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")
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 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")
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")
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")
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")
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")
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")
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")
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")
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")
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")
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))
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
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)
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)
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()
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)
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()
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")
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")
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)
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")
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])
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')
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)
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
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)
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)
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)
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"))
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))
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)
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'))
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"))
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)
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")
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'))
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"))
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")
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)
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
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)
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")
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")
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)
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)
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")
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')
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")
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])
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')
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))
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()
