modif manifest and readme

README.md

@@ -103,13 +103,6 @@ You can install the package in any project with the following command :
 - In order to add our unregistered package, type `add https://github.com/aTrotier/PAPER_subspace_MESE`
 - if you want to use the package : `using Subspace_MESE`
 
-**Additional steps due to issue** https://github.com/aTrotier/PAPER_subspace_MESE/issues/5
-- add a specific version of the package LinearOperatorCollection package : 
-```julia
-using Pkg
-Pkg.add(name="LinearOperatorCollection", version="1.1.2")
-```
-
 ## Reproducing figure 8
 In order to reproduce figure 8, we will run a script from the `docs` project environment which add the dependency to the plotting package `CairoMakie`.
 This folder contains the `Project.toml` and `Manifest.toml` that list all the dependencies and the version used to produce the figure. If you want to use newer 
@@ -123,14 +116,24 @@ In order to run the example you need to :
 - edit the script in `docs/lit/example/subspace_julia_epg.jl` and put the correct path in the variable 
   - line 46 : `path_raw` should point to the bruker folder `10`
   - line 49 : `path_bart` should point to the compiled bart library 
-- run the literate example **(a fix for LinearOperatorCollection has been added and will be removed later issue https://github.com/aTrotier/PAPER_subspace_MESE/issues/5)**:
+- run the literate example using the Manifest.toml files that stores the version of all the packages used to generate the figure 
+  ```julia
+  using Pkg
+  Pkg.instantiate()
+  include("lit/examples/subspace_julia_epg.jl")
+  ```
+
+If you want to start from a fresh environment you need to add the correct version of this repository as well as the plotting library `CairoMakie.jl` (put the correct path to the script `subspace_julia_epg.jl` if you are not in the `docs` folder)
+
   ```julia
   using Pkg
-  Pkg.add(url="https://github.com/aTrotier/PAPER_subspace_MESE")
-  Pkg.add(name="LinearOperatorCollection", version="1.1.2")
+
+  Pkg.add(url="https://github.com/aTrotier/PAPER_subspace_MESE",rev="1.0.1")
+  Pkg.add(name="CairoMakie", version="0.11.3")
   Pkg.instantiate()
   include("lit/examples/subspace_julia_epg.jl")
   ```
+
 The figure will be saved as `fig_bart_julia.png` in the `docs` folder.
 
 ### Note

docs/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.9.4"
 manifest_format = "2.0"
-project_hash = "e571d228757b49f70f03b7fb192617c13c2fc999"
+project_hash = "4e90fb5e21f93d3c968390c8a795a2f903853380"
 
 [[deps.AMD]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"]
@@ -1810,9 +1810,9 @@ version = "0.6.18"
     StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [[deps.Subspace_MESE]]
-deps = ["BartIO", "EPGsim", "FFTW", "LinearAlgebra", "LinearOperatorCollection", "LsqFit", "MRICoilSensitivities", "MRIFiles", "MRIReco"]
-git-tree-sha1 = "184a41a23af05e2c5ea277ab851cae65a81a8a59"
-repo-rev = "main"
+deps = ["BartIO", "EPGsim", "FFTW", "LinearAlgebra", "LsqFit", "MRICoilSensitivities", "MRIFiles", "MRIReco"]
+git-tree-sha1 = "e8bbc9f2a078dc2444c2ee5a933d34dcabc5cfb8"
+repo-rev = "v1.0.0"
 repo-url = "https://github.com/aTrotier/PAPER_subspace_MESE"
 uuid = "03ee4b65-1735-4169-82da-5df6ad43f66c"
 version = "1.0.0"

docs/Project.toml

@@ -1,13 +1,11 @@
 [deps]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-LinearOperatorCollection = "a4a2c56f-fead-462a-a3ab-85921a5f2575"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Subspace_MESE = "03ee4b65-1735-4169-82da-5df6ad43f66c"
 
 [compat]
 CairoMakie = "0.11.3"
 Documenter = "1.2.1"
-LinearOperatorCollection = "1.1.2"
 Literate = "2.16.0"
 julia = "1.9"