Merge branch 'dev' of github.com:CosmoLike/cocoa_lsst_y1 into dev

README.md

@@ -2,29 +2,31 @@
 
 In this tutorial, we assume the user installed Cocoa via the *Conda installation* method, and the name of the Conda environment is `cocoa`. We also presume the user's terminal is in the folder where Cocoa was cloned.
 
- **Step :one:**: activate the cocoa Conda environment, go to the `projects` folder and clone the Cosmolike LSST-Y1 project:
+ **Step :one:**: activate the cocoa Conda environment, go to the `cocoa/Cocoa/projects` folder, and clone the Cosmolike LSST-Y1 project:
 
       conda activate cocoa
       cd ./cocoa/Cocoa/projects
-      git clone --depth 1 https://github.com/CosmoLike/cocoa_lsst_y1.git lsst_y1 
+      ${CONDA_PREFIX}/bin/git clone --depth 1 https://github.com/CosmoLike/cocoa_lsst_y1.git --branch v4.0-beta3 lsst_y1 
 
-By convention, the Cosmolike Organization hosts a Cobaya-Cosmolike project named XXX at `CosmoLike/cocoa_XXX`. However, our scripts and YAML files assume the removal of the `cocoa_` prefix when cloning the repository.
+:warning: Cocoa scripts and YAML files assume the removal of the `cocoa_` prefix when cloning the repository.
 
-📚📚 *Additional Information for experts and developers* 📚📚: Cocoa developers should drop the shallow clone option `--depth 1`, which prevents git from downloading the entire repository history. Developers should also authenticate to GitHub via SSH keys:
+:interrobang: If the user is a developer, then type the following instead *(at your own risk!)*
 
-      $CONDA_PREFIX/bin/git clone [email protected]:CosmoLike/cocoa_lsst_y1.git lsst_y1
+      ${CONDA_PREFIX}/bin/git clone [email protected]:CosmoLike/cocoa_lsst_y1.git lsst_y1
       
- **Step :two:**: go back to the Cocoa main folder, and activate the private Python environment
+ **Step :two:**: go back to the Cocoa main folder and activate the private Python environment
 
       cd ../
-      source start_cocoa
+      source start_cocoa.sh
 
-:warning::warning: Remember to run the start_cocoa script only **after cloning** the project repository. 
+:warning: Remember to run the `start_cocoa.sh` shell script only **after cloning** the project repository (or if you already in the `(.local)` environment, run `start_cocoa.sh` again). 
 
 **Step :three:**: compile the project
 
       source ./projects/lsst_y1/scripts/compile_lsst_y1
 
+:interrobang: The script `compile_cocoa.sh` also compiles every Cosmolike project on the `cocoa/Cocoa/projects/` folder.
+
 **Step :four:**: select the number of OpenMP cores (below, we set it to 4), and run a template YAML file
 
       export OMP_PROC_BIND=close; export OMP_NUM_THREADS=4
@@ -39,11 +41,15 @@ MCMC:
 
 ## Deleting Cosmolike projects <a name="running_cosmolike_projects"></a>
 
-:warning::warning: Never delete the `lsst_y1` folder from the project folder without running `stop_cocoa` first; otherwise, Cocoa will have ill-defined soft links.
-
-Where the ill-defined soft-links will be located? They will be at `Cocoa/cobaya/cobaya/likelihoods/`, `Cocoa/external_modules/code/` and `Cocoa/external_modules/data/`. The script `stop_cocoa` deletes them.
+Do not delete the `lsst_y1` folder from the project folder without first running the shell script `stop_cocoa.sh`. Otherwise, Cocoa will have ill-defined soft links. 
 
-Why this behaviour exists? The script `start_cocoa` creates symbolic links so cobaya can see the likelihood and data files. It also adds the *Cobaya-Cosmolike interface* of all projects to `LD_LIBRARY_PATH` and `PYTHONPATH` paths.
+:interrobang: Where the ill-defined soft links will be located? 
+
+     Cocoa/cobaya/cobaya/likelihoods/
+     Cocoa/external_modules/code/
+     Cocoa/external_modules/data/ 
+
+:interrobang: Why does Cocoa behave like this? The shell script `start_cocoa.sh` creates symbolic links so Cobaya can see the likelihood and data files. Cocoa also adds the Cobaya-Cosmolike interface of all cosmolike-related projects to the `LD_LIBRARY_PATH` and `PYTHONPATH` environmental variables.
 
 ## MCMC Convergence Criteria <a name="running_cosmolike_projects"></a>
 
@@ -53,4 +59,4 @@ Why this behaviour exists? The script `start_cocoa` creates symbolic links so co
     # Gelman-Rubin R-1 on std deviations
     Rminus1_cl_stop: 0.15
 
-For most applications, these settings are overkill, except when computing some tension and goodness of fit metrics. Please adjust these settings to your needs. 
+These settings are overkill for most applications, except when computing some tension and goodness of fit metrics. Please adjust these settings to your needs.