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248 inconsistency between edgepopulationiter connections and edgesiter connections #249

Merged
merged 8 commits into from
Jan 31, 2024
Merged

248 inconsistency between edgepopulationiter connections and edgesiter connections #249

merged 8 commits into from
Jan 31, 2024

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edasubert
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@edasubert edasubert linked an issue Nov 28, 2023 that may be closed by this pull request
inconsistency between EdgePopulation.iter_connections and Edges.iter_connections #248
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@edasubert edasubert self-assigned this Nov 28, 2023
@edasubert edasubert marked this pull request as ready for review November 28, 2023 10:24
joni-herttuainen
joni-herttuainen reviewed Nov 30, 2023
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codecov-commenter commented Dec 1, 2023 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (c9162f7) 100.00% compared to head (9cd14bc) 100.00%.

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@@            Coverage Diff            @@
##            master      #249   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           32        32           
  Lines         2728      2706   -22     
=========================================
- Hits          2728      2706   -22
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@joni-herttuainen
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pinged @GianlucaFicarelli for an extra pair of eyes

joni-herttuainen
joni-herttuainen reviewed Dec 1, 2023
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LGTM. Let's discuss the versioning on stand-up on Monday. Otherwise, I'm ready to approve.

GianlucaFicarelli
GianlucaFicarelli reviewed Dec 4, 2023
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LGTM, but before merging, the version 2.1.0 should be released, unless all the new changes are going to be released together in 3.0.0 (but in this case, the changelog should be updated).

Side note, I don't remember if it was discussed if these changes can affect the performance of iter_connections(), and at what degree.

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Using the same circuit ("/gpfs/bbp.cscs.ch/project/proj30/home/subert/tickets/NSETM-2250-test-psp/sonata/circuit_sonata.json")

on current master:

In [3]: len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
Out[3]: 104521

In [4]: %timeit len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
1.93 s ± 4.07 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

In [5]: %timeit len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
1.92 s ± 8.32 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

In [6]: %timeit len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
1.85 s ± 57.3 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

In [7]: list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN"))[:5]
Out[7]: [(14123, 5018), (14123, 5025), (14123, 5026), (14123, 5031), (14123, 5048)]

on this branch:

In [3]: len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
Out[3]: 104521

In [4]: %timeit len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
1.9 s ± 1.8 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

In [5]: %timeit len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
1.89 s ± 1.44 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

In [6]: %timeit len(list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN")))
1.89 s ± 1.01 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

In [7]: list(circuit.edges["thalamus_neurons__thalamus_neurons__chemical"].iter_connections("bAC_IN"))[:5]
Out[7]: 
[(CircuitNodeId(population='thalamus_neurons', id=14123),
  CircuitNodeId(population='thalamus_neurons', id=5018)),
 (CircuitNodeId(population='thalamus_neurons', id=14123),
  CircuitNodeId(population='thalamus_neurons', id=5025)),
 (CircuitNodeId(population='thalamus_neurons', id=14123),
  CircuitNodeId(population='thalamus_neurons', id=5026)),
 (CircuitNodeId(population='thalamus_neurons', id=14123),
  CircuitNodeId(population='thalamus_neurons', id=5031)),
 (CircuitNodeId(population='thalamus_neurons', id=14123),
  CircuitNodeId(population='thalamus_neurons', id=5048))]

@edasubert
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this MR is now blocking my psp-validation upgrade, which is my fault, because I forgot about it, but still it would help me if we could merge this 🙂

@joni-herttuainen
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joni-herttuainen commented Jan 30, 2024 •
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I'm fine going all the way to 3.0.0 without releasing 2.1.0. AAMOF, since we are going to break stuff, I might just change that deprecated validate to completely removed validate -> validate-simulation + validate-circuit.

That being said, I have no issues with the PR, provided CHANGELOG is modified accordingly.

edasubert and others added 2 commits January 30, 2024 15:40
@edasubert
Merge remote-tracking branch 'origin/master' into 248-inconsistency-b…
99b1b42 
…etween-edgepopulationiter_connections-and-edgesiter_connections
@edasubert
3.0.0 release (#253)
9cd14bc 
changelog tuning
@edasubert edasubert merged commit dea9ac5 into master Jan 31, 2024
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@edasubert edasubert deleted the 248-inconsistency-between-edgepopulationiter_connections-and-edgesiter_connections branch January 31, 2024 13:30
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inconsistency between EdgePopulation.iter_connections and Edges.iter_connections
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