setup_hybrid

#!/usr/bin/env python

"""Set up MICOM on Google colab.

Do not use this on o local machine, especially not as an admin!
"""

import os
import sys
import shutil
from subprocess import Popen, PIPE

r = Popen(["pip", "install", "rich"])
r.wait()
from rich.console import Console  # noqa
con = Console()

COBRAPY_URL = "git+https://github.com/cdiener/cobrapy@feature/hybrid_solver"
MICOM_URL = "git+https://github.com/micom-dev/micom@feature/hybrid_solver"
OPTLANG_URL = "git+https://github.com/cdiener/optlang@feature/hybrid_solver"


def has_hybrid():
    try:
        import micom as mm
        from cobra.util.solver import interface_to_str
        com = mm.Community(mm.data.test_taxonomy(), solver="hybrid")
        assert "hybrid" in interface_to_str(com.solver.problem)
    except Exception:
        return False
    return True


def cleanup():
    """Remove downloaded files."""
    if os.path.exists("/content/sample_data"):
        shutil.rmtree("/content/sample_data")
    con.log(":broom: Cleaned up unneeded files.")


def run_and_check(args, check, message, failure, success, console=con):
    """Run a command and check that it worked."""
    console.log(message)
    r = Popen(args, env=os.environ, stdout=PIPE, stderr=PIPE,
              universal_newlines=True)
    o, e = r.communicate()
    out = o + e
    if r.returncode == 0 and check in out:
        console.log("[blue]%s[/blue]" % success)
    else:
        console.log("[red]%s[/red]" % failure, out)
        cleanup()
        sys.exit(1)


if __name__ == "__main__":
    if not has_hybrid():
        run_and_check(
            ["python", "-m", "pip", "install", COBRAPY_URL, MICOM_URL, "Cython", "biom-format"],
            "done",
            ":stew: Installing MICOM...",
            "failed installing MICOM :sob:",
            ":white_check_mark: Done."
        )

        run_and_check(
            ["pip", "install", "--no-deps", "highspy", OPTLANG_URL],
            "done",
            ":stew: Installing the hybrid solver...",
            "failed installing the solver :sob:",
            ":white_check_mark: Done."
        )
    else:
        con.log(":snake: Everything already installed and working. Skipped.")

    cleanup()

    con.log("[green]Everything is A-OK. "
            "You can start using MICOM now :thumbs_up:[/green]")