Support AiiDA 2.0 and new AiiDAlab Docker image

.github/workflows/ci.yml

@@ -1,46 +1,110 @@
-# Run basic tests for this app on the latest aiidalab-docker image.
+# Run basic tests for this app on the latest aiidalab/full-stack docker image.
 
 name: continuous-integration
 
 on:
-  [push]
+    [push]
 
 jobs:
 
+  # Adapted from: https://github.com/aiidalab/aiidalab-qe
+  pre-commit:
+
+    if: false
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: pip
+          cache-dependency-path: |
+            .pre-commit-config.yaml
+            **/setup.cfg
+            **/pyproject.toml
+            **/requirements*.txt
+
+      - name: Install dependencies
+        run: python -m pip install pre-commit~=2.20
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files || ( git status --short; git diff; exit 1 )
+
+
   test-app:
 
     runs-on: ubuntu-latest
-    timeout-minutes: 10
+    timeout-minutes: 20
+    permissions:
+      packages: read
+      contents: read
 
     strategy:
       matrix:
-        # For now, we're only targeting latest aiidalab image.
-        # tag: [ stable, latest ]
         tag: [latest]
-        # Chrome seems to fail fairly often with timeout errors coming from
-        # the selenium.get_screenshot_as_file()
-        # ```
-        # WARNING: Failed to gather screenshot: Message: timeout: Timed out receiving message from renderer: 10.000
-        # ```
-        # Googling around, this seems to be a common problem so disabling for now.
-        # browser: [ chrome, firefox ]
-        browser: [firefox]
+        image: ["aiidalab/full-stack", "ghcr.io/ispg-group/atmospec"]
+        browser: [Firefox, Chrome]
       fail-fast: false
+    env:
+      IMAGE: ${{ matrix.image }}
+      TAG: ${{ matrix.tag }}
 
     steps:
 
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Check out app
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
-      - name: Test app
-        uses: aiidalab/aiidalab-test-app-action@v2
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
-          image: aiidalab/aiidalab-docker-stack:${{ matrix.tag }}
-          browser: ${{ matrix.browser }}
-          name: aiidalab-ispg
+            python-version: "3.10"
+            cache: pip
+            cache-dependency-path: |
+              **/setup.cfg
+              **/pyproject.toml
+              **/requirements*.txt
+
+      - name: Install dependencies for tests
+        run: pip install -r requirements-test.txt
+
+      - name: Set jupyter token env
+        run: echo "JUPYTER_TOKEN=$(openssl rand -hex 32)" >> $GITHUB_ENV
+
+      # The Firefox and its engine geckodrive need do be installed manually to run
+      # selenium tests.
+      - name: Install Firefox
+        if: matrix.browser == 'Firefox'
+        uses: browser-actions/setup-firefox@latest
+        with:
+          firefox-version: "96.0"
+
+      - name: Install geckodriver
+        if: matrix.browser == 'Firefox'
+        run: |
+          wget -c https://github.com/mozilla/geckodriver/releases/download/v0.30.0/geckodriver-v0.30.0-linux64.tar.gz
+          tar xf geckodriver-v0.30.0-linux64.tar.gz -C /usr/local/bin
+
+      - name: Run pytest
+        run: pytest -sv --driver ${{ matrix.browser }} -o cache_dir=$PYTEST_CACHE_DIR
+
+      - name: Replace slashes in image name
+        if: always()
+        run: echo "IMAGE_NAME=${IMAGE//\//-}" >> $GITHUB_ENV
 
       - name: Upload screenshots as artifacts
-        uses: actions/upload-artifact@v2
+        if: always()
+        uses: actions/upload-artifact@v3
         with:
-          name: Screenshots-${{ matrix.tag }}-${{ matrix.browser }}
-          path: 'screenshots/'
+          name: Screenshots-${{env.IMAGE_NAME}}-${{ matrix.tag }}-${{ matrix.browser }}
+          path: screenshots/
+          if-no-files-found: error

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
       - id: black
         language_version: python3 # Should be a command that runs python3.6+
 
-  - repo: https://gitlab.com/pycqa/flake8
+  - repo: https://github.com/pycqa/flake8
     rev: '3.9.2'
     hooks:
     - id: flake8

aiidalab_ispg/__init__.py

@@ -17,4 +17,4 @@
     "ViewSpectrumStep",
 ]
 
-__version__ = "0.1"
+__version__ = "0.2-alpha"

aiidalab_ispg/conformers.py

@@ -29,8 +29,8 @@
 
 from .utils import calc_boltzmann_weights, argsort, KCALtoKJ, EVtoKJ
 
-StructureData = DataFactory("structure")
-TrajectoryData = DataFactory("array.trajectory")
+StructureData = DataFactory("core.structure")
+TrajectoryData = DataFactory("core.array.trajectory")
 
 # xTB cannot be installed automatically in official AiiDAlab Docker images,
 # because the dependencies are installed via pip,
@@ -198,7 +198,7 @@ def _create_trajectory_node(self, conformers, energies):
         traj = TrajectoryData(
             structurelist=[StructureData(ase=conformer) for conformer in conformers]
         )
-        traj.set_extra("smiles", conformers[0].info["smiles"])
+        traj.base.extras.set("smiles", conformers[0].info["smiles"])
         if energies is not None and len(energies) > 1:
             boltzmann_weights = np.array(
                 calc_boltzmann_weights(energies, T=self._BOLTZMANN_TEMPERATURE)
@@ -207,8 +207,8 @@ def _create_trajectory_node(self, conformers, energies):
                 energies = np.array(energies)
             traj.set_array("energies", energies)
             traj.set_array("boltzmann_weights", boltzmann_weights)
-            traj.set_extra("energy_units", self._ENERGY_UNITS)
-            traj.set_extra("temperature", self._BOLTZMANN_TEMPERATURE)
+            traj.base.extras.set("energy_units", self._ENERGY_UNITS)
+            traj.base.extras.set("temperature", self._BOLTZMANN_TEMPERATURE)
         return traj
 
     # TODO: Automatically filter out conformers with high energy

aiidalab_ispg/qeapp/process.py

@@ -4,7 +4,7 @@
 
 import ipywidgets as ipw
 import traitlets
-from aiida.cmdline.utils.query.calculation import CalculationQueryBuilder
+from aiida.tools.query.calculation import CalculationQueryBuilder
 from aiida.orm import load_node
 
 

aiidalab_ispg/qeapp/widgets.py

@@ -13,7 +13,7 @@
 
 import ipywidgets as ipw
 import traitlets
-from aiida.orm import CalcJobNode
+from aiida.orm import load_node, CalcJobNode
 from aiidalab_widgets_base import register_viewer_widget
 from IPython.display import HTML, Javascript, display
 
@@ -237,7 +237,7 @@ def _observe_value(self, change):
 
 class CalcJobOutputFollower(traitlets.HasTraits):
 
-    calcjob = traitlets.Instance(CalcJobNode, allow_none=True)
+    calcjob_uuid = traitlets.Unicode(allow_none=True)
     filename = traitlets.Unicode(allow_none=True)
     output = traitlets.List(trait=traitlets.Unicode)
     lineno = traitlets.Int()
@@ -253,14 +253,11 @@ def __init__(self, **kwargs):
 
         super().__init__(**kwargs)
 
-    @traitlets.observe("calcjob")
+    @traitlets.observe("calcjob_uuid")
     def _observe_calcjob(self, change):
-        try:
-            if change["old"].pk == change["new"].pk:
-                # Old and new process are identical.
-                return
-        except AttributeError:
-            pass
+        calcjob_uuid = change["new"]
+        if change["old"] == calcjob_uuid:
+            return
 
         with self._lock:
             # Stop following
@@ -278,30 +275,30 @@ def _observe_calcjob(self, change):
             # (Re/)start following
             if change["new"]:
                 self._follow_output_thread = Thread(
-                    target=self._follow_output, args=(change["new"],)
+                    target=self._follow_output, args=(calcjob_uuid,)
                 )
                 self._follow_output_thread.start()
 
-    def _follow_output(self, calcjob):
+    def _follow_output(self, calcjob_uuid):
         """Monitor calcjob and orchestrate pushing and pulling of output."""
-        self._pull_thread = Thread(target=self._pull_output, args=(calcjob,))
+        self._pull_thread = Thread(target=self._pull_output)
         self._pull_thread.start()
-        self._push_thread = Thread(target=self._push_output, args=(calcjob,))
+        self._push_thread = Thread(target=self._push_output, args=(calcjob_uuid,))
         self._push_thread.start()
 
     def _fetch_output(self, calcjob):
         assert isinstance(calcjob, CalcJobNode)
         if "retrieved" in calcjob.outputs:
             try:
-                self.filename = calcjob.attributes["output_filename"]
-                with calcjob.outputs.retrieved.open(self.filename) as f:
+                self.filename = calcjob.base.attributes.get("output_filename")
+                with calcjob.outputs.retrieved.base.repository.open(self.filename) as f:
                     return f.read().splitlines()
             except OSError:
                 return list()
 
         elif "remote_folder" in calcjob.outputs:
             try:
-                fn_out = calcjob.attributes["output_filename"]
+                fn_out = calcjob.base.attributes.get("output_filename")
                 self.filename = fn_out
                 with NamedTemporaryFile() as tmpfile:
                     calcjob.outputs.remote_folder.getfile(fn_out, tmpfile.name)
@@ -313,9 +310,10 @@ def _fetch_output(self, calcjob):
 
     _EOF = None
 
-    def _push_output(self, calcjob, delay=0.2):
+    def _push_output(self, calcjob_uuid, delay=0.2):
         """Push new log lines onto the queue."""
         lineno = 0
+        calcjob = load_node(calcjob_uuid)
         while True:
             try:
                 lines = self._fetch_output(calcjob)
@@ -330,7 +328,7 @@ def _push_output(self, calcjob, delay=0.2):
                     self._output_queue.put(self._EOF)
                     break  # noqa: B012
 
-    def _pull_output(self, calcjob):
+    def _pull_output(self):
         """Pull new log lines from the queue and update traitlets."""
         while True:
             item = self._output_queue.get()
@@ -351,8 +349,8 @@ def __init__(self, calcjob, **kwargs):
         self.output_follower = CalcJobOutputFollower()
         self.log_output = LogOutputWidget()
 
+        self.output_follower.calcjob_uuid = self.calcjob.uuid
         self.output_follower.observe(self._observe_output_follower_lineno, ["lineno"])
-        self.output_follower.calcjob = self.calcjob
 
         super().__init__(
             [ipw.HTML(f"CalcJob: {self.calcjob}"), self.log_output], **kwargs

aiidalab_ispg/spectrum.py

@@ -1,4 +1,4 @@
-"""Widget for displaying UV/VIS spectra in an interactive graph.
+"""Calculating NEA UV/vis spectra and displaying them in an interactive plot.
 
 Authors:
     * Daniel Hollas <daniel.hollas@bristol.ac.uk>
@@ -9,7 +9,7 @@
 from scipy import constants
 import numpy as np
 
-from aiida.orm import QueryBuilder
+from aiida.orm import load_node, QueryBuilder
 from aiida.plugins import DataFactory
 
 # https://docs.bokeh.org/en/latest/docs/user_guide/jupyter.html
@@ -22,9 +22,9 @@
 
 # https://docs.bokeh.org/en/latest/docs/reference/io.html#bokeh.io.output_notebook
 output_notebook(hide_banner=True, load_timeout=5000, verbose=True)
-XyData = DataFactory("array.xy")
-StructureData = DataFactory("structure")
-TrajectoryData = DataFactory("array.trajectory")
+XyData = DataFactory("core.array.xy")
+StructureData = DataFactory("core.structure")
+TrajectoryData = DataFactory("core.array.trajectory")
 
 
 @unique
@@ -48,6 +48,7 @@ class BokehFigureContext(ipw.Output):
     def __init__(self, fig):
         super().__init__()
         self._figure = fig
+        self._handle = None
         self.on_displayed(lambda x: x.set_handle())
 
     def set_handle(self):
@@ -62,7 +63,8 @@ def get_figure(self):
         return self._figure
 
     def update(self):
-        push_notebook(handle=self._handle)
+        if self._handle is not None:
+            push_notebook(handle=self._handle)
 
 
 class Spectrum(object):
@@ -188,7 +190,7 @@ class SpectrumWidget(ipw.VBox):
     # We use SMILES to find matching experimental spectra
     # that are possibly stored in our DB as XyData.
     smiles = traitlets.Unicode(allow_none=True)
-    experimental_spectrum = traitlets.Instance(XyData, allow_none=True)
+    experimental_spectrum_uuid = traitlets.Unicode(allow_none=True)
 
     # For now, we do not allow different intensity units
     intensity_unit = "cm^2 per molecule"
@@ -428,9 +430,10 @@ def _handle_energy_unit_update(self, change):
             kernel=self.kernel_selector.value,
             energy_unit=energy_unit,
         )
-        if self.experimental_spectrum is not None:
+        if self.experimental_spectrum_uuid is not None:
+            node = load_node(self.experimental_spectrum_uuid)
             self._plot_experimental_spectrum(
-                spectrum_node=self.experimental_spectrum, energy_unit=energy_unit
+                spectrum_node=node, energy_unit=energy_unit
             )
 
     def _unhighlight_conformer(self):
@@ -622,7 +625,7 @@ def reset(self):
             self.conformer_transitions = None
             self.conformer_structures = None
             self.smiles = None
-            self.experimental_spectrum = None
+            self.experimental_spectrum_uuid = None
 
         self.disable_controls()
         self.clean_figure()
@@ -701,9 +704,10 @@ def _find_experimental_spectrum(self, smiles: str):
         # TODO: For now let's just assume we have one
         # canonical experimental spectrum per compound.
         # for spectrum in qb.iterall():
-        self.experimental_spectrum = qb.first()[0]
+        experimental_spectrum_node = qb.first()[0]
+        self.experimental_spectrum_uuid = experimental_spectrum_node.uuid
         self._plot_experimental_spectrum(
-            spectrum_node=self.experimental_spectrum,
+            spectrum_node=experimental_spectrum_node,
             energy_unit=self.energy_unit_selector.value,
         )