Merge branch 'master' into feature/connect-to-more-elns

.github/release.yml

@@ -0,0 +1,25 @@
+---
+# Configuration for automatically generated release notes:
+# https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes#configuring-automatically-generated-release-notes
+# We exclude PRs from bots and categorize PRs based on labels
+changelog:
+    exclude:
+        authors:
+            - dependabot
+            - pre-commit-ci
+    categories:
+        - title: Breaking Changes 🛠
+          labels:
+              - breaking
+        - title: New Features 🎉
+          labels:
+              - enhancement
+        - title: Bug fixes 🐛
+          labels:
+              - bug
+        - title: Documentation 📝
+          labels:
+              - docs
+        - title: Other Changes
+          labels:
+              - "*"

.github/workflows/ci.yml

@@ -6,9 +6,12 @@ name: CI
 on:
     push:
         branches:
-            - main
+            - master
     pull_request:
 
+env:
+    FORCE_COLOR: "1"
+    UV_VERSION: "0.4.6"
 
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
@@ -23,7 +26,8 @@ jobs:
         strategy:
             matrix:
                 browser: [Chrome, Firefox]
-                aiida-core-version: [2.1.2, 2.4.3]          # test on the latest and the oldest supported version
+                # test on the latest and the oldest supported version
+                aiida-core-version: [2.1.2, 2.6.2]
             fail-fast: false
 
         runs-on: ubuntu-latest
@@ -39,8 +43,10 @@ jobs:
               with:
                   python-version: '3.10'
 
-            - name: Install uv
-              run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/0.1.44/uv-installer.sh | sh
+            - name: Setup uv
+              uses: astral-sh/setup-uv@v4
+              with:
+                  version: ${{ env.UV_VERSION }}
 
             - name: Install package test dependencies
               # Notebook tests happen in the container, here we only need to install
@@ -82,9 +88,9 @@ jobs:
 
         strategy:
             matrix:
-                python-version: ['3.9', '3.10']
+                python-version: ['3.9', '3.11']
                 # Test on the latest and oldest supported version
-                aiida-core-version: [2.2.2, 2.4.3]
+                aiida-core-version: [2.2.2, 2.6.2]
             fail-fast: false
 
         runs-on: ubuntu-latest
@@ -107,8 +113,10 @@ jobs:
               with:
                   python-version: ${{ matrix.python-version }}
 
-            - name: Install uv
-              run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/0.1.27/uv-installer.sh | sh
+            - name: Setup uv
+              uses: astral-sh/setup-uv@v4
+              with:
+                  version: ${{ env.UV_VERSION }}
 
             - name: Install package
             # NOTE: uv (unlike pip) does not compile python to bytecode after install.
@@ -117,13 +125,13 @@ jobs:
             # Ideally, these would be fixed, but vapory is largely unmaintained,
             # so here we simply keep the pip behaviour with the --compile flag.
             # See https://github.com/astral-sh/uv/issues/1928#issuecomment-1968857514
-              run: uv pip install --compile --system .[dev,smiles,optimade] aiida-core==${{ matrix.aiida-core-version }}
+              run: uv pip install --compile --system -e .[dev,smiles,optimade,eln] aiida-core==${{ matrix.aiida-core-version }}
 
             - name: Run pytest
-              run: pytest -v tests --cov
+              run: pytest -v tests --cov=aiidalab_widgets_base
 
             - name: Upload coverage reports to Codecov
-              uses: codecov/codecov-action@v4
+              uses: codecov/codecov-action@v5
               with:
                   flags: python-${{ matrix.python-version }}
                   token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.5.0
+      rev: v5.0.0
       hooks:
           - id: check-json
           - id: check-yaml
@@ -13,7 +13,7 @@ repos:
             exclude: miscellaneous/structures
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.3.4
+      rev: v0.6.9
       hooks:
           - id: ruff-format
             exclude: ^docs/.*
@@ -27,7 +27,7 @@ repos:
             args: [--preserve-quotes]
 
     - repo: https://github.com/sirosen/check-jsonschema
-      rev: 0.28.1
+      rev: 0.29.3
       hooks:
           - id: check-github-workflows
 

aiidalab_widgets_base/__init__.py

@@ -1,7 +1,5 @@
 """Reusable widgets for AiiDAlab applications."""
 
-from aiida.manage import get_profile
-
 _WARNING_TEMPLATE = """
 <div style="background-color: #f7f7f7; border: 2px solid #e0e0e0; padding: 20px; border-radius: 5px;">
     <p style="font-size: 16px; font-weight: bold; color: #ff5733;">Warning:</p>
@@ -13,6 +11,20 @@
 """
 
 
+def load_default_profile():
+    """Loads the default profile if none loaded and warn of deprecation."""
+    from aiida import load_profile
+
+    load_profile()
+
+    profile = get_profile()
+    assert profile is not None, "Failed to load the default profile"
+
+    # raise a deprecation warning
+    warning = HTML(_WARNING_TEMPLATE.format(profile=profile.name, version="v3.0.0"))
+    display(warning)
+
+
 # We only detect profile and throw a warning if it is on the notebook
 # It is not necessary to do this in the unit tests
 def is_running_in_jupyter():
@@ -27,22 +39,22 @@ def is_running_in_jupyter():
         return False
 
 
-# load the default profile if no profile is loaded, and raise a deprecation warning
-# this is a temporary solution to avoid breaking existing notebooks
-# this will be removed in the next major release
-if is_running_in_jupyter() and get_profile() is None:
-    # if no profile is loaded, load the default profile and raise a deprecation warning
-    from aiida import load_profile
+if is_running_in_jupyter():
+    from pathlib import Path
+
+    from aiida.manage import get_profile
     from IPython.display import HTML, display
 
-    load_profile()
+    # load the default profile if no profile is loaded, and raise a deprecation warning
+    # this is a temporary solution to avoid breaking existing notebooks
+    # this will be removed in the next major release
+    if get_profile() is None:
+        load_default_profile()
 
-    profile = get_profile()
-    assert profile is not None, "Failed to load the default profile"
+    from .utils.loaders import load_css
+
+    load_css(css_path=Path(__file__).parent / "static/styles")
 
-    # raise a deprecation warning
-    warning = HTML(_WARNING_TEMPLATE.format(profile=profile.name, version="v3.0.0"))
-    display(warning)
 
 from .computational_resources import (
     ComputationalResourcesWidget,
@@ -117,4 +129,4 @@ def is_running_in_jupyter():
     "viewer",
 ]
 
-__version__ = "2.2.2"
+__version__ = "2.3.0a2"

aiidalab_widgets_base/computational_resources.py

@@ -1196,16 +1196,26 @@ def on_setup_code(self, _=None):
                 "append_text",
             ]
 
+            containerized_code_additional_items = [
+                "image_name",
+                "engine_command",
+            ]
+
             kwargs = {key: getattr(self, key).value for key in items_to_configure}
 
+            # Check for additional keys needed for orm.ContainerizedCode
+            for container_key in containerized_code_additional_items:
+                if container_key in self.code_setup.keys():
+                    kwargs[container_key] = self.code_setup[container_key]
+
             # set computer from its widget value the UUID of the computer.
             computer = orm.load_computer(self.computer.value)
 
             # Checking if the code with this name already exists
             qb = orm.QueryBuilder()
             qb.append(orm.Computer, filters={"uuid": computer.uuid}, tag="computer")
             qb.append(
-                orm.InstalledCode,
+                orm.AbstractCode,
                 with_computer="computer",
                 filters={"label": kwargs["label"]},
             )
@@ -1223,7 +1233,10 @@ def on_setup_code(self, _=None):
                 return False
 
             try:
-                code = orm.InstalledCode(computer=computer, **kwargs)
+                if "image_name" in kwargs.keys():
+                    code = orm.ContainerizedCode(computer=computer, **kwargs)
+                else:
+                    code = orm.InstalledCode(computer=computer, **kwargs)
             except (common.exceptions.InputValidationError, KeyError) as exception:
                 self.message = wrap_message(
                     f"Invalid input for code creation: <code>{exception}</code>",

aiidalab_widgets_base/elns.py

@@ -2,10 +2,8 @@
 from pathlib import Path
 
 import ipywidgets as ipw
-import requests_cache
 import traitlets as tl
 from aiida import orm
-from aiidalab_eln import get_eln_connector
 from IPython.display import clear_output, display
 
 ELN_CONFIG = Path.home() / ".aiidalab" / "aiidalab-eln-config.json"
@@ -15,6 +13,13 @@
 
 
 def connect_to_eln(eln_instance=None, **kwargs):
+    try:
+        from aiidalab_eln import get_eln_connector
+    except ImportError:
+        return (
+            None,
+            "AiiDAlab-ELN connector not installed. Install with `pip install aiidalab-eln`",
+        )
     # assuming that the connection can only be established to the ELNs
     # with the stored configuration.
     try:
@@ -62,6 +67,8 @@ class ElnImportWidget(ipw.VBox):
     node = tl.Instance(orm.Node, allow_none=True)
 
     def __init__(self, path_to_root="../", **kwargs):
+        import requests_cache
+
         # Used to output additional settings.
         self._output = ipw.Output()
 
@@ -77,8 +84,9 @@ def __init__(self, path_to_root="../", **kwargs):
             return
 
         tl.dlink((eln, "node"), (self, "node"))
+        # Since the requests cache is enabled globally in aiidalab package, we disable it here to get correct results.
+        # This can be removed once https://github.com/aiidalab/aiidalab/issues/196 is fixed.
         with requests_cache.disabled():
-            # Since the cache is enabled in AiiDAlab, we disable it here to get correct results.
             eln.import_data()
 
 
@@ -124,9 +132,8 @@ def _observe_node(self, _=None):
         if self.node is None or self.eln is None:
             return
 
-        if "eln" in self.node.extras:
-            info = self.node.extras["eln"]
-        else:
+        info = self.node.base.extras.get("eln", {})
+        if not info:
             try:
                 q = orm.QueryBuilder().append(
                     orm.Node,
@@ -175,10 +182,13 @@ def get_all_structures_and_geoopts(self, node):
         return all_structures, all_geoopts
 
     def send_to_eln(self, _=None):
+        import requests_cache
+
         if self.eln and self.eln.is_connected:
             self.message.value = f"\u29d7 Sending data to {self.eln.eln_instance}..."
+            # Since the requests cache is enabled globally in aiidalab package, we disable it here to get correct results.
+            # This can be removed once https://github.com/aiidalab/aiidalab/issues/196 is fixed.
             with requests_cache.disabled():
-                # Since the cache is enabled in AiiDAlab, we disable it here to get correct results.
                 self.eln.export_data()
             self.message.value = (
                 f"\u2705 The data were successfully sent to {self.eln.eln_instance}."
@@ -306,6 +316,15 @@ def check_connection(self, _=None):
 
     def display_eln_config(self, value=None):
         """Display ELN configuration specific to the selected type of ELN."""
+        try:
+            from aiidalab_eln import get_eln_connector
+        except ImportError:
+            with self._output:
+                clear_output()
+                msg = "AiiDAlab-ELN connector not installed. Install with `pip install aiidalab-eln`"
+                display(ipw.HTML(f"❌ {msg}"))
+            return
+
         try:
             eln_class = get_eln_connector(self.eln_types.value)
         except NotImplementedError as err:

aiidalab_widgets_base/export.py

@@ -11,7 +11,7 @@ class ExportButtonWidget(ipw.Button):
     def __init__(self, process, **kwargs):
         self.process = process
         if "description" not in kwargs:
-            kwargs["description"] = f"Export workflow ({self.process.id})"
+            kwargs["description"] = f"Export workflow ({self.process.pk})"
         if "layout" not in kwargs:
             kwargs["layout"] = {}
         kwargs["layout"]["width"] = "initial"
@@ -28,7 +28,7 @@ def export_aiida_subgraph(self, change=None):  # pylint: disable=unused-argument
 
         fname = os.path.join(tempfile.mkdtemp(), "export.aiida")
         subprocess.call(
-            ["verdi", "archive", "create", fname, "-N", str(self.process.id)]
+            ["verdi", "archive", "create", fname, "-N", str(self.process.pk)]
         )
         with open(fname, "rb") as fobj:
             b64 = base64.b64encode(fobj.read())
@@ -41,6 +41,6 @@ def export_aiida_subgraph(self, change=None):  # pylint: disable=unused-argument
             document.body.appendChild(link);
             link.click();
             document.body.removeChild(link);
-            """.format(payload=payload, filename=f"export_{self.process.id}.aiida")
+            """.format(payload=payload, filename=f"export_{self.process.pk}.aiida")
         )
         display(javas)

aiidalab_widgets_base/nodes.py

@@ -7,7 +7,6 @@
 import traitlets as tl
 from aiida import common, engine, orm
 from aiida.cmdline.utils.ascii_vis import calc_info
-from aiidalab.app import _AiidaLabApp
 from IPython.display import clear_output, display
 
 CALCULATION_TYPES = [
@@ -326,6 +325,8 @@ def find_node(self, pk, namespaces=None):
 
 class _AppIcon:
     def __init__(self, app, path_to_root, node):
+        from aiidalab.app import _AiidaLabApp
+
         name = app["name"]
         app_object = _AiidaLabApp.from_id(name)
         self.logo = app_object.metadata["logo"]

aiidalab_widgets_base/process.py

@@ -249,7 +249,7 @@ def show_selected_output(self, change=None):
             clear_output()
             if change["new"]:
                 selected_output = self.process.outputs[change["new"]]
-                self.info.value = f"PK: {selected_output.id}"
+                self.info.value = f"PK: {selected_output.pk}"
                 display(viewer(selected_output))
 
 
@@ -537,7 +537,7 @@ def __init__(self, title="Running Job Output", **kwargs):
         self.title = title
         self.selection = ipw.Dropdown(
             description="Select calculation:",
-            options=tuple((p.id, p) for p in get_running_calcs(self.process)),
+            options=tuple((p.pk, p) for p in get_running_calcs(self.process)),
             style={"description_width": "initial"},
         )
         self.output = CalcJobOutputWidget()
@@ -551,7 +551,7 @@ def update(self):
         with self.hold_trait_notifications():
             old_label = self.selection.label
             self.selection.options = tuple(
-                (str(p.id), p) for p in get_running_calcs(self.process)
+                (str(p.pk), p) for p in get_running_calcs(self.process)
             )
             # If the selection remains the same.
             if old_label in self.selection.options: