link everything to the docs

docs/make.jl

@@ -57,7 +57,6 @@ makedocs(
     ),
     authors = "The developers of COBREXA.jl",
     linkcheck = !("skiplinks" in ARGS),
-    warnonly = true, # TODO: remove later
     pages = [
         "Home" => "index.md",
         "Examples" => [
@@ -72,11 +71,10 @@ makedocs(
             "Contents" => "concepts.md"
             find_mds("concepts")
         ],
-        "Reference" => "reference.md",
-        #[ # TODO re-add this when the reference gets bigger
-        #"Contents" => "reference.md"
-        #find_mds("reference")
-        #],
+        "API reference" => [
+            "Contents" => "reference.md"
+            find_mds("reference")
+        ],
     ],
 )
 

docs/src/reference.md

@@ -1,66 +1,6 @@
 # API reference
 
-## Helper types
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/types.jl"]
-```
-
-## Model loading and saving
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/io.jl"]
-```
-
-## Solver interface
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/solver.jl"]
-```
-
-## Constraint system building
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/builders/core.jl"]
-```
-
-### Genetic constraints
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/builders/genes.jl"]
+```@contents
+Pages = ["reference/core.md", "reference/frontend.md", "reference/builders.md", "reference/analysis.md", "reference/misc.md"]
+Depth = 2
 ```
-
-### Objective function helpers
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/builders/objectives.jl"]
-```
-
-### Bounds&tolerances helpers
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/misc/bounds.jl"]
-```
-
-## Analysis functions
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/analysis/flux_balance.jl", "src/analysis/parsimonious_flux_balance.jl"]
-```
-
-### Analysis modifications
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/analysis/modifications.jl"]
-```
-
-## Distributed analysis

docs/src/reference/analysis.md

@@ -0,0 +1,28 @@
+
+# Specialized analysis functions
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/solver.jl"]
+```
+
+## Parsimonious analyses
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/parsimonious.jl"]
+```
+
+## Ensemble solving
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/screen.jl", "src/analysis/variability.jl", "src/analysis/envelope.jl" ]
+```
+
+## Sampling
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/sample.jl"]
+```

docs/src/reference/builders.md

@@ -1,21 +1,53 @@
 
-## Constraint system building
+# Constraint system builders
+
+## Generic constraints
+
+### Comparisons
 
 ```@autodocs
 Modules = [COBREXA]
-Pages = ["src/builders/core.jl"]
+Pages = ["src/builders/compare.jl"]
 ```
 
-### Genetic constraints
+### Constraint scaling
 
 ```@autodocs
 Modules = [COBREXA]
-Pages = ["src/builders/genes.jl"]
+Pages = ["src/builders/scale.jl"]
 ```
 
-### Objective function helpers
+### Sign splitting
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/builders/unsigned.jl"]
+```
+
+### Objectives
 
 ```@autodocs
 Modules = [COBREXA]
 Pages = ["src/builders/objectives.jl"]
 ```
+
+## FBC constraint systems
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/builders/fbc.jl"]
+```
+
+## Analysis-specific constriants
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/builders/loopless.jl", "src/builders/knockout.jl", "src/builders/enzymes.jl"]
+```
+
+## Interfacing of constraint systems
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/builders/interface.jl"]
+```

docs/src/reference/core.md

@@ -0,0 +1,37 @@
+
+# Core functionality
+
+## Model I/O
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/io.jl"]
+```
+
+## Types
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/types.jl"]
+```
+
+## Configuration
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/config.jl"]
+```
+
+## Solver interface
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/solver.jl"]
+```
+
+## Task distribution support
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/worker_data.jl"]
+```

docs/src/reference/frontend.md

@@ -0,0 +1,71 @@
+
+# Front-end user interface
+
+## Flux balance analysis
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/balance.jl"]
+```
+
+## Flux variability analysis
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/variability.jl"]
+```
+
+## Parsimonious flux balance analysis
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/parsimonious.jl"]
+```
+
+## Enzyme-mass-constrained models
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/enzymes.jl"]
+```
+
+## Community models
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/community.jl"]
+```
+
+## Production envelopes
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/envelope.jl"]
+```
+
+## Knockout models
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/knockout.jl"]
+```
+
+## Loopless flux balance analysis
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/loopless.jl"]
+```
+
+## Max-Min Driving Force analysis
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/mmdf.jl"]
+```
+
+## Sampling
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/analysis/sample.jl"]
+```

docs/src/reference/misc.md

@@ -0,0 +1,7 @@
+
+# Miscellaneous functions
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/misc/bounds.jl", "src/misc/breaks.jl", "src/misc/maybe.jl", "src/misc/settings.jl", "src/misc/trees.jl"]
+```