aind-dynamic-foraging-data-utils 0.1.0__tar.gz
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- aind_dynamic_foraging_data_utils-0.1.0/.flake8 +8 -0
- aind_dynamic_foraging_data_utils-0.1.0/.github/ISSUE_TEMPLATE/bug_report.md +38 -0
- aind_dynamic_foraging_data_utils-0.1.0/.github/ISSUE_TEMPLATE/feature_request.md +20 -0
- aind_dynamic_foraging_data_utils-0.1.0/.github/ISSUE_TEMPLATE/user-story.md +27 -0
- aind_dynamic_foraging_data_utils-0.1.0/.github/workflows/init.yml +52 -0
- aind_dynamic_foraging_data_utils-0.1.0/.github/workflows/tag_and_publish.yml +87 -0
- aind_dynamic_foraging_data_utils-0.1.0/.github/workflows/test_and_lint.yml +26 -0
- aind_dynamic_foraging_data_utils-0.1.0/.gitignore +139 -0
- aind_dynamic_foraging_data_utils-0.1.0/LICENSE +21 -0
- aind_dynamic_foraging_data_utils-0.1.0/PKG-INFO +125 -0
- aind_dynamic_foraging_data_utils-0.1.0/README.md +102 -0
- aind_dynamic_foraging_data_utils-0.1.0/doc_template/Makefile +20 -0
- aind_dynamic_foraging_data_utils-0.1.0/doc_template/make.bat +35 -0
- aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/_static/dark-logo.svg +129 -0
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- aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/conf.py +54 -0
- aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/index.rst +22 -0
- aind_dynamic_foraging_data_utils-0.1.0/examples/make_dataframes.py +32 -0
- aind_dynamic_foraging_data_utils-0.1.0/pyproject.toml +83 -0
- aind_dynamic_foraging_data_utils-0.1.0/setup.cfg +4 -0
- aind_dynamic_foraging_data_utils-0.1.0/setup.py +4 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils/__init__.py +3 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils/alignment.py +573 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils/nwb_utils.py +599 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/PKG-INFO +125 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/SOURCES.txt +621 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/dependency_links.txt +1 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/requires.txt +13 -0
- aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/top_level.txt +1 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/__init__.py +3 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-14_11-12-44.nwb +0 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-15_10-02-05.nwb +0 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-16_10-06-43.nwb +0 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-17_09-32-04.nwb +0 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-20_10-39-40.nwb +0 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/.zattrs +7 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/.zgroup +3 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/.zmetadata +4403 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/.zgroup +3 -0
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- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/FIP_falling_time/data/1 +0 -0
- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/FIP_falling_time/data/2 +0 -0
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- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/FIP_falling_time/timestamps/3 +0 -0
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- aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/FIP_rising_time/data/1 +0 -0
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If applicable, add screenshots to help explain your problem.
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**Smartphone (please complete the following information):**
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- Device: [e.g. iPhone6]
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- OS: [e.g. iOS8.1]
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- Version [e.g. 22]
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**Additional context**
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Add any other context about the problem here.
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@@ -0,0 +1,20 @@
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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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+
|
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+
---
|
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9
|
+
|
|
10
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**Is your feature request related to a problem? Please describe.**
|
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
|
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+
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**Describe the solution you'd like**
|
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A clear and concise description of what you want to happen.
|
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**Describe alternatives you've considered**
|
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A clear and concise description of any alternative solutions or features you've considered.
|
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**Additional context**
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Add any other context or screenshots about the feature request here.
|
|
@@ -0,0 +1,27 @@
|
|
|
1
|
+
---
|
|
2
|
+
name: User story
|
|
3
|
+
about: This template provides a basic structure for user story issues.
|
|
4
|
+
title: ''
|
|
5
|
+
labels: ''
|
|
6
|
+
assignees: ''
|
|
7
|
+
|
|
8
|
+
---
|
|
9
|
+
|
|
10
|
+
# User story
|
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11
|
+
As a ..., I want to ..., so I can ...
|
|
12
|
+
|
|
13
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+
*Ideally, this is in the issue title, but if not, you can put it here. If so, delete this section.*
|
|
14
|
+
|
|
15
|
+
# Acceptance criteria
|
|
16
|
+
- [ ] This is something that can be verified to show that this user story is satisfied.
|
|
17
|
+
|
|
18
|
+
# Sprint Ready Checklist
|
|
19
|
+
- [ ] 1. Acceptance criteria defined
|
|
20
|
+
- [ ] 2. Team understands acceptance criteria
|
|
21
|
+
- [ ] 3. Team has defined solution / steps to satisfy acceptance criteria
|
|
22
|
+
- [ ] 4. Acceptance criteria is verifiable / testable
|
|
23
|
+
- [ ] 5. External / 3rd Party dependencies identified
|
|
24
|
+
- [ ] 6. Ticket is prioritized and sized
|
|
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|
+
|
|
26
|
+
# Notes
|
|
27
|
+
*Add any helpful notes here.*
|
|
@@ -0,0 +1,52 @@
|
|
|
1
|
+
# Workflow runs only once when the template is first used.
|
|
2
|
+
# File can be safely deleted after repo is initialized.
|
|
3
|
+
name: Initialize repository
|
|
4
|
+
on:
|
|
5
|
+
push:
|
|
6
|
+
branches:
|
|
7
|
+
- main
|
|
8
|
+
|
|
9
|
+
jobs:
|
|
10
|
+
initialize-package:
|
|
11
|
+
name: Initialize the package
|
|
12
|
+
if: ${{github.event.repository.name != 'aind-library-template'}}
|
|
13
|
+
runs-on: ubuntu-latest
|
|
14
|
+
env:
|
|
15
|
+
REPO_NAME: ${{ github.event.repository.name }}
|
|
16
|
+
GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
|
|
17
|
+
steps:
|
|
18
|
+
- name: Checkout
|
|
19
|
+
uses: actions/checkout@v3
|
|
20
|
+
- name: Rename package
|
|
21
|
+
run: |
|
|
22
|
+
pkg_name=$(echo "${REPO_NAME}" | tr - _)
|
|
23
|
+
current_description='description = "Prints messages to stdout. Simple boilerplate for libraries."'
|
|
24
|
+
new_description='description = "Generated from aind-library-template"'
|
|
25
|
+
readme_description='Template for a minimal, basic repository for an AIND library.'
|
|
26
|
+
new_readme_description='Generated from aind-library-template'
|
|
27
|
+
echo "Package Name ${pkg_name}"
|
|
28
|
+
mkdir src/${pkg_name}
|
|
29
|
+
touch src/${pkg_name}/__init__.py
|
|
30
|
+
echo '"""Init package"""' >> src/${pkg_name}/__init__.py
|
|
31
|
+
echo '__version__ = "0.0.0"' >> src/${pkg_name}/__init__.py
|
|
32
|
+
sed -i "s/aind_library_template/${pkg_name}/" pyproject.toml
|
|
33
|
+
sed -i "s/aind-library-template/${REPO_NAME}/" pyproject.toml
|
|
34
|
+
sed -i "s/aind_library_template/${pkg_name}/" doc_template/source/conf.py
|
|
35
|
+
sed -i "s/${current_description}/${new_description}/" pyproject.toml
|
|
36
|
+
sed -i "/pandas/d" pyproject.toml
|
|
37
|
+
sed -i "s/aind-library-template/${REPO_NAME}/" README.md
|
|
38
|
+
sed -i "s/${readme_description}/${new_readme_description}/" README.md
|
|
39
|
+
- name: Commit changes
|
|
40
|
+
uses: EndBug/add-and-commit@v9
|
|
41
|
+
with:
|
|
42
|
+
default_author: github_actions
|
|
43
|
+
message: "ci: version bump [skip actions]"
|
|
44
|
+
add: '["pyproject.toml", "README.md", "src/*", "doc_template/source/conf.py"]'
|
|
45
|
+
remove: '["-r src/aind_library_template", "tests/test_message_handler.py"]'
|
|
46
|
+
- name: Add first tag
|
|
47
|
+
run: |
|
|
48
|
+
git tag v0.0.0
|
|
49
|
+
git push origin v0.0.0
|
|
50
|
+
- name: Disable workflow
|
|
51
|
+
run: |
|
|
52
|
+
gh workflow disable -R $GITHUB_REPOSITORY "${{ github.workflow }}"
|
|
@@ -0,0 +1,87 @@
|
|
|
1
|
+
name: Tag and publish
|
|
2
|
+
on:
|
|
3
|
+
push:
|
|
4
|
+
branches:
|
|
5
|
+
- main
|
|
6
|
+
# Remove line 61 to enable automated semantic version bumps.
|
|
7
|
+
# Change line 67 from "if: false" to "if: true" to enable PyPI publishing.
|
|
8
|
+
# Requires that svc-aindscicomp be added as an admin to repo.
|
|
9
|
+
jobs:
|
|
10
|
+
update_badges:
|
|
11
|
+
runs-on: ubuntu-latest
|
|
12
|
+
continue-on-error: true
|
|
13
|
+
steps:
|
|
14
|
+
- uses: actions/checkout@v3
|
|
15
|
+
with:
|
|
16
|
+
ref: ${{ env.DEFAULT_BRANCH }}
|
|
17
|
+
fetch-depth: 0
|
|
18
|
+
token: ${{ secrets.SERVICE_TOKEN }}
|
|
19
|
+
- name: Set up Python 3.8
|
|
20
|
+
uses: actions/setup-python@v3
|
|
21
|
+
with:
|
|
22
|
+
python-version: 3.8
|
|
23
|
+
- name: Install dependencies
|
|
24
|
+
run: |
|
|
25
|
+
python -m pip install -e .[dev] --no-cache-dir
|
|
26
|
+
- name: Get Python version and Update README.md
|
|
27
|
+
run: |
|
|
28
|
+
python_version=$(grep "requires-python" pyproject.toml | grep -o ">=[^\"]*")
|
|
29
|
+
python_badge=$(grep -o 'python-[^)]*' README.md)
|
|
30
|
+
new_python_badge="python-$python_version-blue?logo=python"
|
|
31
|
+
sed -i "s/$python_badge/$new_python_badge/g" README.md
|
|
32
|
+
- name: Get interrogate values and Update README.md
|
|
33
|
+
run: |
|
|
34
|
+
interrogate_val=$(interrogate . | grep -o 'actual: [0-9]*\.[0-9]*' | awk '{print $2}')
|
|
35
|
+
interrogate_badge=$(grep -o 'interrogate-[^)]*' README.md)
|
|
36
|
+
if (( $(echo "$interrogate_val >= 90.00" | bc -l) )); then
|
|
37
|
+
new_interrogate_badge="interrogate-$interrogate_val%25-brightgreen"
|
|
38
|
+
elif (( $(echo "$interrogate_val < 80.00" | bc -l) )); then
|
|
39
|
+
new_interrogate_badge="interrogate-$interrogate_val%25-red"
|
|
40
|
+
else
|
|
41
|
+
new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
|
|
42
|
+
fi
|
|
43
|
+
sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
|
|
44
|
+
- name: Get Coverage values and Update README.md
|
|
45
|
+
run: |
|
|
46
|
+
coverage run -m unittest discover
|
|
47
|
+
coverage_val=$(coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
|
|
48
|
+
coverage_badge=$(grep -o "coverage-[^?]*" README.md)
|
|
49
|
+
if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then
|
|
50
|
+
new_coverage_badge="coverage-$coverage_val%25-brightgreen"
|
|
51
|
+
elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
|
|
52
|
+
new_coverage_badge="coverage-$coverage_val%25-red"
|
|
53
|
+
else
|
|
54
|
+
new_coverage_badge="coverage-$coverage_val%25-yellow"
|
|
55
|
+
fi
|
|
56
|
+
sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
|
|
57
|
+
- name: Commit changes
|
|
58
|
+
uses: EndBug/add-and-commit@v9
|
|
59
|
+
with:
|
|
60
|
+
default_author: github_actions
|
|
61
|
+
add: '["README.md"]'
|
|
62
|
+
tag:
|
|
63
|
+
needs: update_badges
|
|
64
|
+
uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
|
|
65
|
+
secrets:
|
|
66
|
+
SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
|
|
67
|
+
publish:
|
|
68
|
+
needs: tag
|
|
69
|
+
if: true
|
|
70
|
+
runs-on: ubuntu-latest
|
|
71
|
+
steps:
|
|
72
|
+
- uses: actions/checkout@v3
|
|
73
|
+
- name: Pull latest changes
|
|
74
|
+
run: git pull origin main
|
|
75
|
+
- name: Set up Python 3.8
|
|
76
|
+
uses: actions/setup-python@v2
|
|
77
|
+
with:
|
|
78
|
+
python-version: 3.8
|
|
79
|
+
- name: Install dependencies
|
|
80
|
+
run: |
|
|
81
|
+
pip install --upgrade setuptools wheel twine build
|
|
82
|
+
python -m build
|
|
83
|
+
twine check dist/*
|
|
84
|
+
- name: Publish on PyPI
|
|
85
|
+
uses: pypa/gh-action-pypi-publish@release/v1
|
|
86
|
+
with:
|
|
87
|
+
password: ${{ secrets.AIND_PYPI_TOKEN }}
|
|
@@ -0,0 +1,26 @@
|
|
|
1
|
+
name: Lint and run tests
|
|
2
|
+
|
|
3
|
+
on:
|
|
4
|
+
pull_request:
|
|
5
|
+
branches:
|
|
6
|
+
- main
|
|
7
|
+
|
|
8
|
+
jobs:
|
|
9
|
+
ci:
|
|
10
|
+
runs-on: ubuntu-latest
|
|
11
|
+
strategy:
|
|
12
|
+
matrix:
|
|
13
|
+
python-version: [ '3.8', '3.9', '3.10' ]
|
|
14
|
+
steps:
|
|
15
|
+
- uses: actions/checkout@v3
|
|
16
|
+
- name: Set up Python ${{ matrix.python-version }}
|
|
17
|
+
uses: actions/setup-python@v3
|
|
18
|
+
with:
|
|
19
|
+
python-version: ${{ matrix.python-version }}
|
|
20
|
+
- name: Install dependencies
|
|
21
|
+
run: |
|
|
22
|
+
python -m pip install -e .[dev]
|
|
23
|
+
- name: Run linter checks
|
|
24
|
+
run: flake8 . && interrogate --verbose .
|
|
25
|
+
- name: Run tests and coverage
|
|
26
|
+
run: coverage run -m unittest discover && coverage report
|
|
@@ -0,0 +1,139 @@
|
|
|
1
|
+
# Byte-compiled / optimized / DLL files
|
|
2
|
+
__pycache__/
|
|
3
|
+
*.py[cod]
|
|
4
|
+
*$py.class
|
|
5
|
+
|
|
6
|
+
# C extensions
|
|
7
|
+
*.so
|
|
8
|
+
|
|
9
|
+
# Distribution / packaging
|
|
10
|
+
.Python
|
|
11
|
+
build/
|
|
12
|
+
develop-eggs/
|
|
13
|
+
dist/
|
|
14
|
+
downloads/
|
|
15
|
+
eggs/
|
|
16
|
+
.eggs/
|
|
17
|
+
lib/
|
|
18
|
+
lib64/
|
|
19
|
+
parts/
|
|
20
|
+
sdist/
|
|
21
|
+
var/
|
|
22
|
+
wheels/
|
|
23
|
+
pip-wheel-metadata/
|
|
24
|
+
share/python-wheels/
|
|
25
|
+
*.egg-info/
|
|
26
|
+
.installed.cfg
|
|
27
|
+
*.egg
|
|
28
|
+
MANIFEST
|
|
29
|
+
|
|
30
|
+
# PyInstaller
|
|
31
|
+
# Usually these files are written by a python script from a template
|
|
32
|
+
# before PyInstaller builds the exe, so as to inject date/other infos into it.
|
|
33
|
+
*.manifest
|
|
34
|
+
*.spec
|
|
35
|
+
|
|
36
|
+
# Installer logs
|
|
37
|
+
pip-log.txt
|
|
38
|
+
pip-delete-this-directory.txt
|
|
39
|
+
|
|
40
|
+
# Unit test / coverage reports
|
|
41
|
+
htmlcov/
|
|
42
|
+
.tox/
|
|
43
|
+
.nox/
|
|
44
|
+
.coverage
|
|
45
|
+
.coverage.*
|
|
46
|
+
.cache
|
|
47
|
+
nosetests.xml
|
|
48
|
+
coverage.xml
|
|
49
|
+
*.cover
|
|
50
|
+
*.py,cover
|
|
51
|
+
.hypothesis/
|
|
52
|
+
.pytest_cache/
|
|
53
|
+
|
|
54
|
+
# Translations
|
|
55
|
+
*.mo
|
|
56
|
+
*.pot
|
|
57
|
+
|
|
58
|
+
# Django stuff:
|
|
59
|
+
*.log
|
|
60
|
+
local_settings.py
|
|
61
|
+
db.sqlite3
|
|
62
|
+
db.sqlite3-journal
|
|
63
|
+
|
|
64
|
+
# Flask stuff:
|
|
65
|
+
instance/
|
|
66
|
+
.webassets-cache
|
|
67
|
+
|
|
68
|
+
# Scrapy stuff:
|
|
69
|
+
.scrapy
|
|
70
|
+
|
|
71
|
+
# Sphinx documentation
|
|
72
|
+
docs/_build/
|
|
73
|
+
|
|
74
|
+
# PyBuilder
|
|
75
|
+
target/
|
|
76
|
+
|
|
77
|
+
# Jupyter Notebook
|
|
78
|
+
.ipynb_checkpoints
|
|
79
|
+
|
|
80
|
+
# IPython
|
|
81
|
+
profile_default/
|
|
82
|
+
ipython_config.py
|
|
83
|
+
|
|
84
|
+
# pyenv
|
|
85
|
+
.python-version
|
|
86
|
+
|
|
87
|
+
# pipenv
|
|
88
|
+
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
|
|
89
|
+
# However, in case of collaboration, if having platform-specific dependencies or dependencies
|
|
90
|
+
# having no cross-platform support, pipenv may install dependencies that don't work, or not
|
|
91
|
+
# install all needed dependencies.
|
|
92
|
+
#Pipfile.lock
|
|
93
|
+
|
|
94
|
+
# PEP 582; used by e.g. github.com/David-OConnor/pyflow
|
|
95
|
+
__pypackages__/
|
|
96
|
+
|
|
97
|
+
# Celery stuff
|
|
98
|
+
celerybeat-schedule
|
|
99
|
+
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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MIT License
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Copyright (c) 2022 Allen Institute for Neural Dynamics
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.1
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Name: aind-dynamic-foraging-data-utils
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Version: 0.1.0
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Summary: Functions to help with postprocessing dynamic foraging data.
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Author: Allen Institute for Neural Dynamics
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License: MIT
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Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.7
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: pandas
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Requires-Dist: numpy
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Requires-Dist: pynwb
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Requires-Dist: hdmf_zarr
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Provides-Extra: dev
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Requires-Dist: black; extra == "dev"
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Requires-Dist: coverage; extra == "dev"
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Requires-Dist: flake8; extra == "dev"
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Requires-Dist: interrogate; extra == "dev"
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Requires-Dist: isort; extra == "dev"
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Requires-Dist: Sphinx; extra == "dev"
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Requires-Dist: furo; extra == "dev"
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# aind-dynamic-foraging-data-utils
|
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[](LICENSE)
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+

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[](https://github.com/semantic-release/semantic-release)
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+

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## Scope
|
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Purpose: Ingests NWB and spits out dataframes with the relevant information. Focused on dynamic foraging. Other tasks can branch and build task-specific utils.
|
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Inputs are nwbs, outputs are dataframes (tidy and not)
|
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Dependencies: xarray (includes numpy and pandas), scikit-learn (includes scipy), matplotlib
|
|
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|
+
|
|
41
|
+
|
|
42
|
+
|
|
43
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|
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## Installation
|
|
45
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To use the software, in the root directory, run
|
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```bash
|
|
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|
+
pip install -e .
|
|
48
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+
```
|
|
49
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+
|
|
50
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To develop the code, run
|
|
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```bash
|
|
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pip install -e .[dev]
|
|
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+
```
|
|
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+
|
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## Contributing
|
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+
|
|
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|
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### Linters and testing
|
|
58
|
+
|
|
59
|
+
There are several libraries used to run linters, check documentation, and run tests.
|
|
60
|
+
|
|
61
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+
- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
|
|
62
|
+
|
|
63
|
+
```bash
|
|
64
|
+
coverage run -m unittest discover && coverage report
|
|
65
|
+
```
|
|
66
|
+
|
|
67
|
+
- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
|
|
68
|
+
|
|
69
|
+
```bash
|
|
70
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+
interrogate .
|
|
71
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+
```
|
|
72
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+
|
|
73
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- Use **flake8** to check that code is up to standards (no unused imports, etc.):
|
|
74
|
+
```bash
|
|
75
|
+
flake8 .
|
|
76
|
+
```
|
|
77
|
+
|
|
78
|
+
- Use **black** to automatically format the code into PEP standards:
|
|
79
|
+
```bash
|
|
80
|
+
black .
|
|
81
|
+
```
|
|
82
|
+
|
|
83
|
+
- Use **isort** to automatically sort import statements:
|
|
84
|
+
```bash
|
|
85
|
+
isort .
|
|
86
|
+
```
|
|
87
|
+
|
|
88
|
+
### Pull requests
|
|
89
|
+
|
|
90
|
+
For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
|
|
91
|
+
```text
|
|
92
|
+
<type>(<scope>): <short summary>
|
|
93
|
+
```
|
|
94
|
+
|
|
95
|
+
where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
|
|
96
|
+
|
|
97
|
+
- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
|
|
98
|
+
- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
|
|
99
|
+
- **docs**: Documentation only changes
|
|
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|
+
- **feat**: A new feature
|
|
101
|
+
- **fix**: A bugfix
|
|
102
|
+
- **perf**: A code change that improves performance
|
|
103
|
+
- **refactor**: A code change that neither fixes a bug nor adds a feature
|
|
104
|
+
- **test**: Adding missing tests or correcting existing tests
|
|
105
|
+
|
|
106
|
+
### Semantic Release
|
|
107
|
+
|
|
108
|
+
The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
|
|
109
|
+
|
|
110
|
+
| Commit message | Release type |
|
|
111
|
+
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
|
|
112
|
+
| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
|
|
113
|
+
| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
|
|
114
|
+
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
|
|
115
|
+
|
|
116
|
+
### Documentation
|
|
117
|
+
To generate the rst files source files for documentation, run
|
|
118
|
+
```bash
|
|
119
|
+
sphinx-apidoc -o doc_template/source/ src
|
|
120
|
+
```
|
|
121
|
+
Then to create the documentation HTML files, run
|
|
122
|
+
```bash
|
|
123
|
+
sphinx-build -b html doc_template/source/ doc_template/build/html
|
|
124
|
+
```
|
|
125
|
+
More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
|
|
@@ -0,0 +1,102 @@
|
|
|
1
|
+
# aind-dynamic-foraging-data-utils
|
|
2
|
+
|
|
3
|
+
|
|
4
|
+
[](LICENSE)
|
|
5
|
+

|
|
6
|
+
[](https://github.com/semantic-release/semantic-release)
|
|
7
|
+

|
|
8
|
+

|
|
9
|
+

|
|
10
|
+
|
|
11
|
+
|
|
12
|
+
|
|
13
|
+
## Scope
|
|
14
|
+
Purpose: Ingests NWB and spits out dataframes with the relevant information. Focused on dynamic foraging. Other tasks can branch and build task-specific utils.
|
|
15
|
+
Inputs are nwbs, outputs are dataframes (tidy and not)
|
|
16
|
+
Dependencies: xarray (includes numpy and pandas), scikit-learn (includes scipy), matplotlib
|
|
17
|
+
|
|
18
|
+
|
|
19
|
+
|
|
20
|
+
|
|
21
|
+
## Installation
|
|
22
|
+
To use the software, in the root directory, run
|
|
23
|
+
```bash
|
|
24
|
+
pip install -e .
|
|
25
|
+
```
|
|
26
|
+
|
|
27
|
+
To develop the code, run
|
|
28
|
+
```bash
|
|
29
|
+
pip install -e .[dev]
|
|
30
|
+
```
|
|
31
|
+
|
|
32
|
+
## Contributing
|
|
33
|
+
|
|
34
|
+
### Linters and testing
|
|
35
|
+
|
|
36
|
+
There are several libraries used to run linters, check documentation, and run tests.
|
|
37
|
+
|
|
38
|
+
- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
|
|
39
|
+
|
|
40
|
+
```bash
|
|
41
|
+
coverage run -m unittest discover && coverage report
|
|
42
|
+
```
|
|
43
|
+
|
|
44
|
+
- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
|
|
45
|
+
|
|
46
|
+
```bash
|
|
47
|
+
interrogate .
|
|
48
|
+
```
|
|
49
|
+
|
|
50
|
+
- Use **flake8** to check that code is up to standards (no unused imports, etc.):
|
|
51
|
+
```bash
|
|
52
|
+
flake8 .
|
|
53
|
+
```
|
|
54
|
+
|
|
55
|
+
- Use **black** to automatically format the code into PEP standards:
|
|
56
|
+
```bash
|
|
57
|
+
black .
|
|
58
|
+
```
|
|
59
|
+
|
|
60
|
+
- Use **isort** to automatically sort import statements:
|
|
61
|
+
```bash
|
|
62
|
+
isort .
|
|
63
|
+
```
|
|
64
|
+
|
|
65
|
+
### Pull requests
|
|
66
|
+
|
|
67
|
+
For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
|
|
68
|
+
```text
|
|
69
|
+
<type>(<scope>): <short summary>
|
|
70
|
+
```
|
|
71
|
+
|
|
72
|
+
where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
|
|
73
|
+
|
|
74
|
+
- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
|
|
75
|
+
- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
|
|
76
|
+
- **docs**: Documentation only changes
|
|
77
|
+
- **feat**: A new feature
|
|
78
|
+
- **fix**: A bugfix
|
|
79
|
+
- **perf**: A code change that improves performance
|
|
80
|
+
- **refactor**: A code change that neither fixes a bug nor adds a feature
|
|
81
|
+
- **test**: Adding missing tests or correcting existing tests
|
|
82
|
+
|
|
83
|
+
### Semantic Release
|
|
84
|
+
|
|
85
|
+
The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
|
|
86
|
+
|
|
87
|
+
| Commit message | Release type |
|
|
88
|
+
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
|
|
89
|
+
| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
|
|
90
|
+
| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
|
|
91
|
+
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
|
|
92
|
+
|
|
93
|
+
### Documentation
|
|
94
|
+
To generate the rst files source files for documentation, run
|
|
95
|
+
```bash
|
|
96
|
+
sphinx-apidoc -o doc_template/source/ src
|
|
97
|
+
```
|
|
98
|
+
Then to create the documentation HTML files, run
|
|
99
|
+
```bash
|
|
100
|
+
sphinx-build -b html doc_template/source/ doc_template/build/html
|
|
101
|
+
```
|
|
102
|
+
More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
# Minimal makefile for Sphinx documentation
|
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+
#
|
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3
|
+
|
|
4
|
+
# You can set these variables from the command line, and also
|
|
5
|
+
# from the environment for the first two.
|
|
6
|
+
SPHINXOPTS ?=
|
|
7
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+
SPHINXBUILD ?= sphinx-build
|
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+
SOURCEDIR = source
|
|
9
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+
BUILDDIR = build
|
|
10
|
+
|
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|
+
# Put it first so that "make" without argument is like "make help".
|
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+
help:
|
|
13
|
+
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
|
|
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|
+
|
|
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+
.PHONY: help Makefile
|
|
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|
+
|
|
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|
+
# Catch-all target: route all unknown targets to Sphinx using the new
|
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+
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
|
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+
%: Makefile
|
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+
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
|