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How to use check_installed method in avocado

Best Python code snippet using avocado_python

test_make_prodigal.py

Source:test_make_prodigal.py

...32    """33    # check installed softs before installing panacota34    cmd = "python3 make"35    error = "Error trying to install PanACoTA from base"36    assert not utils.check_installed("barrnap")37    assert utils.check_installed("prodigal")38    assert not utils.check_installed("mash")39    assert not utils.check_installed("PanACoTA")40    # install panacota and check installation41    utils.run_cmd(cmd, error)42    assert not utils.check_installed("barrnap")43    assert not utils.check_installed("mash")44    assert utils.check_installed("prodigal")45    assert utils.check_installed("PanACoTA")46    # Check that dist-info file exists (pip3 has panacota module)47    cmd = "pip3 show PanACoTA"48    err = "error pip3"49    stdout = "stdout_pip3show.out"50    with open(stdout, "w") as stdof:51        utils.run_cmd(cmd, err, stdout=stdof, stderr=stdof)52    with open(stdout, "r") as stdof:53        for line in stdof:54            if line.startswith("Location"):55                loc = line.split()[-1]56                assert glob.glob(os.path.join(loc, r'PanACoTA*dist-info'))57    os.remove(stdout)58    logfile = "install.log"59    content = ["Installing PanACoTA",60               "Some dependencies needed for some subcommands of PanACoTA are "61               "not installed. Here is the list of missing dependencies, and for what they are "62               "used. If you plan to use the subcommands hereafter, first install required "63               "dependencies:",64               "- mmseqs (for pangenome subcommand)",65               "- mafft (to align persistent genomes in order to infer a phylogenetic tree "66               "after)",67               "- mash (for prepare subcommand, to filter genomes)",68               "- prokka (for annotate subcommand, with syntaxic + functional annotation). "69               "If you only need syntaxic annotation, prodigal is enough.",70               "- barrnap. If you use Prokka for functional annotation, it will not predict RNA.",71               "- One of the 4 following softwares, used to infer a phylogenetic tree:",72               "* FastTree (see README or documentation for more information on how to "73               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)"]74    # Check output logfile content. Check that all content is present, in any order.75    with open(logfile, "r") as logf:76        logf_content = "".join(logf.readlines())77        for linec in content:78            assert linec in logf_content79    # Check that needed packages are installed80    assert utils.is_package_installed("argparse")81    assert utils.is_package_installed("progressbar")82    assert utils.is_package_installed("numpy")83    assert utils.is_package_installed("matplotlib")84    assert utils.is_package_installed("Bio")85def test_upgrade(install_panacota):86    """87    Test upgrading PanACoTA when dependencies (only prodigal) are still installed88    # """89    assert not utils.check_installed("barrnap")90    assert not utils.check_installed("prokka")91    assert utils.check_installed("PanACoTA")92    assert utils.check_installed("prodigal")93    cmd = "python3 make upgrade"94    error = "Error upgrade"95    utils.run_cmd(cmd, error)96    assert not utils.check_installed("barrnap")97    assert not utils.check_installed("prokka")98    assert utils.check_installed("prodigal")99    assert utils.check_installed("PanACoTA")100    logfile = "install.log"101    with open(logfile, "r") as logf:102        lines = logf.readlines()103        assert len(lines) == 2104        assert "Upgrading PanACoTA" in lines[0]105        assert "DONE" in lines[1]106def test_uninstall(install_panacota):107    """108    Test uninstalling PanACoTA109    """110    assert utils.check_installed("prodigal")111    assert not utils.check_installed("barrnap")112    assert not utils.check_installed("prokka")113    assert utils.check_installed("PanACoTA")114    cmd = "python3 make uninstall"115    error = "Error uninstalling"116    utils.run_cmd(cmd, error)117    assert utils.check_installed("prodigal")118    assert not utils.check_installed("prokka")119    assert not utils.check_installed("barrnap")120    assert not utils.check_installed("PanACoTA")121    logfile = "install.log"122    with open(logfile, "r") as logf:123        lines = logf.readlines()124        assert len(lines) == 2125        assert ":: INFO :: Uninstalling PanACoTA" in lines[0]126        assert "DONE" in lines[1]127def test_develop():128    """129    Test installing PanACoTA in developer mode, when prodigal is already installed130    """131    assert not utils.check_installed("PanACoTA")132    assert utils.check_installed("prodigal")133    assert not utils.check_installed("prokka")134    assert not utils.check_installed("barrnap")135    cmd = "python3 make develop"136    error = "Error develop"137    utils.run_cmd(cmd, error)138    assert utils.check_installed("PanACoTA")139    assert utils.check_installed("prodigal")140    assert not utils.check_installed("prokka")141    assert not utils.check_installed("barrnap")142    cmd = "pip3 show PanACoTA"143    err = "error pip3"144    stdout = "stdout_pip3show.out"145    with open(stdout, "w") as stdof:146        utils.run_cmd(cmd, err, stdout=stdof, stderr=stdof)147    with open(stdout, "r") as stdof:148        for line in stdof:149            if line.startswith("Location"):150                loc = line.split()[-1]151                assert glob.glob(os.path.join(loc, r'PanACoTA*egg-info'))152    os.remove(stdout)153    logfile = "install.log"154    content = ["Installing developer packages needed for PanACoTA",155               "- mash (for prepare subcommand, to filter genomes)",156               "Some dependencies needed for some subcommands of PanACoTA are "157               "not installed. Here is the list of missing dependencies, and for what they are "158               "used. If you plan to use the subcommands hereafter, first install required "159               "dependencies:",160               "- mmseqs (for pangenome subcommand)",161               "- barrnap. If you use Prokka for functional annotation, it will not predict RNA.",162               "- mafft (to align persistent genomes in order to infer a phylogenetic tree "163               "after)",164               "- prokka (for annotate subcommand, with syntaxic + functional annotation). "165               "If you only need syntaxic annotation, prodigal is enough.",166               "- One of the 4 following softwares, used to infer a phylogenetic tree:",167               "* FastTree (see README or documentation for more information on how to "168               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)", "DONE"]169    # Check output logfile content. Check that all content is present, in any order.170    with open(logfile, "r") as logf:171        logf_content = "".join(logf.readlines())172        for linec in content:173            assert linec in logf_content174    # Check that needed packages are installed175    assert utils.is_package_installed("argparse")176    assert utils.is_package_installed("progressbar")177    assert utils.is_package_installed("numpy")178    assert utils.is_package_installed("matplotlib")179    assert utils.is_package_installed("Bio")180    assert utils.is_package_installed("sphinx")181    assert utils.is_package_installed("coverage")182def test_install_user():183    """184    Test that when installing from a computer in user mode, it really installs185    PanACoTA in user mode186    """187    assert utils.check_installed("prodigal")188    assert not utils.check_installed("barrnap")189    assert not utils.check_installed("prokka")190    assert not utils.check_installed("PanACoTA")191    cmd = "python3 make --user"192    error = "Error trying to install PanACoTA from base"193    utils.run_cmd(cmd, error)194    assert utils.check_installed("prodigal")195    assert not utils.check_installed("prokka")196    assert not utils.check_installed("barrnap")197    assert utils.check_installed("PanACoTA")198    # Check logfile content199    logfile = "install.log"200    content = ["Installing PanACoTA in user mode...",201               "Some dependencies needed for some subcommands of PanACoTA are "202               "not installed. Here is the list of missing dependencies, and for what they are "203               "used. If you plan to use the subcommands hereafter, first install required "204               "dependencies:",205               "- mash (for prepare subcommand, to filter genomes)",206               "- mmseqs (for pangenome subcommand)",207               "- barrnap. If you use Prokka for functional annotation, it will not predict RNA.",208               "- mafft (to align persistent genomes in order to infer a phylogenetic tree "209               "after)",210               "- prokka (for annotate subcommand, with syntaxic + functional annotation). "211               "If you only need syntaxic annotation, prodigal is enough.",...

test_make_prokka-quicktree.py

Source:test_make_prokka-quicktree.py

...27    """28    Test that when installing from a computer containing only prokka and quicktree, it installs29    PanACoTA, and returns the list of missing dependencies30    """31    assert not utils.check_installed("barrnap")32    assert not utils.check_installed("prodigal")33    assert utils.check_installed("quicktree")34    assert not utils.check_installed("iqtree")35    assert utils.check_installed("prokka")36    assert not utils.check_installed("PanACoTA")37    assert utils.check_installed('quicktree')38    cmd = "python3 make"39    error = "Error trying to install PanACoTA from base"40    utils.run_cmd(cmd, error)41    assert not utils.check_installed("barrnap")42    assert utils.check_installed("prokka")43    assert utils.check_installed("PanACoTA")44    assert utils.check_installed('quicktree')45    cmd = "pip3 show PanACoTA"46    err = "error pip3"47    stdout = "stdout_pip3show.out"48    with open(stdout, "w") as stdof:49        utils.run_cmd(cmd, err, stdout=stdof, stderr=stdof)50    with open(stdout, "r") as stdof:51        for line in stdof:52            if line.startswith("Location"):53                loc = line.split()[-1]54                assert glob.glob(os.path.join(loc, r'PanACoTA*dist-info'))55    os.remove(stdout)56    logfile = "install.log"57    content = ["Installing PanACoTA...", "DONE",58               "Some dependencies needed for some subcommands of PanACoTA are "59               "not installed. Here is the list of missing dependencies, and for what they are "60               "used. If you plan to use the subcommands hereafter, first install required "61               "dependencies:",62               "- mmseqs (for pangenome subcommand)",63               "- mash (for prepare subcommand, to filter genomes)",64               "- mafft (to align persistent genomes in order to infer a phylogenetic tree "65               "after)",66               "See more information on how to download/install those softwares in README or in "67               "documentation.",68               "- barrnap. If you use Prokka for functional annotation, it will not predict RNA."69               ]70    with open(logfile, "r") as logf:71        logf_content = "".join(logf.readlines())72        for linec in content:73            assert linec in logf_content74    # Check that needed packages are installed75    assert utils.is_package_installed("argparse")76    assert utils.is_package_installed("progressbar")77    assert utils.is_package_installed("numpy")78    assert utils.is_package_installed("matplotlib")79    assert utils.is_package_installed("Bio")80    os.remove(logfile)81def test_upgrade(install_panacota):82    """83    Test upgrading PanACoTA when dependencies are still installed84    """85    assert not utils.check_installed("barrnap")86    assert utils.check_installed("prokka")87    assert utils.check_installed("PanACoTA")88    assert utils.check_installed('quicktree')89    cmd = "python3 make upgrade"90    error = "Error upgrade"91    utils.run_cmd(cmd, error)92    assert not utils.check_installed("barrnap")93    assert utils.check_installed("prokka")94    assert utils.check_installed("PanACoTA")95    assert utils.check_installed('quicktree')96    logfile = "install.log"97    with open(logfile, "r") as logf:98        lines = logf.readlines()99        assert len(lines) == 2100        assert "Upgrading PanACoTA" in lines[0]101        assert "DONE" in lines[1]102def test_uninstall_withdep(install_panacota):103    """104    Test uninstalling PanACoTA when dependencies are still installed105    """106    assert not utils.check_installed("barrnap")107    assert utils.check_installed("prokka")108    assert utils.check_installed("quicktree")109    assert utils.check_installed("PanACoTA")110    cmd = "python3 make uninstall"111    error = "Error uninstalling"112    utils.run_cmd(cmd, error)113    assert not utils.check_installed("barrnap")114    assert utils.check_installed("prokka")115    assert not utils.check_installed("PanACoTA")116    assert utils.check_installed('quicktree')117def test_develop():118    """119    Test installing PanACoTA in developer mode, when prokka and barrnap are already installed120    """121    assert not utils.check_installed("PanACoTA")122    assert not utils.check_installed("barrnap")123    assert utils.check_installed('quicktree')124    assert utils.check_installed("prokka")125    cmd = "python3 make develop"126    error = "Error develop"127    utils.run_cmd(cmd, error)128    assert not utils.check_installed("barrnap")129    assert utils.check_installed("prokka")130    assert utils.check_installed("PanACoTA")131    assert utils.check_installed('quicktree')132    cmd = "pip3 show PanACoTA"133    err = "error pip3"134    stdout = "stdout_pip3show.out"135    with open(stdout, "w") as stdof:136        utils.run_cmd(cmd, err, stdout=stdof, stderr=stdof)137    # Check installation in develop mode138    with open(stdout, "r") as stdof:139        for line in stdof:140            if line.startswith("Location"):141                loc = line.split()[-1]142                assert glob.glob(os.path.join(loc, r'PanACoTA*egg-info'))143    os.remove(stdout)144    logfile = "install.log"145    content = ["Installing PanACoTA...",146               "Installing developer packages needed for PanACoTA",147               "Some dependencies needed for some subcommands of PanACoTA are "148               "not installed. Here is the list of missing dependencies, and for what they are "149               "used. If you plan to use the subcommands hereafter, first install required "150               "dependencies:",151               "- mmseqs (for pangenome subcommand)",152               "- mafft (to align persistent genomes in order to infer a phylogenetic tree "153               "after)",154               "- mash (for prepare subcommand, to filter genomes)",155               "- barrnap. If you use Prokka for functional annotation, it will not predict RNA.",156               "See more information on how to download/install those softwares in README or in "157               "documentation."]158    with open(logfile, "r") as logf:159        logf_content = "".join(logf.readlines())160        for linec in content:161            assert linec in logf_content162    # Check that needed packages are installed163    assert utils.is_package_installed("argparse")164    assert utils.is_package_installed("progressbar")165    assert utils.is_package_installed("numpy")166    assert utils.is_package_installed("matplotlib")167    assert utils.is_package_installed("Bio")168    os.remove(logfile)169def test_install_user():170    """171    Test that when installing from a computer containing only prokka, in user mode, it installs172    PanACoTA in /Users and returns list of dependencies173    """174    assert not utils.check_installed("barrnap")175    assert not utils.check_installed("mash")176    assert utils.check_installed("prokka")177    assert utils.check_installed("quicktree")178    assert not utils.check_installed("PanACoTA")179    cmd = "python3 make --user"180    error = "Error trying to install PanACoTA from base"181    utils.run_cmd(cmd, error)182    assert not utils.check_installed("barrnap")183    assert not utils.check_installed("mash")184    assert utils.check_installed("prokka")185    assert utils.check_installed("quicktree")186    assert utils.check_installed("PanACoTA")187    # Check logfile content188    logfile = "install.log"189    content = ["Installing PanACoTA in user mode...",190               "Some dependencies needed for some subcommands of PanACoTA are "191               "not installed. Here is the list of missing dependencies, and for what they are "192               "used. If you plan to use the subcommands hereafter, first install required "193               "dependencies:",194               "- mmseqs (for pangenome subcommand)",195               "- mafft (to align persistent genomes in order to infer a phylogenetic tree "196               "after)",197               "- mash (for prepare subcommand, to filter genomes)",198               "See more information on how to download/install those softwares in README or in "199               "documentation."]200    with open(logfile, "r") as logf:...

test_make_all-installed.py

Source:test_make_all-installed.py

...30    Test that when installing from a computer containing only all dependencies, it returns a message without any warning: everything is ok31    """32    cmd = "python3 make"33    error = "Error trying to install PanACoTA from base"34    assert not utils.check_installed("PanACoTA")35    assert utils.check_installed("barrnap")36    assert utils.check_installed("prokka")37    assert utils.check_installed("mash")38    assert utils.check_installed("FastTreeMP")39    # Install panacota40    utils.run_cmd(cmd, error)41    assert utils.check_installed("PanACoTA")42    assert utils.check_installed("barrnap")43    assert utils.check_installed("prokka")44    assert utils.check_installed("mash")45    assert utils.check_installed("FastTreeMP")46    # Check that panacota is installed (pip3 module exists)47    assert utils.is_package_installed("PanACoTA")48    # Check that it is installed in "final mode"49    cmd = "pip3 show PanACoTA"50    err = "error pip3"51    stdout = "stdout_pip3show.out"52    with open(stdout, "w") as stdof:53        utils.run_cmd(cmd, err, stdout=stdof, stderr=stdof)54    with open(stdout, "r") as stdof:55        for line in stdof:56            if line.startswith("Location"):57                loc = line.split()[-1]58                assert glob.glob(os.path.join(loc, r'PanACoTA*dist-info'))59    os.remove(stdout)60    # Check not installed in user mode61    cmd = "pip list --user"62    list_user_packages = str(subprocess.check_output(shlex.split(cmd)))63    assert "PanACoTA" not in list_user_packages64    # Check output logfile content. Check that all content is present, in any order.65    logfile = "install.log"66    content = ["Installing PanACoTA...", "DONE"]67    with open(logfile, "r") as logf:68        logf_content = "".join(logf.readlines())69        for linec in content:70            assert linec in logf_content71    # Check that needed packages are installed72    assert utils.is_package_installed("argparse")73    assert utils.is_package_installed("progressbar")74    assert utils.is_package_installed("numpy")75    assert utils.is_package_installed("matplotlib")76    assert utils.is_package_installed("Bio")77    print("test_installed done")78def test_upgrade(install_panacota):79    """80    Test upgrading PanACoTA when dependencies are still installed81    """82    assert utils.check_installed("barrnap")83    assert utils.check_installed("prokka")84    assert utils.check_installed("FastTreeMP")85    assert utils.check_installed("PanACoTA")86    # Upgrade PanACoTA87    cmd = "python3 make upgrade"88    error = "Error upgrade"89    utils.run_cmd(cmd, error)90    assert utils.check_installed("barrnap")91    assert utils.check_installed("prokka")92    assert utils.check_installed("PanACoTA")93    assert utils.check_installed("FastTreeMP")94    logfile = "install.log"95    with open(logfile, "r") as logf:96        lines = logf.readlines()97        assert len(lines) == 298        assert "Upgrading PanACoTA" in lines[0]99        assert "DONE" in lines[1]100    print("test_upgrade done")101def test_upgrade_notinstalled():102    """103    Test upgrading PanACoTA when dependencies are not installed (only barrnap),104    and PanACoTA is not installed. It just installs PanACoTA, without prokka dep105    """106    assert utils.check_installed("barrnap")107    assert utils.check_installed("prokka")108    assert utils.check_installed("FastTreeMP")109    assert not utils.check_installed("PanACoTA")110    cmd = "python3 make upgrade"111    error = "Error upgrade"112    utils.run_cmd(cmd, error)113    assert utils.check_installed("barrnap")114    assert utils.check_installed("prokka")115    assert utils.check_installed("PanACoTA")116    assert utils.check_installed("FastTreeMP")117    logfile = "install.log"118    with open(logfile, "r") as logf:119        lines = logf.readlines()120        assert len(lines) == 2121        assert "Upgrading PanACoTA" in lines[0]122        assert "DONE" in lines[1]123    os.remove(logfile)124    print("test_upgrade_notinstalled done")125def test_uninstall(install_panacota):126    """127    Test uninstalling PanACoTA when dependencies are still installed128    """129    assert utils.check_installed("barrnap")130    assert utils.check_installed("prokka")131    assert utils.check_installed("PanACoTA")132    assert utils.check_installed("FastTreeMP")133    cmd = "python3 make uninstall"134    error = "Error uninstalling"135    utils.run_cmd(cmd, error)136    assert not utils.check_installed("PanACoTA")137    assert utils.check_installed("barrnap")138    assert utils.check_installed("prokka")139    assert utils.check_installed("mash")140    assert utils.check_installed("FastTreeMP")141    assert utils.check_installed("quicktree")142    assert utils.check_installed("iqtree") or utils.check_installed("iqtree2")143    logfile = "install.log"144    with open(logfile, "r") as logf:145        lines = logf.readlines()146        assert len(lines) == 2147        assert "Uninstalling PanACoTA" in lines[0]148        assert "DONE" in lines[1]149    print("test_uninstall done")150def test_develop():151    """152    Test installing PanACoTA in developer mode, when prokka and barrnap are already installed153    """154    assert not utils.check_installed("PanACoTA")155    assert utils.check_installed("barrnap")156    assert utils.check_installed("prokka")157    cmd = "python3 make develop"158    error = "Error develop"159    utils.run_cmd(cmd, error)160    assert utils.check_installed("barrnap")161    assert utils.check_installed("prokka")162    assert utils.check_installed("PanACoTA")163    # Check installed in developper mode (egg-info file is present)164    cmd = "pip3 show PanACoTA"165    err = "error pip3"166    stdout = "stdout_pip3show.out"167    with open(stdout, "w") as stdof:168        utils.run_cmd(cmd, err, stdout=stdof, stderr=stdof)169    # Check installation in develop mode170    with open(stdout, "r") as stdof:171        lines = stdof.readlines()172        for line in lines:173            if line.startswith("Location"):174                loc = line.split()[-1]175                assert glob.glob(os.path.join(loc, r'PanACoTA*egg-info'))176    os.remove(stdout)177    # Check not installed in user mode178    cmd = "pip list --user"179    list_user_packages = str(subprocess.check_output(shlex.split(cmd)))180    assert "PanACoTA" not in list_user_packages181    # check logfile content182    logfile = "install.log"183    content = ["Installing PanACoTA...",184               "Installing developer packages needed for PanACoTA", "DONE"]185    with open(logfile, "r") as logf:186        logf_content = "".join(logf.readlines())187        for linec in content:188            assert linec in logf_content189    # Check that needed packages are installed190    assert utils.is_package_installed("argparse")191    assert utils.is_package_installed("progressbar")192    assert utils.is_package_installed("numpy")193    assert utils.is_package_installed("matplotlib")194    assert utils.is_package_installed("Bio")195    assert utils.is_package_installed("sphinx")196    assert utils.is_package_installed("numpydoc")197    assert utils.is_package_installed("pytest")198    assert utils.is_package_installed("coverage")199    print("test_develop done")200def test_install_user():201    """202    Test that when installing from a computer in user mode, it really installs203    PanACoTA in user mode (pip showing PanACoTA when asking for user installed packages)204    """205    cmd = "python3 make --user"206    error = "Error trying to install PanACoTA from base"207    assert utils.check_installed("barrnap")208    assert utils.check_installed("prokka")209    assert not utils.check_installed("PanACoTA")210    assert utils.check_installed("FastTreeMP")211    utils.run_cmd(cmd, error)212    assert utils.check_installed("barrnap")213    assert utils.check_installed("prokka")214    assert utils.check_installed("PanACoTA")215    assert utils.check_installed("FastTreeMP")216    # Check logfile content217    logfile = "install.log"218    content = ["Installing PanACoTA in user mode...", "DONE"]219    with open(logfile, "r") as logf:220        logf_content = "".join(logf.readlines())221        for linec in content:222            assert linec in logf_content223    # Check that needed packages are installed224    assert utils.is_package_installed("argparse")225    assert utils.is_package_installed("progressbar")226    assert utils.is_package_installed("numpy")227    assert utils.is_package_installed("matplotlib")...

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