Merge branch 'main' into dependabot/pip/docs/urllib3-2.2.2

Dockerfile

@@ -86,7 +86,7 @@ COPY --from=qe_conda_env ${QE_DIR} ${QE_DIR}
 
 USER root
 COPY ./before-notebook.d/* /usr/local/bin/before-notebook.d/
-RUN fix-permissions "${CONDA_DIR}"
+
 # Remove content of $HOME
 # '-mindepth=1' ensures that we do not remove the home directory itself.
 RUN find /home/${NB_USER}/ -mindepth 1 -delete

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

@@ -5,10 +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 as install_qe_codes
-
 # The default profile name of AiiDAlab container.
 _DEFAULT_PROFILE = "default"
 
@@ -22,9 +18,12 @@ def cli():
 @click.option("-f", "--force", is_flag=True)
 @click.option("-p", "--profile", default=_DEFAULT_PROFILE)
 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_qe_codes(force=force):
+        for msg in install(force=force):
             click.echo(msg)
         assert codes_are_setup()
         click.secho("Codes are setup!", fg="green")
@@ -45,7 +44,8 @@ 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)
 
@@ -68,7 +68,7 @@ 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(
@@ -90,9 +90,11 @@ 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

@@ -1,215 +1,18 @@
 from pathlib import Path
-from shutil import which
-from subprocess import CalledProcessError, run
 from threading import Thread
 
 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",
 ]
 
-FN_LOCKFILE = Path.home().joinpath(".install-qe-on-localhost.lock")
 FN_DO_NOT_SETUP = Path.cwd().joinpath(".do-not-setup-on-localhost")
 
-QE_VERSION = "7.2"
-
-
-def get_qe_env():
-    # QE is already pre-installed in the QE image
-    path = Path(f"/opt/conda/envs/quantum-espresso-{QE_VERSION}")
-    if path.exists():
-        return path
-    else:
-        return Path.home().joinpath(".conda", "envs", f"quantum-espresso-{QE_VERSION}")
-
-
-# Add all QE codes with the calcjob entry point in the aiida-quantumespresso.
-CODE_NAMES = (
-    "pw",
-    "projwfc",
-    "dos",
-    "cp",
-    "epw",
-    "matdyn",
-    "neb",
-    "open_grid",
-    "ph",
-    "pp",
-    "pw2gw",
-    "pw2wannier90",
-    "q2r",
-    "xspectra",
-    "hp",
-)
-
-
-def qe_installed():
-    return get_qe_env().exists()
-
-
-def install_qe():
-    run(
-        [
-            "conda",
-            "create",
-            "--yes",
-            "--override-channels",
-            "--channel",
-            "conda-forge",
-            "--prefix",
-            str(get_qe_env()),
-            f"qe={QE_VERSION}",
-        ],
-        capture_output=True,
-        check=True,
-    )
-
-
-def _code_is_setup(name):
-    try:
-        load_code(f"{name}-{QE_VERSION}@localhost")
-    except NotExistent:
-        return False
-    else:
-        return True
-
-
-def codes_are_setup():
-    return all(_code_is_setup(code_name) for code_name in CODE_NAMES)
-
-
-def _generate_header_to_setup_code():
-    """Generate the header string to setup a code for a given computer."""
-    header_code = """
-from aiida.orm.nodes.data.code.installed import InstalledCode
-from aiida.orm import load_computer
-from aiida import load_profile
-load_profile()
-
-"""
-    return header_code
-
-
-def _generate_string_to_setup_code(code_name, computer_name="localhost"):
-    """Generate the Python string to setup an AiiDA code for a given computer.
-
-    Tries to load an existing code and if not existent,
-    generates Python code to create and store a new code setup."""
-    try:
-        load_code(f"{code_name}-{QE_VERSION}@{computer_name}")
-    except NotExistent:
-        label = f"{code_name}-{QE_VERSION}"
-        description = f"{code_name}.x ({QE_VERSION}) setup by AiiDAlab."
-        filepath_executable = get_qe_env().joinpath("bin", f"{code_name}.x")
-        default_calc_job_plugin = f"quantumespresso.{code_name}"
-        prepend_text = f'eval "$(conda shell.posix hook)"\\nconda activate {get_qe_env()}\\nexport OMP_NUM_THREADS=1'
-        python_code = """
-computer = load_computer('{}')
-code = InstalledCode(computer=computer,
-                    label='{}',
-                    description='{}',
-                    filepath_executable='{}',
-                    default_calc_job_plugin='{}',
-                    prepend_text='{}'
-                    )
-
-code.store()
-""".format(  # noqa: UP032
-            computer_name,
-            label,
-            description,
-            filepath_executable,
-            default_calc_job_plugin,
-            prepend_text,
-        )
-        return python_code
-    else:
-        # the code already exists
-        return ""
-
-
-def setup_codes():
-    python_code = _generate_header_to_setup_code()
-    for code_name in CODE_NAMES:
-        python_code += _generate_string_to_setup_code(code_name)
-    try:
-        run(["python", "-c", python_code], capture_output=True, check=True)
-    except CalledProcessError as error:
-        raise RuntimeError(f"Failed to setup codes: {error}") from None
-
-
-def install(force=False):
-    """Install Quantum ESPRESSO and the corresponding AiiDA codes.
-
-    Args:
-        force: Ignore previously failed attempts and install anyways.
-    """
-    # Check for "do not install file" and skip actual check. The purpose of
-    # this file is to not re-try this process on every app start in case that
-    # there are issues.
-    if not force and FN_DO_NOT_SETUP.exists():
-        raise RuntimeError("Installation failed in previous attempt.")
-
-    yield "Checking installation status..."
-
-    conda_installed = which("conda")
-    try:
-        with FileLock(FN_LOCKFILE, timeout=5):
-            # We assume that if the codes are already setup, everything is in
-            # order. Only if they are not present, should we take action,
-            # however we only do so if the environment has a conda binary
-            # present (`which conda`). If that is not the case then we assume
-            # that this is a custom user environment in which case we also take
-            # no further action.
-            if codes_are_setup():
-                return  # Already setup
-
-            if not conda_installed:
-                raise RuntimeError(
-                    "Unable to automatically install Quantum ESPRESSO, conda "
-                    "is not available."
-                )
-
-            if not qe_installed():
-                # First, install Quantum ESPRESSO.
-                yield "Installing QE..."
-                try:
-                    install_qe()
-                except CalledProcessError as error:
-                    raise RuntimeError(
-                        f"Failed to create conda environment: {error}"
-                    ) from None
-
-            # After installing QE, we install the corresponding
-            # AiiDA codes:
-            python_code = _generate_header_to_setup_code()
-            for code_name in CODE_NAMES:
-                if not _code_is_setup(code_name):
-                    yield f"Preparing setup script for ({code_name})..."
-                    code_string = _generate_string_to_setup_code(code_name)
-                    python_code += code_string
-            try:
-                yield "Setting up all codes..."
-                run(["python", "-c", python_code], capture_output=True, check=True)
-            except CalledProcessError as error:
-                raise RuntimeError(f"Failed to setup codes: {error}") from None
-
-    except Timeout:
-        # Assume that the installation was triggered by a different process.
-        yield "Installation was already started, waiting for it to finish..."
-        with FileLock(FN_LOCKFILE, timeout=120):
-            if not codes_are_setup():
-                raise RuntimeError(
-                    "Installation process did not finish in the expected time."
-                ) from None
-
 
 class QESetupWidget(ipw.VBox):
     installed = traitlets.Bool(allow_none=True).tag(readonly=True)