def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("cp ../CHANGES.rst change_log.rst")
        ctx.run("sphinx-apidoc -d 6 -o . -f ../pymatgen_diffusion")
        ctx.run("rm pymatgen_diffusion*.tests.rst")
        for f in glob.glob("*.rst"):
            if f.startswith('pymatgen_diffusion') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("pymatgen") and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        # Avoid ths use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("cp ../CHANGES.rst change_log.rst")
        ctx.run("sphinx-apidoc -d 6 -o . -f ../matgendb")
        ctx.run("rm matgendb*.tests.rst")
        for f in glob.glob("*.rst"):
            if f.startswith('matgendb') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("pymatgen") and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")
        ctx.run("cp _static/* ../docs/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        # Avoid ths use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #3
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def make_doc(ctx):
    with open("CHANGES.rst") as f:
        contents = f.read()

    toks = re.split("\-{3,}", contents)
    n = len(toks[0].split()[-1])
    changes = [toks[0]]
    changes.append("\n" + "\n".join(toks[1].strip().split("\n")[0:-1]))
    changes = ("-" * n).join(changes)

    with open("docs_rst/latest_changes.rst", "w") as f:
        f.write(changes)

    with cd("examples"):
        ctx.run("jupyter nbconvert --to html *.ipynb")
        ctx.run("mv *.html ../docs_rst/_static")

    with cd("docs_rst"):
        ctx.run("cp ../CHANGES.rst change_log.rst")
        ctx.run("sphinx-apidoc --separate -d 6 -o . -f ../pymatgen")
        ctx.run("rm pymatgen*.tests.*rst")
        for f in glob.glob("*.rst"):
            if f.startswith('pymatgen') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith(
                                    "pymatgen"
                            ) and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")

        ctx.run("cp _static/* ../docs/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")
        ctx.run("rm -r _sources")

        # This makes sure pymatgen.org works to redirect to the Gihub page
        ctx.run("echo \"pymatgen.org\" > CNAME")
        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #4
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def update_doc(ctx):
    with cd("docs/_build/html/"):
        ctx.run("git pull")
    make_doc(ctx)
    with cd("docs/_build/html/"):
        ctx.run("git add .")
        ctx.run('git commit -a -m "Update dev docs"')
        ctx.run("git push origin gh-pages")
Exemple #5
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def update_doc(ctx):
    with cd("docs/_build/html/"):
        ctx.run("git pull")
    make_doc(ctx)
    with cd("docs/_build/html/"):
        ctx.run("git add .")
        ctx.run("git commit -a -m \"Update dev docs\"")
        ctx.run("git push origin gh-pages")
Exemple #6
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("sphinx-apidoc -o . -f ../amset")
        ctx.run("make html")
        ctx.run("cp -r build/html/* ../docs")

    with cd("docs"):
        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #7
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def make_doc(ctx):
    with open("CHANGES.rst") as f:
        contents = f.read()

    toks = re.split("\-{3,}", contents)
    n = len(toks[0].split()[-1])
    changes = [toks[0]]
    changes.append("\n" + "\n".join(toks[1].strip().split("\n")[0:-1]))
    changes = ("-" * n).join(changes)

    with open("docs_rst/latest_changes.rst", "w") as f:
        f.write(changes)

    with cd("examples"):
       ctx.run("jupyter nbconvert --to html *.ipynb")
       ctx.run("mv *.html ../docs_rst/_static")

    with cd("docs_rst"):
        ctx.run("cp ../CHANGES.rst change_log.rst")
        ctx.run("sphinx-apidoc --separate -d 6 -o . -f ../pymatgen")
        ctx.run("rm pymatgen*.tests.*rst")
        for f in glob.glob("*.rst"):
            if f.startswith('pymatgen') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("pymatgen") and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")
        
        ctx.run("cp _static/* ../docs/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")
        ctx.run("rm -r _sources")

        # This makes sure pymatgen.org works to redirect to the Gihub page
        ctx.run("echo \"pymatgen.org\" > CNAME")
        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("sphinx-apidoc -f -o source ../robocrys " + exclude_paths)
        ctx.run("make html")
        ctx.run("cp -r build/html/* ../docs")

    with cd("docs"):
        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #9
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("sphinx-apidoc -o . -f ../fireworks")
        ctx.run("make html")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")

        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #10
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("sphinx-apidoc -o api/ -f ../turbomoleio")
        ctx.run("make html")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")

        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #11
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("sphinx-apidoc -o . -f ../rocketsled")
        ctx.run("make html")
        ctx.run("cp _static/* ../docs/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")

        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #12
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("python featurizer_summary.py > featurizer_summary.rst")
        ctx.run("sphinx-apidoc -o . -f ../matminer")
        ctx.run("make html")
        ctx.run("cp _static/* ../docs/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")

        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #13
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def make_doc(ctx):
    """
    Generate API documentation + run Sphinx.

    :param ctx:
    """
    # with open("CHANGES.rst") as f:
    #     contents = f.read()
    #
    # toks = re.split(r"\-{3,}", contents)
    # n = len(toks[0].split()[-1])
    # changes = [toks[0]]
    # changes.append("\n" + "\n".join(toks[1].strip().split("\n")[0:-1]))
    # changes = ("-" * n).join(changes)

    # with open("docs_rst/latest_changes.rst", "w") as f:
    #     f.write(changes)

    ctx.run("cp README.rst api-docs-source/index.rst")

    with cd("api-docs-source"):
        ctx.run("rm maml.*.rst", warn=True)
        ctx.run("sphinx-apidoc --separate -P -d 7 -o . -f ../maml")
        ctx.run("rm maml*.tests.*rst", warn=True)
        for f in glob.glob("maml*.rst"):
            newoutput = []
            with open(f, 'r') as fid:
                for line in fid:
                    if re.search("maml.*\._.*", line):
                        continue
                    else:
                        newoutput.append(line)

            with open(f, 'w') as fid:
                fid.write("".join(newoutput))
        ctx.run("rm maml*._*.rst")

    ctx.run("rm -r docs", warn=True)

    ctx.run("sphinx-build -b html api-docs-source docs")

    # ctx.run("cp _static/* ../docs/html/_static", warn=True)

    with cd("docs"):
        ctx.run("rm -r .doctrees", warn=True)

        # This makes sure maml.org works to redirect to the Github page
        # ctx.run("echo \"maml.org\" > CNAME")
        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #14
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("python featurizer_summary.py > featurizer_summary.rst")
        ctx.run("python dataset_summary.py > dataset_summary.rst")
        ctx.run("sphinx-apidoc -o . -f ../matminer")
        ctx.run("make html")
        ctx.run("cp _static/* ../docs/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")

        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #15
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def makedoc(c, preview=False, port=8000):
    c.run("sphinx-apidoc --separate -d 6 -o build -f maggma")
    c.run("make html")
    if preview:
        with cd("build/html"):
            print("Serving docs preview at http://localhost:{}".format(port))
            c.run("python -m http.server {}".format(port))
Exemple #16
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 def get_directories_in_queue(self):
     user_name = getpass.getuser()
     if self.queue_type == 'PBS':
         get_job_ids = ['qstat', '-u', user_name]
         check_job_info = ['qstat', '-f']
         workdir_str = 'PBS_O_WORKDIR'
         split_str = ','
     elif self.queue_type == 'SLURM':
         get_job_ids = ['squeue', '-u', user_name]
         check_job_info = ['scontrol', 'show', 'job']
         workdir_str = 'WorkDir'
         split_str = '\n'
     scan = subprocess.Popen(get_job_ids, stdout=subprocess.PIPE)
     scan.wait()
     scan_out = scan.stdout.read().split('\n')
     ids = [i.split()[0] for i in scan_out if user_name in i]
     dirs = []
     for id in ids:
         scan1 = subprocess.Popen(check_job_info + [id],
                                  stdout=subprocess.PIPE)
         out = scan1.stdout.read().split(split_str)
         line = [i for i in out if workdir_str in i][0]
         dir = line.replace('\n\t', '').split('=')[1]
         with cd(dir):
             dir_orig = os.getcwd()
             dirs.append(dir_orig)
     return dirs
Exemple #17
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def pytest(ctx):
    pytest_cmd = r"""\
pytest -n 2 --cov-config=.coveragerc --cov=abipy -v --doctest-modules pseudo_dojo \
    --ignore=pseudo_dojo/integration_tests
"""
    with cd(DOJO_ROOTDIR):
        ctx.run(pytest_cmd, pty=True)
Exemple #18
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    def gnuplot(self):
        """
        Plot the results with gnuplot.
        Based on the `replot.sh` script provided by the oncvpsp code.
        """
        outfile = self.filepath
        base = os.path.basename(outfile)
        gnufile = base + ".scr"
        plotfile = base + ".plot"
        temp = base + ".tmp"

        from monty.os import cd
        from subprocess import check_call
        workdir = tempfile.mkdtemp()
        print("Working in %s" % workdir)

        with cd(workdir):
            check_call("awk 'BEGIN{out=0};/GNUSCRIPT/{out=0}; {if(out == 1) {print}}; \
                                /DATA FOR PLOTTING/{out=1}' %s > %s" % (outfile, plotfile), shell=True)

            check_call("awk 'BEGIN{out=0};/END_GNU/{out=0}; {if(out == 1) {print}}; \
                                /GNUSCRIPT/{out=1}' %s > %s" % (outfile, temp), shell=True)

            check_call('sed -e 1,1000s/t1/"%s"/ %s > %s' % (plotfile, temp, gnufile), shell=True)

            try:
                check_call(["gnuplot", gnufile])
            except KeyboardInterrupt:
                print("Received KeyboardInterrupt")

        os.rmdir(workdir)
Exemple #19
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 def test_continue(self):
     # Test the continuation functionality
     with cd(os.path.join(test_dir, 'postprocess')):
         # Test default functionality
         with ScratchDir('.', copy_from_current_on_enter=True) as d:
             v = VaspJob("hello", auto_continue=True)
             v.setup()
             self.assertTrue(os.path.exists("continue.json"), "continue.json not created")
             v.setup()
             self.assertEqual(Poscar.from_file("CONTCAR").structure,
                              Poscar.from_file("POSCAR").structure)
             self.assertEqual(Incar.from_file('INCAR')['ISTART'], 1)
             v.postprocess()
             self.assertFalse(os.path.exists("continue.json"),
                              "continue.json not deleted after postprocessing")
         # Test explicit action functionality
         with ScratchDir('.', copy_from_current_on_enter=True) as d:
             v = VaspJob("hello", auto_continue=[{"dict": "INCAR",
                                                  "action": {"_set": {"ISTART": 1}}}])
             v.setup()
             v.setup()
             self.assertNotEqual(Poscar.from_file("CONTCAR").structure,
                                 Poscar.from_file("POSCAR").structure)
             self.assertEqual(Incar.from_file('INCAR')['ISTART'], 1)
             v.postprocess()
Exemple #20
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def write_input(temp, params, xkeys, parr=True, func='pbe'):
    '''
    Method to write QE input file in scratch dir from template.
    :param temp (list): Returned from get_template() method.
    :param params (dict): Dict of parameters to pass into template. Keys
        are the strings within the placeholders in the template.
    :param xkeys ([str]): Parameters to distinguish between different
        input files.
    :param parr (bool): Whether use parallel mode (send the calculation
        to computational nodes). Default to True. Note in non-parallel
        (serial, run the calculation on login nodes), you need to cp the
        psp files into scratch dir.
    :param func (str): Functional used. Default to GGA. Refer to the
        format of filename of template files.
    :return: None
    '''
    t, info = temp
    pl = [str(params[k]) for k in xkeys]
    jobname = "_".join(info+pl)
    if parr:
        c = Composition(info[0])
        elements = [e.symbol for e in c.elements]
        psp = {}
        for e in elements:
            psp[e] = os.path.abspath(glob.glob('../%s.%s*.UPF' % (e, func))[0])
        os.makedirs(jobname)
        with cd(jobname):
            _write_input_from_temp(t, jobname, params)
            for e in psp.keys():
                shutil.copyfile(psp[e],os.path.split(psp[e])[1])
    else:
        _write_input_from_temp(t, jobname, params)
Exemple #21
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def update_coverage(ctx):
    with cd("docs/_build/html/"):
        ctx.run("git pull")
    ctx.run(
        "nosetests --config=nose.cfg --cover-html --cover-html-dir=docs/_build/html/coverage"
    )
    update_doc()
Exemple #22
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def make_doc(ctx):
    with cd("docs"):
        ctx.run("sphinx-apidoc -o . -f ../custodian")
        ctx.run("rm custodian*.tests.rst")
        for f in glob.glob("docs/*.rst"):
            if f.startswith('docs/custodian') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("custodian") and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))

        ctx.run("make html")
Exemple #23
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def makedoc(ctx):
    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "matgendb.webui.settings")
    with cd("docs"):
        ctx.run("sphinx-apidoc -o . -f ../matgendb")
        ctx.run("rm matgendb*.tests.rst")
        for f in glob.glob("docs/*.rst"):
            if f.startswith('docs/matgendb') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("matgendb") and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))

        ctx.run("make html")
        ctx.run("cp favicon.ico _build/html/_static/favicon.ico")
Exemple #24
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def write_input(temp, params, xkeys, parr=True, func='pbe'):
    '''
    Method to write QE input file in scratch dir from template.
    :param temp (list): Returned from get_template() method.
    :param params (dict): Dict of parameters to pass into template. Keys
        are the strings within the placeholders in the template.
    :param xkeys ([str]): Parameters to distinguish between different
        input files.
    :param parr (bool): Whether use parallel mode (send the calculation
        to computational nodes). Default to True. Note in non-parallel
        (serial, run the calculation on login nodes), you need to cp the
        psp files into scratch dir.
    :param func (str): Functional used. Default to GGA. Refer to the
        format of filename of template files.
    :return: None
    '''
    t, info = temp
    pl = [str(params[k]) for k in xkeys]
    jobname = "_".join(info + pl)
    if parr:
        c = Composition(info[0])
        elements = [e.symbol for e in c.elements]
        psp = {}
        for e in elements:
            psp[e] = os.path.abspath(glob.glob('../%s.%s*.UPF' % (e, func))[0])
        os.makedirs(jobname)
        with cd(jobname):
            _write_input_from_temp(t, jobname, params)
            for e in psp.keys():
                shutil.copyfile(psp[e], os.path.split(psp[e])[1])
    else:
        _write_input_from_temp(t, jobname, params)
Exemple #25
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def make_doc(ctx):
    with cd("docs"):
        ctx.run("sphinx-apidoc -d 6 -o . -f ../custodian")
        ctx.run("rm custodian*.tests.rst")
        for f in glob.glob("*.rst"):
            if f.startswith('custodian') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("custodian") and not clean.endswith(
                                    "tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")
        # ctx.run("cp _static/* _build/html/_static")

        # This makes sure pymatgen.org works to redirect to the Gihub page
        # ctx.run("echo \"pymatgen.org\" > _build/html/CNAME")
        # Avoid ths use of jekyll so that _dir works as intended.
        ctx.run("touch _build/html/.nojekyll")
Exemple #26
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    def test_postprocess(self):
        with cd(os.path.join(test_dir, "postprocess")):
            with ScratchDir(".", copy_from_current_on_enter=True):
                shutil.copy("INCAR", "INCAR.backup")

                v = VaspJob("hello",
                            final=False,
                            suffix=".test",
                            copy_magmom=True)
                v.postprocess()
                incar = Incar.from_file("INCAR")
                incar_prev = Incar.from_file("INCAR.test")

                for f in [
                        "INCAR",
                        "KPOINTS",
                        "CONTCAR",
                        "OSZICAR",
                        "OUTCAR",
                        "POSCAR",
                        "vasprun.xml",
                ]:
                    self.assertTrue(os.path.isfile(f"{f}.test"))
                    os.remove(f"{f}.test")
                shutil.move("INCAR.backup", "INCAR")

                self.assertAlmostEqual(incar["MAGMOM"],
                                       [3.007, 1.397, -0.189, -0.189])
                self.assertAlmostEqual(incar_prev["MAGMOM"], [5, -5, 0.6, 0.6])
Exemple #27
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    def test_recover_errors(self):
        fw, launch_id = self.lp.reserve_fw(self.fworker, self.launch_dir)
        fw = self.lp.get_fw_by_id(1)
        with cd(self.launch_dir):
            setup_offline_job(self.lp, fw, launch_id)

        # remove the directory to cause an exception
        shutil.rmtree(self.launch_dir)

        # recover ignoring errors
        self.assertIsNotNone(
            self.lp.recover_offline(launch_id,
                                    ignore_errors=True,
                                    print_errors=True))

        fw = self.lp.get_fw_by_id(launch_id)

        self.assertEqual(fw.state, 'RESERVED')

        #fizzle
        self.assertIsNotNone(
            self.lp.recover_offline(launch_id, ignore_errors=False))

        fw = self.lp.get_fw_by_id(launch_id)

        self.assertEqual(fw.state, 'FIZZLED')
Exemple #28
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def make_doc(ctx):
    with cd("docs"):
        ctx.run("sphinx-apidoc -o . -f ../monty")
        for f in glob.glob("docs/*.rst"):
            if f.startswith('docs/monty') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("monty") and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")

        #This makes sure monty.org works to redirect to the Gihub page
        ctx.run("echo \"monty.org\" > _build/html/CNAME")
        #Avoid ths use of jekyll so that _dir works as intended.
        ctx.run("touch _build/html/.nojekyll")
def build_conda(ctx, pkg, nopy27=False):
    with cd(os.path.join(module_dir, "conda-skeletons")):
        print("Building %s" % pkg)
        ctx.run("conda build --user matsci %s" % pkg)
        if not nopy27:
            # Py27 versions
            ctx.run("conda build --user matsci --python 2.7 %s" % pkg)
Exemple #30
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def get_directories_VaspJobNotDone(root_dir):
    with cd(root_dir):  ### avoid the link problems
        root_dir_real = os.getcwd()
    scan = subprocess.Popen(['find', root_dir_real, '-name', 'POSCAR'],
                            stdout=subprocess.PIPE)
    scan.wait()
    pos_coll = scan.stdout.read().split()
    pos_dirs = [os.path.split(i)[0] for i in pos_coll]
    vaspjob_dirs = []
    for dir in pos_dirs:
        try:
            pos = Poscar.from_file(os.path.join(dir, 'POSCAR'))
            pot = Potcar.from_file(os.path.join(dir, 'POTCAR'))
            incar = Incar.from_file(os.path.join(dir, 'INCAR'))
            kpt = Kpoints.from_file(os.path.join(dir, 'KPOINTS'))
        except:
            print 'input files are not ready in %s' % dir
        else:
            try:
                out = Outcar(os.path.join(dir, 'OUTCAR'))
                if len(out.run_stats) != 7:
                    vaspjob_dir.append(dir)
            except:
                vaspjob_dirs.append(dir)
    return vaspjob_dirs
Exemple #31
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def pytest(ctx):
    pytest_cmd = r"""\
pytest -n 2 --cov-config=.coveragerc --cov=abiflows -v --doctest-modules abiflows \
    --ignore=abiflows/fireworks/integration_tests
"""
    with cd(ROOTDIR):
        ctx.run(pytest_cmd, pty=True)
Exemple #32
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def temp_dir(delete, changedir=True):
    """
    Context manager that creates a temporary directory with tempfile.mkdtemp and cd to it with monty.os.cd.

    Args:
        delete (bool): if True the directory will be deleted at the end of the job, if False it will be preserved.
        changedir (bool): if True inside the context manager will make a cd to the temporary directoy.

    Yields:
        the path to the temporary directory created.
    """

    testdir = tempfile.mkdtemp()
    if not delete:
        print("Running folder: {}".format(testdir))

    try:
        if changedir:
            with cd(testdir):
                yield testdir
        else:
            yield testdir
    finally:
        if delete:
            shutil.rmtree(testdir, ignore_errors=True)
Exemple #33
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def pytest(ctx):
    pytest_cmd = r"""\
pytest -n 2 --cov-config=.coveragerc --cov=abiflows -v --doctest-modules abiflows \
    --ignore=abiflows/fireworks/integration_tests
"""
    with cd(ROOTDIR):
        ctx.run(pytest_cmd, pty=True)
Exemple #34
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    def test_postprocess(self):
        # test gzipped and zipping of additional files
        with cd(os.path.join(test_files_lobster3)):
            with ScratchDir('.', copy_from_current_on_enter=True) as d:
                shutil.copy('lobsterin', 'lobsterin.orig')
                v = LobsterJob("hello",
                               gzipped=True,
                               add_files_to_gzip=VASP_OUTPUT_FILES)
                v.postprocess()
                self.assertTrue(os.path.exists("WAVECAR.gz"))
                self.assertTrue(os.path.exists("lobsterin.gz"))
                self.assertTrue(os.path.exists("lobsterout.gz"))
                self.assertTrue(os.path.exists("INCAR.gz"))
                self.assertTrue(os.path.exists("lobsterin.orig.gz"))

            with ScratchDir('.', copy_from_current_on_enter=True) as d:
                shutil.copy('lobsterin', 'lobsterin.orig')
                v = LobsterJob("hello",
                               gzipped=False,
                               add_files_to_gzip=VASP_OUTPUT_FILES)
                v.postprocess()
                self.assertTrue(os.path.exists("WAVECAR"))
                self.assertTrue(os.path.exists("lobsterin"))
                self.assertTrue(os.path.exists("lobsterout"))
                self.assertTrue(os.path.exists("INCAR"))
                self.assertTrue(os.path.exists("lobsterin.orig"))
Exemple #35
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    def test_postprocess(self):
        neb_outputs = ['INCAR', 'KPOINTS', 'POTCAR', 'vasprun.xml']
        neb_sub_outputs = [
            'CHG', 'CHGCAR', 'CONTCAR', 'DOSCAR', 'EIGENVAL', 'IBZKPT',
            'PCDAT', 'POSCAR', 'REPORT', 'PROCAR', 'OSZICAR', 'OUTCAR',
            'WAVECAR', 'XDATCAR'
        ]

        with cd(os.path.join(test_dir, 'postprocess_neb')):
            postprocess_neb = os.path.abspath(".")

            v = VaspNEBJob("hello", final=False, suffix=".test")
            v.postprocess()

            for f in neb_outputs:
                self.assertTrue(os.path.isfile('{}.test'.format(f)))
                os.remove('{}.test'.format(f))

            sub_folders = glob.glob("[0-9][0-9]")
            for sf in sub_folders:
                os.chdir(os.path.join(postprocess_neb, sf))
                for f in neb_sub_outputs:
                    if os.path.exists(f):
                        self.assertTrue(os.path.isfile('{}.test'.format(f)))
                        os.remove('{}.test'.format(f))
Exemple #36
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    def gnuplot(self):
        """
        Plot the results with gnuplot.
        Based on the `replot.sh` script provided by the oncvpsp code.
        """
        outfile = self.filepath
        base = os.path.basename(outfile)
        gnufile = base + ".scr"
        plotfile = base + ".plot"
        temp = base + ".tmp"

        from monty.os import cd
        from subprocess import check_call
        workdir = tempfile.mkdtemp()
        print("Working in %s" % workdir)

        with cd(workdir):
            check_call("awk 'BEGIN{out=0};/GNUSCRIPT/{out=0}; {if(out == 1) {print}}; \
                                /DATA FOR PLOTTING/{out=1}' %s > %s" % (outfile, plotfile), shell=True)

            check_call("awk 'BEGIN{out=0};/END_GNU/{out=0}; {if(out == 1) {print}}; \
                                /GNUSCRIPT/{out=1}' %s > %s" % (outfile, temp), shell=True)

            check_call('sed -e 1,1000s/t1/"%s"/ %s > %s' % (plotfile, temp, gnufile), shell=True)

            try:
                check_call(["gnuplot", gnufile])
            except KeyboardInterrupt:
                print("Received KeyboardInterrupt")

        os.rmdir(workdir)
Exemple #37
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 def test_postprocess(self):
     with cd(test_dir):
         with ScratchDir('.', copy_from_current_on_enter=True):
             f = FeffJob("hello", backup=True, gzipped=True)
             f.postprocess()
             self.assertTrue(os.path.exists('feff_out.1.tar.gz'))
             f.postprocess()
             self.assertTrue(os.path.exists('feff_out.2.tar.gz'))
Exemple #38
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 def test_cd_exception(self):
     try:
         with cd(test_dir):
             self.assertTrue(os.path.exists("empty_file.txt"))
             raise RuntimeError()
     except:
         pass
     self.assertFalse(os.path.exists("empty_file.txt"))
Exemple #39
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def pytest(ctx):
    pytest_cmd = r"""\
pytest -n 2 --cov-config=.coveragerc --cov=abipy -v --doctest-modules abipy \
    --ignore=abipy/integration_tests --ignore=abipy/data/refs --ignore=abipy/scripts/ \
    --ignore=abipy/examples/plot --ignore=abipy/examples/flows --ignore=abipy/gui
"""
    with cd(ABIPY_ROOTDIR):
        ctx.run(pytest_cmd, pty=True)
Exemple #40
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def make_doc(ctx):
    with cd("docs"):
        ctx.run("sphinx-apidoc -o . -f .")
        ctx.run("make html")
        # ctx.run("cp _static/* ../docs/html/_static")
        ctx.run("cp -r build/html/* .")
        ctx.run("rm -r build")
        ctx.run("touch .nojekyll")
Exemple #41
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 def test_postprocess(self):
     with cd(test_dir):
         with ScratchDir('.', copy_from_current_on_enter=True):
             f = FeffJob("hello", backup=True, gzipped=True)
             f.postprocess()
             self.assertTrue(os.path.exists('feff_out.1.tar.gz'))
             f.postprocess()
             self.assertTrue(os.path.exists('feff_out.2.tar.gz'))
Exemple #42
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 def test_cd_exception(self):
     try:
         with cd(test_dir):
             self.assertTrue(os.path.exists("empty_file.txt"))
             raise RuntimeError()
     except:
         pass
     self.assertFalse(os.path.exists("empty_file.txt"))
Exemple #43
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def make_doc(ctx):

    with cd("docs_rst"):
        ctx.run("sphinx-apidoc --separate -d 6 -o . -f ../veidt")
        ctx.run("rm veidt*.tests.*rst")
        ctx.run("make html")
        ctx.run("cp _static/* ../docs/html/_static", warn=True)

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")
        ctx.run("rm -r _sources")

        # This makes sure veidt.org works to redirect to the Gihub page
        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #44
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def pytest(ctx):
    pytest_cmd = r"""\
pytest -n 2 --cov-config=.coveragerc --cov=abipy -v --doctest-modules abipy \
    --ignore=abipy/integration_tests --ignore=abipy/data/refs --ignore=abipy/scripts/ \
    --ignore=abipy/examples/plot --ignore=abipy/examples/flows --ignore=abipy/gui
"""
    with cd(ABIPY_ROOTDIR):
        ctx.run(pytest_cmd, pty=True)
Exemple #45
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def proc_dic(rootfolder, filename, sub):

    filename_pre = rootfolder.rsplit('/', 1)[-1]
    rename = filename_pre + '.' + filename.split('.')[-1]
    command = 'mv F.out {}'.format(rename)
    # print filename
    with cd(rootfolder):
        os.system(command)
    print command
Exemple #46
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 def test_setup(self):
     with cd(test_dir):
         with ScratchDir('.', copy_from_current_on_enter=True) as d:
             v = VaspJob("hello")
             v.setup()
             incar = Incar.from_file("INCAR")
             count = multiprocessing.cpu_count()
             if count > 1:
                 self.assertGreater(incar["NPAR"], 1)
 def test_setup(self):
     with cd(test_dir):
         with ScratchDir('.', copy_from_current_on_enter=True) as d:
             v = VaspJob("hello", auto_npar=True)
             v.setup()
             incar = Incar.from_file("INCAR")
             count = multiprocessing.cpu_count()
             # Need at least 3 CPUs for NPAR to be greater than 1
             if count > 3:
                 self.assertGreater(incar["NPAR"], 1)
Exemple #48
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def contribute_dash(ctx):
    make_dash(ctx)
    ctx.run('cp pymatgen.tgz ../Dash-User-Contributions/docsets/pymatgen/pymatgen.tgz')
    with cd("../Dash-User-Contributions/docsets/pymatgen"):
        with open("docset.json", "rt") as f:
            data = json.load(f)
            data["version"] = NEW_VER
        with open("docset.json", "wt") as f:
            json.dump(data, f, indent=4)
        ctx.run('git commit -a -m "Update to v%s"' % NEW_VER)
        ctx.run('git push')
    ctx.run("rm pymatgen.tgz")
Exemple #49
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("sphinx-apidoc --separate -d 6 -o . -f ../monty")
        for f in glob.glob("*.rst"):
            if f.startswith('monty') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith(
                                    "monty") and not clean.endswith("tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")

        # ctx.run("cp _static/* ../docs/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")
        ctx.run("rm -r _sources")

        # This makes sure pymatgen.org works to redirect to the Gihub page
        # ctx.run("echo \"pymatgen.org\" > CNAME")
        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #50
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    def test_setup(self):
        with cd(test_dir):
            with ScratchDir('.', copy_from_current_on_enter=True):
                f = FeffJob("hello", backup=True)
                f.setup()

                parameter = Tags.from_file('feff.inp')
                parameter_orig = Tags.from_file('feff.inp.orig')
                self.assertEqual(parameter, parameter_orig)

                atom = Atoms.cluster_from_file('feff.inp')
                atom_origin = Atoms.cluster_from_file('feff.inp.orig')
                self.assertEqual(atom, atom_origin)
Exemple #51
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def submit_dash_pr(ctx):
    with cd("../Dash-User-Contributions/docsets/pymatgen"):

        payload = {
          "title": "Update pymatgen docset to v%s" % NEW_VER,
          "body": "Update pymatgen docset to v%s" % NEW_VER,
          "head": "Dash-User-Contributions:master",
          "base": "master"
        }
        response = requests.post(
            "https://api.github.com/repos/materialsvirtuallab/Dash-User-Contributions/pulls",
            data=json.dumps(payload))
        print(response.text)
Exemple #52
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def make_doc(ctx):
    with cd("docs_rst"):
        ctx.run("sphinx-apidoc -d 6 -o . -f ../custodian")
        ctx.run("rm custodian*.tests.rst")
        for f in glob.glob("*.rst"):
            if f.startswith('custodian') and f.endswith('rst'):
                newoutput = []
                suboutput = []
                subpackage = False
                with open(f, 'r') as fid:
                    for line in fid:
                        clean = line.strip()
                        if clean == "Subpackages":
                            subpackage = True
                        if not subpackage and not clean.endswith("tests"):
                            newoutput.append(line)
                        else:
                            if not clean.endswith("tests"):
                                suboutput.append(line)
                            if clean.startswith("custodian") and not clean.endswith(
                                    "tests"):
                                newoutput.extend(suboutput)
                                subpackage = False
                                suboutput = []

                with open(f, 'w') as fid:
                    fid.write("".join(newoutput))
        ctx.run("make html")
        # ctx.run("cp _static/* _build/html/_static")

    with cd("docs"):
        ctx.run("cp -r html/* .")
        ctx.run("rm -r html")
        ctx.run("rm -r doctrees")
        ctx.run("rm -r _sources")

        # Avoid the use of jekyll so that _dir works as intended.
        ctx.run("touch .nojekyll")
Exemple #53
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    def test__recover_completed(self):
        fw, launch_id = self.lp.reserve_fw(self.fworker, self.launch_dir)
        fw = self.lp.get_fw_by_id(1)
        with cd(self.launch_dir):
            setup_offline_job(self.lp, fw, launch_id)

            # launch rocket without launchpad to trigger offline mode
            launch_rocket(launchpad=None, fworker=self.fworker, fw_id=1)

        self.assertIsNone(self.lp.recover_offline(launch_id))

        fw = self.lp.get_fw_by_id(launch_id)

        self.assertEqual(fw.state, 'COMPLETED')
Exemple #54
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    def test_setup(self):
        with cd(os.path.join(test_dir, 'setup_neb')):
            with ScratchDir('.', copy_from_current_on_enter=True) as d:
                v = VaspNEBJob("hello", half_kpts=True)
                v.setup()

                incar = Incar.from_file("INCAR")
                count = multiprocessing.cpu_count()
                if count > 3:
                    self.assertGreater(incar["NPAR"], 1)

                kpt = Kpoints.from_file("KPOINTS")
                kpt_pre = Kpoints.from_file("KPOINTS.orig")
                self.assertEqual(kpt_pre.style.name, "Monkhorst")
                self.assertEqual(kpt.style.name, "Gamma")
Exemple #55
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    def test_postprocess(self):
        with cd(os.path.join(test_dir, 'postprocess')):
            with ScratchDir('.', copy_from_current_on_enter=True) as d:
                shutil.copy('INCAR', 'INCAR.backup')

                v = VaspJob("hello", final=False, suffix=".test", copy_magmom=True)
                v.postprocess()
                incar = Incar.from_file("INCAR")
                incar_prev = Incar.from_file("INCAR.test")

                for f in ['INCAR', 'KPOINTS', 'CONTCAR', 'OSZICAR', 'OUTCAR',
                          'POSCAR', 'vasprun.xml']:
                    self.assertTrue(os.path.isfile('{}.test'.format(f)))
                    os.remove('{}.test'.format(f))
                shutil.move('INCAR.backup', 'INCAR')

                self.assertAlmostEqual(incar['MAGMOM'], [3.007, 1.397, -0.189, -0.189])
                self.assertAlmostEqual(incar_prev["MAGMOM"], [5, -5, 0.6, 0.6])
Exemple #56
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    def test_recover_errors(self):
        fw, launch_id = self.lp.reserve_fw(self.fworker, self.launch_dir)
        fw = self.lp.get_fw_by_id(1)
        with cd(self.launch_dir):
            setup_offline_job(self.lp, fw, launch_id)

        # remove the directory to cause an exception
        shutil.rmtree(self.launch_dir)

        # recover ignoring errors
        self.assertIsNotNone(self.lp.recover_offline(launch_id, ignore_errors=True, print_errors=True))

        fw = self.lp.get_fw_by_id(launch_id)

        self.assertEqual(fw.state, 'RESERVED')

        #fizzle
        self.assertIsNotNone(self.lp.recover_offline(launch_id, ignore_errors=False))

        fw = self.lp.get_fw_by_id(launch_id)

        self.assertEqual(fw.state, 'FIZZLED')
Exemple #57
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    def test_postprocess(self):
        neb_outputs = ['INCAR', 'KPOINTS', 'POTCAR', 'vasprun.xml']
        neb_sub_outputs = ['CHG', 'CHGCAR', 'CONTCAR', 'DOSCAR',
                           'EIGENVAL', 'IBZKPT', 'PCDAT', 'POSCAR',
                           'REPORT', 'PROCAR', 'OSZICAR', 'OUTCAR',
                           'WAVECAR', 'XDATCAR']

        with cd(os.path.join(test_dir, 'postprocess_neb')):
            postprocess_neb = os.path.abspath(".")

            v = VaspNEBJob("hello", final=False, suffix=".test")
            v.postprocess()

            for f in neb_outputs:
                self.assertTrue(os.path.isfile('{}.test'.format(f)))
                os.remove('{}.test'.format(f))

            sub_folders = glob.glob("[0-9][0-9]")
            for sf in sub_folders:
                os.chdir(os.path.join(postprocess_neb, sf))
                for f in neb_sub_outputs:
                    if os.path.exists(f):
                        self.assertTrue(os.path.isfile('{}.test'.format(f)))
                        os.remove('{}.test'.format(f))
Exemple #58
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def check_resub_relax2(args):



    if args.debug:
        logging.basicConfig(level=logging.DEBUG)


    dir_entry = parse_entry(args)
    for ele in dir_entry:

        with cd(ele):

            logging.debug('Current dir path is: {}'.format(os.getcwd()))

            if not os.path.exists('Complete'):
                os.makedirs('Complete')

            exclude = set(['Complete'])

            result_dir_entry = [f for f in os.listdir('.') if f not in exclude]

            for subdir in result_dir_entry:
                check_command = 'check_CONTCARRELAX2 {} -st Yes -stdic Complete/'.format(subdir)
                subprocess.call(check_command,shell=True)

            no_relax2_file = [f for f in os.listdir('.') if f not in exclude]

            for dir_ele in no_relax2_file:
                resub_command = submit_command(args,dir_ele)
                restore_command = 'restoretoinital {}'.format(dir_ele)
                subprocess.call(restore_command,shell=True)
                subprocess.call(resub_command,shell=True)


            logging.debug('Folder with no_relax2_file is: {}'.format(no_relax2_file))
def launch_rocket_to_queue(launchpad, fworker, qadapter, launcher_dir='.', reserve=False,
                           strm_lvl='INFO', create_launcher_dir=False, fill_mode=False,
                           fw_id=None):
    """
    Submit a single job to the queue.

    Args:
        launchpad (LaunchPad)
        fworker (FWorker)
        qadapter (QueueAdapterBase)
        launcher_dir (str): The directory where to submit the job
        reserve (bool): Whether to queue in reservation mode
        strm_lvl (str): level at which to stream log messages
        create_launcher_dir (bool): Whether to create a subfolder launcher+timestamp, if needed
        fill_mode (bool): whether to submit jobs even when there is nothing to run
            (only in non-reservation mode)
        fw_id (int): specific fw_id to reserve (reservation mode only)
    """
    fworker = fworker if fworker else FWorker()
    launcher_dir = os.path.abspath(launcher_dir)
    l_logger = get_fw_logger('queue.launcher', l_dir=launchpad.logdir, stream_level=strm_lvl)

    l_logger.debug('getting queue adapter')
    qadapter = load_object(qadapter.to_dict())  # make a defensive copy, mainly for reservation mode

    fw, launch_id = None, None  # only needed in reservation mode

    if not os.path.exists(launcher_dir):
        raise ValueError('Desired launch directory {} does not exist!'.format(launcher_dir))

    if '--offline' in qadapter['rocket_launch'] and not reserve:
        raise ValueError("Must use reservation mode (-r option) of qlaunch "
                         "when using offline option of rlaunch!!")

    if reserve and 'singleshot' not in qadapter.get('rocket_launch', ''):
        raise ValueError('Reservation mode of queue launcher only works for singleshot Rocket Launcher!')

    if fill_mode and reserve:
        raise ValueError("Fill_mode cannot be used in conjunction with reserve mode!")

    if fw_id and not reserve:
        raise ValueError("qlaunch for specific fireworks may only be used in reservation mode.")

    if fill_mode or launchpad.run_exists(fworker):
        launch_id = None
        try:
            if reserve:
                if fw_id:
                    l_logger.debug('finding a FW to reserve...')
                fw, launch_id = launchpad.reserve_fw(fworker, launcher_dir, fw_id=fw_id)
                if not fw:
                    l_logger.info('No jobs exist in the LaunchPad for submission to queue!')
                    return False
                l_logger.info('reserved FW with fw_id: {}'.format(fw.fw_id))

                # update qadapter job_name based on FW name
                job_name = get_slug(fw.name)[0:QUEUE_JOBNAME_MAXLEN]
                qadapter.update({'job_name': job_name})

                if '_queueadapter' in fw.spec:
                    l_logger.debug('updating queue params using Firework spec..')
                    qadapter.update(fw.spec['_queueadapter'])

                # reservation mode includes --fw_id in rocket launch
                qadapter['rocket_launch'] += ' --fw_id {}'.format(fw.fw_id)

                # update launcher_dir if _launch_dir is selected in reserved fw
                if '_launch_dir' in fw.spec:
                    fw_launch_dir = os.path.expandvars(fw.spec['_launch_dir'])

                    if not os.path.isabs(fw_launch_dir):
                        fw_launch_dir = os.path.join(launcher_dir, fw_launch_dir)

                    launcher_dir = fw_launch_dir

                    makedirs_p(launcher_dir)

                    launchpad.change_launch_dir(launch_id, launcher_dir)
                elif create_launcher_dir:
                    # create launcher_dir
                    launcher_dir = create_datestamp_dir(launcher_dir, l_logger, prefix='launcher_')
                    launchpad.change_launch_dir(launch_id, launcher_dir)

            elif create_launcher_dir:
                # create launcher_dir
                launcher_dir = create_datestamp_dir(launcher_dir, l_logger, prefix='launcher_')

            # move to the launch directory
            l_logger.info('moving to launch_dir {}'.format(launcher_dir))

            with cd(launcher_dir):

                if '--offline' in qadapter['rocket_launch']:
                    setup_offline_job(launchpad, fw, launch_id)

                l_logger.debug('writing queue script')
                with open(SUBMIT_SCRIPT_NAME, 'w') as f:
                    queue_script = qadapter.get_script_str(launcher_dir)
                    f.write(queue_script)

                l_logger.info('submitting queue script')
                reservation_id = qadapter.submit_to_queue(SUBMIT_SCRIPT_NAME)
                if not reservation_id:
                    raise RuntimeError('queue script could not be submitted, check queue '
                                       'script/queue adapter/queue server status!')
                elif reserve:
                    launchpad.set_reservation_id(launch_id, reservation_id)
            return reservation_id

        except:
            log_exception(l_logger, 'Error writing/submitting queue script!')
            if reserve and launch_id is not None:
                try:
                    l_logger.info('Un-reserving FW with fw_id, launch_id: {}, {}'.format(
                        fw.fw_id, launch_id))
                    launchpad.cancel_reservation(launch_id)
                    launchpad.forget_offline(launch_id)
                except:
                    log_exception(l_logger, 'Error unreserving FW with fw_id {}'.format(fw.fw_id))

            return False

    else:
        l_logger.info('No jobs exist in the LaunchPad for submission to queue!')
        return None  # note: this is a hack (rather than False) to indicate a soft failure to rapidfire()