Release/1.0.0b19 (#221)

.github/workflows/ci.yml

@@ -31,7 +31,7 @@ jobs:
 
     strategy:
       matrix:
-        tag: [ stable, latest ]
+        tag: [ stable ]
         browser: [ chrome, firefox ]
       fail-fast: false
 

.github/workflows/publish.yml

@@ -0,0 +1,86 @@
+name: Publish on Test PyPI and PyPI
+
+on:
+  push:
+    branches:
+      # Commits pushed to release/ branches are published on Test PyPI if they
+      # have a new version number.
+      - "release/**"
+    tags:
+      # Tags that start with the "v" prefix are published on PyPI.
+      - "v*"
+
+jobs:
+
+  build-and-publish-test:
+
+    name: Build and publish on TestPyPI
+    if: startsWith(github.ref, 'refs/heads/release/')
+
+    runs-on: ubuntu-latest
+    environment:
+      name: Test PyPI
+      url: https://test.pypi.org/project/aiidalab-widgets-base/
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install pypa/build
+        run: python -m pip install build
+
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Publish distribution on Test PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+
+  build-and-publish:
+
+    name: Build and publish on PyPI
+    if: startsWith(github.ref, 'refs/tags')
+
+    runs-on: ubuntu-latest
+    environment:
+      name: PyPI
+      url: https://pypi.org/project/aiidalab-widgets-base/
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install pypa/build
+        run: python -m pip install build
+
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Publish distribution on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -18,3 +18,9 @@ repos:
     hooks:
       - id: flake8
         args: [--count, --show-source, --statistics]
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.6.4
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]

aiidalab_widgets_base/__init__.py

@@ -3,13 +3,11 @@
 
 load_profile()
 
-from .codes import CodeDropdown, AiiDACodeSetup
-from .computers import SshComputerSetup
-from .computers import AiidaComputerSetup
-from .computers import ComputerDropdown
+from .codes import AiiDACodeSetup, CodeDropdown
+from .computers import AiidaComputerSetup, ComputerDropdown, SshComputerSetup
 from .databases import (
-    CodQueryWidget,
     CodeDatabaseWidget,
+    CodQueryWidget,
     ComputerDatabaseWidget,
     OptimadeQueryWidget,
 )
@@ -28,24 +26,21 @@
     RunningCalcJobOutputWidget,
     SubmitButtonWidget,
 )
-from .structures import StructureManagerWidget
 from .structures import (
+    BasicStructureEditor,
+    SmilesWidget,
     StructureBrowserWidget,
     StructureExamplesWidget,
+    StructureManagerWidget,
     StructureUploadWidget,
-    SmilesWidget,
 )
-from .structures import BasicStructureEditor
-from .viewers import viewer
-from .viewers import register_viewer_widget
-
-from .wizard import WizardAppWidget
-from .wizard import WizardAppWidgetStep
-
+from .viewers import AiidaNodeViewWidget, register_viewer_widget, viewer
+from .wizard import WizardAppWidget, WizardAppWidgetStep
 
 __all__ = [
     "AiiDACodeSetup",
     "AiidaComputerSetup",
+    "AiidaNodeViewWidget",
     "BasicStructureEditor",
     "CodQueryWidget",
     "CodeDatabaseWidget",
@@ -79,4 +74,4 @@
     "viewer",
 ]
 
-__version__ = "1.0.0b18"
+__version__ = "1.0.0b19"

aiidalab_widgets_base/bug_report.py

@@ -0,0 +1,181 @@
+"""Provide more user friendly error messages and automated reporting.
+
+Authors:
+
+    * Carl Simon Adorf <simon.adorf@epfl.ch>
+"""
+import base64
+import json
+import platform
+import re
+import sys
+import zlib
+from textwrap import wrap
+from urllib.parse import urlencode, urlsplit, urlunsplit
+
+import ipywidgets as ipw
+from aiidalab.utils import find_installed_packages
+from ansi2html import Ansi2HTMLConverter
+
+
+def get_environment_fingerprint(encoding="utf-8"):
+    packages = find_installed_packages()
+    data = {
+        "version": 1,
+        "platform": {
+            "architecture": platform.architecture(),
+            "python_version": platform.python_version(),
+            "version": platform.version(),
+        },
+        "packages": {package.name: package.version for package in packages},
+    }
+    json_data = json.dumps(data, separators=(",", ":"))
+    return base64.urlsafe_b64encode(zlib.compress(json_data.encode(encoding), level=9))
+
+
+def parse_environment_fingerprint(data, encoding="utf-8"):
+    packages = json.loads(
+        zlib.decompress(base64.urlsafe_b64decode(data)).decode(encoding)
+    )
+    return packages
+
+
+ERROR_MESSAGE = """<div class="alert alert-danger">
+<p><strong>
+    <i class="fa fa-bug" aria-hidden="true"></i> Oh no... the application crashed due to an unexpected error.
+</strong></p>
+<a href="{issue_url}" target="_blank" class="btn btn-primary">
+    <i class="fa fa-share" aria-hidden="true"></i> Create bug report
+</a>
+<button
+    onclick="Jupyter.notebook.clear_all_output(); Jupyter.notebook.restart_run_all({{confirm: false}})"
+    type="button"
+    class="btn btn-success">
+        <i class="fa fa-refresh" aria-hidden="true"></i> Restart app
+</button>
+<div style="padding-top: 1em">
+    <details style="border: 1px solid #aaa; border-radius: 4px; padding: .5em .5em 0; ">
+        <summary style="font-weight: bold; margin: -.5em -.5em 0; padding: .5em">
+            <i class="fa fa-code" aria-hidden="true"></i> View the full traceback
+        </summary>
+      <pre style="color: #333; background: #f8f8f8;"><code>{traceback}</code></pre>
+    </details>
+</div></div>"""
+
+
+BUG_REPORT_TITLE = """Bug report: Application crashed with {exception_type}"""
+
+BUG_REPORT_BODY = """## Automated report
+
+_This issue was created with the app's automated bug reporting feature.
+Attached to this issue is the full traceback as well as an environment
+fingerprint that contains information about the operating system as well as all
+installed libraries._
+
+## Additional comments (optional):
+
+_Example: I submitted a band structure calculation for Silica._
+
+## Attachments
+
+<details>
+<summary>Traceback</summary>
+
+```python-traceback
+{traceback}
+```
+</details>
+
+<details>
+<summary>Environment fingerprint</summary>
+<pre>{environment_fingerprint}</pre>
+</details>
+
+**By submitting this issue I confirm that I am aware that this information can
+potentially be used to determine what kind of calculation was performed at the
+time of error.**
+"""
+
+
+def _strip_ansi_codes(msg):
+    """Remove any ANSI codes (e.g. color codes)."""
+    return re.sub(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])", "", msg)
+
+
+def _convert_ansi_codes_to_html(msg):
+    """Convert any ANSI codes (e.g. color codes) into HTML."""
+    converter = Ansi2HTMLConverter()
+    return converter.produce_headers().strip() + converter.convert(msg, full=False)
+
+
+def _format_truncated_traceback(traceback, max_num_chars=3000):
+    """Truncate the traceback to the given character length."""
+    n = 0
+    for i, line in enumerate(reversed(traceback)):
+        n += len(_strip_ansi_codes(line)) + 2  # add 2 for newline control characters
+        if n > max_num_chars:
+            break
+    return _strip_ansi_codes("\n".join(traceback[-i:]))
+
+
+_ORIGINAL_EXCEPTION_HANDLER = None
+
+
+def install_create_github_issue_exception_handler(output, url, labels=None):
+    """Install a GitHub bug report exception handler.
+
+    After installing this handler, kernel exception will show a generic error
+    message to the user, with the option to file an automatic bug report at the
+    given URL.
+    """
+    global _ORIGINAL_EXCEPTION_HANDLER
+
+    if labels is None:
+        labels = []
+
+    ipython = get_ipython()  # noqa
+    _ORIGINAL_EXCEPTION_HANDLER = _ORIGINAL_EXCEPTION_HANDLER or ipython._showtraceback
+
+    def create_github_issue_exception_handler(exception_type, exception, traceback):
+        try:
+            output.clear_output()
+
+            bug_report_query = {
+                "title": BUG_REPORT_TITLE.format(
+                    exception_type=str(exception_type.__name__)
+                ),
+                "body": BUG_REPORT_BODY.format(
+                    # Truncate the traceback to a maximum of 3000 characters
+                    # and strip all ansi control characters:
+                    traceback=_format_truncated_traceback(traceback, 3000),
+                    # Determine and format the environment fingerprint to be
+                    # included with the bug report:
+                    environment_fingerprint="\n".join(
+                        wrap(get_environment_fingerprint().decode("utf-8"), 100)
+                    ),
+                ),
+                "labels": ",".join(labels),
+            }
+            issue_url = urlunsplit(
+                urlsplit(url)._replace(query=urlencode(bug_report_query))
+            )
+
+            with output:
+                msg = ipw.HTML(
+                    ERROR_MESSAGE.format(
+                        issue_url=issue_url,
+                        traceback=_convert_ansi_codes_to_html("\n".join(traceback)),
+                        len_url=len(issue_url),
+                    )
+                )
+                display(msg)  # noqa
+        except Exception as error:
+            print(f"Error while generating bug report: {error}", file=sys.stderr)
+            _ORIGINAL_EXCEPTION_HANDLER(exception_type, exception, traceback)
+
+    def restore_original_exception_handler():
+        ipython._showtraceback = _ORIGINAL_EXCEPTION_HANDLER
+
+    ipython._showtraceback = create_github_issue_exception_handler
+
+    return restore_original_exception_handler

aiidalab_widgets_base/codes.py

@@ -3,11 +3,11 @@
 from subprocess import check_output
 
 import ipywidgets as ipw
+from aiida.orm import Code, Computer, QueryBuilder, User
+from aiida.plugins.entry_point import get_entry_point_names
 from IPython.display import clear_output
 from traitlets import Bool, Dict, Instance, Unicode, Union, dlink, link, validate
 
-from aiida.orm import Code, Computer, QueryBuilder, User
-from aiida.plugins.entry_point import get_entry_point_names
 from aiidalab_widgets_base.computers import ComputerDropdown
 
 
@@ -269,7 +269,7 @@ def _setup_code(self, _=None):
 
     def exists(self):
         """Returns True if the code exists, returns False otherwise."""
-        from aiida.common import NotExistent, MultipleObjectsError
+        from aiida.common import MultipleObjectsError, NotExistent
 
         try:
             Code.get_from_string(f"{self.label}@{self.computer.name}")