Prevent user from declaring variables and functions with same name by pramodk · Pull Request #1992 · neuronsimulator/nrn

pramodk · 2022-09-23T12:03:00Z

Today user can "declare" a variable in the NEURON block and then PROCEDURE or FUNCTION with the same name. For example, the below doesn't raise any error today:
```
NEURON {
    SUFFIX glia
    RANGE alfa
}

FUNCTION alfa(v(mV)) {
    alfa = exp(v)
}
```
The reason this works is that the RANGE alfa declaration in the NEURON block is not complete (i.e. variable needs to be "defined" in blocks like ASSIGNED, PARAMETER, etc) and hence doesn't appear anywhere in the generated code. If we try to use alfa as a variable then that is a warning and resulted in a compilation error.
This behavior kind of works but is error-prone. Apart from corner cases and confusing behavior, it's difficult to do certain analyses that we would like to do (e.g. in new NMODL code generation).

So for robustness and simplicity, we now throw an error if a user tries to declare a variable and function with the same name.

    $ ./bin/nocmodl mod_x/test.mod Translating mod_x/test.mod into mod_x/test.cpp
        Error: alfa used as both variable and function in file mod/test.mod

Once there is a wheel, I will launch ModelDB CI to check if any MOD files need to be fixed
A PR to dbbs-lab/dbbs-mod-collection would be nice! Avoid declaring RANGE variables with same name as function dbbs-lab/dbbs-mod-collection#7
Update dentate model Make vecevent.mod and Gfluct3.mod compatible with the upcoming NEURON release (& current master) soltesz-lab/dentate#4
Update tests like testcorenrn and reduced_dentate

ModelDB PRs

* Today use can "declarae" a variable in NEURON block and then PROCEDURE or FUNCTION with the same name. For example, below doesn't raise any error today: ```python NEURON { SUFFIX glia RANGE alfa } FUNCTION alfa(v(mV)) { alfa = exp(v) } ``` * The reason this works is that the `RANGE alfa` declaration in NEURON block id not complete (i.e. variable needs to be "defined" in block like ASSIGNED, PARAMETER etc) and hence doesn't appear anywhere in the generated code. If we try to use `alfa` as variable then that is warning and resulted into compilation error. * This behaviour kind of works but error prone. Apart from corner cases and confusing behaviour, it's difficult to do certain analysis that we would like to do (e.g. in new NMODL code generation). * So for the robustness and simplicity, we now throw an error if user try to declarte variable and function with the same name. ```console $ ./bin/nocmodl mod_x/test.mod Translating mod_x/test.mod into mod_x/test.cpp Error: alfa used as both variable and function in file mod/test.mod ```

See neuronsimulator/nrn#1992

azure-pipelines · 2022-09-23T12:55:27Z

✔️ 7c4660b -> Azure artifacts URL

See neuronsimulator/nrn#1992

nrnhines

yes. should raise error.

See neuronsimulator/nrn#1992

codecov-commenter · 2022-09-23T14:01:27Z

Codecov Report

Merging #1992 (f0fe629) into master (d2564ff) will increase coverage by 0.00%.
The diff coverage is 76.92%.

@@           Coverage Diff           @@
##           master    #1992   +/-   ##
=======================================
  Coverage   46.48%   46.48%           
=======================================
  Files         527      527           
  Lines      119181   119191   +10     
=======================================
+ Hits        55402    55410    +8     
- Misses      63779    63781    +2

Impacted Files	Coverage Δ
src/nmodl/io.cpp	`65.06% <0.00%> (ø)`
src/nmodl/nocpout.cpp	`93.25% <ø> (ø)`
src/nmodl/consist.cpp	`79.59% <83.33%> (+0.10%)`	⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

release (current master) * MOD file translation is being changed from C to C++ and requires certain changes for type safety. These are all syntax changes. See https://nrn.readthedocs.io/en/latest/guide/porting_mechanisms_to_cpp.html * Gfluct3.mod declares a variable of the same name as RANGE variable. This will be an error in the upcoming release. See neuronsimulator/nrn/pull/1992

azure-pipelines · 2022-09-23T14:05:42Z

✔️ f0fe629 -> Azure artifacts URL

pramodk · 2022-09-23T14:15:36Z

ModelDB models / mod files that needs to be fixed are:

➜  nrn-modeldb-ci git:(master) ✗ grep "both variable and function in file" log
Error: new_seed used as both variable and function in file ./cache/138205/Schizophr/Gfluct.mod
Error: new_seed used as both variable and function in file ./cache/155601/ProdduturEtAl2013/Gfluct2.mod
Error: new_seed used as both variable and function in file ./cache/190559/MiglioreEJN2016/Gfluct.mod
Error: minf used as both variable and function in file ./cache/139657/Kopp-Scheinpflug2011/lva.mod
Error: new_seed used as both variable and function in file ./cache/139657/Kopp-Scheinpflug2011/mhh_Gfluct.mod
Error: new_seed used as both variable and function in file ./cache/124513/dentate_gyrus/Gfluct2.mod
Error: new_seed used as both variable and function in file ./cache/262115/demo_destexhe-pare-1999/corrgen8.mod
Error: r used as both variable and function in file ./cache/139656/network/Golgi_hcn1.mod
Error: alfa used as both variable and function in file ./cache/139656/network/GRC_NA.mod
Error: diffusione used as both variable and function in file ./cache/116835/GrC/GRC_GABA.mod
Error: alfa used as both variable and function in file ./cache/116835/GrC/GRC_NA.mod
Error: new_seed used as both variable and function in file ./cache/232876/TCR/high_conductance_state/Gfluct.mod
Error: new_seed used as both variable and function in file ./cache/240116/modeldb-bulb3d/sim/Gfluct.mod
Error: new_seed used as both variable and function in file ./cache/217882/LombardoHarrington2016/Gfluctdv.mod
Error: curr used as both variable and function in file ./cache/151825/Demo/epsp.mod
Error: new_seed used as both variable and function in file ./cache/97917/splitcell/pardentategyrus/Gfluct2.mod
Error: new_seed used as both variable and function in file ./cache/183949/Discharge_hysteresis/Gfluctdv.mod
Error: new_seed used as both variable and function in file ./cache/155602/YuEtAl2013/Gfluct2.mod
Error: r used as both variable and function in file ./cache/127021/Golgi_cell_NaKATPAse/Golgi_hcn1.mod
Error: new_seed used as both variable and function in file ./cache/143671/PowersEtAl2012/code/Gfluctdv.mod
Error: new_seed used as both variable and function in file ./cache/144482/Pyramidal_STDP_Gomez_Delgado_2010/mechanism/mechanism_cell1/Gfluct.mod
Error: minf used as both variable and function in file ./cache/53893/ca_t_lva/lva.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/04_GrC_2020_accelerating/mod_files/GRC_NA_FHF.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/04_GrC_2020_accelerating/mod_files/GRC_NA.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/02_GrC_2020_mild_adapting/mod_files/GRC_NA_FHF.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/02_GrC_2020_mild_adapting/mod_files/GRC_NA.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/03_GrC_2020_adapting/mod_files/GRC_NA_FHF.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/03_GrC_2020_adapting/mod_files/GRC_NA.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/01_GrC_2020_regular/mod_files/GRC_NA_FHF.mod
Error: alfa used as both variable and function in file ./cache/265584/Granule_cell_2020/01_GrC_2020_regular/mod_files/GRC_NA.mod
Error: r used as both variable and function in file ./cache/232023/cerebellar_granular_network/mechanisms/Golgi_CL/Golgi_hcn1.mod
Error: new_seed used as both variable and function in file ./cache/150024/CNModel_May2013/Ifluct8.mod
Error: new_seed used as both variable and function in file ./cache/122329/GPSingleCompartment/syn.mod
Error: new_seed used as both variable and function in file ./cache/141273/Vierling-ClaassenEtAl2010/Gfluct.mod
Error: new_seed used as both variable and function in file ./cache/83590/Arsiero_et_al2007/mechanisms/Ifluct1.mod

See neuronsimulator/nrn#1992

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk · 2022-09-24T10:27:05Z

As PRs to respective ModelDB models are created, I will merge this.

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

* Update MOD files to avoid conflicting variable and function name * This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992 * Update README.html Co-authored-by: ramcdougal <robert.mcdougal@yale.edu>

pramodk requested review from alkino and nrnhines September 23, 2022 12:03

pramodk force-pushed the pramodk/avoid-var-function-conflict branch from 45982a6 to 7c4660b Compare September 23, 2022 12:03

pramodk added a commit to pramodk/dbbs-mod-collection that referenced this pull request Sep 23, 2022

Avoid declaring RANGE variables with same name as function

b6615e5

See neuronsimulator/nrn#1992

pramodk mentioned this pull request Sep 23, 2022

Avoid declaring RANGE variables with same name as function dbbs-lab/dbbs-mod-collection#7

Merged

pramodk added a commit to neuronsimulator/testcorenrn that referenced this pull request Sep 23, 2022

Avoid declaring unnecessary variable as function

0840875

See neuronsimulator/nrn#1992

pramodk mentioned this pull request Sep 23, 2022

Avoid declaring unnecessary variable as function name neuronsimulator/testcorenrn#12

Merged

nrnhines approved these changes Sep 23, 2022

View reviewed changes

pramodk added a commit to neuronsimulator/testcorenrn that referenced this pull request Sep 23, 2022

Avoid declaring unnecessary variable as function (#12)

014aab9

See neuronsimulator/nrn#1992

pramodk added a commit to neuronsimulator/reduced_dentate that referenced this pull request Sep 23, 2022

Avoid declaring unnecessary variable as function name

8290cac

See neuronsimulator/nrn#1992

pramodk mentioned this pull request Sep 23, 2022

Avoid declaring unnecessary variable as function name neuronsimulator/reduced_dentate#6

Merged

pramodk added a commit to neuronsimulator/reduced_dentate that referenced this pull request Sep 23, 2022

Avoid declaring unnecessary variable as function name (#6)

58ad389

See neuronsimulator/nrn#1992

make clang-format happy; update test repos with necessary fixes

f0fe629

pramodk mentioned this pull request Sep 23, 2022

Make vecevent.mod and Gfluct3.mod compatible with the upcoming NEURON release (& current master) soltesz-lab/dentate#4

Merged

pramodk marked this pull request as draft September 23, 2022 14:22

Helveg pushed a commit to dbbs-lab/dbbs-mod-collection that referenced this pull request Sep 23, 2022

Avoid declaring RANGE variables with same name as function (#7)

c4386fe

See neuronsimulator/nrn#1992

pramodk added a commit to ModelDBRepository/138205 that referenced this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name

b18acfc

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk mentioned this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name ModelDBRepository/138205#1

Merged

pramodk added a commit to ModelDBRepository/155601 that referenced this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name

3c70c37

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk added a commit to ModelDBRepository/190559 that referenced this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name

8076e15

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk added a commit to ModelDBRepository/139657 that referenced this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name

39cb0c6

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk added a commit to ModelDBRepository/124513 that referenced this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name

5cabc0a

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk added a commit to ModelDBRepository/262115 that referenced this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name

580d897

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk added a commit to ModelDBRepository/139656 that referenced this pull request Sep 24, 2022

Update MOD files to avoid conflicting variable and function name

171fe7d

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

pramodk marked this pull request as ready for review September 24, 2022 10:22

pramodk merged commit 02574e7 into master Sep 24, 2022

pramodk deleted the pramodk/avoid-var-function-conflict branch September 24, 2022 10:28

ramcdougal pushed a commit to ModelDBRepository/155601 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#2)

046522a

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/190559 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

11ad93b

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/139657 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

3c37527

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/124513 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

9dd11bd

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/139656 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

433a053

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/116835 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

46908b9

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/232876 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

2d4e0b3

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/240116 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

3f71b30

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/217882 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

c27a63c

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/151825 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

f8c0c36

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/97917 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#3)

03957ad

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/183949 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

3587347

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/155602 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#2)

2d3be61

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/127021 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

ca342f3

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/143671 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

9c79854

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/144482 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

dbe4700

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/53893 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

603dfbe

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/265584 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#2)

ca4c26c

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/232023 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

d0ea7ee

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/150024 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

efb5957

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/122329 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

c739b74

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/141273 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

496d35c

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

ramcdougal pushed a commit to ModelDBRepository/83590 that referenced this pull request Nov 4, 2022

Update MOD files to avoid conflicting variable and function name (#1)

76b48c1

* This will be an error in the upcoming NEURON 9.0 release * For details, see neuronsimulator/nrn#1992

olupton mentioned this pull request May 30, 2023

Do not re-use names as variables and functions ModelDBRepository/267355#1

Merged

olupton mentioned this pull request Jun 26, 2023

Curate skipped models neuronsimulator/nrn-modeldb-ci#33

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