Merge branch 'develop'

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.2
+current_version = 1.1.3-dev
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?

.travis.yml

@@ -1,3 +1,4 @@
+#rabbitMQ only works with trusty according to travis website
 dist: trusty
 language: python
 python: 2.7
@@ -9,7 +10,7 @@ services:
 - rabbitmq
 addons:
   postgresql: '9.5'
-  apt: # copied from wannier90's travis.yml
+  apt: # adapted from wannier90's travis.yml
     packages:
       - gfortran
       - libblas-dev
@@ -21,6 +22,7 @@ before_install:
 # now unpack the secrets (pypi_credentials and ssh key to download the KKR code
 - tar -zxvf secrets.tar.gz && rm secrets.tar.gz
 # Now we install the needed dependencies
+#- sudo apt-get update && sudo apt-get upgrade && sudo apt-get install software-properties-common -y && sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y && sudo apt-get update && sudo apt-get install gfortran-8 -y && sudo apt-get update
 - sudo apt-get install locate
 - sudo service postgresql stop
 - sudo apt-get remove postgresql
@@ -42,16 +44,26 @@ script:
 - echo "iffgit.fz-juelich.de,134.94.161.83 ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBH2UDrT0bZP+WmJGGbtLPtFyC5FgQgOM1XvVJ6u5XBJrYMnKNVb9jAttL+k8VvDgcK6b3dFJnvt7eiXtG/hnqCo=" >> ~/.ssh/known_hosts
 # clone the code and install
 - cd aiida_kkr/tests && ./jukkr_installation.sh
-# Now run all tests
-- pwd && ./run_all.sh
-allow_failures:
-  - pytest -s --cov-report=term-missing --cov=aiida_kkr -k Test_dos_workflow
-  - pytest -s --cov-report=term-missing --cov=aiida_kkr -k Test_gf_writeout_workflow
-# (needs allow failure so that after_success is executed)
+## First check if rabbitmq communication is working
+#- ./check_pika-rabbitmq.py | tee out_rmq_check
+#- ./verify_rmq_check.py
+# Then run all tests
+- ./run_all.sh
+#- travis_wait 30 ./run_all.sh
+matrix:
+  allow_failures: # (needs allow failure so that after_success is executed)
+    # these tests fail at the moment because gfortran is too old
+    - pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_dos_workflow
+    - pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_gf_writeout_workflow
+    - pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_scf_workflow
+    # these are fail because gfortran compilation of kkrimp does not work
+    - pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_kkrimp_scf_workflow
+    - pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_kkrimp_full_workflow
+
 after_success:
 - codecov
-#deploy to pypi
+#deploy to pypi using poetry
 - cd ../../ && rm -rf aiida_kkr/tests/{submit_test/,__pycache__/,jukkr} id_rsa_travis #remove test output before publishing
-- pip install poetry && ./publish_to_pypi.sh
+- pip install poetry && ./publish_to_pypi.sh # publish_to_pypi script does poetry publish with autentification information
 git:
   depth: 3

aiida_kkr/__init__.py

@@ -3,4 +3,4 @@
 
 """
 
-__version__ = "1.1.2"
+__version__ = "1.1.3-dev"

aiida_kkr/tests/check_pika-rabbitmq.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+
+import pika
+from time import sleep, time
+import timeout_decorator
+
+@timeout_decorator.timeout(5)
+def rmq_listen():
+    channel.start_consuming()
+
+# Part 1: send message
+print "Start sending message..."
+connection = pika.BlockingConnection(pika.ConnectionParameters('localhost'))
+channel = connection.channel()
+channel.queue_declare(queue='hello')
+msg = 'Hello World! {}'.format(time())
+channel.basic_publish(exchange='',routing_key='hello', body=msg)
+print " [x] Sent '{}'".format(msg)
+connection.close()
+
+print "done sending message. Wait for 5 seconds and start receiving..."
+sleep(5)
+
+# Part 2: receive message
+connection = pika.BlockingConnection(pika.ConnectionParameters(host='localhost'))
+channel = connection.channel()
+channel.queue_declare(queue='hello')
+print ' [*] Waiting 5 seconds for messages.'
+def callback(ch, method, properties, body):
+    print " [x] Received %r" % (body,)
+channel.basic_consume(queue='hello',on_message_callback=callback,auto_ack=False)
+try:
+    rmq_listen()
+except timeout_decorator.timeout_decorator.TimeoutError:
+    print "Done waiting, now close connection"
+    connection.close()

aiida_kkr/tests/dbsetup.py

@@ -0,0 +1,81 @@
+
+import os
+
+
+# some global settings
+
+kkr_codename = 'kkrhost'
+kkrimp_codename = 'kkrimp'
+voro_codename = 'voronoi'
+computername = 'localhost'
+queuename = ''
+
+cwd = os.getcwd()
+workdir = cwd+'/jukkr/work'
+codelocation = cwd+'/jukkr/'
+
+
+
+def prepare_computer(computername, workdir):
+    """Create new computer in db or read computer from db if it already exists."""
+    from aiida.orm import Computer
+    from aiida.orm.backend import construct_backend
+    from aiida.orm.querybuilder import QueryBuilder
+    # 
+    # first check if computer exists already in database
+    qb = QueryBuilder()
+    qb.append(Computer, tag='computer')
+    all_computers = qb.get_results_dict()
+    computer_found_in_db = False
+    if len(all_computers)>0:
+        for icomp in range(len(all_computers)):
+            c = all_computers[icomp].get('computer').get('*')
+            if c.get_name() == computername:
+                computer_found_in_db = True
+                comp = c 
+    # if it is not there create a new one
+    if not computer_found_in_db:
+        #comp = Computer(computername, 'test computer', transport_type='local', scheduler_type='direct', workdir=workdir)
+        b = construct_backend()
+        comp = b.computers.create(computername, 'test computer', transport_type='local', scheduler_type='direct', workdir=workdir)
+        comp.set_default_mpiprocs_per_machine(4)
+        comp.store()
+        print 'computer stored now cofigure'
+        comp.configure()
+    else:
+        print 'found computer in database'
+    # return computer
+    return comp
+
+
+def prepare_code(codename, codelocation, computername, workdir):
+    """."""
+    # first create or read computer
+    comp = prepare_computer(computername, workdir)
+    # now decide which code to add
+    if codename == 'kkrhost':
+        execname = 'kkr.x'
+        pluginname = 'kkr.kkr'
+    elif codename == 'voronoi':
+        execname = 'voronoi.exe'
+        pluginname = 'kkr.voro'
+    elif codename == 'kkrimp':
+        execname = 'kkrflex.exe'
+        pluginname = 'kkr.kkrimp'
+    else:
+        raise ValueError('unknown codename')
+    # then get code from database or create a new code
+    from aiida.orm import Code
+    from aiida.common.exceptions import NotExistent
+    try:
+        code = Code.get_from_string(codename+'@'+computername)
+    except NotExistent as exception:
+        code = Code()
+        code.label = codename
+        code.description = ''
+        code.set_remote_computer_exec((comp, codelocation+execname))
+        code.set_input_plugin_name(pluginname)
+        if codename == 'voronoi':
+            code.set_prepend_text('ln -s '+codelocation+'ElementDataBase .')
+        code.store()
+

aiida_kkr/tests/jukkr_installation.sh

@@ -8,20 +8,20 @@ cd jukkr/
 
 # build voronoi code
 # cannot build with gfortran at the moment, needs fixing on jukkr side
-./install.py --program=voronoi --compiler=ifort --parallelization=serial
-#./install.py --program=voronoi --compiler=gfortran --parallelization=serial
+#./install.py --program=voronoi --compiler=ifort --parallelization=serial
+./install.py --program=voronoi --compiler=gfortran --parallelization=serial
 cd build/ && make -j4 && cp voronoi.exe ../
 cd ..
 
 # build kkrhost code
-./install.py --program=kkrhost --compiler=ifort --parallelization=serial
-#./install.py --program=kkrhost --compiler=gfortran --parallelization=serial -d
-cd build/ && make -j4 && cp kkr.x ../
-cd ..
+#./install.py --program=kkrhost --compiler=ifort --parallelization=serial
+#./install.py --program=kkrhost --compiler=gfortran --parallelization=serial
+#cd build/ && make -j4 && cp kkr.x ../
+#cd ..
 
 # build kkrimp code
 # cannot build with gfortran at the moment, needs fixing on jukkr side
-./install.py --program=kkrimp --compiler=ifort --parallelization=serial
+#./install.py --program=kkrimp --compiler=ifort --parallelization=serial
 #./install.py --program=kkrimp --compiler=gfortran --parallelization=serial
-cd build/ && make -j4 && cp kkrflex.exe ../
-cd ..
+#cd build/ && make -j4 && cp kkrflex.exe ../
+#cd ..

aiida_kkr/tests/run_all.sh

@@ -2,6 +2,18 @@
 export AIIDA_PATH='.';
 mkdir -p '.aiida';
 #pytest -sv
-#pytest -v
-#pytest --cov-report=term-missing --cov=aiida_kkr --ignore=test_scf_wc_simple.py
-pytest --cov-report=term-missing --cov=aiida_kkr --ignore=test_scf_wc_simple.py --ignore=test_vorostart_wc.py --ignore=test_dos_wc.py --ignore=test_gf_writeout_wc.py --ignore=test_kkrimp_sub_wc.py --ignore=test_kkrimp_full_wc.py --ignore=jukkr
+
+# tests without running actual calculations
+pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=workflows --ignore=jukkr
+
+# test running full workflows, need compiled codes and execute them
+pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_vorostart_workflow
+
+# these tests fail at the moment because gfortran is too old
+#pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_dos_workflow
+#pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_gf_writeout_workflow
+#pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_scf_workflow
+
+# these are deactivated becaus gfortran compilation of kkrimp does not work
+#pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_kkrimp_scf_workflow
+#pytest --cov-report=term-missing --cov-append --cov=aiida_kkr --ignore=jukkr -k Test_kkrimp_full_workflow

aiida_kkr/tests/run_all_covhtml.sh

@@ -10,4 +10,4 @@
 #pytest -s --cov-report=html --cov=aiida_kkr --ignore=jukkr -k Test_dos_workflow
 #pytest -s --cov-report=html --cov=aiida_kkr --ignore=jukkr -k Test_gf_writeout_workflow -k Test_dos_workflow
 #pytest --cov-report=html --cov=aiida_kkr --ignore=jukkr --ignore=test_scf_wc_simple.py --ignore=test_vorostart_wc.py --ignore=test_kkrimp_sub_wc.py --ignore=test_kkrimp_full_wc.py
-pytest -s --cov-report=html --cov=aiida_kkr --ignore=jukkr
+pytest -v -s --cov-report=html --cov=aiida_kkr --ignore=jukkr