Merge pull request #110 from sphuber/fix/ci

Fix CI and correct the `setup.json`

.github/workflows/ci.yml

@@ -9,10 +9,10 @@ jobs:
  runs-on: ubuntu-18.04
 
  steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v2
 
  - name: Set up Python 3.7
- uses: actions/setup-python@v1
+ uses: actions/setup-python@v2
  with:
  python-version: 3.7
 
@@ -41,7 +41,7 @@ jobs:
  timeout-minutes: 30
 
  steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v2
 
  - name: Cache python dependencies
  id: cache-pip
@@ -53,18 +53,17 @@ jobs:
  pip-pre-commit-
 
  - name: Set up Python 3.7
- uses: actions/setup-python@v1
+ uses: actions/setup-python@v2
  with:
  python-version: 3.7
 
  - name: Install python dependencies
- run:
- pip install git+https://github.com/aiidateam/aiida-testing@export_cache
+ run: |
  pip install .[pre-commit,testing]
  pip freeze
 
  - name: Run pre-commit
- run: 
+ run:
  pre-commit run --all-files || (git status --short; git diff ; exit 1)
 
  tests:
@@ -74,10 +73,24 @@ jobs:
 
  strategy:
  matrix:
- python-version: ['3.8', '3.7', '3.6']
+ python-version: [3.6, 3.7, 3.8, 3.9]
+
+ services:
+ postgres:
+ image: postgres:10
+ env:
+ POSTGRES_DB: test_${{ matrix.backend }}
+ POSTGRES_PASSWORD: ''
+ POSTGRES_HOST_AUTH_METHOD: trust
+ ports:
+ - 5432:5432
+ rabbitmq:
+ image: rabbitmq:latest
+ ports:
+ - 5672:5672
 
  steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v2
 
  - name: Cache python dependencies
  id: cache-pip
@@ -89,26 +102,18 @@ jobs:
  pip-${{ matrix.python-version }}-tests
 
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v1
+ uses: actions/setup-python@v2
  with:
  python-version: ${{ matrix.python-version }}
 
  - name: Install system dependencies
  run: |
- wget -O - "https://github.com/rabbitmq/signing-keys/releases/download/2.0/rabbitmq-release-signing-key.asc" | sudo apt-key add -
- echo 'deb https://dl.bintray.com/rabbitmq-erlang/debian bionic erlang' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
- echo 'deb https://dl.bintray.com/rabbitmq/debian bionic main' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
  sudo apt update
- sudo apt install postgresql postgresql-server-dev-all postgresql-client
- sudo apt install rabbitmq-server
- sudo systemctl status rabbitmq-server.service
+ sudo apt install postgresql-10
 
  - name: Install python dependencies
  run: |
- pip install numpy==1.16.4
- pip install PyCifRW~=4.4
- # install aiida-testing manually
- #pip install git+https://github.com/broeder-j/aiida-testing.git@fa44c3ba4e57192fdbdee1cf3581576acc93800c
+ pip install --upgrade wheel setuptools
  pip install git+https://github.com/aiidateam/aiida-testing.git@export_cache
  pip install .[testing]
  reentry scan
@@ -118,9 +123,9 @@ jobs:
  # create fake codes for tests to work on ci
  cd ./tests/
  touch local_exe/inpgen && chmod +x local_exe/inpgen
- touch local_exe/fleur && chmod +x local_exe/fleur 
+ touch local_exe/fleur && chmod +x local_exe/fleur
  ./run_all_cov.sh
- 
+
  - name: Upload report to Codecov
  uses: codecov/codecov-action@v1
  with:

aiida_fleur/tools/common_fleur_wf.py

@@ -632,7 +632,7 @@ def find_last_submitted_calcjob(restart_wc):
  from aiida.common.exceptions import NotExistent
  from aiida.orm import CalcJobNode
  links = restart_wc.get_outgoing().all()
- calls = list([x for x in links if isinstance(x.node, CalcJobNode)])
+ calls = [x for x in links if isinstance(x.node, CalcJobNode)]
  if calls:
  calls = sorted(calls, key=lambda x: x.node.pk)
  return calls[-1].node.uuid
@@ -648,7 +648,7 @@ def find_last_submitted_workchain(restart_wc):
  from aiida.common.exceptions import NotExistent
  from aiida.orm import WorkChainNode
  links = restart_wc.get_outgoing().all()
- calls = list([x for x in links if isinstance(x.node, WorkChainNode)])
+ calls = [x for x in links if isinstance(x.node, WorkChainNode)]
  if calls:
  calls = sorted(calls, key=lambda x: x.node.pk)
  return calls[-1].node.uuid

aiida_fleur/workflows/create_magnetic_film.py

@@ -195,7 +195,7 @@ def start(self):
  return self.exit_codes.ERROR_INVALID_INPUT_CONFIG
 
  if 'relax' in inputs and 'distance_suggestion' not in inputs:
- if 'eos' or 'eos_output' in inputs:
+ if 'eos' in inputs or 'eos_output' in inputs:
  self.report('ERROR: relax wc input was given but distance_suggestion was not.')
  return self.exit_codes.ERROR_INVALID_INPUT_CONFIG
 

aiida_fleur/workflows/dmi.py

@@ -528,7 +528,7 @@ def get_results(self):
  for k in six.moves.range(i, i + num_ang - 1, 1):
  t_energydict[k] -= ref_enrg
 
- if e_u == 'Htr' or 'htr':
+ if e_u in ['Htr', 'htr']:
  for labels, energies in t_energydict.items():
  t_energydict[labels] = energies * HTR_TO_EV
  except AttributeError:

aiida_fleur/workflows/eos.py

@@ -220,7 +220,7 @@ def return_results(self):
 
  t_e = outpara.get('total_energy', float('nan'))
  e_u = outpara.get('total_energy_units', 'eV')
- if e_u == 'Htr' or 'htr':
+ if e_u in ['Htr', 'htr']:
  t_e = t_e * HTR_TO_EV
  dis = outpara.get('distance_charge', float('nan'))
  dis_u = outpara.get('distance_charge_units', 'me/bohr^3')

aiida_fleur/workflows/mae.py

@@ -475,7 +475,7 @@ def get_results(self):
 
  minenergy = min(t_energydict)
 
- if e_u == 'Htr' or 'htr':
+ if e_u in ['Htr', 'htr']:
  t_energydict = [HTR_TO_EV * (x - minenergy) for x in t_energydict]
  else:
  t_energydict = [(x - minenergy) for x in t_energydict]

aiida_fleur/workflows/mae_conv.py

@@ -182,7 +182,7 @@ def get_results(self):
  self.ctx.warnings.append(message)
  continue
  e_u = outpara.get('total_energy_units', 'Htr')
- if e_u == 'Htr' or 'htr':
+ if e_u in ['Htr', 'htr']:
  t_e = t_e * HTR_TO_EV
  t_energydict[label] = t_e
 

aiida_fleur/workflows/ssdisp.py

@@ -474,7 +474,7 @@ def get_results(self):
  # Find a minimal value of SpSp and count it as 0
  minenergy = min(t_energydict)
 
- if e_u == 'Htr' or 'htr':
+ if e_u in ['Htr', 'htr']:
  t_energydict = [HTR_TO_EV * (x - minenergy) for x in t_energydict]
  else:
  t_energydict = [(x - minenergy) for x in t_energydict]

aiida_fleur/workflows/ssdisp_conv.py

@@ -185,7 +185,7 @@ def get_results(self):
  self.ctx.warnings.append(message)
  continue
  e_u = outpara.get('total_energy_units', 'Htr')
- if e_u == 'Htr' or 'htr':
+ if e_u in ['Htr', 'htr']:
  t_e = t_e * htr_to_eV
  t_energydict[label] = t_e
 

setup.json

@@ -12,32 +12,31 @@
  "Operating System :: POSIX :: Linux",
  "Operating System :: MacOS :: MacOS X",
  "Programming Language :: Python :: 3",
- "Programming Language :: Python :: 3.5",
  "Programming Language :: Python :: 3.6",
  "Programming Language :: Python :: 3.7",
+ "Programming Language :: Python :: 3.8",
+ "Programming Language :: Python :: 3.9",
  "Environment :: Plugins",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Physics",
  "Natural Language :: English"
  ],
  "keywords": "fleur aiida inpgen workflows flapw juelich dft all-electron",
  "include_package_data": true,
+ "python_requires": ">=3.6",
  "setup_requires": [
  "reentry"
  ],
  "reentry_register": true,
  "install_requires": [
- "aiida-core>=1.3.0,<2.0.0",
- "lxml >= 3.6.4",
- "pytest-cov >= 2.5.0",
- "numpy>=1.16.4,<1.20.0",
+ "aiida-core[atomic_tools]>=1.3.0,<2.0.0",
+ "lxml>=3.6.4",
+ "numpy~=1.16,>=1.16.4",
  "sympy",
- "masci-tools>=0.3.12-dev4",
+ "masci-tools>=0.3.12-dev4,<0.4.0",
  "future",
- "ase",
- "pymatgen",
  "pyhull",
- "PyCifRW~=4.4"
+ "sqlalchemy<1.4"
  ],
  "extras_require": {
  "graphs ": [

tests/tools/test_common_aiida.py

@@ -154,7 +154,7 @@ def test_get_nodes_from_group():
 
  w = get_nodes_from_group(group, return_format='uuid')
  assert len(w) == 3
- assert all([isinstance(x, str) for x in w])
+ assert all(isinstance(x, str) for x in w)
 
  w = get_nodes_from_group(group, return_format='pk')
  assert len(w) == 3