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 Installation for Windows Using Git Bash
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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
      <https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html>`_.
   -  **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.

2. Open Git Bash and install ``make``:

   .. code:: bash

      choco install make

#. Clone the repository:

   .. code:: bash

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

#. Initialize conda for Git Bash in the Anaconda prompt:

   .. code:: bash

      conda init bash

#. Create the conda environment:

   .. code:: bash

      cd chemsmart
      conda env create -f environment.yml

#. Activate the environment:

   .. code:: bash

      conda activate chemsmart

.. note::

   You may need to run ``conda init`` first on Windows.

*******************
 Make Installation
*******************

#. Install the package and dependencies:

   .. code:: bash

      make install

#. For developers, install additional packages:

   .. code:: bash

      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:

.. code:: bash

   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:

.. code:: bash

   source ~/.bashrc

After this, you can verify the installation:

.. code:: bash

   chemsmart --version

or

.. code:: bash

   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
   :doc:`installation-windows-powershell`.