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fee5846
feat: add cell builder utilities
sanjayankur31 Jun 18, 2021
7880bfa
feat: propagate validation result to writer
sanjayankur31 Jun 18, 2021
a885a4d
feat: add cell builder utility
sanjayankur31 Jun 18, 2021
47b5cab
feat: add unit tests for cell builder utility
sanjayankur31 Jun 18, 2021
819e76d
feat: add pytest to CI
sanjayankur31 Jun 18, 2021
4e9d4db
fix: correct type hinting for list of floats
sanjayankur31 Jun 19, 2021
a5df48b
fix: use Python 2 compatible type hinting syntax
sanjayankur31 Jun 19, 2021
c4cca51
fix: drop f-strings for Python 2 compatibility
sanjayankur31 Jun 19, 2021
4b2feb8
refactor(ci): move pytest to test scripts
sanjayankur31 Jun 19, 2021
3fb3111
feat: add fraction_along to add_segment
sanjayankur31 Jun 23, 2021
107352e
feat: set default fraction_along in segment parent
sanjayankur31 Jun 23, 2021
731ddcd
feat: add summary doc string to add_segment
sanjayankur31 Jun 23, 2021
95994db
chore: remove stray doc string line
sanjayankur31 Jun 23, 2021
ec46850
feat: allow omission of proximal point in add_segment
sanjayankur31 Jun 23, 2021
3daaa24
fix: make sure p is defined even when prox is None
sanjayankur31 Jun 23, 2021
a2cca2f
feat: do not repeat includes
sanjayankur31 Jun 23, 2021
29de814
feat(cellbuilder): define a dict to store neurolex ids
sanjayankur31 Jun 24, 2021
bf5a553
feat(cellbuilder): add default segment groups
sanjayankur31 Jun 24, 2021
098df66
feat(cellbuilder): add utilities to easily find segment groups
sanjayankur31 Jun 24, 2021
04ce495
feat(cellbuilder): add newly created segments to default segments
sanjayankur31 Jun 24, 2021
91345a4
fix: correct type annotations
sanjayankur31 Jun 24, 2021
8fadf0d
chore(cellbuilder): add note about order of segment groups in NML files
sanjayankur31 Jun 24, 2021
9735a51
refactor(cellbuilder): migrate segment getters to nml.py in libNeuroML
sanjayankur31 Jun 25, 2021
ff1b0de
refactor(cellbuilder): use update nml.py methods and make conventiona…
sanjayankur31 Jun 25, 2021
b6123c4
feat(cell-builder): use py3 type annotations
sanjayankur31 Jul 26, 2022
49d687e
chore: format with black
sanjayankur31 Jul 26, 2022
ffadf98
chore(ci): remove duplicate pytest command
sanjayankur31 Jul 26, 2022
2f9eac0
feat(deps): set version constraint: libNeuroML>= 0.3.1
sanjayankur31 Jul 26, 2022
429d0a8
docs: add CellBuilder to sphinx docs
sanjayankur31 Jul 26, 2022
313c262
test(CellBuilder): re-enable skipped tests
sanjayankur31 Jul 26, 2022
8b604f5
chore: correct section heading in docs
sanjayankur31 Jul 26, 2022
8066c59
feat(cell-builder): add missing check
sanjayankur31 Jul 26, 2022
f6ba895
feat: handle exception when a segment group does not exist
sanjayankur31 Jul 27, 2022
911ed4b
test(cell-builder): add new tests
sanjayankur31 Jul 27, 2022
c3b0b89
chore: use is for comparison with None instead of ==
sanjayankur31 Jul 27, 2022
0ab7859
fix(cell-builder): append to resistivities instead of overwriting
sanjayankur31 Aug 4, 2022
311c561
fix(cell-builder): correct append function call
sanjayankur31 Aug 4, 2022
18fedd3
fix(cell-builder): append to list of InitMembPotentials
sanjayankur31 Aug 4, 2022
1ff8211
improvement(cell-builder): re-order function args
sanjayankur31 Aug 4, 2022
32d2e05
feat(cell-builder): add generic channel density helper
sanjayankur31 Aug 4, 2022
f42acf3
test(cell-builder): add test for generic conductance density adder
sanjayankur31 Aug 4, 2022
3e9b2e6
feat(cell-builder): add generic method to add membrane properties
sanjayankur31 Aug 4, 2022
fdd9e99
feat(utils): add general component factory function
sanjayankur31 Aug 4, 2022
f418f5a
improvement(utils): make component factory case sensitive
sanjayankur31 Aug 4, 2022
8cbc383
chore(utils): remove wrong doc noting names are case insensitive
sanjayankur31 Aug 4, 2022
f42dda8
test(cell-builder): correct tests
sanjayankur31 Aug 4, 2022
4b84a33
chore: add missing blank line
sanjayankur31 Aug 4, 2022
0eb1220
feat(cell-builder): add generic function to add intracellular properties
sanjayankur31 Aug 4, 2022
381e9a5
test(cell-builder): test intracellular and membrane property helpers
sanjayankur31 Aug 4, 2022
6e7ae42
test(utils): add tests for factory helper function
sanjayankur31 Aug 4, 2022
627a7ed
feat(utils): add function to check for compulsory parameters
sanjayankur31 Aug 4, 2022
a74a26c
Merge branch 'development' into feat/cell-builder-methods-105
sanjayankur31 Aug 19, 2022
be491cc
fix(component-factory): return created component
sanjayankur31 Aug 22, 2022
813217e
test(plot): disable interactive
sanjayankur31 Aug 22, 2022
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2 changes: 0 additions & 2 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,6 @@ jobs:
run: |
python -m pip install --upgrade pip
pip install -r requirements-dev.txt
pip install pytest
pip install .

- name: List packages so far
Expand All @@ -63,7 +62,6 @@ jobs:

- name: Run tests
run: |
pytest --cov=pyneuroml .
pynml -h

./test-ghactions.sh -neuron
Expand Down
2 changes: 1 addition & 1 deletion .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ install:
#- pip install git+https://github.com/NeuralEnsemble/pyelectro.git

- pip install --upgrade pip
- pip install flake8
- pip install flake8 pytest
- pip install .

script:
Expand Down
1 change: 1 addition & 0 deletions docs/source/pyneuroml.rst
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ Subpackages
pyneuroml.swc
pyneuroml.tune
pyneuroml.neuron
pyneuroml.utils


pyneuroml.pynml module
Expand Down
16 changes: 16 additions & 0 deletions docs/source/pyneuroml.utils.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
pyneuroml.utils package
==========================

.. automodule:: pyneuroml.utils
:members:
:undoc-members:
:show-inheritance:

pyneuroml.utils.CellBuilder module
---------------------------------------------

.. automodule:: pyneuroml.utils.CellBuilder
:members:
:undoc-members:
:show-inheritance:

3 changes: 1 addition & 2 deletions pyneuroml/pynml.py
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
"""

from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals

# py3.7, 3.8 require this to use standard collections as generics
Expand Down Expand Up @@ -1094,7 +1093,7 @@ def write_neuroml2_file(
writers.NeuroMLWriter.write(nml2_doc, nml2_file_name)

if validate:
validate_neuroml2(nml2_file_name, verbose_validate)
return validate_neuroml2(nml2_file_name, verbose_validate)


def read_lems_file(
Expand Down
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