Update setup info and scripts

Author: peterrrock2

Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.2"
+julia_version = "1.11.3"
 manifest_format = "2.0"
 project_hash = "92713d8d40a9172e59b96f0da75d24fab6398141"
 

README.md

@@ -49,19 +49,18 @@ This repository is not complete at this time.
 
 ## Simple Setup
 
-To set up this project to run some of the analysis scripts contained within, you 
-can simply invoke
-
-```console
-source setup_all.sh
-```
-
-sourcing is necessary to make sure that the Julia project is set up correctly.
-You will need to have Julia, Cargo, and RStudio installed in order for this to run without 
-errors. (Note: This script requires the use of a Unix based operating system, such as 
-MacOS or Linux. Windows users may invoke this by setting up the subsystem for Linux)
-
+Note: These instructions are intended for Mac and Linux users. Windows users
+may follow along by using the 
+[Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/install) 
+and
+[Windows Terminal](https://apps.microsoft.com/detail/9n0dx20hk701?ocid=webpdpshare)
+which allow for the use of Linux commands within a Windows environment. Windows users
+will also need to install the appropriate subsystem, for which we recommend 
+[Ubuntu 22.04.5 LTS](https://apps.microsoft.com/detail/9pn20msr04dw?ocid=webpdpshare)
+due to the ease-of-use and quantity of support documentation for Ubuntu users.
 
+To set up this project to run some of the analysis scripts contained within, you 
+must make sure that you have Cargo, Julia, and R (or RStudio) installed.
 To install Cargo, visit the 
 [Rustup Download Page](https://doc.rust-lang.org/cargo/getting-started/installation.html)
 and follow the instructions for your operating system. Likewise, to install Julia,
@@ -78,9 +77,19 @@ than installing from the Julia website.)
 > :warning: There appears to be a memory leak bug that sometimes appears when running the `redist`
 > package. This memory leak appears to be an issue with the R interpreter not freeing memory
 > appropriately when the R base language and the relevant RCpp and Rarmadillo libraries
-> are compiled with an earler version of gcc. To avoid this bug, please make sure to have
-> R version >= 4.4.2 and a gcc released after 15 May 2024. Relevant gdal and fortran compilation
-> libraries should also be up-to-date.
+> are compiled with an earler version of gcc/gfortran. To avoid this bug, please make sure to have
+> R version >= 4.4.2 and a verson ofgcc released after 15 May 2024. Relevant gdal and fortran
+> compilation libraries should also be up-to-date.
+
+
+After making sure the appropriate programming languages are installed on your 
+machine, you can simply invoke
+
+```console
+source setup_all.sh
+```
+
+sourcing is necessary to make sure that the Julia project is set up correctly.
 
 ## More Detailed Setup instructions in case the script fails
 
@@ -116,11 +125,11 @@ To run the Sequential Monte Carlo (SMC) code for this repository, you will need
 appropriate version of R (you don't _need_ RStudio, but it is nice to have) installed, as
 well as the following packages:
 
-- argparser
-- dplyr
-- ggplot2
-- remotes
-- sf
+- `argparser`
+- `dplyr`
+- `ggplot2`
+- `remotes`
+- `sf`
 
 To install these packages, you can simply invoke the R terminal (or open RStudio)
 and call
@@ -183,12 +192,50 @@ If you are on mac, then the corresponding brew packages would be:
 brew update && brew install \
   gdal \
   geos \
+  gfortran \
   proj \
   udunits \
   openssl \
   cairo
 ```
 
+In some versions of R, especially on newer Mac installations, there can be a slight issue 
+during the installation of the `redist` package. Specifically, you might see something like
+
+```console
+ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found
+ld: warning: search path '/opt/gfortran/lib' not found
+ld: library 'gfortran' not found
+clang++: error: linker command failed with exit code 1 (use -v to see invocation)
+make: *** [redist.so] Error 1
+ERROR: compilation failed for package 'redist'
+* removing '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/redist'
+Warning message:
+In i.p(...) :
+  installation of package '/var/folders/r_/xjlnv23j48v1p28d0tq18wcc0000gn/T//RtmpxA09fJ/file130a75c9fcf76/redist_4.1.2.tar.gz' had non-zero exit status
+```
+
+In this message, the key line is
+
+```console
+ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found
+```
+
+which indicates that R is trying to grab a gfortran library that was not installed with the
+brew package manager. The easiest way to try and fix this is to just adjust the compilation
+flags for R (i.e. edit the file `~/.R/Makevars/`). Most likely, you have never touched
+this file before, so the easiest way to fix this is to invoke the following from the console:
+
+```console
+mkdir -p ~/.R && echo "CC = clang
+CXX = clang++
+FC = /opt/homebrew/bin/gfortran
+F77 = /opt/homebrew/bin/gfortran
+FLIBS = -L/opt/homebrew/opt/gcc/lib/gcc/current -lgfortran -lquadmath -lm" > ~/.R/Makevars
+```
+
+
+
 ### Other dependencies
 
 In order to convert the "atlas" format that is output by the MSMS code to an assignment-vector 

cli_files/smc_cli.R

@@ -122,8 +122,6 @@ p <- add_argument(p,
 )
 
 argv <- parse_args(p)
-options(redist.adjust_labels = FALSE)
-
 vtds <- st_read(dsn = paste0(argv$shapefile))
 
 population <- sum(vtds[[argv$pop_col]])
@@ -176,10 +174,5 @@ if (argv$print) {
     file_name <- argv$output_file
     dir.create(dirname(file_name), recursive = TRUE, showWarnings = FALSE)
     write.csv(plans, file_name)
-    if (argv$resample) {
-        write.csv(t(as.matrix(attr(plans, "old_plans"))), paste0(tools::file_path_sans_ext(file_name), "_assignments_before_resample.csv"))
-        write.csv(t(as.matrix(attr(plans, "resample_indices"))), paste0(tools::file_path_sans_ext(file_name), "_parent_indices_for_reshuffle.csv"))
-        write.csv(t(as.matrix(attr(plans, "resample_wgts"))), paste0(tools::file_path_sans_ext(file_name), "_parent_weights_for_reshuffle.csv"))
-    }
     write.csv(t(as.matrix(plans)), paste0(tools::file_path_sans_ext(file_name), "_assignments.csv"))
 }

data_processing/other_processing_scripts/make_7_enum_ben.sh

@@ -4,12 +4,14 @@
 SCRIPT_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
 TOP_DIR=$(realpath "$SCRIPT_DIR/../..")
 
-# This makes the 4x4 -> 4 omino ensemble. The 7x7 takes a while. So this
+# This makes the 5x5 -> 5 omino ensemble. The 7x7 takes a while. So this
 # is left in for testing purposes.
+echo "Running 5x5 to 5 enumeration"
 julia "$TOP_DIR/data_processing/other_processing_scripts/gridenum.jl" 5 5 5 5 > "$TOP_DIR/other_data_files/processed_data_files/5x5_to_5_enumeration.jsonl"
 python "$TOP_DIR/data_processing/other_processing_scripts/tree_counter.py" "$TOP_DIR/other_data_files/processed_data_files/5x5_to_5_enumeration.jsonl" 5 5 5
 rm "$TOP_DIR/other_data_files/processed_data_files/5x5_to_5_enumeration.jsonl"
 
+# echo "Running 7x7 to 7 enumeration"
 # julia "$TOP_DIR/data_processing/other_processing_scripts/gridenum.jl" 7 7 7 7 > "$TOP_DIR/other_data_files/processed_data_files/7x7_to_7_enumeration.jsonl"
 # python "$TOP_DIR/data_processing/other_processing_scripts/tree_counter.py" "$TOP_DIR/other_data_files/processed_data_files/7x7_to_7_enumeration.jsonl" 7 7 7
 # rm "$TOP_DIR/other_data_files/processed_data_files/7x7_to_7_enumeration.jsonl"

setup_all.sh

@@ -21,6 +21,7 @@ fi
 
 cargo install binary-ensemble --version 0.2.0
 cargo install --git https://github.com/peterrrock2/msms_parser.git --rev 3c37fc5a57b1b9480b95d3d01cad9c37e6564f59
+cargo install --git https://github.com/peterrock2/smc_parser.git --rev 03edd583e40e6198045d62e9eeb8a3e543bb1551
 cargo install --git https://github.com/mggg/frcw.rs --rev b28260bc1eba425731b7ae6a194ab4a2cd4532b6
 cargo install --path ./data_processing/Ben_Tally