Restored-acro-r-installation-guide (#37)

* Restore-acro-r-installation-guide and reverted back to the installation guide for acro-r, including virtual environment setup and troubleshooting steps.

* Updated Python version requirement to 3.10 or higher

Author: JessUWE

inst/INSTALL.md

@@ -1,42 +1,143 @@
 # Installation Guides
 
-This document is intended to provide help installing and running acro-r.
+This document is intended to provide help installing and running acro-r in different settings.
 
-## Prerequisites
+Keeping this comprehensive will require input from the community.
 
-- **Python 3.10+**: You must have Python installed on your system.
-- **R**: You need a working installation of R.
+So please email sacro.contact@uwe.ac.uk, or [raise an issue on the GitHub repository](https://github.com/AI-SDC/ACRO-R/issues/new/choose) if:
+ - you have a setting that is not covered, or
+ - the steps outlined below do not work for you,
 
-## Installation
+**Please note**: most of the scenarios below assume that
+- you have a working version of Python 3 (version 3.10 or higher) on your system
+- you are able to access a terminal or command prompt to write and execute some commands.
 
-### Step 1: Install the R package
+---
 
-Install the **acro** package from CRAN:
+## Step 1 create a python virtual environment and install the base python package *acro*
+**In every case** we recommend that you create what is called a 'python virtual environment' called **r-acro**.
+Virtual environments (*venv's*) are recommended best practice.
+This is because they isolate the impact of any changes you make in one venv - such as adding or updating a package- from the rest of your system.
 
-```r
-install.packages("acro")
+There are many tutorials available on the web if you get stuck.
+We do not endorse any particular site, but here are some examples:
+- [an overview with examples  for windows/linux/mac](https://python.land/virtual-environments/virtualenv)
+- [another that also contains instructions for VSCode and Pycharm](https://realpython.com/python-virtual-environments-a-primer/)
+
+**For individual users** we suggest that you do this in your home directory where you should have write permission.
+
+**To install site-wide** we assume you have access rights and know where your organisation's preferred locations are (for example, this might be ```/usr/local``` on a linux system).
+
+### Make a dedicated virtual environment
+You can make a new virtual environment  via:
+- the Anaconda GUI interface to the conda system
+- command line access - by opening a terminal or command prompt and entering the command:
+ ```sh
+  conda create --n r-acro
+  ```
+if you have a version of conda installed or
+ ```sh
+python -m venv ./r-acro
 ```
+to use the native python *venv* package.
 
-### Step 2: Initialize ACRO
+### Change to that virtual environment and install acro
+Anaconda comes with its own GUI to makes this process easy.
+
+**On any system** using *conda* from the command line :
+```sh
+conda activate r-acro
+conda install conda-forge::acro
+
+#assuming this completes successfully you can now exit
+conda deactivate r-acro
+```
 
-The `acro` package interfaces with the Python `acro` library. The package provides a helper function to set up the necessary Python environment and dependencies automatically.
+**On Windows**from the command line with python's *pip* package manager:
+```sh
+# In cmd.exe
+r-acro\Scripts\activate.bat
+# In PowerShell
+r-acro\Scripts\Activate.ps1
+```
+followed by
+```sh
+python -m pip install acro
+#assuming this completes successfully you can now exit the virtual environment
+deactivate
+```
 
-Run the following in your R console:
+**On linux/mac** using conda:
 
-```r
-library("acro")
-acro_init()
+```sh
+source r-acro/bin/activate
+#you should see the your command prompt change to show (r-acro)
+python -m pip install acro
+#assuming this completes successfully you can now exit the virtual environment
+deactivate
 ```
+---
+
+## Step 2 Install the R packages *reticulate* and *acro*
+
+The *reticulate* package is the industry-standard method for supporting communications between R and Python.
+It provides the `plumbing` between the R `front-end'
 
-This command will:
-1. Check for a valid Python installation.
-2. Create a virtual environment named `r-acro`.
-3. Install the required Python `acro` package into this environment.
+These commands should work whether you are
+- working on a machine outside the TRE: in which case packages should install from a mirror of the CRAN service
+- working on a machine inside a TRE: in which case the administrator should have set up a local mirror of approved packages from CRAN
+
+**For individual users**  without permission to make site-wide or machine-wide changes
+Open your preferred R interface - for  example, RStudio, and in a R window type
+```R
+install.packages*("reticulate")
+install.packages("acro")
+```
+
+**For administrators wishing to install for all users site-wide** the commands are  the same but you will need to run them in *sudo* mode.
+
+---
+
+## Step 3: Telling R and reticulate to use the new python virtual environment
+The final step of the process is to tell the R package reticulate which version of python to use.
+
+What we need to do is to set the value of a global variable ```RETICULATE_PYTHON```
+The [R documentation for doing this](https://rstudio.github.io/reticulate/articles/versions.html) is a little inconsistent here, but the following  options all seem to work.
+
+### Option 1- For individuals using RStudio
+If you follow the menu items from ```Tools->Project Options ->Python``` or ```Tools->Global Options->Python``` you can tell it to use the version of python from the virtual environment you create in step 1, either for a specific R project or for all your sessions as shown below
+
+![This is what it looks like: step0](Images/settingpython-rstudio-step0.png)
+
+![This is what it looks like: step1](Images/settingpython-rstudio-step1.png)
+
+![This is what it looks like: step2](Images/settingpython-rstudio-step2.png)
+
+![This is what it looks like: step3](Images/settingpython-rstudio-step3.png)
+
+### Option 2 - Adding code to an individual project file
+    you add add one of the following lines at the start of your file
+   ```R
+   #Either
+    use_python("~/r-acro/bin/python")
+   #or
+   use_virtualenv("~/r-acro")
+   #or
+   use_condaenv("r-acro")
+   #finally followed by
+  library(reticulate)
+  library("acro)"
+   ```
+
+### Option 3 - Editing your personal R preferences
+In your home directory create (or edit) the file ```.Rprofile``` file, adding the lines
+
+```R
+Sys.setenv(RETICULATE_PYTHON=file.path(Sys.getenv("USERPROFILE"),"r-acro/bin/python"))
+Sys.setenv(RETICULATE_PYTHON_ENV=file.path(Sys.getenv("USERPROFILE"),"r-acro"))
+```
 
-Once initialized, you are ready to use ACRO-R!
 
-## Troubleshooting
 
-If you encounter issues during `acro_init()`:
-- Ensure Python 3.10+ is installed and added to your system PATH.
-- If you are on a restricted network, you may need to configure proxy settings for Python package installation.
+### Option 4- Making site-wide changes
+ You can also edit the [site-wide Rprofile]() file to add these global environment variables, using replacing *~/r-acro* with the path to wherever you created the dedicated virtual environment.