Skip to content

Commit b365cd3

Browse files
pgleesonpgleeson
authored
Merge pull request #257 from NeuroML/development
 Changes for NML v2.3 release
2 parents 3af5ab2 + 9bdb814 commit b365cd3

File tree

160 files changed

+142422
-1380
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

160 files changed

+142422
-1380
lines changed

‎.all-contributorsrc‎

Lines changed: 178 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,178 @@
1+
{
2+
"projectName": "pyNeuroML",
3+
"projectOwner": "NeuroML",
4+
"repoType": "github",
5+
"repoHost": "https://github.com",
6+
"files": [
7+
"README.md"
8+
],
9+
"imageSize": 100,
10+
"commit": true,
11+
"commitConvention": "angular",
12+
"contributors": [
13+
{
14+
"login": "pgleeson",
15+
"name": "Padraig Gleeson",
16+
"avatar_url": "https://avatars.githubusercontent.com/u/1556687?v=4",
17+
"profile": "http://www.opensourcebrain.org/",
18+
"contributions": [
19+
"bug",
20+
"code",
21+
"content",
22+
"data",
23+
"doc",
24+
"design",
25+
"eventOrganizing",
26+
"ideas",
27+
"infra",
28+
"maintenance",
29+
"mentoring",
30+
"platform",
31+
"projectManagement",
32+
"question",
33+
"research",
34+
"review",
35+
"tool",
36+
"tutorial",
37+
"talk",
38+
"userTesting"
39+
]
40+
},
41+
{
42+
"login": "sanjayankur31",
43+
"name": "Ankur Sinha",
44+
"avatar_url": "https://avatars.githubusercontent.com/u/102575?v=4",
45+
"profile": "https://ankursinha.in/",
46+
"contributions": [
47+
"bug",
48+
"code",
49+
"content",
50+
"data",
51+
"doc",
52+
"design",
53+
"eventOrganizing",
54+
"ideas",
55+
"mentoring",
56+
"platform",
57+
"question",
58+
"research"
59+
]
60+
},
61+
{
62+
"login": "borismarin",
63+
"name": "Boris Marin",
64+
"avatar_url": "https://avatars.githubusercontent.com/u/3452783?v=4",
65+
"profile": "https://github.com/borismarin",
66+
"contributions": [
67+
"bug",
68+
"code",
69+
"content",
70+
"data",
71+
"doc",
72+
"design",
73+
"eventOrganizing",
74+
"ideas",
75+
"infra",
76+
"maintenance",
77+
"platform",
78+
"question",
79+
"research",
80+
"review",
81+
"tool",
82+
"userTesting"
83+
]
84+
},
85+
{
86+
"login": "rgerkin",
87+
"name": "Richard C Gerkin",
88+
"avatar_url": "https://avatars.githubusercontent.com/u/549787?v=4",
89+
"profile": "http://rick.gerk.in/",
90+
"contributions": [
91+
"bug",
92+
"code",
93+
"ideas",
94+
"maintenance",
95+
"platform",
96+
"research",
97+
"review",
98+
"tool",
99+
"userTesting"
100+
]
101+
},
102+
{
103+
"login": "lungd",
104+
"name": "David Lung",
105+
"avatar_url": "https://avatars.githubusercontent.com/u/5890526?v=4",
106+
"profile": "https://github.com/lungd",
107+
"contributions": [
108+
"bug",
109+
"code",
110+
"maintenance",
111+
"tool",
112+
"userTesting"
113+
]
114+
},
115+
{
116+
"login": "mwatts15",
117+
"name": "Mark Watts",
118+
"avatar_url": "https://avatars.githubusercontent.com/u/1487560?v=4",
119+
"profile": "https://www.thispersondoesnotexist.com/",
120+
"contributions": [
121+
"bug",
122+
"code"
123+
]
124+
},
125+
{
126+
"login": "ccluri",
127+
"name": "Chaitanya Chintaluri ",
128+
"avatar_url": "https://avatars.githubusercontent.com/u/546703?v=4",
129+
"profile": "https://chchaitanya.wordpress.com/",
130+
"contributions": [
131+
"bug",
132+
"code"
133+
]
134+
},
135+
{
136+
"login": "34383c",
137+
"name": "34383c",
138+
"avatar_url": "https://avatars.githubusercontent.com/u/17238193?v=4",
139+
"profile": "https://github.com/34383c",
140+
"contributions": [
141+
"bug",
142+
"code"
143+
]
144+
},
145+
{
146+
"login": "jrieke",
147+
"name": "Johannes Rieke",
148+
"avatar_url": "https://avatars.githubusercontent.com/u/5103165?v=4",
149+
"profile": "https://github.com/jrieke",
150+
"contributions": [
151+
"bug",
152+
"code"
153+
]
154+
},
155+
{
156+
"login": "andrisecker",
157+
"name": "András Ecker",
158+
"avatar_url": "https://avatars.githubusercontent.com/u/13274870?v=4",
159+
"profile": "https://github.com/andrisecker",
160+
"contributions": [
161+
"bug",
162+
"code"
163+
]
164+
},
165+
{
166+
"login": "RokasSt",
167+
"name": "Rokas Stanislovas",
168+
"avatar_url": "https://avatars.githubusercontent.com/u/12904422?v=4",
169+
"profile": "https://github.com/RokasSt",
170+
"contributions": [
171+
"bug",
172+
"code"
173+
]
174+
}
175+
],
176+
"contributorsPerLine": 7,
177+
"linkToUsage": true
178+
}

‎.github/workflows/ci.yml‎

Lines changed: 20 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -2,24 +2,32 @@ name: Continuous builds
22

33
on:
44
push:
5-
branches: [ master, development, experimental, test* ]
5+
branches:
6+
- master
7+
- development
8+
- experimental
9+
- 'test*'
610
pull_request:
7-
branches: [ master, development, experimental, test* ]
11+
branches:
12+
- master
13+
- development
14+
- experimental
15+
- 'test*'
816

917
jobs:
1018
build:
1119

1220
runs-on: ubuntu-latest
1321
strategy:
1422
matrix:
15-
python-version: [3.7, 3.8, 3.9]
23+
python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
1624
fail-fast: false
1725

1826
steps:
1927

20-
- uses: actions/checkout@v2
28+
- uses: actions/checkout@v3
2129
- name: Set up Python ${{ matrix.python-version }}
22-
uses: actions/setup-python@v2
30+
uses: actions/setup-python@v4
2331
with:
2432
python-version: ${{ matrix.python-version }}
2533

@@ -28,35 +36,21 @@ jobs:
2836
echo "github.ref is: ${{ github.ref }}"
2937
echo "github.base_ref is: ${{ github.base_ref }}"
3038
31-
- name: Install deps from development
32-
if: ${{ github.ref == 'refs/heads/development' || github.base_ref == 'development' }}
39+
- name: Upgrade pip, install inspyred
3340
run: |
34-
echo "Using deps from development for our repos"
35-
sed -E -i 's/((libNeuroML|NeuroMLlite|pylems|pyelectro|neurotune).git)@master/\1@development/' requirements-dev.txt
36-
sed -E -i 's/((modelspec).git)@main/\1@development/' requirements-dev.txt
37-
38-
- name: Install deps from experimental
39-
if: ${{ github.ref == 'refs/heads/experimental' || github.base_ref == 'experimental' }}
40-
run: |
41-
echo "Using deps from experimental - assuming development in others"
42-
sed -E -i 's/((libNeuroML|NeuroMLlite|pylems|pyelectro|neurotune).git)@master/\1@development/' requirements-dev.txt
43-
sed -E -i 's/((modelspec).git)@main/\1@development/' requirements-dev.txt
41+
python -m pip install --upgrade pip
42+
pip install git+https://github.com/aarongarrett/inspyred.git@master#egg=inspyred
43+
pip install .[dev]
4444
45-
- name: Install package
45+
- name: List packages so far
4646
run: |
47-
python -m pip install --upgrade pip
48-
pip install -r requirements-dev.txt
49-
pip install pytest
50-
pip install .
47+
pip list
5148
5249
- name: Run tests
5350
run: |
54-
pytest .
5551
pynml -h
5652
57-
# For now, only test neuron related examples on py3
58-
if [[ ${{ matrix.python-version }} == "3."* ]]; then argnrn=-neuron ; fi
59-
./test-ghactions.sh $argnrn
53+
./test-ghactions.sh -neuron
6054
6155
- name: Lint with flake8
6256
run: |

‎.github/workflows/python-publish.yml‎

Lines changed: 36 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,36 @@
1+
# This workflow will upload a Python Package using Twine when a release is created
2+
# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
3+
4+
# This workflow uses actions that are not certified by GitHub.
5+
# They are provided by a third-party and are governed by
6+
# separate terms of service, privacy policy, and support
7+
# documentation.
8+
9+
name: Upload Python Package
10+
11+
on:
12+
release:
13+
types: [published]
14+
15+
jobs:
16+
deploy:
17+
18+
runs-on: ubuntu-latest
19+
20+
steps:
21+
- uses: actions/checkout@v3
22+
- name: Set up Python
23+
uses: actions/setup-python@v4
24+
with:
25+
python-version: '3.x'
26+
- name: Install dependencies
27+
run: |
28+
python -m pip install --upgrade pip
29+
pip install build
30+
- name: Build package
31+
run: python -m build
32+
- name: Publish package
33+
uses: pypa/gh-action-pypi-publish@release/v1
34+
with:
35+
user: __token__
36+
password: ${{ secrets.PYPI_API_TOKEN }}

‎.gitignore‎

Lines changed: 43 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -122,3 +122,46 @@ examples/results/*.dat
122122
/examples/test_data/ca1/*.hoc
123123
.venv/
124124
/examples/LEMS_NML2_Ex5_DetCell_brian2.py
125+
/examples/*.gen.so
126+
*_eden.py
127+
/examples/test_data/Purk2M9s.nml.png
128+
/examples/test_data/*.pov
129+
/examples/test_data/ca1/*.pov
130+
/examples/test_data/ca1/TestOLMNet.net.nml.png
131+
/examples/test_data/complex_cell.cell.png
132+
/examples/test_data/simple_cell.cell.png
133+
/examples/test_data/complex_cell.morph.png
134+
/examples/test_data/simple_cell.morph.png
135+
/examples/LEMS_NML2_Ex5_DetCell_moose.py
136+
/examples/NET_NML2_Ex5_DetCell.net.nml
137+
138+
.mypy_cache/
139+
/examples/test_data/TwoCell.net.png
140+
/examples/test_data/Purk2M9s.png
141+
/.coverage
142+
/Nav.channel.nml
143+
/iv_izh2007RS0.net.nml
144+
/leak_chan.channel.nml
145+
/test_analysis_if.png
146+
/test_analysis_iv.png
147+
/test_analysis_traces.png
148+
/test_cell_analysis.cell.nml
149+
/tests/DoubExpSyn.channel.nml
150+
/tests/Nav.channel.nml
151+
/tests/iv_izh2007RS0.net.nml
152+
/tests/leak_chan.channel.nml
153+
/tests/test_cell_analysis.cell.nml
154+
arm64
155+
*.neux
156+
/test_*plot*png
157+
/examples/plot.py
158+
/tests/utils/test_rotation.net.nml
159+
/tests/utils/test_rotation.net.png
160+
/tests/analysis/test_analysis_if.png
161+
/tests/analysis/test_analysis_iv.png
162+
/tests/analysis/test_analysis_traces.png
163+
/tests/analysis/test_cell_analysis.cell.nml
164+
/tests/plot/test_schematic_plot_2d_test_cell_nml_xy.png
165+
/tests/plot/test_schematic_plot_2d_test_cell_nml_xz.png
166+
/tests/plot/test_schematic_plot_2d_test_cell_nml_yz.png
167+
/tests/analysis/*png

‎.pre-commit-config.yaml‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
# See https://pre-commit.com for more information
2+
# See https://pre-commit.com/hooks.html for more hooks
3+
repos:
4+
- repo: https://github.com/pre-commit/pre-commit-hooks
5+
rev: v4.4.0
6+
hooks:
7+
- id: trailing-whitespace
8+
- id: end-of-file-fixer
9+
- id: check-added-large-files
10+
- repo: https://github.com/psf/black
11+
rev: 23.3.0
12+
hooks:
13+
- id: black

‎.readthedocs.yaml‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
1+
version: 2
2+
3+
build:
4+
os: ubuntu-22.04
5+
tools:
6+
python: "3.11"
7+
8+
9+
sphinx:
10+
configuration: docs/source/conf.py
11+
12+
13+
python:
14+
install:
15+
- method: pip
16+
path: .
17+
extra_requirements:
18+
- doc

0 commit comments

Comments
 (0)