Migrate to aiida 2 (#23)

* update aiida-core dependency * run aiida-upgrade * fix yapf * update ci
nanotech-empa · Nov 21, 2022 · 1f603e1 · 1f603e1
1 parent e2dd422
commit 1f603e1
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Showing 10 changed files with 95 additions and 112 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -4,12 +4,30 @@ on: [push, pull_request]
 
 jobs:
 
+ pre-commit:
+ runs-on: ubuntu-latest
+ timeout-minutes: 15
+ steps:
+ - uses: actions/checkout@v1
+ - name: Set up Python 3.8
+ uses: actions/setup-python@v1
+ with:
+ python-version: 3.8
+ - name: Install python dependencies
+ run: |
+ pip install --upgrade pip
+ pip install -e .[pre-commit]
+ - name: Run pre-commit
+ run: |
+ pre-commit install
+ pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
  tests:
  runs-on: ubuntu-latest
  timeout-minutes: 30
  services:
  postgres:
- image: postgres:10
+ image: postgres:12
  ports:
  - 5432:5432
  rabbitmq:
@@ -19,51 +37,24 @@ jobs:
  strategy:
  matrix:
  python-version: [3.8]
- backend: ['django']
  steps:
  - uses: actions/checkout@v2
 
  - 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: |
- sudo apt update
- sudo apt install postgresql-12
-
  - name: Install python dependencies
  run: |
  pip install --upgrade pip
  pip install -e .[testing]
- reentry scan -r aiida
 
  - name: Run test suite
  env:
- AIIDA_TEST_BACKEND: ${{ matrix.backend }}
  # show timings of tests
  PYTEST_ADDOPTS: "--durations=0"
  COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
  run: |
  py.test --cov aiida_gaussian --cov-append .
  coveralls
-
- pre-commit:
- runs-on: ubuntu-latest
- timeout-minutes: 15
- steps:
- - uses: actions/checkout@v1
- - name: Set up Python 3.8
- uses: actions/setup-python@v1
- with:
- python-version: 3.8
- - name: Install python dependencies
- run: |
- pip install --upgrade pip
- pip install -e .[pre-commit]
- reentry scan -r aiida
- - name: Run pre-commit
- run: |
- pre-commit install
- pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
diff --git a/aiida_gaussian/calculations/gaussian.py b/aiida_gaussian/calculations/gaussian.py
@@ -11,7 +11,7 @@
 
 import pymatgen.io.gaussian as mgaus
 
-StructureData = DataFactory("structure")
+StructureData = DataFactory("core.structure")
 
 
 class GaussianCalculation(CalcJob):

diff --git a/aiida_gaussian/tests/test_gaussian.py b/aiida_gaussian/tests/test_gaussian.py
@@ -52,7 +52,7 @@ def test_gaussian(fixture_code):
  inputs = {
  'code': fixture_code('gaussian'), #load_code("gaussian09@localhost"),
  'structure': structure,
- 'parameters': Dict(dict=parameters),
+ 'parameters': Dict(parameters),
  'metadata': {
  'options': {
  'resources': {

diff --git a/aiida_gaussian/workchains/base.py b/aiida_gaussian/workchains/base.py
@@ -10,7 +10,7 @@
 from aiida.plugins import CalculationFactory, DataFactory
 
 GaussianCalculation = CalculationFactory('gaussian')
-StructureData = DataFactory('structure')
+StructureData = DataFactory('core.structure')
 
 
 class GaussianBaseWorkChain(BaseRestartWorkChain):
@@ -96,7 +96,7 @@ def handle_scf_failure(self, node):
 
  # Update the params Dict
  route_params['scf'] = new_scf
- self.ctx.inputs.parameters = Dict(dict=params)
+ self.ctx.inputs.parameters = Dict(params)
 
  return ProcessHandlerReport(True)
 

diff --git a/aiida_gaussian/workchains/cubes.py b/aiida_gaussian/workchains/cubes.py
@@ -282,7 +282,7 @@ def cubegen_step(self):
  builder.parent_calc_folder = self.ctx.formchk_node.outputs.remote_folder
  builder.code = self.inputs.cubegen_code
  builder.stencil = SinglefileData(io.BytesIO(stencil))
- builder.parameters = Dict(dict=params_dict)
+ builder.parameters = Dict(params_dict)
  builder.retrieve_cubes = self.inputs.retrieve_cubes
 
  builder.parser_params = self.inputs.cubegen_parser_params

diff --git a/examples/example_01_opt.py b/examples/example_01_opt.py
@@ -28,26 +28,24 @@ def example_dft(gaussian_code):
  memory_mb = 300
 
  # Main parameters: geometry optimization
- parameters = Dict(
- dict={
- 'link0_parameters': {
- '%chk': 'aiida.chk',
- '%mem': "%dMB" % memory_mb,
- '%nprocshared': num_cores,
+ parameters = Dict({
+ 'link0_parameters': {
+ '%chk': 'aiida.chk',
+ '%mem': "%dMB" % memory_mb,
+ '%nprocshared': num_cores,
+ },
+ 'functional': 'BLYP',
+ 'basis_set': '6-31g',
+ 'charge': 0,
+ 'multiplicity': 1,
+ 'route_parameters': {
+ 'scf': {
+ 'cdiis': None,
  },
- 'functional': 'BLYP',
- 'basis_set': '6-31g',
- 'charge': 0,
- 'multiplicity': 1,
- 'route_parameters': {
- 'scf': {
- 'cdiis': None,
- },
- 'nosymm': None,
- 'opt': None,
- },
- }
- )
+ 'nosymm': None,
+ 'opt': None,
+ },
+ })
 
  # Construct process builder
 

diff --git a/examples/example_02_output_wfx.py b/examples/example_02_output_wfx.py
@@ -30,24 +30,22 @@ def example_dft(gaussian_code):
  memory_mb = 300
 
  # parameters
- parameters = Dict(
- dict={
- 'link0_parameters': {
- '%chk': 'aiida.chk',
- '%mem': '%dMB' % memory_mb,
- '%nprocshared': num_cores,
- },
- 'functional': 'PBE1PBE',
- 'basis_set': '6-31g',
- 'route_parameters': {
- 'nosymm': None,
- 'Output': 'WFX'
- },
- 'input_parameters': {
- 'output.wfx': None
- },
- }
- )
+ parameters = Dict({
+ 'link0_parameters': {
+ '%chk': 'aiida.chk',
+ '%mem': '%dMB' % memory_mb,
+ '%nprocshared': num_cores,
+ },
+ 'functional': 'PBE1PBE',
+ 'basis_set': '6-31g',
+ 'route_parameters': {
+ 'nosymm': None,
+ 'Output': 'WFX'
+ },
+ 'input_parameters': {
+ 'output.wfx': None
+ },
+ })
 
  # Construct process builder
 

diff --git a/examples/example_03_base_workflow.py b/examples/example_03_base_workflow.py
@@ -32,33 +32,31 @@ def example_dft(gaussian_code):
  memory_mb = 300
 
  # Main parameters: geometry optimization
- parameters = Dict(
- dict={
- 'link0_parameters': {
- '%chk': 'aiida.chk',
- '%mem': "%dMB" % memory_mb,
- '%nprocshared': num_cores,
+ parameters = Dict({
+ 'link0_parameters': {
+ '%chk': 'aiida.chk',
+ '%mem': "%dMB" % memory_mb,
+ '%nprocshared': num_cores,
+ },
+ 'functional': 'B3LYP',
+ 'basis_set': '6-31g',
+ 'charge': 0,
+ 'multiplicity': 1,
+ 'route_parameters': {
+ 'scf': {
+ 'conver': 7,
+ 'maxcycle': 140,
  },
- 'functional': 'B3LYP',
- 'basis_set': '6-31g',
- 'charge': 0,
- 'multiplicity': 1,
- 'route_parameters': {
- 'scf': {
- 'conver': 7,
- 'maxcycle': 140,
- },
- 'sp': None,
- },
- }
- )
+ 'sp': None,
+ },
+ })
 
  # Construct process builder
 
  builder = GaussianBaseWorkChain.get_builder()
 
  # Handle the ASyTop error
- builder.handler_overrides = Dict(dict={'handle_asytop_error': True})
+ builder.handler_overrides = Dict({'handle_asytop_error': True})
 
  builder.gaussian.structure = structure
  builder.gaussian.parameters = parameters

diff --git a/examples/example_cubes_workchain.py b/examples/example_cubes_workchain.py
@@ -37,27 +37,25 @@ def example(gaussian_code, formchk_code, cubegen_code):
  builder = GaussianCalculation.get_builder()
  builder.code = gaussian_code
  builder.structure = struct_node
- builder.parameters = Dict(
- dict={
- 'link0_parameters': {
- '%chk': 'aiida.chk',
- '%mem': "%dMB" % memory_mb,
- '%nprocshared': str(num_cores),
+ builder.parameters = Dict({
+ 'link0_parameters': {
+ '%chk': 'aiida.chk',
+ '%mem': "%dMB" % memory_mb,
+ '%nprocshared': str(num_cores),
+ },
+ 'functional': 'UB3LYP',
+ 'basis_set': '6-31g',
+ 'charge': 0,
+ 'multiplicity': 1,
+ 'route_parameters': {
+ 'scf': {
+ 'cdiis': None,
  },
- 'functional': 'UB3LYP',
- 'basis_set': '6-31g',
- 'charge': 0,
- 'multiplicity': 1,
- 'route_parameters': {
- 'scf': {
- 'cdiis': None,
- },
- 'guess': 'mix',
- 'nosymm': None,
- 'sp': None,
- },
- }
- )
+ 'guess': 'mix',
+ 'nosymm': None,
+ 'sp': None,
+ },
+ })
  builder.metadata.options.resources = {
  "tot_num_mpiprocs": num_cores,
  "num_machines": 1,

diff --git a/pyproject.toml b/pyproject.toml
@@ -21,7 +21,7 @@ classifiers = [
 ]
 requires-python = ">=3.7"
 dependencies = [
- "aiida-core>=1.0.0,<2.0.0",
+ "aiida-core>=2.0.0,<3.0.0",
  "pymatgen>=2020.4,<2022.0.0",
  "cclib>=1.6.1,<=1.7",
  "ase",