Add more ZnDraw-features

[phohenberger]

• Move len(zndraw) call in update loop to avoid socket-call
• Allow non-Jupyter use postponed due to unsolved runaway server problems
• Allow multiple frames in the same file using different tokens
• Asynchronous Server startup
• Add color gradients for particle colors depending on the distance to reference
• Make constraints proportionate to the box dimension, update ZnDraw shape
  • Add clipping mechanism for 2D shapes that cross the box boundaries
• Make the box center the origin, instead of a box corner (confusing when rotating the box view)
• Expose the ZnDraw script interface to Python
  • At least provide a way to set the camera angle from Python
• Fix inconsistencies in server communication
  • on lama, ZnDraw creates a white rectangle in Jupyter instead of displaying the GUI (works fine in Chrome, on Firefox one can still click on the server URL to open the visualizer in a new tab and see everything)
    • solution: completely deactivate cookie blocking in the web browser settings (not just from third-party or unvisited sites, allow all cookies)
  • on CIP pool machines, using Firefox, once a ZnDraw server was used in a Notebook, when opening another Notebook in the same Jupyter session, ZnDraw cannot load the particle data
  • on other web browsers like GNOME Web, ZnDraw cannot load the particle data
• Find out if datamodel-code-generator can be made a soft dependency (it has a lot of dependencies) not possible
• Visualize ext_forces

[jngrad]

Here is a one-line change to make the complete CI/CD pipeline happy:

diff --git a/testsuite/scripts/importlib_wrapper.py b/testsuite/scripts/importlib_wrapper.py
index f3dd8e5b44..5bc879338c 100644
--- a/testsuite/scripts/importlib_wrapper.py
+++ b/testsuite/scripts/importlib_wrapper.py
@@ -396,3 +396,3 @@ class GetEspressomdVisualizerImports(ast.NodeVisitor):
     def __init__(self):
-        self.visualizers = {"visualization"}
+        self.visualizers = {"visualization", "zn"}
         self.namespace_visualizers = {

[PythonFZ]

• Visualize ext_forces

[phohenberger]

@jngrad Regarding the cookie issue, are you sure that you have enable all cookies? On firefox for example I worked fine when using blocking cross-site tracking cookies and isolate other cross-site cookies or is this lama specific?

[jngrad]

I did not try all options, but the two specifically mentioned were not resolving the issue. I gave up and allowed everything.

[jngrad]

After updating to ZnDraw 0.4.6, I can no longer start a ZnDraw server on Chrome and Firefox:

Starting ZnDraw server, this may take a few seconds
WARNING:zndraw.zndraw:Connection failed. Retrying...
WARNING:zndraw.zndraw:Connection failed. Retrying...
WARNING:zndraw.zndraw:Connection failed. Retrying...
WARNING:zndraw.zndraw:Connection failed. Retrying...
ConnectionError                           Traceback (most recent call last)
/work/jgrad/espresso-fork-PR/zndraw/lib/python3.10/site-packages/zndraw/zndraw.py in __post_init__(self)
    118                 self.socket.sleep(self.timeout["connection"])
    119                 if idx == self.timeout["connect_retries"]:
--> 120                     raise socketio.exceptions.ConnectionError(
    121                         f"Unable to connect to ZnDraw server at '{self.url}'. Is the server running?"
    122                     ) from err
ConnectionError: Unable to connect to ZnDraw server at 'ws://127.0.0.1:1234'. Is the server running?

pip freeze

(zndraw) jgrad@lama:/work/jgrad/espresso-fork-PR$ pip freeze
amqp==5.2.0
annotated-types==0.7.0
argcomplete==3.5.0
ase==3.23.0
async-timeout==4.0.3
bidict==0.23.1
billiard==4.2.0
black==24.8.0
blinker==1.8.2
celery==5.4.0
certifi==2024.7.4
charset-normalizer==3.3.2
click==8.1.7
click-didyoumean==0.3.1
click-plugins==1.1.1
click-repl==0.3.0
contourpy==1.2.1
cycler==0.12.1
datamodel-code-generator==0.25.9
dnspython==2.6.1
email_validator==2.2.0
eventlet==0.36.1
Flask==2.3.3
Flask-SocketIO==5.3.6
fonttools==4.53.1
genson==1.3.0
greenlet==3.0.3
h11==0.14.0
idna==3.7
inflect==5.6.2
isort==5.13.2
itsdangerous==2.2.0
Jinja2==3.1.4
kiwisolver==1.4.5
kombu==5.4.0
lazy_loader==0.4
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.9.2
mdurl==0.1.2
mypy-extensions==1.0.0
networkx==3.3
numpy==1.26.4
packaging==24.1
pandas==2.2.2
pathspec==0.12.1
pillow==10.4.0
platformdirs==4.2.2
plotly==5.23.0
prompt_toolkit==3.0.47
pydantic==2.8.2
pydantic_core==2.20.1
Pygments==2.18.0
pyparsing==3.1.2
python-dateutil==2.9.0.post0
python-engineio==4.9.1
python-socketio==5.11.3
pytz==2024.1
PyYAML==6.0.2
redis==5.0.8
requests==2.32.3
rich==13.7.1
scipy==1.14.1
shellingham==1.5.4
simple-websocket==1.0.0
six==1.16.0
splines==0.3.2
SQLAlchemy==2.0.32
tenacity==9.0.0
toml==0.10.2
tomli==2.0.1
tqdm==4.66.5
typer==0.12.4
typing_extensions==4.12.2
tzdata==2024.1
urllib3==2.2.2
vine==5.1.0
wcwidth==0.2.13
websocket-client==1.8.0
Werkzeug==3.0.4
wsproto==1.2.0
zndraw==0.4.6
znjson==0.2.4
znsocket==0.1.8

[phohenberger]

What. I tested in on some of the most common browsers. Chrome, Firefox, Edge, Brave all worked with no issues at all. The internal ZnDraw tests for starting a server also passed.

Is the problem you are facing simply using the Visualizer as provided by the PR, or your work on making it run on binder?

[jngrad]

I used your PR on the lama workstation, and accepted cookies.

[jngrad]

We created a new user account to get a fresh Firefox/Chrome/JupyterLab installation, and your PR now works.