Mig/2.x (#172)

- Add CLI to run
- migrate to support AiiDA 2.x
- new YAML to setup pw/ph executables

.github/workflows/ci.yml

@@ -8,8 +8,6 @@ on: [push, pull_request]
 jobs:
 
     pre-commit:
-    # Adapted from: https://github.com/CasperWA/voila-optimade-client
-
         runs-on: ubuntu-latest
 
         steps:
@@ -18,11 +16,56 @@ jobs:
             - name: Setup Python
               uses: actions/setup-python@v2
               with:
-                  python-version: 3.9
+                  python-version: '3.10'
 
             - name: Install dependencies
-              run: |
-                  python -m pip install pre-commit==2.11.1
-                  python -m pip install virtualenv==20.0.33
+              run: pip install -U pre-commit==2.10.0
+
             - name: Run pre-commit
               run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+    test:
+        needs: [pre-commit]
+
+        strategy:
+            matrix:
+                python-version: ['3.9']
+
+        services:
+            rabbitmq:
+                image: rabbitmq:3.8.14-management
+                ports:
+                    - 5672:5672
+                    - 15672:15672
+
+        runs-on: ubuntu-latest
+        timeout-minutes: 40
+
+        steps:
+            - uses: eWaterCycle/setup-singularity@v7 # for containerized code test
+              with:
+                  singularity-version: 3.8.7
+
+            - uses: actions/checkout@v2
+
+            - name: Cache Python dependencies
+              uses: actions/cache@v1
+              with:
+                  path: ~/.cache/pip
+                  key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+                  restore-keys: pip-${{ matrix.python-version }}-tests
+
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                  python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies for test
+              run: |
+                  pip install -U pip==22.3.1
+                  pip install -U .[tests]
+
+            # - name: Pull the image and Run pytest
+            #   run: |
+            #     singularity run docker://containers4hpc/qe-mpich314:0.1.0 which pw.x
+            #     pytest -v tests/test_nightly.py -s

.pre-commit-config.yaml

@@ -14,11 +14,6 @@ repos:
           - id: trailing-whitespace
             exclude: *exclude_pre_commit_hooks
 
-    - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
-      rev: 0.1.0
-      hooks:
-          - id: yamlfmt
-
     - repo: https://github.com/ikamensh/flynt/
       rev: '0.76'
       hooks:
@@ -55,23 +50,12 @@ repos:
                     ^docs/ |
                 )
 
-    - repo: https://github.com/hadialqattan/pycln
-      rev: v1.2.5
-      hooks:
-          - id: pycln
-            args: [--config=pyproject.toml]
-
     - repo: https://github.com/pycqa/isort
-      rev: 5.10.1
+      rev: 5.12.0
       hooks:
           - id: isort
             args: [--profile, black, --filter-files]
 
-    - repo: https://github.com/asottile/setup-cfg-fmt
-      rev: v1.20.0
-      hooks:
-          - id: setup-cfg-fmt
-
     - repo: https://github.com/sirosen/check-jsonschema
       rev: 0.14.0
       hooks:

README.md

@@ -2,7 +2,7 @@
 
 ## Initial dual (E_rho/E_wfc) for convergence test
 
-For NC psp we use dual start from 4, PAW/US use dual from 8 for most of elements but 18 for high dual elements which we found usually high charge density cutoff are needed. 
+For NC psp we use dual start from 4, PAW/US use dual from 8 for most of elements but 18 for high dual elements which we found usually high charge density cutoff are needed.
 They are O,Fe,Hf, Mn, Co, Ni, Cr.
 
 ## Logic of convergence test on different criteria protocol

aiida_sssp_workflow/calculations/calculate_delta.py

@@ -124,9 +124,9 @@ def delta_analyze(element, configuration, V0, B0, B1, natoms) -> orm.Dict:
         B0,
         B1,
         config_string=None,
-        prefact=400,  # XXX: re-inspect this value and set it in protocol
-        weight_b0=1 / 8,
-        weight_b1=1 / 64,
+        prefact=1,
+        weight_b0=1 / 20,
+        weight_b1=1 / 400,
     )
 
     return orm.Dict(

aiida_sssp_workflow/cli/__init__.py

@@ -2,20 +2,18 @@
 # pylint: disable=wrong-import-position,wildcard-import
 """Module for the command line interface."""
 import click
-import click_completion
-from aiida.cmdline.params import options as options_core
-from aiida.cmdline.params import types
-
-# Activate the completion of parameter types provided by the click_completion package
-click_completion.init()
+from aiida.cmdline.groups import VerdiCommandGroup
+from aiida.cmdline.params import options, types
 
 
 @click.group(
-    "aiida-sssp-workflow", context_settings={"help_option_names": ["-h", "--help"]}
+    "aiida-sssp-workfloww",
+    cls=VerdiCommandGroup,
+    context_settings={"help_option_names": ["-h", "--help"]},
 )
-@options_core.PROFILE(type=types.ProfileParamType(load_profile=True))
-def cmd_root(profile):  # pylint: disable=unused-argument
+@options.PROFILE(type=types.ProfileParamType(load_profile=True), expose_value=False)
+def cmd_root():
     """CLI for the `aiida-sssp-workflow` plugin."""
 
 
-from aiida_sssp_workflow.cli.tools import dump_output
+from .run import launch