Updated clt documentation

docs/libraries/clt/index.md

@@ -5,21 +5,76 @@ layout: default
 
 The [SenNet Command-Line Transfer (CLT)](https://pypi.org/project/atlas-consortia-clt/) tool streamlines the download of individual files and directories from multiple datasets and uploads. Files and directories are specified in a manifest file and given to the CLT.
 
-
 ## Installation
 
 The CLT uses the [Globus Connect Personal](https://www.globus.org/globus-connect-personal) (GCP) application to download the specified files and directories to your computer. GCP and the CLT require a SenNet account. This account is the same account used to log in to the SenNet Data Sharing Portal. Windows users should follow [additional instructions](gcp-windows) to correctly setup GCP.
 
-The CLT requires Python 3.9 or above. The CLT can be installed through PyPI using the following command:
+The CLT requires Python 3.9 or above.
+
+### pip
+
+Install the CLT globally using pip:
+```bash
+pip install atlas-consortia-clt
+```
+
+### pip with a virtual environment
 
+Installing in a virtual environment keeps the CLT and its dependencies isolated from other Python projects.
+
+**macOS/Linux:**
+```bash
+python3 -m venv clt-env # creates virtual environment named clt-env in the current directory
+source clt-env/bin/activate # activates the virtual environment
+pip install atlas-consortia-clt
 ```
+
+**Windows:**
+```bash
+python -m venv clt-env # creates virtual environment named clt-env in the current directory
+clt-env\Scripts\activate # activates the virtual environment
 pip install atlas-consortia-clt
 ```
 
+To use the CLT in the future, activate the virtual environment first:
+
+**macOS/Linux:**
+```bash
+source clt-env/bin/activate
+```
+
+**Windows:**
+```bash
+clt-env\Scripts\activate
+```
+
+To deactivate the virtual environment, run the following command on any platform:
+```bash
+deactivate
+```
+
+### pipx
+
+[pipx](https://pipx.pypa.io) installs the CLT in its own isolated environment and automatically exposes the `sennet-clt` commands on your `PATH`, without affecting other Python packages.
+
+Install pipx if you don't have it. Check the [pipx documentation](https://pipx.pypa.io/stable/#install-pipx) for detailed installation instructions.
+
+Then install the CLT. The CLT relies on the `globus-cli` package and must also be installed via pipx.
+```bash
+pipx install atlas-consortia-clt globus-cli
+```
+
+To upgrade:
+```bash
+pipx upgrade atlas-consortia-clt globus-cli
+```
+
 ## Manifest File
+
 Files and directories of interest are specified in a manifest file. A manifest is a text file that contains the dataset id and the path to the dataset, separated by a space. Multiple files or directories can be specified by placing each on a separate line. A directory can be specified by ending the path with a slash `/`. An optional header can be specified at the top of the file. Text after the path will be ignored and can be used for comments.
 
 ### Example
+
 ```
 dataset_id file_or_dir_specifier    #optional header line is ignored
 SNT123.ABCD.456 /metadata.tsv       #download the metadata.tsv file for dataset SNT123.ABCD.456
@@ -38,48 +93,49 @@ at the top left of the table.<br>
 ## Usage
 
 Usage documentation can also be found by running the following command:
-```
+```bash
 sennet-clt -h
 ```
 
 ### Login
 
-A one-time login is required for any download session. For non-public data, you must log in with your SenNet account. For publicly available data, you can log in with any account accepted by the login form (Google and ORCID). Log in can be initiated using the following command:
+A one-time login is required for any download session. For non-public data, you must log in with your SenNet account. For publicly available data, you can log in with any account accepted by the login form (Google and ORCID). Login can be initiated using the following command:
 
-``` 
+```bash
 sennet-clt login
 ```
 
-In the scenario that you cannot utilize a browser you will have to utilize Globus' CLI [`--no-local-server`
-option](https://docs.globus.org/cli/reference/login/#options-no-local-server). This will present you with a URL to be
-copied onto another device with browser support to perform authentication. Once complete you will be presented with an
-authorization code to be entered in the original console.
+By default, login will automatically open a browser window to complete authentication. If you are in a headless environment (e.g. a remote server without a browser), use the `--no-browser` flag. This will display a URL in the terminal that you can copy and open in a browser on another device to complete the login:
+
+```bash
+sennet-clt login --no-browser
+```
 
 ### Logout
 
 Logout can be used to log out the current user.
-```
+```bash
 sennet-clt logout
 ```
 
 ### Transfer
 
 A data transfer and download can be initiated using the transfer command and a manifest file. You must be logged in to use the transfer command.
-```
+```bash
 sennet-clt transfer <PATH/TO/MANIFEST/FILE> 
 ```
 An optional destination argument can be specified. The destination is the directory on the user's computer where data will be downloaded. The directory will be created if it doesn't exist. The destination argument is relative to the user's home directory (~). For example, `--destination Desktop/sennet-data` corresponds to an absolute path of `~/Desktop/sennet-data`. The default destination directory is `~/sennet-downloads`.
-```
+```bash
 sennet-clt transfer <PATH/TO/MANIFEST/FILE> --destination <PATH/TO/DESTINATION/DIRECTORY>
 ```
 An optional `--from-protected-space` flag can be specified to download protected data belonging to a published protected `Dataset`. By default, the CLT will download public data only. The user must have access to the protected data in order for the transfer to be successful.
-```
+```bash
 sennet-clt transfer <PATH/TO/MANIFEST/FILE> --from-protected-space
 ```
 
 ### Whoami
 
 Whoami can be used to display the information of the currently logged in user.
-``` 
+```bash
 sennet-clt whoami
 ```