Update setup files

Fixed indentation inconsistencies and renamed folder to 'setup'

README.md

@@ -73,7 +73,7 @@ pypef --help
 ```
 
 The detailed routine for setting up a new virtual environment with Anaconda, installing the necessary Python packages for that environment, and running the Jupyter notebook tutorial can be found below in the Tutorial section.
-A quick file setup and run test can be performed running files in [/easy_setup](/easy_setup) containing a Batch script for Windows and a Bash script for Linux (the latter requires conda, i.e. Miniconda3 or Anaconda3, already being installed).
+A quick file setup and run test can be performed running files in [/setup](/setup) containing a Batch script for Windows and a Bash script for Linux (the latter requires conda, i.e. Miniconda3 or Anaconda3, already being installed).
 
 <a name="requirements"></a>
 ## Requirements

easy_setup/linux/conda_install_test.sh → setup/linux/conda_install_test.sh

@@ -1,13 +1,13 @@
 #!/bin/bash
 
-# Run we with ./conda_install_test.sh
 
-# Easy "installer" for downloading repository and running local Python files (not pip-installed).
+# Easy "installer" for downloading repository and running pip-installed PyPEF version.
 # Testing a few PyPEF commands on downloaded test data.
 # Requires conda, i.e. Anaconda3 or Miniconda3 [https://docs.conda.io/en/latest/miniconda.html].
 
 # 1. wget https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.2-0-Linux-x86_64.sh
 # 2. bash Miniconda3-py310_23.5.2-0-Linux-x86_64.sh
+# 3. Run this file with ./conda_install_test.sh
 
 
 # Echo on
@@ -30,18 +30,18 @@ while true; do
     read -p "Test PyPEF installation (downloads PyPEF example test set files and runs a Python test script, ~ 1 h run time) [Y/N]? " yn
     case $yn in
         [Yy]* ) 
-			mkdir test_dataset_avgfp
-			wget https://raw.githubusercontent.com/Protein-Engineering-Framework/PyPEF/master/workflow/test_dataset_avgfp/avGFP.csv
-			wget https://raw.githubusercontent.com/Protein-Engineering-Framework/PyPEF/master/workflow/test_dataset_avgfp/uref100_avgfp_jhmmer_119.a2m
-			wget https://raw.githubusercontent.com/Protein-Engineering-Framework/PyPEF/master/workflow/api_encoding_train_test.py
-			mv avGFP.csv ./test_dataset_avgfp/avGFP.csv
-			mv uref100_avgfp_jhmmer_119.a2m ./test_dataset_avgfp/uref100_avgfp_jhmmer_119.a2m
-			python3 ./api_encoding_train_test.py
-			break;;
+      mkdir test_dataset_avgfp
+      wget https://raw.githubusercontent.com/Protein-Engineering-Framework/PyPEF/master/workflow/test_dataset_avgfp/avGFP.csv
+      wget https://raw.githubusercontent.com/Protein-Engineering-Framework/PyPEF/master/workflow/test_dataset_avgfp/uref100_avgfp_jhmmer_119.a2m
+      wget https://raw.githubusercontent.com/Protein-Engineering-Framework/PyPEF/master/workflow/api_encoding_train_test.py
+      mv avGFP.csv ./test_dataset_avgfp/avGFP.csv
+      mv uref100_avgfp_jhmmer_119.a2m ./test_dataset_avgfp/uref100_avgfp_jhmmer_119.a2m
+      python3 ./api_encoding_train_test.py
+      break;;
         [Nn]* ) 
-			break;;
+      break;;
         * ) 
-			echo "Please answer yes or no.";;
+      echo "Please answer yes or no.";;
     esac
 done
 

setup/windows/README.md

@@ -0,0 +1,8 @@
+Double-clicking the Batch (BAT) file Installs Miniconda3 locally in working/download directory, 
+adds a Python 3.10 environment, and installs the latest PyPEF version for that environment 
+(requires the two PowerShell (PS1) scripts in the same directory as the BAT script).
+Note that invoking the PS scripts requires setting the PowerShell 
+[execution policy](https://learn.microsoft.com/en-us/powershell/module/microsoft.powershell.core/about/about_execution_policies?view=powershell-7.3) 
+with Administrator rights to Bypass  
+(`powershell.exe -ExecutionPolicy Bypass -File`) 
+for running the Batch file successfully.

easy_setup/windows/download_install_miniconda.ps1 → setup/windows/download_install_miniconda.ps1

@@ -3,11 +3,9 @@
 (
     $minicondaUrl = "https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe",
     $downloadPath = "Miniconda3-latest-Windows-x86_64.exe",
-	$fullInstallPath = (Get-Item .).FullName + "\Miniconda3"
+    $fullInstallPath = (Get-Item .).FullName + "\Miniconda3"
 )
 
-#New-Item -Path "." -Name "Miniconda3" -ItemType "directory"
-
 Write-Host "Downloading Miniconda..."
 (New-Object Net.WebClient).DownloadFile($minicondaUrl, $downloadPath)