Merge branch 'develop', drop python 3.4 support, bumpversion -> v1.1.10

Dropped support for python 3.4 since the latest AiiDA-core requires graphviz==0.13 which is not available there
JuDFTteam · Jan 27, 2020 · e1296b1 · e1296b1
2 parents 0a10f0c + 57816eb
commit e1296b1
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Showing 15 changed files with 435 additions and 96 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.9
+current_version = 1.1.10
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?

diff --git a/.codacy.yml b/.codacy.yml
@@ -0,0 +1,3 @@
+
+exclude_paths:
+  - 'aiida_kkr/tests/**'
diff --git a/.travis.yml b/.travis.yml
@@ -3,7 +3,6 @@ dist: trusty
 language: python
 python:
   - "2.7"
-  - "3.4"
   - "3.5"
   - "3.6"
 matrix:
@@ -12,6 +11,7 @@ matrix:
   include:
     - python: 3.7
       dist: xenial
+      env: NO_RMQ='t'
 notifications:
   slack:
     on_success: never

diff --git a/aiida_kkr/__init__.py b/aiida_kkr/__init__.py
@@ -2,4 +2,4 @@
 AiiDA KKR
 """
 
-__version__ = "1.1.9"
+__version__ = "1.1.10"
diff --git a/aiida_kkr/calculations/kkrimp.py b/aiida_kkr/calculations/kkrimp.py
@@ -31,7 +31,7 @@
 __copyright__ = (u"Copyright (c), 2018, Forschungszentrum Jülich GmbH, "
                  "IAS-1/PGI-1, Germany. All rights reserved.")
 __license__ = "MIT license, see LICENSE.txt file"
-__version__ = "0.5.0"
+__version__ = "0.5.1"
 __contributors__ = (u"Philipp Rüßmann", u"Fabian Bertoldo")
 
 #TODO: implement 'ilayer_center' consistency check
@@ -693,7 +693,8 @@ def get_remote_symlink(self, local_copy_list):
         with comp.get_transport() as connection:
             # do this for GMAT
             uuid_GF = GF_local_copy_info[0]
-            GF_remote_path = os.path.join(GFpath_remote, uuid_GF, GF_local_copy_info[1])
+            filename = GF_local_copy_info[1]
+            GF_remote_path = os.path.join(GFpath_remote, uuid_GF, filename)
             # check if file exists on remote
             if connection.isfile(GF_remote_path):
                 # remove GF from local copy list and add to remote symlink list
@@ -702,12 +703,17 @@ def get_remote_symlink(self, local_copy_list):
 
             # do the same for TMAT
             uuid_TM = TM_local_copy_info[0]
-            TM_remote_path = os.path.join(GFpath_remote, uuid_TM, TM_local_copy_info[1])
+            filename = TM_local_copy_info[1]
+            TM_remote_path = os.path.join(GFpath_remote, uuid_TM, filename)
             # check if file exists on remote
             if connection.isfile(TM_remote_path):
                 # remove TMAT from local copy list and add to remote symlink list
                 local_copy_list.remove(TM_local_copy_info)
                 remote_symlink_list.append((comp.uuid, TM_remote_path, filename))
 
+        # print symlink and local copy list (for debugging purposes)
+        print('local_copy_list: {}'.format(local_copy_list))
+        print('symlink_list: {}'.format(remote_symlink_list))
+
         # now return updated remote_symlink and local_copy lists
         return remote_symlink_list, local_copy_list
diff --git a/aiida_kkr/tests/run_all.sh b/aiida_kkr/tests/run_all.sh
@@ -11,7 +11,17 @@ mkdir -p '.aiida';
 # if the environment variable is unset or the empty string then the corresponding tests will be ignored 
 
 usage(){
-  echo "$0 usage:" && grep " .)\ #" $0; exit 0;
+  echo "$0 usage:" && grep " .)\ #" $0;
+  echo
+  echo "Default behavior is to run only tests that do not require running an actual calculation (i.e. skip workflow tests)."
+  echo "Additional settings with the environment variables (set to something or unset to remove setting):";
+  echo "  'RUN_ALL': run all tests";
+  echo "  'SKIP_NOWORK': skip workflow tests";
+  echo "  'RUN_VORONOI': run voronoi tests";
+  echo "  'RUN_KKRHOST': run kkrhost tests";
+  echo "  'RUN_KKRIMP': run kkrimp tests";
+  echo
+  exit 0;
 }
 
 addopt=""
@@ -51,6 +61,11 @@ else
   else
     echo "skip workflows tests using KKRimp (set 'RUN_KKRIMP' env to activate this)"
   fi
+  if [[ ! -z "$NO_RMQ" ]]; then
+    echo "do not run workflows and workfuntions that need rabbitMQ (unset 'NO_RMQ' env to prevent this)"
+  else
+    echo "run workflows and workfunctions also with rabbitMQ (set 'NO_RMQ' env to deactivate this)"
+  fi
 fi
 echo "============="
 echo
@@ -63,18 +78,24 @@ if [[ ! -z "$RUN_ALL" ]]; then
   pytest --cov-report=term-missing --cov=aiida_kkr --cov-append --ignore=jukkr --ignore=workflows --mpl -p no:warnings $addopt # then run non-workflow tests
 else
   # tests without running actual calculations
-  if [[ -z "$SKIP_NOWORK" ]]; then
+  if [[ -z "$SKIP_NOWORK" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run non-workflow tests"
     pytest --cov-report=term-missing --cov=aiida_kkr --ignore=workflows --ignore=jukkr --mpl -p no:warnings $addopt
   else
-    echo "skipping tests that are not workflows"
+    # skip things that need rabbitMQ
+    if [[ -z "$SKIP_NOWORK" ]] && [[ ! -z "$NO_RMQ" ]]; then
+      echo "run non-workflow tests"
+      pytest --cov-report=term-missing --cov=aiida_kkr --ignore=workflows --ignore=jukkr --ignore=calculations --ignore=test_common_workfunctions_with_rmq.py --ignore=test_plot_kkr.py --mpl -p no:warnings $addopt
+    else
+      echo "skipping tests that are not workflows"
+    fi
   fi
 
   # test running full workflows, need compiled codes and execute them
 
   # tests using only voronoi
 
-  if [[ ! -z "$RUN_VORONOI" ]]; then
+  if [[ ! -z "$RUN_VORONOI" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run vorostart workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_vorostart_workflow $addopt
   else
@@ -83,25 +104,25 @@ else
 
   # tests using kkrhost (and voronoi)
 
-  if [[ ! -z "$RUN_KKRHOST" ]]; then
+  if [[ ! -z "$RUN_KKRHOST" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run kkr_dos workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_dos_workflow $addopt
   else
     echo "skipping kkr_dos workflow test"
   fi
-  if [[ ! -z "$RUN_KKRHOST" ]]; then
+  if [[ ! -z "$RUN_KKRHOST" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run kkr_gf_writeout workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_gf_writeout_workflow $addopt
   else
     echo "skipping kkr_gf_writeout workflow test"
   fi
-  if [[ ! -z "$RUN_VORONOI" ]] && [[ ! -z "$RUN_KKRHOST" ]]; then
+  if [[ ! -z "$RUN_VORONOI" ]] && [[ ! -z "$RUN_KKRHOST" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run kkr_scf workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_scf_workflow $addopt
   else
     echo "skipping kkr_scf workflow test"
   fi
-  if [[ ! -z "$RUN_VORONOI" ]] && [[ ! -z "$RUN_KKRHOST" ]]; then
+  if [[ ! -z "$RUN_VORONOI" ]] && [[ ! -z "$RUN_KKRHOST" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run kkr_eos workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_eos_workflow $addopt
   else
@@ -110,19 +131,19 @@ else
 
   # tests using kkrimp (and kkrhost/voronoi)
 
-  if [[ ! -z "$RUN_KKRIMP" ]]; then
+  if [[ ! -z "$RUN_KKRIMP" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run kkrimp_scf workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_kkrimp_scf_workflow $addopt
   else
     echo "skipping kkrimp_scf workflow test"
   fi
-  if [[ ! -z "$RUN_KKRIMP" ]] && [[ ! -z "$RUN_KKRHOST" ]] && [[ ! -z "$RUN_VORONOI" ]]; then
+  if [[ ! -z "$RUN_KKRIMP" ]] && [[ ! -z "$RUN_KKRHOST" ]] && [[ ! -z "$RUN_VORONOI" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run kkrimp_full workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_kkrimp_full_workflow $addopt
   else
     echo "skipping kkrimp_full workflow test"
   fi
-  if [[ ! -z "$RUN_KKRIMP" ]] && [[ ! -z "$RUN_KKRHOST" ]]; then
+  if [[ ! -z "$RUN_KKRIMP" ]] && [[ ! -z "$RUN_KKRHOST" ]] && [[ -z "$NO_RMQ" ]]; then
     echo "run kkrimp_dos workflow test"
     pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_kkrimp_dos_workflow $addopt
   else

diff --git a/aiida_kkr/tests/test_common_workfunctions.py b/aiida_kkr/tests/test_common_workfunctions.py
@@ -141,62 +141,6 @@ def test_check_2Dinput_consistency_5(self):
         assert list(input_check[1]).sort() == list("3D info given in parameters but structure is 2D\nstructure is 2D? {}\ninput has 2D info? {}\nset keys are: {}".format(False, True, ['ZPERIODL', '<NRBASIS>', '<RBLEFT>', 'INTERFACE', '<NLBASIS>', 'ZPERIODR', '<RBRIGHT>'])).sort()
 
 
-    def test_update_params_wf(self):
-        from aiida_kkr.tools.common_workfunctions import update_params_wf
-        from masci_tools.io.kkr_params import kkrparams
-        from aiida.plugins import DataFactory
-        Dict = DataFactory('dict')
-
-        k = kkrparams(LMAX=2)
-        node1 = Dict(dict=k.values)
-        node2 = Dict(dict={'nodename': 'my_changed_name', 'nodedesc': 'My description text', 'EMIN': -1, 'RMAX': 10.})
-
-        unode = update_params_wf(node1, node1)
-        assert unode.get_dict() == node1.get_dict()
-
-        unode = update_params_wf(node1, node2)
-
-        d0 = node1.get_dict()
-        for i in list(d0.keys()):
-            if d0[i] is None:
-                d0.pop(i)
-
-        d1 = unode.get_dict()
-        for i in list(d1.keys()):
-            if d1[i] is None:
-                d1.pop(i)
-
-        l_identical, l_diff = [], []
-        for i in list(d0.keys()):
-            if i in list(d1.keys()):
-                l_identical.append([i, d0[i], d1[i]])
-            else:
-                l_diff.append([0, i, d0[i]])
-        for i in list(d1.keys()):
-            if i not in list(d0.keys()):
-                l_diff.append([1, i, d1[i]])
-
-        assert l_identical ==  [[u'LMAX', 2, 2]]
-        assert l_diff.sort() == [[1, u'RMAX', 10.0], [1, u'EMIN', -1.0]].sort()
-        return node1, node2, unode
-
-
-    def test_neworder_potential_wf(self):
-        from numpy import loadtxt
-        from aiida.orm import load_node
-        from aiida.plugins import DataFactory
-        from aiida_kkr.tools.common_workfunctions import neworder_potential_wf
-        from aiida.tools.importexport import import_data
-        Dict = DataFactory('dict')
-        import_data('files/db_dump_kkrflex_create.tar.gz')
-        GF_host_calc = load_node('baabef05-f418-4475-bba5-ef0ee3fd5ca6').outputs
-        neworder_pot1 = [int(i) for i in loadtxt(GF_host_calc.retrieved.open('scoef'), skiprows=1)[:,3]-1]
-        settings_dict = {'pot1': 'out_potential',  'out_pot': 'potential_imp', 'neworder': neworder_pot1}
-        settings = Dict(dict=settings_dict)
-        startpot_imp_sfd = neworder_potential_wf(settings_node=settings, parent_calc_folder=GF_host_calc.remote_folder)
-        assert startpot_imp_sfd.get_object_content(startpot_imp_sfd.filename)[::1000] == u'C12807143D556463084.6+55 7D117 9D-87 0+25\n20.70351.75\n0521259.2+491.0-462. 02621D74112D03547T00 4D02116D502 6D39\n96.20261.50941.4944.7+30 98-29 .5-3625D07193.58104D0773D27252285417D341 9.506544D548447094.9+38 91063 54-08 6D28277.60909.98111'
-
-
     def test_vca_check(self):
         from aiida_kkr.tools.common_workfunctions import vca_check
         pass

diff --git a/aiida_kkr/tests/test_common_workfunctions_with_rmq.py b/aiida_kkr/tests/test_common_workfunctions_with_rmq.py
@@ -0,0 +1,74 @@
+# -*- coding: utf-8 -*-
+"""
+@author: ruess
+"""
+from __future__ import print_function
+from __future__ import absolute_import
+from builtins import object
+import pytest
+from six.moves import range
+from numpy import sort
+
+@pytest.mark.usefixtures("aiida_env")
+class Test_common_workfunctions_rmq(object):
+    """
+    Tests for the common workfunctions from tools.common_workfunctions,
+    i.e. functions commonly used in this plugin that depend on aiida stuff to work
+    these tests use rabbitMQ
+    """
+
+    def test_update_params_wf(self):
+        from aiida_kkr.tools.common_workfunctions import update_params_wf
+        from masci_tools.io.kkr_params import kkrparams
+        from aiida.plugins import DataFactory
+        Dict = DataFactory('dict')
+
+        k = kkrparams(LMAX=2)
+        node1 = Dict(dict=k.values)
+        node2 = Dict(dict={'nodename': 'my_changed_name', 'nodedesc': 'My description text', 'EMIN': -1, 'RMAX': 10.})
+
+        unode = update_params_wf(node1, node1)
+        assert unode.get_dict() == node1.get_dict()
+
+        unode = update_params_wf(node1, node2)
+
+        d0 = node1.get_dict()
+        for i in list(d0.keys()):
+            if d0[i] is None:
+                d0.pop(i)
+
+        d1 = unode.get_dict()
+        for i in list(d1.keys()):
+            if d1[i] is None:
+                d1.pop(i)
+
+        l_identical, l_diff = [], []
+        for i in list(d0.keys()):
+            if i in list(d1.keys()):
+                l_identical.append([i, d0[i], d1[i]])
+            else:
+                l_diff.append([0, i, d0[i]])
+        for i in list(d1.keys()):
+            if i not in list(d0.keys()):
+                l_diff.append([1, i, d1[i]])
+
+        assert l_identical ==  [[u'LMAX', 2, 2]]
+        assert l_diff.sort() == [[1, u'RMAX', 10.0], [1, u'EMIN', -1.0]].sort()
+        return node1, node2, unode
+
+
+    def test_neworder_potential_wf(self):
+        from numpy import loadtxt
+        from aiida.orm import load_node
+        from aiida.plugins import DataFactory
+        from aiida_kkr.tools.common_workfunctions import neworder_potential_wf
+        from aiida.tools.importexport import import_data
+        Dict = DataFactory('dict')
+        import_data('files/db_dump_kkrflex_create.tar.gz')
+        GF_host_calc = load_node('baabef05-f418-4475-bba5-ef0ee3fd5ca6').outputs
+        neworder_pot1 = [int(i) for i in loadtxt(GF_host_calc.retrieved.open('scoef'), skiprows=1)[:,3]-1]
+        settings_dict = {'pot1': 'out_potential',  'out_pot': 'potential_imp', 'neworder': neworder_pot1}
+        settings = Dict(dict=settings_dict)
+        startpot_imp_sfd = neworder_potential_wf(settings_node=settings, parent_calc_folder=GF_host_calc.remote_folder)
+        assert startpot_imp_sfd.get_object_content(startpot_imp_sfd.filename)[::1000] == u'C12807143D556463084.6+55 7D117 9D-87 0+25\n20.70351.75\n0521259.2+491.0-462. 02621D74112D03547T00 4D02116D502 6D39\n96.20261.50941.4944.7+30 98-29 .5-3625D07193.58104D0773D27252285417D341 9.506544D548447094.9+38 91063 54-08 6D28277.60909.98111'
+
diff --git a/aiida_kkr/tests/workflows/test_kkrimp_dos_wc.py b/aiida_kkr/tests/workflows/test_kkrimp_dos_wc.py
@@ -76,6 +76,7 @@ def test_dos_startpot_wc(self):
         from aiida.engine import run
         print(builder)
         out = run(builder)
+        print(out)
 
         assert 'last_calc_info' in out.keys()
         assert 'last_calc_output_parameters' in out.keys()