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Fix scripts after refactoring

This commit is contained in:
Matteo Giantomassi 2017-03-10 23:30:24 +01:00
parent 981eb56e65
commit 804ab3f5db
5 changed files with 32 additions and 25 deletions
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3
abipy/electrons/tests/test_ebands.py
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@ -202,7 +202,8 @@ class ElectronBandsPlotterTest(AbipyTest):
if self.has_matplotlib(): if self.has_matplotlib():
plotter.combiplot(title="Silicon band structure", show=False) plotter.combiplot(title="Silicon band structure", show=False)
plotter.combiboxplot(title="Silicon band structure", show=False) if self.has_seaborn():
plotter.combiboxplot(title="Silicon band structure", show=False)
plotter.gridplot(title="Silicon band structure", show=False) plotter.gridplot(title="Silicon band structure", show=False)
plotter.boxplot(title="Silicon band structure", swarm=True, show=False) plotter.boxplot(title="Silicon band structure", swarm=True, show=False)
plotter.animate(show=False) plotter.animate(show=False)

13
abipy/flowapi/abiphonopy.py
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@ -7,10 +7,15 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
import os import os
import numpy as np import numpy as np
from phonopy import Phonopy, file_IO try:
from phonopy.structure.atoms import Atoms as PhonopyAtoms from phonopy import Phonopy, file_IO
from phonopy.interface.vasp import read_vasp_from_strings from phonopy.interface.vasp import read_vasp_from_strings
from phonopy.interface.abinit import parse_set_of_forces from phonopy.interface.abinit import parse_set_of_forces
except ImportError:
import warnings
warnings.warn("phonopy is required by abiphonopy. Install it with conda or pip")
from pymatgen.io.abinit.works import Work from pymatgen.io.abinit.works import Work
from abipy.core.structure import Structure from abipy.core.structure import Structure
from abipy.abio.inputs import AbinitInput from abipy.abio.inputs import AbinitInput

17
abipy/scripts/abirun.py
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@ -87,7 +87,7 @@ def flowdir_wname_tname(dirname):
""" """
if dirname is None: dirname = os.getcwd() if dirname is None: dirname = os.getcwd()
dirname = os.path.abspath(dirname) dirname = os.path.abspath(dirname)
if os.path.exists(os.path.join(dirname, abilab.Flow.PICKLE_FNAME)): if os.path.exists(os.path.join(dirname, flowapi.Flow.PICKLE_FNAME)):
return dirname, None, None return dirname, None, None
# Handle works or tasks. # Handle works or tasks.
@ -96,7 +96,7 @@ def flowdir_wname_tname(dirname):
for i in range(2): for i in range(2):
head, tail = os.path.split(head) head, tail = os.path.split(head)
if i == 0: tail_1 = tail if i == 0: tail_1 = tail
if os.path.exists(os.path.join(head, abilab.Flow.PICKLE_FNAME)): if os.path.exists(os.path.join(head, flowapi.Flow.PICKLE_FNAME)):
if i == 0: if i == 0:
# We have a work: /root/flow_dir/w[num] # We have a work: /root/flow_dir/w[num]
wname = tail wname = tail
@ -529,7 +529,7 @@ Specify the files to open. Possible choices:
qtype = options.qtype qtype = options.qtype
if qtype == "script": if qtype == "script":
manager = abilab.TaskManager.from_user_config() manager = flowapi.TaskManager.from_user_config()
script = manager.qadapter.get_script_str( script = manager.qadapter.get_script_str(
job_name="job_name", job_name="job_name",
launch_dir="workdir", launch_dir="workdir",
@ -543,7 +543,7 @@ Specify the files to open. Possible choices:
print(script) print(script)
else: else:
print(abilab.TaskManager.autodoc()) print(flowapi.TaskManager.autodoc())
print("qtype supported: %s" % flowapi.all_qtypes()) print("qtype supported: %s" % flowapi.all_qtypes())
print("Use `abirun.py . manager slurm` to have the list of qparams for slurm.\n") print("Use `abirun.py . manager slurm` to have the list of qparams for slurm.\n")
@ -555,12 +555,11 @@ Specify the files to open. Possible choices:
if options.command == "doc_scheduler": if options.command == "doc_scheduler":
print("Options that can be specified in scheduler.yml:") print("Options that can be specified in scheduler.yml:")
print(abilab.PyFlowScheduler.autodoc()) print(flowapi.PyFlowScheduler.autodoc())
return 0 return 0
if options.command == "abibuild": if options.command == "abibuild":
#abilab.abicheck(): abinit_build = flowapi.AbinitBuild()
abinit_build = abilab.AbinitBuild()
print() print()
print(abinit_build) print(abinit_build)
print() print()
@ -597,7 +596,7 @@ Specify the files to open. Possible choices:
options.flowdir, wname, tname = flowdir_wname_tname(options.flowdir) options.flowdir, wname, tname = flowdir_wname_tname(options.flowdir)
# Read the flow from the pickle database. # Read the flow from the pickle database.
flow = abilab.Flow.pickle_load(options.flowdir, remove_lock=options.remove_lock) flow = flowapi.Flow.pickle_load(options.flowdir, remove_lock=options.remove_lock)
#flow.show_info() #flow.show_info()
# If we have selected a work/task, we have to convert wname/tname into node ids (nids) # If we have selected a work/task, we have to convert wname/tname into node ids (nids)
@ -642,7 +641,7 @@ Specify the files to open. Possible choices:
elif options.command == "new_manager": elif options.command == "new_manager":
# Read the new manager from file. # Read the new manager from file.
new_manager = abilab.TaskManager.from_file(options.manager_file) new_manager = flowapi.TaskManager.from_file(options.manager_file)
# Default status for new_manager is QCritical # Default status for new_manager is QCritical
if options.task_status is None: if options.task_status is None:

6
tests/test_managers.py
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@ -4,9 +4,9 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
import os import os
import abipy.data as abidata import abipy.data as abidata
import abipy.flowapi as flowapi
from abipy.core.testing import AbipyTest from abipy.core.testing import AbipyTest
from abipy import abilab
class ManagerTest(AbipyTest): class ManagerTest(AbipyTest):
@ -17,7 +17,7 @@ class ManagerTest(AbipyTest):
yaml_paths = [os.path.join(root, f) for f in os.listdir(root) if f.endswith(".yml") and "_manager" in f] yaml_paths = [os.path.join(root, f) for f in os.listdir(root) if f.endswith(".yml") and "_manager" in f]
assert yaml_paths assert yaml_paths
for p in yaml_paths: for p in yaml_paths:
manager = abilab.TaskManager.from_file(p) manager = flowapi.TaskManager.from_file(p)
print(manager) print(manager)
shell = manager.to_shell_manager(mpi_procs=2) shell = manager.to_shell_manager(mpi_procs=2)
#assert 0 #assert 0
@ -28,7 +28,7 @@ class ManagerTest(AbipyTest):
yaml_paths = [os.path.join(root, f) for f in os.listdir(root) if f.endswith(".yml") and "_scheduler" in f] yaml_paths = [os.path.join(root, f) for f in os.listdir(root) if f.endswith(".yml") and "_scheduler" in f]
assert yaml_paths assert yaml_paths
for p in yaml_paths: for p in yaml_paths:
sched = abilab.PyFlowScheduler.from_file(p) sched = flowapi.PyFlowScheduler.from_file(p)
print(sched) print(sched)
#assert 0 #assert 0

18
tests/test_scripts.py
View File

@ -4,6 +4,7 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
import os import os
import abipy.data as abidata import abipy.data as abidata
import abipy.flowapi as flowapi
from scripttest import TestFileEnvironment from scripttest import TestFileEnvironment
from monty.inspect import all_subclasses from monty.inspect import all_subclasses
@ -26,13 +27,14 @@ def test_if_all_scripts_are_tested():
for i, s in enumerate(not_tested): for i, s in enumerate(not_tested):
print("[%d] %s" % (i, s)) print("[%d] %s" % (i, s))
assert not_tested == set([ assert len(not_tested) == 0
"abiGWprint.py", #assert not_tested == set([
"abiGWstore.py", # "abiGWprint.py",
"abiGWoutput.py", # "abiGWstore.py",
"abiphonons.py", # "abiGWoutput.py",
"abiGWsetup.py", # "abiphonons.py",
]) # "abiGWsetup.py",
#])
class ScriptTest(AbipyTest): class ScriptTest(AbipyTest):
@ -177,7 +179,7 @@ class TestAbirun(ScriptTest):
# Build a flow. # Build a flow.
flowdir = env.base_path flowdir = env.base_path
scf_input, nscf_input = make_scf_nscf_inputs() scf_input, nscf_input = make_scf_nscf_inputs()
flow = abilab.bandstructure_flow(flowdir, scf_input, nscf_input, manager=None) flow = flowapi.bandstructure_flow(flowdir, scf_input, nscf_input, manager=None)
flow.build_and_pickle_dump() flow.build_and_pickle_dump()
# Test abirun commands requiring a flow (no submission) # Test abirun commands requiring a flow (no submission)