Installing Python and pip

Installing Python and pip

MoleditPy is installed with pip, so you need a working Python first. This page covers getting Python and pip onto Windows, macOS and Linux, and the problems people most often hit along the way. If you already have Python, check the version below and go straight to your platform's installation page.

MoleditPy supports Python 3.9 through 3.14. Any of them works; a recent version such as 3.12 or 3.13 is a good choice.

Prefer conda? If you use Anaconda or Miniconda, you already have Python and pip. Follow the Conda method on the Windows or macOS page instead.

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Check what you have

Open a terminal (Windows: PowerShell or Command Prompt; macOS: Terminal) and run:

python --version
python -m pip --version

On macOS and Linux the command is usually python3:

python3 --version
python3 -m pip --version

If both print a version and the Python version is 3.9–3.14, you are ready — skip to Next steps.

Use python -m pip, not bare pip. If more than one Python is installed, pip may belong to a different one than python, and MoleditPy ends up installed somewhere you are not running. python -m pip always uses the Python you named. The commands on this page follow that rule.

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Windows

1. Download the installer from python.org/downloads.

2. Run it and, on the first screen, tick "Add python.exe to PATH" before clicking Install Now. pip is included.

3. Open a new PowerShell window and check:

   python --version
   python -m pip --version

If python is still not found, the Python Launcher always works: use py in place of python (for example py -m pip install moleditpy-installer).

Typing python opens the Microsoft Store

Windows ships a placeholder python command that opens the Store. Either install Python from python.org as above, or turn the placeholder off: Settings › Apps › Advanced app settings › App execution aliases, and switch off python.exe and python3.exe.

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macOS

macOS may already have a python3 command, but it belongs to Apple's developer tools and can be older than you want. Install your own Python with one of these:

Option 1: python.org installer (recommended)

1. Download the macOS installer from python.org/downloads and run it.

2. When it finishes, a Finder window opens on /Applications/Python 3.x. Double-click Install Certificates.command in it. Do not skip this step — see SSL certificate errors on macOS for why.

3. Open a new Terminal window and check:

   python3 --version
   python3 -m pip --version

Option 2: Homebrew

If you use Homebrew:

brew install python

Homebrew's Python uses Homebrew's own certificates, so the certificate step above is not needed. Homebrew's Python refuses pip install into itself (externally-managed-environment), so install MoleditPy into a virtual environment.

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Linux

Most distributions include Python 3. Install pip and the venv module from the package manager:

# Debian / Ubuntu
sudo apt update
sudo apt install python3 python3-pip python3-venv

# Fedora
sudo dnf install python3 python3-pip

Recent distributions block pip install into the system Python (externally-managed-environment), so install MoleditPy into a virtual environment — see Method B on Installation for Linux.

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Next steps

Install MoleditPy with:

python -m pip install moleditpy-installer
python -m moleditpy_installer

(python3 on macOS and Linux.) The platform pages explain the options and how to upgrade and uninstall:

• Installation for Windows
• Installation for macOS
• Installation for Linux

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Troubleshooting

SSL certificate errors on macOS

Symptom: MoleditPy installs and runs, but anything that downloads from the internet fails — the Plugin Installer cannot reach the registry, PubChem lookups fail, and plugins that call an online service report a network error. The log or the terminal shows something like:

ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate

Cause: the python.org installer for macOS does not set up the root certificates that Python uses to check HTTPS connections. pip is not affected, because it carries its own certificate bundle — which is why installation succeeds and only the app's own downloads fail.

Fix: run the certificate installer that came with Python. Double-click Install Certificates.command in /Applications/Python 3.x (use the folder for the version you installed), or run it from Terminal, adjusting the version number:

open "/Applications/Python 3.13/Install Certificates.command"

Then restart MoleditPy. If you install another Python version later, run that version's Install Certificates.command too.

Pythons from Homebrew or conda do not have this problem.

Network errors behind a proxy or firewall

On a university or company network, downloads can fail with timeouts or ProxyError. If your network uses an HTTP proxy, give it to pip:

python -m pip install --proxy http://proxy.example.com:8080 moleditpy-installer

To let MoleditPy and its plugins use the proxy too, set it in the environment before starting the app:

# macOS / Linux
export HTTPS_PROXY=http://proxy.example.com:8080
export HTTP_PROXY=http://proxy.example.com:8080

# Windows (PowerShell)
$env:HTTPS_PROXY = "http://proxy.example.com:8080"
$env:HTTP_PROXY = "http://proxy.example.com:8080"

Ask your IT department for the proxy address. If the network inspects HTTPS traffic with its own certificate, you will also see CERTIFICATE_VERIFY_FAILED; IT can give you that certificate to install.

pip: command not found / 'pip' is not recognized

Use python -m pip (or python3 -m pip, or py -m pip on Windows). If that also fails, pip is missing: reinstall Python from python.org, or on Linux install the python3-pip package.

error: externally-managed-environment

Your system or Homebrew Python is protected from pip install. Create a virtual environment and install MoleditPy into it:

python3 -m venv ~/moleditpy-env
source ~/moleditpy-env/bin/activate
python -m pip install moleditpy-installer

Activate the environment (source ~/moleditpy-env/bin/activate) each time before running moleditpy from a terminal; the shortcut created by moleditpy-installer remembers the environment for you.

Wrong Python version

moleditpy needs Python 3.9–3.14. If pip says it cannot find a matching version, check python --version. On Windows, py -0 lists every installed Python and py -3.13 -m pip ... picks one; on macOS and Linux, call a specific version such as python3.13.

See also

• Installation for Windows / macOS / Linux / with Docker
• Troubleshooting Common Issues