Fix scripts after refactoring

abipy/electrons/tests/test_ebands.py

@@ -202,7 +202,8 @@ class ElectronBandsPlotterTest(AbipyTest):
 
         if self.has_matplotlib():
             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.boxplot(title="Silicon band structure", swarm=True, show=False)
             plotter.animate(show=False)

abipy/flowapi/abiphonopy.py

@@ -7,10 +7,15 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
 import os
 import numpy as np
 
-from phonopy import Phonopy, file_IO
-from phonopy.structure.atoms import Atoms as PhonopyAtoms
-from phonopy.interface.vasp import read_vasp_from_strings
-from phonopy.interface.abinit import parse_set_of_forces
+try:
+    from phonopy import Phonopy, file_IO
+    from phonopy.interface.vasp import read_vasp_from_strings
+    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 abipy.core.structure import Structure
 from abipy.abio.inputs import AbinitInput

abipy/scripts/abirun.py

@@ -87,7 +87,7 @@ def flowdir_wname_tname(dirname):
     """
     if dirname is None: dirname = os.getcwd()
     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
 
     # Handle works or tasks.
@@ -96,7 +96,7 @@ def flowdir_wname_tname(dirname):
     for i in range(2):
         head, tail = os.path.split(head)
         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:
                 # We have a work: /root/flow_dir/w[num]
                 wname = tail
@@ -529,7 +529,7 @@ Specify the files to open. Possible choices:
         qtype = options.qtype
 
         if qtype == "script":
-            manager = abilab.TaskManager.from_user_config()
+            manager = flowapi.TaskManager.from_user_config()
             script = manager.qadapter.get_script_str(
                 job_name="job_name",
                 launch_dir="workdir",
@@ -543,7 +543,7 @@ Specify the files to open. Possible choices:
             print(script)
 
         else:
-            print(abilab.TaskManager.autodoc())
+            print(flowapi.TaskManager.autodoc())
             print("qtype supported: %s" % flowapi.all_qtypes())
             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":
         print("Options that can be specified in scheduler.yml:")
-        print(abilab.PyFlowScheduler.autodoc())
+        print(flowapi.PyFlowScheduler.autodoc())
         return 0
 
     if options.command == "abibuild":
-        #abilab.abicheck():
-        abinit_build = abilab.AbinitBuild()
+        abinit_build = flowapi.AbinitBuild()
         print()
         print(abinit_build)
         print()
@@ -597,7 +596,7 @@ Specify the files to open. Possible choices:
         options.flowdir, wname, tname = flowdir_wname_tname(options.flowdir)
 
     # 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()
 
     # 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":
         # 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
         if options.task_status is None:

tests/test_managers.py

@@ -4,9 +4,9 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
 
 import os
 import abipy.data as abidata
+import abipy.flowapi as flowapi
 
 from abipy.core.testing import AbipyTest
-from abipy import abilab
 
 
 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]
         assert yaml_paths
         for p in yaml_paths:
-            manager = abilab.TaskManager.from_file(p)
+            manager = flowapi.TaskManager.from_file(p)
             print(manager)
             shell = manager.to_shell_manager(mpi_procs=2)
         #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]
         assert yaml_paths
         for p in yaml_paths:
-            sched = abilab.PyFlowScheduler.from_file(p)
+            sched = flowapi.PyFlowScheduler.from_file(p)
             print(sched)
 
         #assert 0

tests/test_scripts.py

@@ -4,6 +4,7 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
 
 import os
 import abipy.data as abidata
+import abipy.flowapi as flowapi
 
 from scripttest import TestFileEnvironment
 from monty.inspect import all_subclasses
@@ -26,13 +27,14 @@ def test_if_all_scripts_are_tested():
         for i, s in enumerate(not_tested):
             print("[%d] %s" % (i, s))
 
-    assert not_tested == set([
-        "abiGWprint.py",
-        "abiGWstore.py",
-        "abiGWoutput.py",
-        "abiphonons.py",
-        "abiGWsetup.py",
-    ])
+    assert len(not_tested) == 0
+    #assert not_tested == set([
+    #    "abiGWprint.py",
+    #    "abiGWstore.py",
+    #    "abiGWoutput.py",
+    #    "abiphonons.py",
+    #    "abiGWsetup.py",
+    #])
 
 
 class ScriptTest(AbipyTest):
@@ -177,7 +179,7 @@ class TestAbirun(ScriptTest):
         # Build a flow.
         flowdir = env.base_path
         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()
 
         # Test abirun commands requiring a flow (no submission)