Merge branch 'main' into hq

README.md

@@ -5,8 +5,8 @@
 
 ## About
 
-This is a early-development implementation of an AiiDAlab application for Quantum ESPRESSO workflow.
-The app allows the execution of a workflow with Quantum ESPRESSO that includes the selection of an input structure, its relaxation, and the bands structure calculation.
+This is an AiiDAlab application for Quantum ESPRESSO workflows.
+The app allows the execution of a workflow with Quantum ESPRESSO that includes the selection of an input structure, its relaxation, the bands structure calculation, and more!
 
 **The app is currently in an early development stage!**
 
@@ -41,6 +41,16 @@ Then, you can run the integration tests with:
 pytest --driver Chrome tests_integration
 ```
 
+### Published Docker images
+
+Supported tags released on [Github Container Registry](https://ghcr.io/aiidalab):
+
+- `edge` – the latest commit on the default branch (`main`)
+- `latest` – the latest stable release
+- `$version` – the version of a specific release (ex. `2022.1001`)
+
+Pull requests into the default branch are further released on ghcr.io with the `pr-###` tag to simplify the testing of development versions.
+
 ## For maintainers
 
 To create a new release, clone the repository, install development dependencies with `pip install '.[dev]'`, and then execute `bumpver update`.

src/aiidalab_qe/__main__.py

@@ -5,12 +5,6 @@
 
 import click
 
-from aiida import load_profile
-from aiidalab_qe.common.setup_codes import codes_are_setup
-from aiidalab_qe.common.setup_codes import (
-    install_and_setup as install_and_setup_qe_codes,
-)
-
 # The default profile name of AiiDAlab container.
 _DEFAULT_PROFILE = "default"
 
@@ -24,10 +18,14 @@ def cli():
 @click.option("-f", "--force", is_flag=True)
 @click.option("--computer")
 @click.option("-p", "--profile", default=_DEFAULT_PROFILE)
-def install_qe(force, profile, computer):
+
+def install_qe(force, profile):
+    from aiida import load_profile
+    from aiidalab_qe.setup.codes import codes_are_setup, install
+
     load_profile(profile)
     try:
-        for msg in install_and_setup_qe_codes(computer=computer, force=force):
+        for msg in install(computer=computer, force=force):
             click.echo(msg)
         assert codes_are_setup(computer=computer)
         click.secho("Codes are setup!", fg="green")
@@ -48,7 +46,8 @@ def install_pseudos(profile, source):
     """Install pseudopotentials from a local folder if source is specified,
     otherwise download from remote repositories.
     """
-    from aiidalab_qe.common.setup_pseudos import install
+    from aiida import load_profile
+    from aiidalab_qe.setup.pseudos import install
 
     load_profile(profile)
 
@@ -71,7 +70,7 @@ def install_pseudos(profile, source):
     type=click.Path(exists=True, path_type=Path, resolve_path=True),
 )
 def download_pseudos(dest):
-    from aiidalab_qe.common.setup_pseudos import EXPECTED_PSEUDOS, _install_pseudos
+    from aiidalab_qe.setup.pseudos import EXPECTED_PSEUDOS, _install_pseudos
 
     try:
         for progress in _install_pseudos(
@@ -93,9 +92,11 @@ def download_pseudos(dest):
 )
 @click.option("-p", "--profile", default=_DEFAULT_PROFILE)
 def test_plugin(plugin_name, profile):
-    load_profile(profile)
+    from aiida import load_profile
     from aiidalab_qe.app.utils import test_plugin_functionality
 
+    load_profile(profile)
+
     try:
         success, message = test_plugin_functionality(plugin_name)
         if success:

src/aiidalab_qe/app/configuration/advanced.py

@@ -18,8 +18,8 @@
 from aiida_quantumespresso.workflows.pw.base import PwBaseWorkChain
 from aiidalab_qe.app.parameters import DEFAULT_PARAMETERS
 from aiidalab_qe.common.panel import Panel
-from aiidalab_qe.common.setup_pseudos import PseudoFamily
 from aiidalab_qe.common.widgets import HubbardWidget
+from aiidalab_qe.setup.pseudos import PseudoFamily
 
 from .pseudos import PseudoFamilySelector, PseudoSetter
 

src/aiidalab_qe/app/configuration/pseudos.py

@@ -11,7 +11,7 @@
 from aiida.plugins import DataFactory, GroupFactory
 from aiida_quantumespresso.workflows.pw.base import PwBaseWorkChain
 from aiidalab_qe.app.parameters import DEFAULT_PARAMETERS
-from aiidalab_qe.common.setup_pseudos import (
+from aiidalab_qe.setup.pseudos import (
     PSEUDODOJO_VERSION,
     SSSP_VERSION,
     PseudoFamily,

src/aiidalab_qe/common/setup_codes.py

@@ -5,11 +5,9 @@
 
 import ipywidgets as ipw
 import traitlets
-from filelock import FileLock, Timeout
 
-from aiida.common.exceptions import NotExistent
-from aiida.orm import load_code
-from aiidalab_qe.common.widgets import ProgressBar
+from ..setup.codes import QE_VERSION, install
+from .widgets import ProgressBar
 
 __all__ = [
     "QESetupWidget",
@@ -251,6 +249,7 @@ def _setup(computer):
                     "Installation process did not finish in the expected time."
                 ) from None
 
+FN_DO_NOT_SETUP = Path.cwd().joinpath(".do-not-setup-on-localhost")
 
 class QESetupWidget(ipw.VBox):
     installed = traitlets.Bool(allow_none=True).tag(readonly=True)

src/aiidalab_qe/common/setup_pseudos.py

@@ -1,230 +1,12 @@
 from __future__ import annotations
 
-import os
-from collections.abc import Iterable
-from dataclasses import dataclass, field
-from pathlib import Path
-from subprocess import run
 from threading import Thread
 
 import ipywidgets as ipw
 import traitlets
-from aiida_pseudo.groups.family import PseudoPotentialFamily
-from filelock import FileLock, Timeout
 
-from aiida.orm import QueryBuilder
-from aiidalab_qe.common.widgets import ProgressBar
-
-SSSP_VERSION = "1.3"
-PSEUDODOJO_VERSION = "0.4"
-
-EXPECTED_PSEUDOS = {
-    f"SSSP/{SSSP_VERSION}/PBE/efficiency",
-    f"SSSP/{SSSP_VERSION}/PBE/precision",
-    f"SSSP/{SSSP_VERSION}/PBEsol/efficiency",
-    f"SSSP/{SSSP_VERSION}/PBEsol/precision",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/standard/upf",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/SR/standard/upf",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/SR/stringent/upf",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/SR/stringent/upf",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/FR/standard/upf",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/FR/standard/upf",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBE/FR/stringent/upf",
-    f"PseudoDojo/{PSEUDODOJO_VERSION}/PBEsol/FR/stringent/upf",
-}
-
-
-FN_LOCKFILE = Path.home().joinpath(".install-sssp.lock")
-
-
-@dataclass
-class PseudoFamily:
-    """The dataclass to deal with pseudo family strings.
-
-    Attributes:
-    library: the library name of the pseudo family, e.g. SSSP or PseudoDojo.
-    cmd_library_name: the sub command name used in aiida-pseudo command line.
-    version: the version of the pseudo family, e.g. 1.2
-    functional: the functional of the pseudo family, e.g. PBE, PBEsol.
-    accuracy: the accuracy of the pseudo family, which is protocol in aiida-pseudo, e.g. efficiency, precision, standard, stringent.
-    relativistic: the relativistic treatment of the pseudo family, e.g. SR, FR.
-    file_type: the file type of the pseudo family, e.g. upf, psml, currently only used for PseudoDojo.
-    """
-
-    library: str
-    version: str
-    functional: str
-    accuracy: str
-    cmd_library_name: str = field(init=False)
-    relativistic: str | None = None
-    file_type: str | None = None
-
-    def __post_init__(self):
-        """Post init operations and checks."""
-        if self.library == "SSSP":
-            self.cmd_library_name = "sssp"
-        elif self.library == "PseudoDojo":
-            self.cmd_library_name = "pseudo-dojo"
-        else:
-            raise ValueError(f"Unknown pseudo library {self.library}")
-
-    @classmethod
-    def from_string(cls, pseudo_family_string: str) -> PseudoFamily:
-        """Initialize from a pseudo family string."""
-        # We support two pseudo families: SSSP and PseudoDojo
-        # They are formatted as follows:
-        # SSSP: SSSP/<version>/<functional>/<accuracy>
-        # PseudoDojo: PseudoDojo/<version>/<functional>/<relativistic>/<accuracy>/<file_type>
-        # where <relativistic> is either 'SR' or 'FR' and <file_type> is either 'upf' or 'psml'
-        # Before we unify the format of family strings, the conditions below are necessary
-        # to distinguish between the two families
-        library = pseudo_family_string.split("/")[0]
-        if library == "SSSP":
-            version, functional, accuracy = pseudo_family_string.split("/")[1:]
-            relativistic = None
-            file_type = None
-        elif library == "PseudoDojo":
-            (
-                version,
-                functional,
-                relativistic,
-                accuracy,
-                file_type,
-            ) = pseudo_family_string.split("/")[1:]
-        else:
-            raise ValueError(
-                f"Not able to parse valid library name from {pseudo_family_string}"
-            )
-
-        return cls(
-            library=library,
-            version=version,
-            functional=functional,
-            accuracy=accuracy,
-            relativistic=relativistic,
-            file_type=file_type,
-        )
-
-
-def pseudos_to_install() -> set[str]:
-    """Query the database and return the list of pseudopotentials that are not installed."""
-    qb = QueryBuilder()
-    qb.append(
-        PseudoPotentialFamily,
-        filters={
-            "or": [
-                {"label": {"like": "SSSP/%"}},
-                {"label": {"like": "PseudoDojo/%"}},
-            ]
-        },
-        project="label",
-    )
-    labels = set(qb.all(flat=True))
-    return EXPECTED_PSEUDOS - labels
-
-
-def _construct_cmd(
-    pseudo_family_string: str, download_only: bool = False, cwd: Path | None = None
-) -> list:
-    """Construct the command for installation of pseudopotentials.
-
-    If ``cwd`` is not None, and ``download_only`` is True the, only download the
-    pseudopotential files to the ``cwd`` folder.
-    If ``download_only`` is False and ``cwd`` is not None, the the pseudos will be installed from the ``cwd`` where the pseudos are downloaded to.
-
-    NOTE: download_only has nothing to do with cwd, it will not download the pseudos to cwd if cwd is specified.
-    The control to download to cwd is in the ``_install_pseudos`` function below.
-    """
-    pseudo_family = PseudoFamily.from_string(pseudo_family_string)
-
-    # the library used in command line is lowercase
-    # e.g. SSSP -> sssp and PseudoDojo -> pseudo-dojo
-    library = pseudo_family.cmd_library_name
-    version = pseudo_family.version
-    functional = pseudo_family.functional
-    accuracy = pseudo_family.accuracy
-    cmd = [
-        "aiida-pseudo",
-        "install",
-        library,
-        "--functional",
-        functional,
-        "--version",
-        version,
-        "-p",  # p for protocol which is the accuracy of the library
-        accuracy,
-    ]
-
-    # extra arguments for PseudoDojo
-    if library == "pseudo-dojo":
-        relativistic = pseudo_family.relativistic
-        file_type = pseudo_family.file_type
-        cmd.extend(
-            [
-                "--relativistic",
-                relativistic,
-                "--pseudo-format",
-                file_type,
-            ]
-        )
-
-    if download_only:
-        cmd.append("--download-only")
-
-    # if cwd source folder specified, then install the pseudos from the folder
-    # download file name is replace `/` with `_` of the pseudo family string with `.aiida_pseudo` extension
-    if not download_only and cwd is not None:
-        file_path = cwd / f"{pseudo_family_string.replace('/', '_')}.aiida_pseudo"
-        if file_path.exists():
-            cmd.extend(["--from-download", str(file_path)])
-
-    return cmd
-
-
-def run_cmd(cmd: list, env: dict | None = None, cwd: Path | None = None):
-    """Run the command with specific env in the workdir specified."""
-    run(cmd, env=env, cwd=cwd, capture_output=True, check=True)
-
-
-def _install_pseudos(
-    pseudo_families: set[str], download_only: bool = False, cwd: Path | None = None
-) -> Iterable[float]:
-    """Go through the list of pseudo families and install them."""
-    env = os.environ.copy()
-    env["PATH"] = f"{env['PATH']}:{Path.home() / '.local' / 'bin'}"
-
-    mult = 1.0 / len(pseudo_families)
-    yield mult * 0
-    for i, pseudo_family in enumerate(pseudo_families):
-        cmd = _construct_cmd(pseudo_family, download_only, cwd=cwd)
-
-        run_cmd(cmd, env=env, cwd=cwd)
-
-        yield mult * (i + 1)
-
-
-def install(
-    download_only: bool = False, cwd: Path | None = None
-) -> Iterable[tuple[str, float]]:
-    yield "Checking installation status...", 0.1
-    try:
-        with FileLock(FN_LOCKFILE, timeout=5):
-            if len(pseudos := pseudos_to_install()) > 0:
-                yield "Installing...", 0.1
-                for progress in _install_pseudos(pseudos, download_only, cwd):
-                    yield "Installing...", progress
-
-    except Timeout:
-        # Assume that the installation was triggered by a different process.
-        yield (
-            "Installation was already started elsewhere, waiting for it to finish...",
-            ProgressBar.AnimationRate(1.0),
-        )
-        with FileLock(FN_LOCKFILE, timeout=300):
-            if len(pseudos_to_install()) > 0:
-                raise RuntimeError(
-                    "Installation process did not finish in the expected time."
-                ) from None
+from ..setup.pseudos import install, pseudos_to_install
+from .widgets import ProgressBar
 
 
 class PseudosInstallWidget(ProgressBar):

src/aiidalab_qe/setup/__init__.py

@@ -0,0 +1,5 @@
+"""Package for the QE app CLI for setting up codes and pseudos"""
+
+from .codes import QE_VERSION
+
+__all__ = ["QE_VERSION"]