Installation for Windows Using Git Bash

This guide covers installing CHEMSMART on Windows using Git Bash.

Create Environment

Install the required software:
- Conda: Install either Anaconda3 or Miniconda3 for Windows from the conda installation guide.
- Git: Install Git from https://git-scm.com/downloads (Git Bash is included).
- Chocolatey: Install from https://chocolatey.org/install to enable make support.

Note

Ensure the environment variables for Git and Conda are added correctly.

Open Git Bash and install make:
```
choco install make
```

Clone the repository:

git clone https://github.com/xinglong-zhang/chemsmart.git

Initialize conda for Git Bash in the Anaconda prompt:
```
conda init bash
```

Create the conda environment:

cd chemsmart
conda env create -f environment.yml

Activate the environment:
```
conda activate chemsmart
```

Note

You may need to run conda init first on Windows.

Make Installation

Install the package and dependencies:
```
make install
```
For developers, install additional packages:
```
make install-dev
```

Configure CHEMSMART

Run the make configure command to set up the ~/.chemsmart templates and register the chemsmart command in your Git Bash environment:

make configure

What make configure does on Git Bash:

Copies templates — copies the bundled .chemsmart configuration templates to ~/.chemsmart.
Updates ~/.bashrc — appends export PATH=... and export PYTHONPATH=... lines so that the chemsmart command is available in new Git Bash sessions.
Prompts for software paths — after setting up the shell environment, make configure interactively asks for the installation folders of the following software:
- Gaussian g16
- ORCA
- NCIPLOT
Press Enter to skip any prompt you don’t need. The entered paths are written to ~/.chemsmart/server/*.yaml. These prompts use Python’s click.prompt() and work correctly on all platforms.
Configures the conda path — auto-detects your conda installation via which conda and updates the ~/.chemsmart/server/*.yaml files with the correct conda path for your remote HPC cluster. If conda is not found in PATH, a message is logged — add conda to your PATH and re-run chemsmart config server.
Automatically sources ~/.bashrc — after writing to ~/.bashrc, make configure automatically runs . ~/.bashrc so that chemsmart is active for the rest of the current make session.

Note

make configure sources ~/.bashrc inside its own sub-shell process. Because a child process cannot export environment changes back to its parent, your current Git Bash terminal is not automatically updated. You must run source ~/.bashrc manually in your own terminal, or open a new Git Bash window.

After make configure completes, the chemsmart command is available immediately in any new terminal. To activate it in your current Git Bash session without opening a new one, run:

source ~/.bashrc

After this, you can verify the installation:

chemsmart --version

or

chemsmart --help

Note

If ~/.bashrc already contains a chemsmart section (i.e. make configure has been run before), it will not be modified again to avoid duplicate entries.

Tip

If you prefer to use the Anaconda or Miniconda PowerShell Prompt instead of Git Bash, see Installation for Windows Using Anaconda PowerShell.