qls (#6)

* first commit on branch qls! * wip * starting adding two galaxy species * added 2 species in auto correlations * first cross GNC with twom species, DopplerIntegrated * now R_GNC is computed inside the TPCFs * cross GNC wip * rewritten computation of R_GNC in tpcfs * wip * finished GNC 2 species (I think) * wip on bugs * finished bugs corrections, i hope * bug fixes: s_b_s2 corrected to s_b_s1 in GNC LensingIntegrated * wip on GNCxLD for 2 species, doing Lensig x stuff * finished GNCxLD 2 species, bugs to be still removed * bugs fixed * wip * implemented tests for TwoSpecies.jl * wip on indentation * added first docstring for LD in AutoDoppler * improving docs * finished docstrings for LD auto correlations * wip on cross correlation LD doctrings * still wip * finished focstrings on LD cross correlations * started docstrings on GNCxLD TPCFs * wip * done docstrings GNCxLD Doppler x others * wip * wip on docstrings GNCxLD Integrated x others * done docstrings GNCxLD Lensing x others * done docstrings GNCxLD local x others * wip onn docstrings GNCxLD newtonianxothers * finished docstrings on GNCxLD * added z_spline_lim to CosmoParams and CosmoSplines * implemented z_spline_lim and s_spline_lim, must be tested * corrected bug LensingXNewton for two species * modified README and CHANGELOG * added Dockerfile for image gapse-julia-1.9.1:0.8.0a * added pyplot in Dockerfile * added matplotlib to Dockerfile, bug fixed * bug in README.md * bug in README.md * bug in README.md * README.md * added PRL reference * added readchoosen * correcting docs * correcting docs * correcting docs * correcting docs * correcting docs * correcting docs * test new brand * test new brand * test new brand * test new brand * tests * tests * tests * tests * added tests WindowF_QMultipoles.jl --------- Co-authored-by: Matteo Foglieni <[email protected]>
foglienimatteo · Feb 23, 2024 · e601437 · e601437
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diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,9 @@
+.github/*
+.ipynb_checkpoints/*
+*/.ipynb_checkpoints/*
+build.log
+
+.DS_Store
+*/.DS_Store
+Manifest.toml
+newimage.sh
diff --git a/.github/workflows/DocDeploy.yml b/.github/workflows/DocDeploy.yml
@@ -19,15 +19,16 @@
 
 name: Documentation
 
-# on:
-#  push:
-#    branches:
-#      - main
-#    tags: '*'
-#  pull_request:
-#
+on:
+  push:
+    branches:
+      - main
+      - qls
+    tags: '*'
+  pull_request:
+
 
-on: [push]
+#on: [push]
 #on:
 #  release:
 #    types: [published, edited, prereleased, released]
@@ -36,14 +37,20 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1.8'
+          version: '1.9'
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
         run: julia --project=docs/ docs/make.jl
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src
+      - uses: codecov/codecov-action@v3
+        with:
+          files: lcov.inf
diff --git a/.github/workflows/UnitTests.yml b/.github/workflows/UnitTests.yml
@@ -20,16 +20,17 @@
 
 name: Unit tests
 
-on: [push]
+#on: [push]
 
 #on:
 #  release:
 #    types: [published, edited, prereleased, released]
 
-#on:
-#  push:
-#    branches:
-#      - demo
+on:
+  push:
+    branches:
+      - main
+      - qls
 
 
 
@@ -39,12 +40,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: ['1.8']
+        julia-version: ['1.9']
         os: [macos-latest, ubuntu-latest, windows-latest]
         arch: [x64]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: "Set up Julia"
         # install Julia 
@@ -74,6 +75,6 @@ jobs:
         # run the tests 
         uses: julia-actions/julia-runtest@latest
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v2
         with:
           file: lcov.info
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,21 @@
 
 ## development branch qls
 
+- added `readchoosen` and `readxchoosey` functions in `src/OtherUtils.jl`;
+
+- changed logo of GaPSE;
+
+- added `ipynbs/eBOSS_Window.ipynb` and related files;
+
+- added `Dockerfile` for building the image `gapse-julia-1.9.1:0.8.0a`;
+
+- IMPORTANT CHANGE: NOW YOU CAN GO FURTHER THAN `z=1.5`!
+
+- IMPORTANT CHANGE: TWO TRACERS IMPLEMENTATION!
+  Now you have two comsological biases sets `b1`, `s_b1`, `𝑓_evo1` and `b2`, `s_b2`, `𝑓_evo2` in the `CosmoParams` struct (you cannot specify anymore them as `b`, `s_b`, `𝑓_evo`);
+
+- added all the previously missing docstrings in `GNCxLD` and `LD` TPCFs;
+
 - added `ipynb/Computations_b1p5-sb0-fevo0.ipynb`, `Computations_b1p5-sb0-fevo0.jl` and `Generic_Window.jl` for the analysis of the PNG, even with a generic window function
 
 - added `src/PowerSpectraGenWin.jl` and `src/WindowF_QMultipoles.jl`: now it's possible to compute the PS for a generic window!
@@ -12,10 +27,6 @@
 
 - huge improvements on docstrings and API.
 
-- added `ipynbs/PS_L01234.ipynb` and its Julia script
-
-- modified starting point of FFTLog algorithm (from (1 + ell) ./ plan.x to 1.0 ./ plan.x)
-
 - renamed `src/PowerSpectrum.jl` to `src/PowerSpectra.jl`
 
 - creation of the package `GaPSE.jl`; it will still take a while

diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,20 @@
+FROM jupyter/julia-notebook:julia-1.9.1
+#FROM julia:1.8.5-bullseye
+
+USER root
+
+COPY . /home/jovyan/GaPSE
+WORKDIR /home/jovyan/GaPSE
+RUN chown -R jovyan:users /home/jovyan/GaPSE
+
+USER jovyan
+RUN pip3 install matplotlib
+RUN julia --project=. --eval 'using Pkg; Pkg.instantiate(); Pkg.precompile()'
+RUN julia --project=. --eval 'using Pkg; for p in [  \
+        "Plots", "LaTeXStrings", "PyPlot" \
+    ]; \ 
+    Pkg.add(p); end; Pkg.resolve()'
+
+#ENTRYPOINT ["/bin/bash"]
+
+
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "GaPSE"
 uuid = "d1bf0294-456c-4ffb-813c-36d532d2da2e"
 authors = ["Matteo Foglieni <[email protected]>"]
-version = "0.7.0"
+version = "0.8.0"
 
 [deps]
 ArbNumerics = "7e558dbc-694d-5a72-987c-6f4ebed21442"

diff --git a/README.md b/README.md
diff --git a/data/Ql_multipoles_of_F_REFERENCE_z115.txt b/data/Ql_multipoles_of_F_REFERENCE_z115.txt
diff --git a/docs/make.jl b/docs/make.jl
@@ -19,13 +19,14 @@ Documenter.makedocs(
                "Integrated Window F" => "WindowFIntegrated.md",
           ],
           "Calculating TPCFs multipoles" => [
-               "GNC" => "GNC_Correlations.md",
-               "LD" => "LD_Correlations.md",
-               "GNCxLD" => "GNCxLD_Correlations.md",
-               "LDxGNC" => "GNCxLD_Correlations.md",
+               "GNC" => ["GNC_Correlations_1.md", "GNC_Correlations_2.md", "GNC_Correlations_3.md"],
+               "LD" => ["LD_Correlations_1.md", "LD_Correlations_2.md"],
+               "GNCxLD" => ["GNCxLD_Correlations_1.md", "GNCxLD_Correlations_2.md"],
+               "LDxGNC" => ["LDxGNC_Correlations_1.md", "LDxGNC_Correlations_2.md"],
           ],
           "Calculating TPCFs with the PP Approximation" => "PlaneParallelApprox.md",
           "Calculating Power Spectra" => "PowerSpectra.md",
+          "Power Spectra for a generic window" => "PowerSpectraGenWin.md",
           "implication on PNG" => "PNG.md",
           "Utilities" => [
                "Dictionaries and names" => "Dicts.md",
@@ -37,4 +38,4 @@ Documenter.makedocs(
      ],
 )
 
-deploydocs(repo = "github.com/cosmofico97/GaPSE.jl.git")
+deploydocs(repo = "github.com/foglienimatteo/GaPSE.jl.git")
diff --git a/docs/src/CosmoUtils.md b/docs/src/CosmoUtils.md
@@ -17,4 +17,5 @@ GaPSE.W
 GaPSE.V_survey
 GaPSE.A
 GaPSE.A_prime
+GaPSE.corresponding_redshift
 ```
diff --git a/docs/src/Dicts.md b/docs/src/Dicts.md
@@ -9,6 +9,7 @@ end
 
 ```@docs
 GaPSE.VALID_INTEGRATION_ALGORITHM
+GaPSE.VALID_KWARGS_GNC
 
 GaPSE.GR_EFFECTS_LD
 GaPSE.VEC_ξs_LD

diff --git a/docs/src/GNC_Correlations.md b/docs/src/GNC_Correlations.md
diff --git a/docs/src/GNC_Correlations_1.md b/docs/src/GNC_Correlations_1.md
@@ -0,0 +1,24 @@
+```@meta
+DocTestSetup = quote
+    using GaPSE
+end
+```
+
+# GNC TPCFs
+
+## Two-Point Auto-Correlation Functions
+
+```@docs
+GaPSE.ξ_GNC_Newtonian
+GaPSE.ξ_GNC_Doppler
+GaPSE.ξ_GNC_Lensing
+GaPSE.ξ_GNC_LocalGP
+GaPSE.ξ_GNC_IntegratedGP
+```
+
+## Two-Point Auto-Correlation Functions integrands
+
+```@docs
+GaPSE.integrand_ξ_GNC_Lensing
+GaPSE.integrand_ξ_GNC_IntegratedGP
+```
diff --git a/docs/src/GNC_Correlations_2.md b/docs/src/GNC_Correlations_2.md
@@ -0,0 +1,34 @@
+```@meta
+DocTestSetup = quote
+    using GaPSE
+end
+```
+
+# GNC TPCFs
+
+## Two-Point Cross-Correlation Functions
+
+```@docs
+GaPSE.ξ_GNC_Newtonian_Doppler
+GaPSE.ξ_GNC_Doppler_Newtonian
+GaPSE.ξ_GNC_Newtonian_Lensing
+GaPSE.ξ_GNC_Lensing_Newtonian
+GaPSE.ξ_GNC_Newtonian_LocalGP
+GaPSE.ξ_GNC_LocalGP_Newtonian
+GaPSE.ξ_GNC_Newtonian_IntegratedGP
+GaPSE.ξ_GNC_IntegratedGP_Newtonian
+GaPSE.ξ_GNC_Doppler_Lensing
+GaPSE.ξ_GNC_Lensing_Doppler
+GaPSE.ξ_GNC_Doppler_LocalGP
+GaPSE.ξ_GNC_LocalGP_Doppler
+GaPSE.ξ_GNC_Doppler_IntegratedGP
+GaPSE.ξ_GNC_IntegratedGP_Doppler
+GaPSE.ξ_GNC_Lensing_LocalGP
+GaPSE.ξ_GNC_LocalGP_Lensing
+GaPSE.ξ_GNC_Lensing_IntegratedGP
+GaPSE.ξ_GNC_IntegratedGP_Lensing
+GaPSE.ξ_GNC_LocalGP_IntegratedGP
+GaPSE.ξ_GNC_IntegratedGP_LocalGP
+```
+
+
diff --git a/docs/src/GNC_Correlations_3.md b/docs/src/GNC_Correlations_3.md
@@ -0,0 +1,37 @@
+```@meta
+DocTestSetup = quote
+    using GaPSE
+end
+```
+
+# GNC TPCFs
+
+## Two-Point Cross-Correlation Functions integrands
+
+```@docs
+GaPSE.integrand_ξ_GNC_Newtonian_Lensing
+GaPSE.integrand_ξ_GNC_Newtonian_IntegratedGP
+GaPSE.integrand_ξ_GNC_Doppler_IntegratedGP
+GaPSE.integrand_ξ_GNC_Lensing_Doppler
+GaPSE.integrand_ξ_GNC_Lensing_LocalGP
+GaPSE.integrand_ξ_GNC_Lensing_IntegratedGP
+GaPSE.integrand_ξ_GNC_LocalGP_IntegratedGP
+```
+
+
+## Two-Point Cross-Correlation Function multipoles
+
+```@docs
+GaPSE.integrand_ξ_GNC_multipole
+GaPSE.ξ_GNC_multipole
+GaPSE.map_ξ_GNC_multipole
+GaPSE.print_map_ξ_GNC_multipole
+```
+
+## Two-Point Cross-Correlation Function Sum multipoles
+
+```@docs
+GaPSE.sum_ξ_GNC_multipole
+GaPSE.map_sum_ξ_GNC_multipole
+GaPSE.print_map_sum_ξ_GNC_multipole
+```
diff --git a/docs/src/GNCxLD_Correlations.md → docs/src/GNCxLD_Correlations_1.md b/docs/src/GNCxLD_Correlations.md → docs/src/GNCxLD_Correlations_1.md
@@ -32,19 +32,3 @@ GaPSE.ξ_GNCxLD_IntegratedGP_IntegratedGP
 ```
 
 
-## Two-Point Cross-Correlation Function multipoles
-
-```@docs
-GaPSE.integrand_ξ_GNCxLD_multipole
-GaPSE.ξ_GNCxLD_multipole
-GaPSE.map_ξ_GNCxLD_multipole
-GaPSE.print_map_ξ_GNCxLD_multipole
-```
-
-## Two-Point Cross-Correlation Function Sum multipoles
-
-```@docs
-GaPSE.sum_ξ_GNCxLD_multipole
-GaPSE.map_sum_ξ_GNCxLD_multipole
-GaPSE.print_map_sum_ξ_GNCxLD_multipole
-```