time that the spin spends in any direction ([`duration_state`](@ref)), which is particularly useful in the transverse direction to compute the amount of T2-weighting ([`duration_transverse`](@ref)) and the amount of time spent dephasing to compute the amount of T2*-weighting ([`duration_dephase`](@ref)).
+- the time that the spin spends in each longitudinal and transverse direction, which is particularly useful in the transverse direction to compute the amount of T2-weighting ([`duration_transverse`](@ref)) and the amount of time spent dephasing to compute the amount of T2*-weighting ([`duration_dephase`](@ref)).
 - the diffusion weighting experienced ([`bval`](@ref), [`bmat`](@ref), and [`qvec`](@ref))
 By defining a default pathway for the sequence, the user can now put constraints on any or all of these variables.
 

src/build_sequences.jl

@@ -105,6 +105,13 @@ end
 build_sequence(f::Function, optimiser_constructor; kwargs...) = build_sequence(f, Default_Scanner, optimiser_constructor; kwargs...)
 
 
+"""
+    global_model()
+
+Return the currently set JuMP model.
+
+The model can be set using [`build_sequence`](@ref)
+"""
 function global_model()
     if GLOBAL_MODEL[] == IGNORE_MODEL
         error("No global model has been set. Please embed any sequence creation within an `build_sequence` block.")
@@ -112,6 +119,13 @@ function global_model()
     return GLOBAL_MODEL[]
 end
 
+"""
+    global_scanner()
+
+Return the currently set [`Scanner`](@ref).
+
+The scanner can be set using [`build_sequence`](@ref)
+"""
 function global_scanner()
     if !isfinite(GLOBAL_SCANNER[].gradient)
         error("No valid scanner has been set. Please provide one when calling `build_sequence`.")
@@ -123,8 +137,9 @@ end
 """
     fixed(building_block)
 
-Returns an equiavalent [`BuildingBlock`](@ref) with all free variables replaced by numbers.
-This will only work after calling [`optimize!`](@ref)([`global_model`](@ref)()).
+Return an equiavalent `BuildingBlock` with all free variables replaced by numbers.
+
+This will only work after calling `optimize!`(@ref)([`global_model`](@ref)()).
 It is used internally by [`build_sequence`](@ref).
 """
 fixed(some_value) = some_value

src/parts/helper_functions.jl

@@ -5,7 +5,7 @@ import ..Trapezoids: Trapezoid, opposite_kspace_lines, SliceSelect
 import ..SpoiltSliceSelects: SpoiltSliceSelect
 import ..SliceSelectRephases: SliceSelectRephase
 import ..EPIReadouts: EPIReadout
-import ...BuildSequences: global_model, build_sequence
+import ...BuildSequences: global_model, build_sequence, global_scanner
 import ...Containers: Sequence
 import ...Components: SincPulse, ConstantPulse, InstantPulse, SingleReadout, InstantGradient
 import ...Variables: qvec, flat_time, rise_time, qval, apply_simple_constraint!, variables

src/pathways.jl

@@ -42,8 +42,8 @@ Over the pathway the following values are computed. Each can be accessed by call
 The area under curve, q-values, and b-values are computed separately for each group of gradients (depending on the `group` keyword set during construction).
 - [`qvec`](@ref): Net displacement vector in k-space/q-space.
 - [`qval`](@ref)/[`area_under_curve`](@ref): size of the displacement in k-space/q-space. For a spoiled pathway, this should be large compared with 1/voxel size; for unspoiled pathways it should be (close to) zero.
-- [`bmat`](@ref): Net diffusion weighting due to gradients along the [`Pathway`](@ref) in matrix form.
-- [`bval`](@ref): Net diffusion weighting due to gradients along the [`Pathway`](@ref) as a single number.
+- [`bmat`](@ref): Net diffusion weighting due to gradients along the `Pathway` in matrix form.
+- [`bval`](@ref): Net diffusion weighting due to gradients along the `Pathway` as a single number.
 """
 struct Pathway
     # user provided
@@ -237,7 +237,7 @@ end
 """
 Helper structure for [`PathwayWalker`](@ref), which is itself a helper for `Pathway`.  You are deep down the rabit hole now...
     
-For documentation, see that structure and [`walk_pathway`](@ref) and [`update_walker_gradient!`](@ref).
+For documentation, see that structure and [`walk_pathway!`](@ref) and [`update_walker_gradient!`](@ref).
 """
 mutable struct GradientTracker
     last_gradient_time :: VariableType
@@ -251,7 +251,7 @@ GradientTracker() = GradientTracker(0., zeros(3), zeros(3, 3))
 """
 Helper structure for `Pathway`.
     
-For documentation, see that structure and [`walk_pathway`](@ref).
+For documentation, see that structure and [`walk_pathway!`](@ref).
 """
 mutable struct PathwayWalker
     last_pulse_time :: VariableType

src/variables.jl

@@ -6,8 +6,8 @@ In addition this defines:
 - [`VariableType`](@ref): parent type for any variables (whether number or JuMP variable).
 - [`get_free_variable`](@ref): helper function to create new JuMP variables.
 - [`VariableNotAvailable`](@ref): error raised if variable is not defined for specific [`AbstractBlock`](@ref).
-- [`set_simple_constraints`](@ref): call [`apply_simple_constraint`](@ref) for each keyword argument.
-- [`apply_simple_constraint`](@ref): set a simple equality constraint.
+- [`set_simple_constraints!`](@ref): call [`apply_simple_constraint!`](@ref) for each keyword argument.
+- [`apply_simple_constraint!`](@ref): set a simple equality constraint.
 - [`get_pulse`](@ref)/[`get_gradient`](@ref)/[`get_readout`](@ref): Used to get the pulse/gradient/readout part of a building block
 - [`gradient_orientation`](@ref): returns the gradient orientation of a waveform if fixed.
 """
@@ -36,7 +36,7 @@ end
 
 Returns the adjusted blocks and add any keywords used in the process to `names_used`.
 
-This is a helper function used by [`adjust`](@ref). 
+This is a helper function used by `adjust`. 
 """
 function adjust_internal end