docs kinda build (but 10000 doccheck fails)

LCSB-BioCore · Nov 10, 2023 · 4d1d8d9 · 4d1d8d9
1 parent 77a9dbf
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -14,5 +14,5 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
 
 [compat]
-Documenter = "0.26"
-Literate = "2.8"
+Documenter = "1"
+Literate = "2"
diff --git a/docs/src/reference.md b/docs/src/reference.md
@@ -1,47 +1,6 @@
 # API reference
 
-## Helper types
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/types.jl"]
-```
-
-## Model loading and saving
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/io.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/types.md", "reference/io.md", "reference/builders.md", "reference/solver.md"]
+Depth = 2
 ```
-
-### Objective function helpers
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/builders/objectives.jl"]
-```
-
-## Solver interface
-
-```@autodocs
-Modules = [COBREXA]
-Pages = ["src/solver.jl"]
-```
-
-## Analysis functions
-
-## Distributed analysis
diff --git a/docs/src/reference/analysis.md b/docs/src/reference/analysis.md
diff --git a/docs/src/reference/base.md b/docs/src/reference/base.md
diff --git a/docs/src/reference/builders.md b/docs/src/reference/builders.md
@@ -0,0 +1,21 @@
+
+## Constraint system building
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/builders/core.jl"]
+```
+
+### Genetic constraints
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/builders/genes.jl"]
+```
+
+### Objective function helpers
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/builders/objectives.jl"]
+```
diff --git a/docs/src/reference/io.md b/docs/src/reference/io.md
@@ -1,15 +1,7 @@
-# Input and output
 
-## File I/O and serialization
+# Model loading and saving
 
 ```@autodocs
 Modules = [COBREXA]
-Pages = map(file -> joinpath("io", file), readdir("../src/io"))
-```
-
-## Pretty printing
-
-```@autodocs
-Modules = [COBREXA]
-Pages = map(file -> joinpath("io", "show", file), readdir("../src/io/show"))
+Pages = ["src/io.jl"]
 ```
diff --git a/docs/src/reference/reconstruction.md b/docs/src/reference/reconstruction.md
diff --git a/docs/src/reference/solver.md b/docs/src/reference/solver.md
@@ -0,0 +1,7 @@
+
+# Solver interface
+
+```@autodocs
+Modules = [COBREXA]
+Pages = ["src/solver.jl"]
+```
diff --git a/docs/src/reference/types.md b/docs/src/reference/types.md
@@ -1,20 +1,7 @@
-# Types
 
-## Base types
+# Helper types
 
 ```@autodocs
 Modules = [COBREXA]
-Pages = map(file -> joinpath("base", "types", "abstract", file), readdir("../src/base/types/abstract"))
-```
-
-## Model types and contents
-```@autodocs
-Modules = [COBREXA]
-Pages = map(file -> joinpath("base", "types", file), readdir("../src/base/types"))
-```
-
-## Model type wrappers
-```@autodocs
-Modules = [COBREXA]
-Pages = map(file -> joinpath("base", "types", "wrappers", file), readdir("../src/base/types/wrappers"))
+Pages = ["src/types.jl"]
 ```
diff --git a/docs/src/reference/utils.md b/docs/src/reference/utils.md