Merge branch 'alejandro' into merging

# Conflicts:
#	Manifest.toml
#	src/juobs.jl
#	src/juobs_obs.jl
#	src/juobs_reader.jl
#	src/juobs_tools.jl

src/juobs.jl

@@ -9,9 +9,14 @@ include("juobs_reader.jl")
 include("juobs_tools.jl")
 include("juobs_obs.jl")
 
-export read_mesons, read_mesons_correction, read_ms1, read_ms, read_md, truncate_data!
+export read_mesons, read_mesons_correction, read_ms1, read_ms, read_md, truncate_data!, concat_data!
 export get_matrix, energies, uwdot, uweigvals, uweigvecs, uweigen, invert, getall_eigvals, getall_eigvecs, hess_reduce, uwcholesky, transpose, tridiag_reduction, make_positive_def, invert_covar_matrix
+<<<<<<< HEAD
 export corr_obs, corr_obs_TSM, corr_sym, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine, bayesian_av
 export meff, mpcac, dec_const, dec_const_w, dec_const_pcvc, comp_t0
+=======
+export corr_obs, corr_obs_TSM, corr_sym, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine, bayesian_av, pvalue
+export meff, mpcac, dec_const, dec_const_pcvc, comp_t0
+>>>>>>> alejandro
 
 end # module

src/juobs_obs.jl

@@ -217,8 +217,12 @@ function dec_const(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64},
         T = length(corr_a0p)
         aux = exp.((collect(1:T) .- (T)/2) .* [m for k = 1:T])
     else
+<<<<<<< HEAD
         T = length(corr_a0p)
         aux = exp.((collect(1:T) .- T/2) .* [m for k = 1:T])
+=======
+        aux = exp.((collect(0:T-1) .- (T-1)/2) .* [m for k = 1:T])
+>>>>>>> alejandro
     end
 
     R = corr_a0p .* aux ./ [((corr_pp[T-y0])^2)^(1/4) for k = 1:length(corr_a0p)]
@@ -247,7 +251,7 @@ function dec_const(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64},
             title(string(L"$\kappa_1 = $", kappa[1], L" $\kappa_2 = $", kappa[2]))
         end
         display(gcf())
-        close()
+        #close()
     end
     if !data
         return f

src/juobs_reader.jl

@@ -91,6 +91,10 @@ ADerrors id can be specified as argument. If is not specified, the `id` is fixed
 
 *For the old version (without smearing, distance preconditioning and theta) set legacy=true.
 
+For Julien's most updated inversion code, the sign of the valence derivatives is flipped. Note also that for the new dat files version, no `_d1, _d2` 
+is written by the reader, so you must select by hand (looking at the log files e.g.) which are you derivative correlators. In the log file, the 
+derivative correlators are signaled by `seq_prop=some number`.
+
 Examples:
 ```@example
 read_mesons(path)
@@ -128,6 +132,7 @@ function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union
     ncfg = div(fsize - g_header.hsize - sum(getfield.(c_header, :hsize)), datsize) #(total size - header_size) / data_size
 
     corr_match = findall(x-> (x.type1==t1 || isnothing(t1)) && (x.type2==t2 || isnothing(t2)), c_header)
+    #findall(x-> (x.mu1==0.2209), c_header)
 
         
     seek(data, g_header.hsize + sum(c.hsize for c in c_header))
@@ -679,6 +684,7 @@ function concat_data!(data1::Vector{Vector{CData}}, data2::Vector{Vector{CData}}
             data1[k][r].vcfg = vcat(data1[k][r].vcfg, data2[k][r].vcfg)
             data1[k][r].re_data = vcat(data1[k][r].re_data, data2[k][r].re_data)
             data1[k][r].im_data = vcat(data1[k][r].im_data, data2[k][r].im_data)
+<<<<<<< HEAD
             idx = sortperm(data1[k][r].vcfg)
             data1[k][r].vcfg = data1[k][r].vcfg[idx]
             data1[k][r].re_data = data1[k][r].re_data[idx, :] 
@@ -687,3 +693,9 @@ function concat_data!(data1::Vector{Vector{CData}}, data2::Vector{Vector{CData}}
     end
     return nothing
 end
+=======
+        end
+    end
+    return nothing
+end
+>>>>>>> alejandro