Refactoring on the running and tidy up the repo (#238)

* Extract pseudo info from name and text function

* Use pyproject.toml only with flit as build backend

* Use ruff for precommit lint

* Add more source to test pseudo info extraction

* Renew structure mapping using a script

* Use src path for modules and delete unused legacy modules

* Standardize the structure for each type of verification

* Base and Caching Convergence refactoring

* eos convergence refactoring

* Accept UpfData to contruct builder

* Cohesive energe convergence workflow refac

* Refactor convergence pressure workflow

* Refactoring Band convergence workflow

* Add an element list UNSUPPERTED_ELEMENTS for elements where nat.phys.rev has no structures

* Refactoring phonon convergence test

* Having robust tests for tricky caching cases of bands and phonon frequecies

* Refactoring transferibility verification workflow

* Band structure verification workflow and tidy standard structure collecting function

* Update CI to do unit tests

* Remove parse_pseudo as package move it into aiida_sssp_workflow

* More sophisticate pytest running option.

* Delete computer setup yaml files delete examples

* Test on the main branche of aiida-core

* Compute and write down the success rate to the convergence test output

* Full verification workchain

- Rename measure to transferability and separate bands and eos

* Convergence parser for properties

* More parser

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.docker/tests/conftest.py

@@ -5,7 +5,7 @@
 
 @pytest.fixture(scope="session")
 def docker_compose_file(pytestconfig):  # pylint: disable=unused-argument
-    return f"docker-compose.aiida-sssp-workflow.yml"
+    return "docker-compose.aiida-sssp-workflow.yml"
 
 
 @pytest.fixture(scope="session")

.github/dependabot.yml

@@ -0,0 +1,12 @@
+---
+version: 2
+updates:
+# Maintain dependencies for GitHub Actions
+    - package-ecosystem: github-actions
+      directory: /
+      schedule:
+          interval: monthly
+      groups:
+          gha-dependencies:
+              patterns:
+                  - '*'

.github/workflows/ci.yml

@@ -1,66 +1,106 @@
 ---
 # Run basic tests for this app on the latest aiidalab-docker image.
 
-name: continuous-integration
+name: CI unit test
 
 on: [push, pull_request]
 
 jobs:
 
-    pre-commit:
+
+    fast-tests:
         runs-on: ubuntu-latest
+        timeout-minutes: 10
+
+        services:
+          rabbitmq:
+            image: rabbitmq:3.8.14-management
+            ports:
+            - 5672:5672
+            - 15672:15672
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
 
-            - name: Setup Python
-              uses: actions/setup-python@v2
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v5
               with:
-                  python-version: '3.10'
+                  python-version: "3.10"
 
-            - name: Install dependencies
-              run: pip install -U pre-commit==2.10.0
+            - name: Install dependencies for test
+              run: |
+                  pip install .[dev]
 
-            - name: Run pre-commit
-              run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+            - name: Run pytest
+              run: |
+                  pytest -s tests -m "not slow"
 
-    test:
-        needs: [pre-commit]
+    slow-tests:
 
-        strategy:
-            matrix:
-                python-version: ['3.9', '3.10']
+        runs-on: ubuntu-latest
+        timeout-minutes: 30
 
         services:
-            rabbitmq:
-                image: rabbitmq:3.8.14-management
-                ports:
-                    - 5672:5672
-                    - 15672:15672
-
-        runs-on: ubuntu-latest
-        timeout-minutes: 40
+          rabbitmq:
+            image: rabbitmq:3.8.14-management
+            ports:
+            - 5672:5672
+            - 15672:15672
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
 
-            - name: Cache Python dependencies
-              uses: actions/cache@v1
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v5
               with:
-                  path: ~/.cache/pip
-                  key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
-                  restore-keys: pip-${{ matrix.python-version }}-tests
+                  python-version: "3.10"
+
+            - name: Install dependencies for test
+              run: |
+                  pip install .[dev]
 
-            - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v2
+            - name: Run pytest
+              run: |
+                  pytest -s tests -m "slow"
+
+    edge-aiida-core-tests:
+        # This is to test the plugin is compatible with the main branch of aiida-core
+
+        needs: [slow-tests]
+        runs-on: ubuntu-latest
+        timeout-minutes: 30
+
+        services:
+          rabbitmq:
+            image: rabbitmq:3.8.14-management
+            ports:
+            - 5672:5672
+            - 15672:15672
+
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v5
               with:
-                  python-version: ${{ matrix.python-version }}
+                  python-version: "3.10"
 
-            - name: Install dependencies for test
+            - name: Install dependencies and edge aiida-core for test
               run: |
-                  pip install -U pip==22.3.1
-                  pip install -U .[tests]
+                  pip install .[dev]
+                  pip uninstall --yes aiida-core
+                  git clone --depth 1 https://github.com/aiidateam/aiida-core.git
+                  pip install ./aiida-core
 
-            - name: Pull the image and Run pytest
+            - name: Check aiida-core version is the edget ('post' in version tag)
+              run: |
+                  if verdi --version | grep -q "post"; then
+                    echo $(verdi --version)
+                  else
+                    echo $(verdi --version)
+                    exit 1
+                  fi
+
+            - name: Run pytest
               run: |
-                pytest -sv tests
+                  pytest -s tests

.pre-commit-config.yaml

@@ -9,48 +9,24 @@ repos:
           - id: end-of-file-fixer
             exclude: &exclude_pre_commit_hooks >
                 (?x)^(
-                    run_script/_static/.*/.*|
+                    tests/_statics/upf/.*|
                 )$
           - id: trailing-whitespace
             exclude: *exclude_pre_commit_hooks
 
-    - repo: https://github.com/ikamensh/flynt/
-      rev: '0.76'
-      hooks:
-          - id: flynt
-
-    - repo: https://github.com/psf/black
-      rev: 23.3.0
-      hooks:
-          - id: black
-            language_version: python3 # Should be a command that runs python3.6+
-
-    - repo: https://github.com/PyCQA/flake8
-      rev: 4.0.1
-      hooks:
-          - id: flake8
-            args: [--count, --show-source, --statistics]
-            additional_dependencies:
-                - flake8-bugbear==21.3.1
-            exclude: |
-                (?x)(
-                    ^tests/ |
-                    ^examples/ |
-                    ^docs/ |
-                )
-
-    - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-            args: [--profile, black, --filter-files]
-
-    - repo: https://github.com/sirosen/check-jsonschema
-      rev: 0.14.0
-      hooks:
-          - id: check-github-workflows
-
     - repo: https://github.com/kynan/nbstripout
       rev: 0.6.1
       hooks:
           - id: nbstripout
+
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.4.1
+      hooks:
+      - id: ruff-format
+        exclude: &exclude_ruff >
+          (?x)^(
+            examples/.*|
+          )$
+      - id: ruff
+        exclude: *exclude_ruff
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]