dj.diagram not working after update to 14.1

[troselab-setup]

Hi all, has there been a change to dj.Diagram? I updated to dj 14.1 and now I am receiving this error:

`--------------------------------------------------------------------------- ValueError Traceback (most recent call last) File ~/miniconda3/envs/datajoint/lib/python3.8/site-packages/IPython/core/formatters.py:343, in BaseFormatter.call(self, obj) 341 method = get_real_method(obj, self.print_method) 342 if method is not None: --> 343 return method() 344 return None 345 else:

File ~/miniconda3/envs/datajoint/lib/python3.8/site-packages/datajoint/diagram.py:436, in Diagram._reprsvg(self) 435 def _reprsvg(self): --> 436 return self.make_svg()._reprsvg()

File ~/miniconda3/envs/datajoint/lib/python3.8/site-packages/datajoint/diagram.py:424, in Diagram.make_svg(self) 421 def make_svg(self): 422 from IPython.display import SVG --> 424 return SVG(self.make_dot().create_svg())

File ~/miniconda3/envs/datajoint/lib/python3.8/site-packages/datajoint/diagram.py:371, in Diagram.make_dot(self) 308 label_props = { # http://matplotlib.org/examples/color/named_colors.html 309 None: dict( 310 shape="circle", (...) 364 ), 365 } 366 node_props = { 367 node: label_props[d["node_type"]] 368 for node, d in dict(graph.nodes(data=True)).items() 369 } --> 371 dot = nx.drawing.nx_pydot.to_pydot(graph) 372 for node in dot.get_nodes(): 373 node.set_shape("circle")

File ~/miniconda3/envs/datajoint/lib/python3.8/site-packages/networkx/drawing/nx_pydot.py:309, in to_pydot(N) 298 raise_error = ( 299 _check_colon_quotes(u) 300 or _check_colon_quotes(v) (...) 306 ) 307 ) 308 if raise_error: --> 309 raise ValueError( 310 f'Node names and attributes should not contain ":" unless they are quoted with "".\ 311 For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ 312 Please refer https://github.com/pydot/pydot/issues/258' 313 ) 314 edge = pydot.Edge(u, v, **str_edgedata) 315 P.add_edge(edge)

ValueError: Node names and attributes should not contain ":" unless they are quoted with "". For example the string 'attribute:data1' should be written as '"attribute:data1"'. Please refer https://github.com/pydot/pydot/issues/258`

Reproducibility

Include:

• Linux
• Python 3.8.16

[troselab-setup]

I see this has been raised already here: https://github.com/datajoint/datajoint-python/issues/1065#issue-1444879799

[CBroz1]

I would describe this issue as 'networkx rejects dj.Diagrams with attribute mapping'

Minimal replication

```python import datajoint as dj schema = dj.schema("temp_demo") @schema class A(dj.Manual): definition = """ a : int """ @schema class B(dj.Manual): definition = """ b : int -> A """ if __name__ == "__main__": (dj.Diagram(B) - 1).draw() ```

Error stack

```python 🌸 python 3.9.16 🌸 --------------------------------------------------------------------------- ValueError Traceback (most recent call last) File ~/wrk/spyglass/temp-demo.py:22 15 definition = """ 16 b : int 17 -> A 18 """ 21 if __name__ == "__main__": ---> 22 (dj.Diagram(B) - 1).draw() File ~/wrk/datajoint-python/datajoint/diagram.py:440, in Diagram.draw(self) 438 def draw(self): 439 if plot_active: --> 440 plt.imshow(self.make_image()) 441 plt.gca().axis("off") 442 plt.show() File ~/wrk/datajoint-python/datajoint/diagram.py:431, in Diagram.make_image(self) 429 def make_image(self): 430 if plot_active: --> 431 return plt.imread(self.make_png()) 432 else: 433 raise DataJointError("pyplot was not imported") File ~/wrk/datajoint-python/datajoint/diagram.py:427, in Diagram.make_png(self) 426 def make_png(self): --> 427 return io.BytesIO(self.make_dot().create_png()) File ~/wrk/datajoint-python/datajoint/diagram.py:371, in Diagram.make_dot(self) 308 label_props = { # http://matplotlib.org/examples/color/named_colors.html 309 None: dict( 310 shape="circle", (...) 364 ), 365 } 366 node_props = { 367 node: label_props[d["node_type"]] 368 for node, d in dict(graph.nodes(data=True)).items() 369 } --> 371 dot = nx.drawing.nx_pydot.to_pydot(graph) 372 for node in dot.get_nodes(): 373 node.set_shape("circle") File ~/miniconda3/envs/spy/lib/python3.9/site-packages/networkx/drawing/nx_pydot.py:311, in to_pydot(N) 300 raise_error = ( 301 _check_colon_quotes(u) 302 or _check_colon_quotes(v) (...) 308 ) 309 ) 310 if raise_error: --> 311 raise ValueError( 312 f'Node names and attributes should not contain ":" unless they are quoted with "".\ 313 For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ 314 Please refer https://github.com/pydot/pydot/issues/258' 315 ) 316 edge = pydot.Edge(u, v, **str_edgedata) 317 P.add_edge(edge) ValueError: Node names and attributes should not contain ":" unless they are quoted with "". For example the string 'attribute:data1' should be written as '"attribute:data1"'. Please refer https://github.com/pydot/pydot/issues/258 ```

[trose-neuro]

Hi! Is there an update to this?

[dimitri-yatsenko]

fixing this week :-)

[ethho]

Can reproduce with tests/test_erd.py on b755c84e in a Dev Container running Python 3.11:

Details

``` vscode ➜ /workspaces/datajoint-python (master) $ pytest tests/test_erd.py ========================================================= test session starts ========================================================== platform linux -- Python 3.11.4, pytest-8.2.2, pluggy-1.5.0 rootdir: /workspaces/datajoint-python plugins: Faker-28.4.1, cov-5.0.0 collected 7 items tests/test_erd.py ....FF. [100%] =============================================================== FAILURES =============================================================== ____________________________________________________________ test_repr_svg _____________________________________________________________ schema_adv = Schema `djtest_advanced` def test_repr_svg(schema_adv): erd = dj.ERD(schema_adv, context=dict()) > svg = erd._repr_svg_() tests/test_erd.py:53: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ datajoint/diagram.py:440: in _repr_svg_ return self.make_svg()._repr_svg_() datajoint/diagram.py:428: in make_svg return SVG(self.make_dot().create_svg()) datajoint/diagram.py:371: in make_dot dot = nx.drawing.nx_pydot.to_pydot(graph) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ N = def to_pydot(N): """Returns a pydot graph from a NetworkX graph N. Parameters ---------- N : NetworkX graph A graph created with NetworkX Examples -------- >>> K5 = nx.complete_graph(5) >>> P = nx.nx_pydot.to_pydot(K5) Notes ----- """ import pydot # set Graphviz graph type if N.is_directed(): graph_type = "digraph" else: graph_type = "graph" strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph() name = N.name graph_defaults = N.graph.get("graph", {}) if name == "": P = pydot.Dot("", graph_type=graph_type, strict=strict, **graph_defaults) else: P = pydot.Dot( f'"{name}"', graph_type=graph_type, strict=strict, **graph_defaults ) try: P.set_node_defaults(**N.graph["node"]) except KeyError: pass try: P.set_edge_defaults(**N.graph["edge"]) except KeyError: pass for n, nodedata in N.nodes(data=True): str_nodedata = {str(k): str(v) for k, v in nodedata.items()} # Explicitly catch nodes with ":" in node names or nodedata. n = str(n) raise_error = _check_colon_quotes(n) or ( any( (_check_colon_quotes(k) or _check_colon_quotes(v)) for k, v in str_nodedata.items() ) ) if raise_error: raise ValueError( f'Node names and attributes should not contain ":" unless they are quoted with "".\ For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ Please refer https://github.com/pydot/pydot/issues/258' ) p = pydot.Node(n, **str_nodedata) P.add_node(p) if N.is_multigraph(): for u, v, key, edgedata in N.edges(data=True, keys=True): str_edgedata = {str(k): str(v) for k, v in edgedata.items() if k != "key"} u, v = str(u), str(v) raise_error = ( _check_colon_quotes(u) or _check_colon_quotes(v) or ( any( (_check_colon_quotes(k) or _check_colon_quotes(val)) for k, val in str_edgedata.items() ) ) ) if raise_error: raise ValueError( f'Node names and attributes should not contain ":" unless they are quoted with "".\ For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ Please refer https://github.com/pydot/pydot/issues/258' ) edge = pydot.Edge(u, v, key=str(key), **str_edgedata) P.add_edge(edge) else: for u, v, edgedata in N.edges(data=True): str_edgedata = {str(k): str(v) for k, v in edgedata.items()} u, v = str(u), str(v) raise_error = ( _check_colon_quotes(u) or _check_colon_quotes(v) or ( any( (_check_colon_quotes(k) or _check_colon_quotes(val)) for k, val in str_edgedata.items() ) ) ) if raise_error: > raise ValueError( f'Node names and attributes should not contain ":" unless they are quoted with "".\ For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ Please refer https://github.com/pydot/pydot/issues/258' ) E ValueError: Node names and attributes should not contain ":" unless they are quoted with "". For example the string 'attribute:data1' should be written as '"attribute:data1"'. Please refer https://github.com/pydot/pydot/issues/258 /usr/local/lib/python3.11/site-packages/networkx/drawing/nx_pydot.py:282: ValueError ___________________________________________________________ test_make_image ____________________________________________________________ schema_simp = Schema `djtest_relational` def test_make_image(schema_simp): erd = dj.ERD(schema_simp, context=dict()) > img = erd.make_image() tests/test_erd.py:59: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ datajoint/diagram.py:435: in make_image return plt.imread(self.make_png()) datajoint/diagram.py:431: in make_png return io.BytesIO(self.make_dot().create_png()) datajoint/diagram.py:371: in make_dot dot = nx.drawing.nx_pydot.to_pydot(graph) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ N = def to_pydot(N): """Returns a pydot graph from a NetworkX graph N. Parameters ---------- N : NetworkX graph A graph created with NetworkX Examples -------- >>> K5 = nx.complete_graph(5) >>> P = nx.nx_pydot.to_pydot(K5) Notes ----- """ import pydot # set Graphviz graph type if N.is_directed(): graph_type = "digraph" else: graph_type = "graph" strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph() name = N.name graph_defaults = N.graph.get("graph", {}) if name == "": P = pydot.Dot("", graph_type=graph_type, strict=strict, **graph_defaults) else: P = pydot.Dot( f'"{name}"', graph_type=graph_type, strict=strict, **graph_defaults ) try: P.set_node_defaults(**N.graph["node"]) except KeyError: pass try: P.set_edge_defaults(**N.graph["edge"]) except KeyError: pass for n, nodedata in N.nodes(data=True): str_nodedata = {str(k): str(v) for k, v in nodedata.items()} # Explicitly catch nodes with ":" in node names or nodedata. n = str(n) raise_error = _check_colon_quotes(n) or ( any( (_check_colon_quotes(k) or _check_colon_quotes(v)) for k, v in str_nodedata.items() ) ) if raise_error: raise ValueError( f'Node names and attributes should not contain ":" unless they are quoted with "".\ For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ Please refer https://github.com/pydot/pydot/issues/258' ) p = pydot.Node(n, **str_nodedata) P.add_node(p) if N.is_multigraph(): for u, v, key, edgedata in N.edges(data=True, keys=True): str_edgedata = {str(k): str(v) for k, v in edgedata.items() if k != "key"} u, v = str(u), str(v) raise_error = ( _check_colon_quotes(u) or _check_colon_quotes(v) or ( any( (_check_colon_quotes(k) or _check_colon_quotes(val)) for k, val in str_edgedata.items() ) ) ) if raise_error: raise ValueError( f'Node names and attributes should not contain ":" unless they are quoted with "".\ For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ Please refer https://github.com/pydot/pydot/issues/258' ) edge = pydot.Edge(u, v, key=str(key), **str_edgedata) P.add_edge(edge) else: for u, v, edgedata in N.edges(data=True): str_edgedata = {str(k): str(v) for k, v in edgedata.items()} u, v = str(u), str(v) raise_error = ( _check_colon_quotes(u) or _check_colon_quotes(v) or ( any( (_check_colon_quotes(k) or _check_colon_quotes(val)) for k, val in str_edgedata.items() ) ) ) if raise_error: > raise ValueError( f'Node names and attributes should not contain ":" unless they are quoted with "".\ For example the string \'attribute:data1\' should be written as \'"attribute:data1"\'.\ Please refer https://github.com/pydot/pydot/issues/258' ) E ValueError: Node names and attributes should not contain ":" unless they are quoted with "". For example the string 'attribute:data1' should be written as '"attribute:data1"'. Please refer https://github.com/pydot/pydot/issues/258 /usr/local/lib/python3.11/site-packages/networkx/drawing/nx_pydot.py:282: ValueError ======================================================= short test summary info ======================================================== FAILED tests/test_erd.py::test_repr_svg - ValueError: Node names and attributes should not contain ":" unless they are quoted with "". For example the str... FAILED tests/test_erd.py::test_make_image - ValueError: Node names and attributes should not contain ":" unless they are quoted with "". For example the str... ===================================================== 2 failed, 5 passed in 32.77s ===================================================== vscode ➜ /workspaces/datajoint-python (master) $ conda list bash: conda: command not found vscode ➜ /workspaces/datajoint-python (master) $ pip list Package Version Editable project location -------------------- ----------- ---------------------------- appdirs 1.4.4 argon2-cffi 23.1.0 argon2-cffi-bindings 21.2.0 asttokens 2.4.1 black 24.8.0 blinker 1.8.2 certifi 2024.8.30 cffi 1.17.1 click 8.1.7 comm 0.2.2 contourpy 1.3.0 cov-core 1.15.0 coverage 7.6.1 cryptography 43.0.1 cycler 0.12.1 datajoint 0.14.2 /workspaces/datajoint-python debugpy 1.8.5 decorator 5.1.1 executing 2.1.0 Faker 28.4.1 flake8 7.1.1 Flask 3.0.3 fonttools 4.53.1 gitdb 4.0.11 GitPython 3.1.41 iniconfig 2.0.0 ipykernel 6.29.5 ipython 8.27.0 itsdangerous 2.2.0 jedi 0.19.1 Jinja2 3.1.4 jupyter_client 8.6.2 jupyter_core 5.7.2 kiwisolver 1.4.7 MarkupSafe 2.1.5 matplotlib 3.9.2 matplotlib-inline 0.1.7 mccabe 0.7.0 minio 7.2.8 mypy-extensions 1.0.0 nest-asyncio 1.6.0 networkx 3.3 nose 1.3.7 nose-cov 1.6 numpy 2.1.1 otumat 0.3.1 packaging 24.1 pandas 2.2.2 parso 0.8.4 pathspec 0.12.1 pexpect 4.9.0 pillow 10.4.0 pip 23.1.2 platformdirs 4.2.2 pluggy 1.5.0 prompt_toolkit 3.0.47 psutil 6.0.0 ptyprocess 0.7.0 pure_eval 0.2.3 pycodestyle 2.12.1 pycparser 2.22 pycryptodome 3.20.0 pydot 3.0.1 pyflakes 3.2.0 Pygments 2.18.0 PyMySQL 1.1.1 pyparsing 3.1.4 pytest 8.3.2 pytest-cov 5.0.0 python-dateutil 2.9.0.post0 pytz 2024.1 pyzmq 26.2.0 setuptools 69.0.3 six 1.16.0 smmap 5.0.1 stack-data 0.6.3 tornado 6.4.1 tqdm 4.66.5 traitlets 5.14.3 typing_extensions 4.12.2 tzdata 2024.1 urllib3 2.2.2 watchdog 5.0.2 wcwidth 0.2.13 Werkzeug 3.0.4 wheel 0.40.0 [notice] A new release of pip is available: 23.1.2 -> 24.2 [notice] To update, run: pip install --upgrade pip vscode ➜ /workspaces/datajoint-python (master) $ python --version Python 3.11.4 ```

[ethho]

Duplicates #1065