Dependencies: Update requirement for aiida-core~=2.0 (#804)

The minimum requirement for `aiida-core` is upped to `v2.0` which was
just released. This commit just does the minimum to get the tests
passing. There are a lot of deprecated warnings that will be addressed
later.

Notable necessary changes:

 * Remove the use of `reentry`. This is no longer necessary in
   `aiida-core==2.0` which uses `importlib_metadata` instead.
 * Remove `click_completion` and add `click~=8.0` as requirement which
   now comes with its own auto-completion built-in.
 * The `aiida.cmdline.params.options.VERBOSITY` option was added to the
   root CLI command. This is necessary for the messages printed through
   the `aiida.cmdline.utils.echo` to actually show up. It is this option
   that automatically configures the logging which is used by that
   module and without it, the messages would not end up to stdout.
 * Update requirements for `docs` extra to build documentation.
 * Remove use of `Node._repository` which has been removed
 * Add `core.` prefix to entry point names in reference test files
 * `Node.add_incoming` -> `Node.base.links.add_incoming`
 * Use `QueryBuilder.first(flat=True` when only single projection

.github/workflows/cd.yml

@@ -46,9 +46,7 @@ jobs:
  python-version: '3.8'
 
  - name: Install Python dependencies
- run: |
- pip install --upgrade pip setuptools wheel
- pip install -e .[pre-commit,tests]
+ run: pip install -e .[pre-commit,tests]
 
  - name: Run pre-commit
  run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
@@ -87,10 +85,7 @@ jobs:
  python-version: ${{ matrix.python-version }}
 
  - name: Install Python dependencies
- run: |
- pip install --upgrade pip setuptools wheel
- pip install -e .[tests]
- reentry scan
+ run: pip install -e .[tests]
 
  - name: Run pytest
  run: pytest -sv tests

.github/workflows/ci.yml

@@ -25,9 +25,7 @@ jobs:
  python-version: '3.8'
 
  - name: Install Python dependencies
- run: |
- pip install --upgrade pip setuptools wheel
- pip install -e .[pre-commit,tests]
+ run: pip install -e .[pre-commit,tests]
 
  - name: Run pre-commit
  run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
@@ -65,10 +63,7 @@ jobs:
  python-version: ${{ matrix.python-version }}
 
  - name: Install Python dependencies
- run: |
- pip install --upgrade pip setuptools wheel
- pip install -e .[tests]
- reentry scan
+ run: pip install -e .[tests]
 
  - name: Run pytest
  run: pytest -sv tests

README.md

@@ -12,7 +12,8 @@ The matrix below assumes the user always install the latest patch release of the
 
 | Plugin | AiiDA | Python | Quantum ESPRESSO |
 |-|-|-|-|
-| `v3.5 < v4.0` | ![Compatibility for v3.5][AiiDA v3.4] | [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-quantumespresso.svg)](https://pypi.org/project/aiida-quantumespresso.svg) | ![Quantum ESPRESSO compatibility][QE v6-7] |
+| `v4.0 < v5.0` | ![Compatibility for v4.0][AiiDA v4.0] | [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-quantumespresso.svg)](https://pypi.org/project/aiida-quantumespresso.svg) | ![Quantum ESPRESSO compatibility][QE v6-7] |
+| `v3.5 < v4.0` | ![Compatibility for v3.5][AiiDA v3.5] | [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-quantumespresso.svg)](https://pypi.org/project/aiida-quantumespresso.svg) | ![Quantum ESPRESSO compatibility][QE v6-7] |
 | `v3.4 < v3.5` | ![Compatibility for v3.4][AiiDA v3.4] | [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-quantumespresso.svg)](https://pypi.org/project/aiida-quantumespresso.svg) | ![Quantum ESPRESSO compatibility][QE v6] |
 | `v3.3 < v3.4` | ![Compatibility for v3.3][AiiDA v3.3] | [![PyPI pyversions](https://img.shields.io/pypi/pyversions/aiida-quantumespresso.svg)](https://pypi.org/project/aiida-quantumespresso.svg) | ![Quantum ESPRESSO compatibility][QE v6] |
 | `v3.1 < v3.3` | ![Compatibility for v3.1][AiiDA v3.1] | | ![Quantum ESPRESSO compatibility][QE v6] |
@@ -102,7 +103,7 @@ We acknowledge support from:
 
 <img src="https://raw.githubusercontent.com/aiidateam/aiida-quantumespresso/develop/docs/source/images/swissuniversities.png" width="300px" height="35px"/>
 
-
+[AiiDA v4.0]: https://img.shields.io/badge/AiiDA>=2.0.0,<3.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D
 [AiiDA v3.5]: https://img.shields.io/badge/AiiDA->=1.4.4,<2.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D
 [AiiDA v3.4]: https://img.shields.io/badge/AiiDA->=1.4.4,<2.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D
 [AiiDA v3.3]: https://img.shields.io/badge/AiiDA->=1.4.4,<2.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D

aiida_quantumespresso/cli/__init__.py

@@ -1,17 +1,49 @@
 # -*- coding: utf-8 -*-
-# pylint: disable=wrong-import-position,wildcard-import
+# pylint: disable=wrong-import-position
 """Module for the command line interface."""
 from aiida.cmdline.params import options, types
 import click
-import click_completion
 
-# Activate the completion of parameter types provided by the click_completion package
-click_completion.init()
+
+class VerbosityGroup(click.Group):
+ """Custom command group that automatically adds the ``VERBOSITY`` option to all subcommands."""
+
+ @staticmethod
+ def add_verbosity_option(cmd):
+ """Apply the ``verbosity`` option to the command, which is common to all ``verdi`` commands."""
+ if 'verbosity' not in [param.name for param in cmd.params]:
+ cmd = options.VERBOSITY()(cmd)
+
+ return cmd
+
+ def group(self, *args, **kwargs):
+ """Ensure that sub command groups use the same class but do not override an explicitly set value."""
+ kwargs.setdefault('cls', self.__class__)
+ return super().group(*args, **kwargs)
+
+ def get_command(self, ctx, cmd_name):
+ """Return the command that corresponds to the requested ``cmd_name``.
+
+ This method is overridden from the base class in order to automatically add the verbosity option.
+
+ Note that if the command is not found and ``resilient_parsing`` is set to True on the context, then the latter
+ feature is disabled because most likely we are operating in tab-completion mode.
+ """
+ cmd = super().get_command(ctx, cmd_name)
+
+ if cmd is not None:
+ return self.add_verbosity_option(cmd)
+
+ if ctx.resilient_parsing:
+ return None
+
+ return ctx.fail(f'`{cmd_name}` is not a {self.name} command.')
 
 
 @click.group('aiida-quantumespresso', context_settings={'help_option_names': ['-h', '--help']})
-@options.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)
+@options.VERBOSITY()
+def cmd_root():
  """CLI for the `aiida-quantumespresso` plugin."""
 
 

aiida_quantumespresso/cli/utils/defaults.py

@@ -27,9 +27,9 @@ def get_structure():
  }
 
  builder = QueryBuilder().append(StructureData, filters=filters)
- results = builder.first()
+ structure = builder.first(flat=True)
 
- if not results:
+ if not structure:
  alat = 5.43
  ase_structure = crystal(
  'Si',
@@ -40,7 +40,5 @@ def get_structure():
  )
  structure = StructureData(ase=ase_structure)
  structure.store()
- else:
- structure = results[0]
 
  return structure.uuid

aiida_quantumespresso/parsers/cp.py

@@ -20,7 +20,7 @@ def parse(self, **kwargs):
  retrieved = self.retrieved
 
  # check what is inside the folder
- list_of_files = retrieved._repository.list_object_names()
+ list_of_files = retrieved.list_object_names()
 
  # options.metadata become attributes like this:
  stdout_filename = self.node.get_attribute('output_filename')

docs/source/conf.py

@@ -13,20 +13,15 @@
 # serve to show the default.
 import time
 
-# ensure plugins are loaded
-from reentry import manager
+# Load the dummy profile even if we are running locally, this way the documentation will succeed even if the current
+# default profile of the AiiDA installation does not use a Django backend.
+from aiida.manage.configuration import load_documentation_profile
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 import aiida_quantumespresso
 
-manager.scan()
-
-# Load the dummy profile even if we are running locally, this way the documentation will succeed even if the current
-# default profile of the AiiDA installation does not use a Django backend.
-from aiida.manage.configuration import load_documentation_profile
-
 load_documentation_profile()
 
 # -- Project information -----------------------------------------------------

pyproject.toml

@@ -21,15 +21,15 @@ classifiers = [
 keywords = ['aiida', 'workflows']
 requires-python = '>=3.8'
 dependencies = [
- 'psycopg2-binary<2.9',
- 'aiida_core[atomic_tools]~=1.4,>=1.4.4',
- 'aiida-pseudo~=0.6.1',
+ 'aiida_core[atomic_tools]~=2.0',
+ 'aiida-pseudo~=0.7.0',
+ 'click~=8.0',
+ 'importlib_resources',
  'jsonschema',
+ 'numpy',
  'packaging',
  'qe-tools~=2.0rc1',
- 'xmlschema~=1.2,>=1.2.5',
- 'numpy',
- 'importlib_resources'
+ 'xmlschema~=1.2,>=1.2.5'
 ]
 
 [project.urls]
@@ -39,12 +39,10 @@ Documentation = 'https://aiida-quantumespresso.readthedocs.io'
 
 [project.optional-dependencies]
 docs = [
- 'Sphinx',
- 'docutils',
- 'markupsafe<2.1',
- 'sphinx-copybutton~=0.3.0',
- 'sphinx-book-theme~=0.1.0',
- 'sphinx-click~=2.7.1'
+ 'sphinx~=4.1',
+ 'sphinx-copybutton~=0.5.0',
+ 'sphinx-book-theme~=0.3.2',
+ 'sphinx-click~=4.0',
 ]
 pre-commit = [
  'pre-commit~=2.17',
@@ -190,7 +188,6 @@ testpaths = [
 filterwarnings = [
  'ignore::DeprecationWarning:frozendict:',
  'ignore::DeprecationWarning:pkg_resources:',
- 'ignore::DeprecationWarning:reentry:',
  'ignore::DeprecationWarning:sqlalchemy_utils:',
 ]
 

tests/calculations/test_epw.py

@@ -59,7 +59,7 @@ def test_epw_default(
  }
 
  parameters2 = orm.Dict(dict=qibz)
- parameters2.add_incoming(parent_ph.creator, link_label='output_parameters', link_type=LinkType.CREATE)
+ parameters2.base.links.add_incoming(parent_ph.creator, link_label='output_parameters', link_type=LinkType.CREATE)
  parameters2.store()
 
  inputs = {

tests/conftest.py

@@ -258,7 +258,7 @@ def _generate_calc_job_node(
 
  for link_label, input_node in flatten_inputs(inputs):
  input_node.store()
- node.add_incoming(input_node, link_type=LinkType.INPUT_CALC, link_label=link_label)
+ node.base.links.add_incoming(input_node, link_type=LinkType.INPUT_CALC, link_label=link_label)
 
  node.store()
 
@@ -282,11 +282,11 @@ def _generate_calc_job_node(
  except OSError:
  pass # To test the absence of files in the retrieve_temporary folder
 
- retrieved.add_incoming(node, link_type=LinkType.CREATE, link_label='retrieved')
+ retrieved.base.links.add_incoming(node, link_type=LinkType.CREATE, link_label='retrieved')
  retrieved.store()
 
  remote_folder = orm.RemoteData(computer=computer, remote_path='/tmp')
- remote_folder.add_incoming(node, link_type=LinkType.CREATE, link_label='remote_folder')
+ remote_folder.base.links.add_incoming(node, link_type=LinkType.CREATE, link_label='remote_folder')
  remote_folder.store()
 
  return node
@@ -393,7 +393,7 @@ def _generate_remote_data(computer, remote_path, entry_point_name=None):
  if entry_point_name is not None:
  creator = CalcJobNode(computer=computer, process_type=entry_point)
  creator.set_option('resources', {'num_machines': 1, 'num_mpiprocs_per_machine': 1})
- remote.add_incoming(creator, link_type=LinkType.CREATE, link_label='remote_folder')
+ remote.base.links.add_incoming(creator, link_type=LinkType.CREATE, link_label='remote_folder')
  creator.store()
 
  return remote
@@ -650,7 +650,7 @@ def _generate_workchain_pw(exit_code=None, inputs=None, return_inputs=False, pw_
 
  if pw_outputs is not None:
  for link_label, output_node in pw_outputs.items():
- output_node.add_incoming(pw_node, link_type=LinkType.CREATE, link_label=link_label)
+ output_node.base.links.add_incoming(pw_node, link_type=LinkType.CREATE, link_label=link_label)
  output_node.store()
 
  if exit_code is not None: