bump deps, add a few function headers

Project.toml

@@ -20,7 +20,7 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 AbstractFBCModels = "0.2.2"
 Aqua = "0.7"
 Clarabel = "0.6"
-ConstraintTrees = "0.9.1"
+ConstraintTrees = "0.9.2"
 DistributedData = "0.2"
 DocStringExtensions = "0.8, 0.9"
 Downloads = "1"

src/COBREXA.jl

@@ -39,6 +39,7 @@ using DocStringExtensions
 
 import AbstractFBCModels as A
 import ConstraintTrees as C
+import Distributed as D
 import JuMP as J
 import LinearAlgebra
 import SparseArrays
@@ -50,6 +51,12 @@ include("config.jl")
 include("io.jl")
 include("solver.jl")
 
+# generic analysis functions
+include("analysis/envelope.jl")
+include("analysis/sample.jl")
+include("analysis/screen.jl")
+include("analysis/variability.jl")
+
 # conversion of various stuff to constraint trees
 include("builders/communities.jl")
 include("builders/enzymes.jl")
@@ -63,11 +70,15 @@ include("builders/unsigned.jl")
 
 # simplified front-ends for the above
 include("frontend/balance.jl")
-include("frontend/parsimonious.jl")
+include("frontend/envelope.jl")
+include("frontend/enzymes.jl")
+include("frontend/knockout.jl")
+include("frontend/loopless.jl")
 include("frontend/mmdf.jl")
 include("frontend/moma.jl")
-include("frontend/loopless.jl")
-include("frontend/enzyme_constrained.jl")
+include("frontend/parsimonious.jl")
+include("frontend/sample.jl")
+include("frontend/variability.jl")
 
 # utilities
 include("misc/bounds.jl")

src/analysis/envelope.jl

@@ -0,0 +1,19 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function constraints_objective_envelope(constraints::C.ConstraintTree, grid::Array{C.ConstraintTreeElem}, objective::C.Value; workers = D.workers())
+    #TODO
+end

src/analysis/sample.jl

@@ -0,0 +1,21 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function sample_achr(constraints::C.ConstraintTree, points::Matrix{Float64}; seed, chains, collect_iterations, epsilon, filter_constraints::C.ConstraintTree, workers=D.workers())
+end
+
+function sample_affine_hr(constraints::C.ConstraintTree, points::Matrix{Float64}; seed, chains, collect_iterations, epsilon, mix_points, filter_constraints::C.ConstraintTree, workers=D.workers())
+end

src/analysis/screen.jl

@@ -0,0 +1,27 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function screen(f, model::A.AbstractFBCModel; args::Array{Tuple} = [()], workers=D.workers(), kwargs...)
+    # TODO might belong to the frontend
+end
+
+function screen(f, constraints::C.ConstraintTree; args::Array{Tuple} = [()], workers=D.workers())
+    # TODO
+end
+
+function screen_optimization_model(f, constraints::C.ConstraintTree, args::Maybe{Array}, workers=D.workers())
+    # TODO
+end

src/analysis/variability.jl

@@ -0,0 +1,19 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function constraints_variability(constraints::C.ConstraintTree, targets::C.ConstraintTree; workers = D.workers()) :: C.Tree{Tuple{Maybe{Float64}, Maybe{Float64}}}
+    #TODO
+end

src/builders/communities.jl

@@ -27,7 +27,10 @@ as `:module_name => (module, module.interface)`; the second tuple member may
 also be specified just by name as e.g. `:interface`, or omitted while relying
 on `default_interface`).
 
-Compatible modules with interfaces may be created e.g. by
+Interface parts get merged and constrained to create a new interface; networks
+are intact with disjoint variable sets.
+
+Compatible modules with ready-made interfaces may be created e.g. by
 [`flux_balance_constraints`](@ref).
 """
 function join_module_constraints(

src/frontend/envelope.jl

@@ -0,0 +1,19 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function objective_production_envelope(model::A.AbstractFBCModel, dimensions; optimizer, kwargs...)
+    #TODO
+end

src/frontend/enzyme_constrained.jl → src/frontend/enzymes.jl

@@ -18,7 +18,8 @@
 $(TYPEDEF)
 
 A simple struct storing information about the isozyme composition, including
-subunit stoichiometry and turnover numbers.
+subunit stoichiometry and turnover numbers. Use with
+[`enzyme_constrained_flux_balance_analysis`](@ref).
 
 # Fields
 $(TYPEDFIELDS)

src/frontend/knockout.jl

@@ -0,0 +1,19 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function gene_knockouts(model::A.AbstractFBCModel, genes, n; kwargs...)
+    # TODO just use screen to do this right
+end

src/frontend/sample.jl

@@ -0,0 +1,23 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function flux_sampling_achr(model::A.AbstractFBCModel; optimizer, kwargs...)
+    #TODO
+end
+
+function flux_sampling_affine_hr(model::A.AbstractFBCModel; optimizer, kwargs...)
+    #TODO probably share a lot of the frontend with the above thing
+end

src/frontend/variability.jl

@@ -0,0 +1,19 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+function flux_variability_analysis(model::A.AbstractFBCModel; optimizer, kwargs...)
+    #TODO
+end