Skip to content

Commit 060bfad

Browse files
singlespsinglesp
authored
Initial commit
0 parents  commit 060bfad

File tree

11 files changed

+1801
-0
lines changed

11 files changed

+1801
-0
lines changed

‎.github/workflows/lint_python.yml

Lines changed: 31 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,31 @@
1+
name: Lint Python code
2+
3+
on:
4+
push:
5+
branches:
6+
- main
7+
pull_request:
8+
branches:
9+
- main
10+
11+
defaults:
12+
run:
13+
shell: bash
14+
15+
jobs:
16+
lint:
17+
runs-on: ubuntu-latest
18+
steps:
19+
- uses: actions/checkout@v2
20+
- name: Set up Python 3.8
21+
uses: actions/setup-python@v2
22+
with:
23+
python-version: 3.8
24+
- name: Display Python version
25+
run: python -c "import sys; print(sys.version)"
26+
- name: Install flake8 and related packages
27+
run: python -m pip install -r python_requirements.txt
28+
- name: Check the repository's Python code
29+
run: python -m flake8 .
30+
- name: Check the repository's Jupyter notebooks
31+
run: python -m nbqa flake8 **/*.ipynb

‎.github/workflows/lint_r.yml

Lines changed: 31 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,31 @@
1+
name: Lint R code
2+
3+
on:
4+
push:
5+
branches:
6+
- main
7+
pull_request:
8+
branches:
9+
- main
10+
11+
defaults:
12+
run:
13+
shell: bash
14+
15+
jobs:
16+
lint:
17+
runs-on: ubuntu-latest
18+
steps:
19+
- uses: actions/checkout@v3
20+
- uses: r-lib/actions/setup-r@v2
21+
with:
22+
use-public-rspm: true
23+
- uses: r-lib/actions/setup-r-dependencies@v2
24+
with:
25+
extra-packages: |
26+
r-lib/lintr
27+
local::.
28+
needs: lint
29+
- name: Lint
30+
run: lintr::lint_package()
31+
shell: Rscript {0}

‎.github/workflows/lint_shell.yml

Lines changed: 20 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,20 @@
1+
name: Lint shell code
2+
3+
on:
4+
push:
5+
branches:
6+
- main
7+
pull_request:
8+
branches:
9+
- main
10+
11+
permissions: {}
12+
13+
jobs:
14+
shellcheck:
15+
name: Shellcheck
16+
runs-on: ubuntu-latest
17+
steps:
18+
- uses: actions/checkout@v3
19+
- name: Run ShellCheck
20+
uses: ludeeus/action-shellcheck@master

‎.gitignore

Lines changed: 205 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,205 @@
1+
# Custom (PennLINC) gitignore
2+
.DS_Store
3+
4+
# Python gitignore
5+
# Byte-compiled / optimized / DLL files
6+
__pycache__/
7+
*.py[cod]
8+
*$py.class
9+
10+
# C extensions
11+
*.so
12+
13+
# Distribution / packaging
14+
.Python
15+
build/
16+
develop-eggs/
17+
dist/
18+
downloads/
19+
eggs/
20+
.eggs/
21+
lib/
22+
lib64/
23+
parts/
24+
sdist/
25+
var/
26+
wheels/
27+
share/python-wheels/
28+
*.egg-info/
29+
.installed.cfg
30+
*.egg
31+
MANIFEST
32+
33+
# PyInstaller
34+
# Usually these files are written by a python script from a template
35+
# before PyInstaller builds the exe, so as to inject date/other infos into it.
36+
*.manifest
37+
*.spec
38+
39+
# Installer logs
40+
pip-log.txt
41+
pip-delete-this-directory.txt
42+
43+
# Unit test / coverage reports
44+
htmlcov/
45+
.tox/
46+
.nox/
47+
.coverage
48+
.coverage.*
49+
.cache
50+
nosetests.xml
51+
coverage.xml
52+
*.cover
53+
*.py,cover
54+
.hypothesis/
55+
.pytest_cache/
56+
cover/
57+
58+
# Translations
59+
*.mo
60+
*.pot
61+
62+
# Django stuff:
63+
*.log
64+
local_settings.py
65+
db.sqlite3
66+
db.sqlite3-journal
67+
68+
# Flask stuff:
69+
instance/
70+
.webassets-cache
71+
72+
# Scrapy stuff:
73+
.scrapy
74+
75+
# Sphinx documentation
76+
docs/_build/
77+
78+
# PyBuilder
79+
.pybuilder/
80+
target/
81+
82+
# Jupyter Notebook
83+
.ipynb_checkpoints
84+
85+
# IPython
86+
profile_default/
87+
ipython_config.py
88+
89+
# pyenv
90+
# For a library or package, you might want to ignore these files since the code is
91+
# intended to run in multiple environments; otherwise, check them in:
92+
# .python-version
93+
94+
# pipenv
95+
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
96+
# However, in case of collaboration, if having platform-specific dependencies or dependencies
97+
# having no cross-platform support, pipenv may install dependencies that don't work, or not
98+
# install all needed dependencies.
99+
#Pipfile.lock
100+
101+
# poetry
102+
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
103+
# This is especially recommended for binary packages to ensure reproducibility, and is more
104+
# commonly ignored for libraries.
105+
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
106+
#poetry.lock
107+
108+
# pdm
109+
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
110+
#pdm.lock
111+
# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
112+
# in version control.
113+
# https://pdm.fming.dev/#use-with-ide
114+
.pdm.toml
115+
116+
# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
117+
__pypackages__/
118+
119+
# Celery stuff
120+
celerybeat-schedule
121+
celerybeat.pid
122+
123+
# SageMath parsed files
124+
*.sage.py
125+
126+
# Environments
127+
.env
128+
.venv
129+
env/
130+
venv/
131+
ENV/
132+
env.bak/
133+
venv.bak/
134+
135+
# Spyder project settings
136+
.spyderproject
137+
.spyproject
138+
139+
# Rope project settings
140+
.ropeproject
141+
142+
# mkdocs documentation
143+
/site
144+
145+
# mypy
146+
.mypy_cache/
147+
.dmypy.json
148+
dmypy.json
149+
150+
# Pyre type checker
151+
.pyre/
152+
153+
# pytype static type analyzer
154+
.pytype/
155+
156+
# Cython debug symbols
157+
cython_debug/
158+
159+
# PyCharm
160+
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
161+
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
162+
# and can be added to the global gitignore or merged into this file. For a more nuclear
163+
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
164+
#.idea/
165+
166+
# R gitignore
167+
# History files
168+
.Rhistory
169+
.Rapp.history
170+
171+
# Session Data files
172+
.RData
173+
174+
# User-specific files
175+
.Ruserdata
176+
177+
# Example code in package build process
178+
*-Ex.R
179+
180+
# Output files from R CMD build
181+
/*.tar.gz
182+
183+
# Output files from R CMD check
184+
/*.Rcheck/
185+
186+
# RStudio files
187+
.Rproj.user/
188+
189+
# produced vignettes
190+
vignettes/*.html
191+
vignettes/*.pdf
192+
193+
# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
194+
.httr-oauth
195+
196+
# knitr and R markdown default cache directories
197+
*_cache/
198+
/cache/
199+
200+
# Temporary files created by R markdown
201+
*.utf8.md
202+
*.knit.md
203+
204+
# R Environment Variables
205+
.Renviron

‎.vscode/settings.json

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
{
2+
"python.linting.flake8Enabled": true,
3+
"python.linting.enabled": true
4+
}

‎LICENSE

Lines changed: 21 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
MIT License
2+
3+
Copyright (c) 2023 Lifespan Informatics and Neuroimaging Center
4+
5+
Permission is hereby granted, free of charge, to any person obtaining a copy
6+
of this software and associated documentation files (the "Software"), to deal
7+
in the Software without restriction, including without limitation the rights
8+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9+
copies of the Software, and to permit persons to whom the Software is
10+
furnished to do so, subject to the following conditions:
11+
12+
The above copyright notice and this permission notice shall be included in all
13+
copies or substantial portions of the Software.
14+
15+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21+
SOFTWARE.

‎README.md

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,17 @@
1+
# paper-template
2+
A template repository for scientific projects.
3+
4+
## File organization on CUBIC
5+
6+
```
7+
/path/to/project/
8+
|- code/ # Local clone of the GitHub repository
9+
|- figures/ # Any figures for the manuscript
10+
|_ data/ # Tabular data that may be shared on GitHub
11+
|- data/
12+
|- results/ # Results that cannot be shared on GitHub
13+
|_ reproduction/
14+
|- code/ # Local clone of reproducibilibuddy's fork of GitHub repository
15+
|- data/ # Any data that must be copied and not referenced
16+
|_ results/
17+
```

‎analysis/generate_figure_01.ipynb

Lines changed: 72 additions & 0 deletions
Large diffs are not rendered by default.

0 commit comments

Comments
 (0)