Installation for Windows Using Anaconda PowerShell

This guide covers installing CHEMSMART on Windows using the Anaconda or Miniconda PowerShell prompt.

Create Environment

Install the required software:
- Conda: Install either Anaconda3 or Miniconda3 for Windows. The Anaconda / Miniconda installer registers the Anaconda PowerShell Prompt shortcut in the Start Menu.
- Chocolatey: Install from https://chocolatey.org/install to enable make support.

Note

Ensure the Anaconda / Miniconda environment variables are added correctly during installation (select “Add Anaconda to my PATH environment variable” or run the installer with default settings and use the dedicated Anaconda Prompt).

Open the Anaconda PowerShell Prompt (or Miniconda PowerShell Prompt) from the Start Menu and install make:
```
choco install make
```

Clone the repository:

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

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 powershell once to allow conda environments to be activated inside PowerShell. If prompted, close and reopen the Anaconda PowerShell Prompt afterwards.

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 PowerShell environment:

make configure

What make configure does on Anaconda / Miniconda PowerShell:

Copies templates — copies the bundled .chemsmart configuration templates to ~\.chemsmart (%USERPROFILE%\.chemsmart).
Updates PowerShell profiles — writes a $env:PYTHONPATH entry and a Set-Alias -Name chemsmart -Value chemsmart.exe declaration to:
- ~/Documents/WindowsPowerShell/Microsoft.PowerShell_profile.ps1 (Windows PowerShell 5.x, used by Anaconda / Miniconda prompts)
- ~/Documents/PowerShell/Microsoft.PowerShell_profile.ps1 (PowerShell 7+, if installed)
Note

A ``Set-Alias`` declaration (rather than a bare $env:PATH addition) is used because PowerShell resolves aliases before external commands in PATH. This means that even if a bare POSIX-style chemsmart script (no .exe extension) is present somewhere on PATH — for example in chemsmart/cli/ in a development install — the alias wins and chemsmart.exe (which pip places in the conda Scripts/ directory) is called directly. This avoids the Windows “Open with” popup.

If you previously ran make configure and your profile contained old $env:PATH or function chemsmart entries, re-running make configure will automatically remove the old block and write the new Set-Alias declaration in its place.
Prompts for software paths — after setting up the PowerShell profiles, 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 conda in PATH 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.
Outputs activation instructions — at the end of make configure, the Makefile prints a reminder to run . $PROFILE so that chemsmart is immediately available in the current session.

Note

On Windows, make configure does not execute . $PROFILE automatically — it only prints the instruction. You must run . $PROFILE manually in your Anaconda/Miniconda PowerShell Prompt to load the chemsmart alias into your current session. Alternatively, simply open a new Anaconda PowerShell Prompt.

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

. $PROFILE

After this, you can verify the installation:

chemsmart --version

or

chemsmart --help

Note

Each time make configure is run, the installer replaces the previous chemsmart block in the PS profile with the latest settings. Re-running configure is therefore safe and idempotent.

Troubleshooting

PowerShell execution policy error

If you see an error like cannot be loaded because running scripts is disabled on this system, you need to allow local scripts to run. Open PowerShell as Administrator and run:

Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser

conda not found after make configure

If conda is not in your PATH when make configure runs, the server YAML files will not be updated automatically. Add conda to your PATH (or activate the conda base environment) and then re-run:

chemsmart config server

chemsmart command not found after make configure

Make sure you have reloaded the PowerShell profile:

. $PROFILE

Or open a new Anaconda PowerShell Prompt — the profile is sourced automatically on startup.

chemsmart opens an “Open with” popup instead of running

This means Windows found a bare POSIX script named chemsmart (no .exe extension) in $env:PATH before resolving the alias. Re-run make configure to update the profile with the Set-Alias declaration that takes precedence over external files, then reload the profile:

make configure
. $PROFILE