virtualenv will not activate in Cygwin inside PyCharm and breaks all unix-like commands after the failure

Question

When trying to activate a venv within the terminal embedded in PyCharm, I recieve the following errors:

$ . venv/Scripts/activate
bash: cygpath: command not found
bash: basename: command not found

Furthermore, after this command fails all Unix-like commands are no longer recognized:

$ ls
bash: ls: command not found
()

I have tried using both Cygwin and Git-Bash as Unix-like terminals in PyCharm. I have also added C:\cygwin64\bin to my PATH variable. Virtualenv activates fine in both the standalone windows of Cygwin and Git-Bash.

---

Here are my settings in PyCharm for both Cygwin and Git-Bash:

"C:\Program Files\Git\bin\sh" -lic "cd ${OLDPWD-.}; bash"
"C:\cygwin64\bin\sh" -lic "cd ${OLDPWD-.}; bash"

---

Not sure if this is relevant, but I noticed that the cwd of the embedded terminal is a weird path:

$ pwd
/cygdrive/c/Users/account_name/Documents/python-projects/project

I have tried cd'ing into the 'normal' path but I have the same results.

I don't know enough about shell scripting to look at the activate file and really know what's going on. But I am 99% sure the issue is coming from these lines (mainly because cypath and basename are only found on these lines)

VIRTUAL_ENV="$(if [ "$OSTYPE" "==" "cygwin" ]; then cygpath -u 'C:\Users\account_name\Documents\python-projects\project\venv'; else echo '/C/Users/account_name/Documents/python-projects/project/venv'; fi;)"
export VIRTUAL_ENV

and

if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT-}" ] ; then
    _OLD_VIRTUAL_PS1="$PS1"
    if [ "x" != x ] ; then
        PS1="$PS1"
    else
        PS1="(`basename \"$VIRTUAL_ENV\"`) $PS1"
    fi
    export PS1
fi

Then again, these are commands that come with cygwin (I think) so the Unix-like commands might be crashing out before this line.

---

All other commands seem to be working as intended, but everything stops working as soon as the failed activation happens. When I swap back to the Windows command prompt using cmd, my venv is immediately activated by PyCharm like normal.

Any input would be greatly helpful because I am at a loss!

---

Update:

Was able to get the . venv/Scripts/activate command to work. I decided to try and run the activate script piece by piece by pasting it into the terminal. Oddly enough, nothing crashed here...

Turns out for some reason if I swap the order of execution in the script, everything works.

If anyone could tell me how to avoid this, it would be greatly beneficial - at the moment I am going to have to manually adjust each activate scripts in all my virtual environments.

Working activate script:

VIRTUAL_ENV="$(if [ "$OSTYPE" "==" "cygwin" ]; then cygpath -u 'C:\Users\account_name\Documents\python-projects\project\venv'; else echo '/C/Users/account_name/Documents/python-projects/project/venv'; fi;)"
export VIRTUAL_ENV

_OLD_VIRTUAL_PATH="$PATH"
PATH="$VIRTUAL_ENV/Scripts:$PATH"
export PATH

# unset PYTHONHOME if set
if ! [ -z "${PYTHONHOME+_}" ] ; then
    _OLD_VIRTUAL_PYTHONHOME="$PYTHONHOME"
    unset PYTHONHOME
fi

if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT-}" ] ; then
    _OLD_VIRTUAL_PS1="$PS1"
    if [ "x" != x ] ; then
        PS1="$PS1"
    else
        PS1="(`basename \"$VIRTUAL_ENV\"`) $PS1"
    fi
    export PS1
fi

# Make sure to unalias pydoc if it's already there
alias pydoc 2>/dev/null >/dev/null && unalias pydoc

pydoc () {
    python -m pydoc "$@"
}

# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands.  Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
    hash -r 2>/dev/null
fi

# This file must be used with "source bin/activate" *from bash*
# you cannot run it directly

deactivate () {
    unset -f pydoc >/dev/null 2>&1

    # reset old environment variables
    # ! [ -z ${VAR+_} ] returns true if VAR is declared at all
    if ! [ -z "${_OLD_VIRTUAL_PATH+_}" ] ; then
        PATH="$_OLD_VIRTUAL_PATH"
        export PATH
        unset _OLD_VIRTUAL_PATH
    fi
    if ! [ -z "${_OLD_VIRTUAL_PYTHONHOME+_}" ] ; then
        PYTHONHOME="$_OLD_VIRTUAL_PYTHONHOME"
        export PYTHONHOME
        unset _OLD_VIRTUAL_PYTHONHOME
    fi

    # This should detect bash and zsh, which have a hash command that must
    # be called to get it to forget past commands.  Without forgetting
    # past commands the $PATH changes we made may not be respected
    if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
        hash -r 2>/dev/null
    fi

    if ! [ -z "${_OLD_VIRTUAL_PS1+_}" ] ; then
        PS1="$_OLD_VIRTUAL_PS1"
        export PS1
        unset _OLD_VIRTUAL_PS1
    fi

    unset VIRTUAL_ENV
    if [ ! "${1-}" = "nondestructive" ] ; then
    # Self destruct!
        unset -f deactivate
    fi
}

# unset irrelevant variables
# deactivate nondestructive

Old activate script:

# This file must be used with "source bin/activate" *from bash*
# you cannot run it directly

deactivate () {
    unset -f pydoc >/dev/null 2>&1

    # reset old environment variables
    # ! [ -z ${VAR+_} ] returns true if VAR is declared at all
    if ! [ -z "${_OLD_VIRTUAL_PATH+_}" ] ; then
        PATH="$_OLD_VIRTUAL_PATH"
        export PATH
        unset _OLD_VIRTUAL_PATH
    fi
    if ! [ -z "${_OLD_VIRTUAL_PYTHONHOME+_}" ] ; then
        PYTHONHOME="$_OLD_VIRTUAL_PYTHONHOME"
        export PYTHONHOME
        unset _OLD_VIRTUAL_PYTHONHOME
    fi

    # This should detect bash and zsh, which have a hash command that must
    # be called to get it to forget past commands.  Without forgetting
    # past commands the $PATH changes we made may not be respected
    if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
        hash -r 2>/dev/null
    fi

    if ! [ -z "${_OLD_VIRTUAL_PS1+_}" ] ; then
        PS1="$_OLD_VIRTUAL_PS1"
        export PS1
        unset _OLD_VIRTUAL_PS1
    fi

    unset VIRTUAL_ENV
    if [ ! "${1-}" = "nondestructive" ] ; then
    # Self destruct!
        unset -f deactivate
    fi
}

# unset irrelevant variables
deactivate nondestructive

VIRTUAL_ENV="$(if [ "$OSTYPE" "==" "cygwin" ]; then cygpath -u 'C:\Users\account_name\Documents\python-projects\project\venv'; else echo '/C/Users/account_name/Documents/python-projects/project/venv'; fi;)"
export VIRTUAL_ENV

_OLD_VIRTUAL_PATH="$PATH"
PATH="$VIRTUAL_ENV/Scripts:$PATH"
export PATH

# unset PYTHONHOME if set
if ! [ -z "${PYTHONHOME+_}" ] ; then
    _OLD_VIRTUAL_PYTHONHOME="$PYTHONHOME"
    unset PYTHONHOME
fi

if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT-}" ] ; then
    _OLD_VIRTUAL_PS1="$PS1"
    if [ "x" != x ] ; then
        PS1="$PS1"
    else
        PS1="(`basename \"$VIRTUAL_ENV\"`) $PS1"
    fi
    export PS1
fi

# Make sure to unalias pydoc if it's already there
alias pydoc 2>/dev/null >/dev/null && unalias pydoc

pydoc () {
    python -m pydoc "$@"
}

# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands.  Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
    hash -r 2>/dev/null
fi

Answer 1

VIRTUAL_ENV="$(if [ "$OSTYPE" "==" "cygwin" ]; then cygpath -u 'C:\Users\account_name\Documents\python-projects\project\venv'; else echo '/C/Users/account_name/Documents/python-projects/project/venv'; fi;)"
export VIRTUAL_ENV

_OLD_VIRTUAL_PATH="$PATH"
PATH="$VIRTUAL_ENV/Scripts:$PATH"
export PATH

# unset PYTHONHOME if set
if ! [ -z "${PYTHONHOME+_}" ] ; then
    _OLD_VIRTUAL_PYTHONHOME="$PYTHONHOME"
    unset PYTHONHOME
fi

if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT-}" ] ; then
    _OLD_VIRTUAL_PS1="$PS1"
    if [ "x" != x ] ; then
        PS1="$PS1"
    else
        PS1="(`basename \"$VIRTUAL_ENV\"`) $PS1"
    fi
    export PS1
fi

# Make sure to unalias pydoc if it's already there
alias pydoc 2>/dev/null >/dev/null && unalias pydoc

pydoc () {
    python -m pydoc "$@"
}

# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands.  Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
    hash -r 2>/dev/null
fi

# This file must be used with "source bin/activate" *from bash*
# you cannot run it directly

deactivate () {
    unset -f pydoc >/dev/null 2>&1

    # reset old environment variables
    # ! [ -z ${VAR+_} ] returns true if VAR is declared at all
    if ! [ -z "${_OLD_VIRTUAL_PATH+_}" ] ; then
        PATH="$_OLD_VIRTUAL_PATH"
        export PATH
        unset _OLD_VIRTUAL_PATH
    fi
    if ! [ -z "${_OLD_VIRTUAL_PYTHONHOME+_}" ] ; then
        PYTHONHOME="$_OLD_VIRTUAL_PYTHONHOME"
        export PYTHONHOME
        unset _OLD_VIRTUAL_PYTHONHOME
    fi

    # This should detect bash and zsh, which have a hash command that must
    # be called to get it to forget past commands.  Without forgetting
    # past commands the $PATH changes we made may not be respected
    if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
        hash -r 2>/dev/null
    fi

    if ! [ -z "${_OLD_VIRTUAL_PS1+_}" ] ; then
        PS1="$_OLD_VIRTUAL_PS1"
        export PS1
        unset _OLD_VIRTUAL_PS1
    fi

    unset VIRTUAL_ENV
    if [ ! "${1-}" = "nondestructive" ] ; then
    # Self destruct!
        unset -f deactivate
    fi
}

# unset irrelevant variables
# deactivate nondestructive