aind-dynamic-foraging-data-utils 0.1.0__tar.gz

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  1. aind_dynamic_foraging_data_utils-0.1.0/.flake8 +8 -0
  2. aind_dynamic_foraging_data_utils-0.1.0/.github/ISSUE_TEMPLATE/bug_report.md +38 -0
  3. aind_dynamic_foraging_data_utils-0.1.0/.github/ISSUE_TEMPLATE/feature_request.md +20 -0
  4. aind_dynamic_foraging_data_utils-0.1.0/.github/ISSUE_TEMPLATE/user-story.md +27 -0
  5. aind_dynamic_foraging_data_utils-0.1.0/.github/workflows/init.yml +52 -0
  6. aind_dynamic_foraging_data_utils-0.1.0/.github/workflows/tag_and_publish.yml +87 -0
  7. aind_dynamic_foraging_data_utils-0.1.0/.github/workflows/test_and_lint.yml +26 -0
  8. aind_dynamic_foraging_data_utils-0.1.0/.gitignore +139 -0
  9. aind_dynamic_foraging_data_utils-0.1.0/LICENSE +21 -0
  10. aind_dynamic_foraging_data_utils-0.1.0/PKG-INFO +125 -0
  11. aind_dynamic_foraging_data_utils-0.1.0/README.md +102 -0
  12. aind_dynamic_foraging_data_utils-0.1.0/doc_template/Makefile +20 -0
  13. aind_dynamic_foraging_data_utils-0.1.0/doc_template/make.bat +35 -0
  14. aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/_static/dark-logo.svg +129 -0
  15. aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/_static/favicon.ico +0 -0
  16. aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/_static/light-logo.svg +128 -0
  17. aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/conf.py +54 -0
  18. aind_dynamic_foraging_data_utils-0.1.0/doc_template/source/index.rst +22 -0
  19. aind_dynamic_foraging_data_utils-0.1.0/examples/make_dataframes.py +32 -0
  20. aind_dynamic_foraging_data_utils-0.1.0/pyproject.toml +83 -0
  21. aind_dynamic_foraging_data_utils-0.1.0/setup.cfg +4 -0
  22. aind_dynamic_foraging_data_utils-0.1.0/setup.py +4 -0
  23. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils/__init__.py +3 -0
  24. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils/alignment.py +573 -0
  25. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils/nwb_utils.py +599 -0
  26. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/PKG-INFO +125 -0
  27. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/SOURCES.txt +621 -0
  28. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/dependency_links.txt +1 -0
  29. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/requires.txt +13 -0
  30. aind_dynamic_foraging_data_utils-0.1.0/src/aind_dynamic_foraging_data_utils.egg-info/top_level.txt +1 -0
  31. aind_dynamic_foraging_data_utils-0.1.0/tests/__init__.py +3 -0
  32. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-14_11-12-44.nwb +0 -0
  33. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-15_10-02-05.nwb +0 -0
  34. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-16_10-06-43.nwb +0 -0
  35. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-17_09-32-04.nwb +0 -0
  36. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/697062_2023-11-20_10-39-40.nwb +0 -0
  37. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/.zattrs +7 -0
  38. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/.zgroup +3 -0
  39. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/.zmetadata +4403 -0
  40. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/.zgroup +3 -0
  41. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/FIP_falling_time/.zattrs +7 -0
  42. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/FIP_falling_time/.zgroup +3 -0
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  45. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/FIP_falling_time/data/0 +0 -0
  46. 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
  47. 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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  69. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/acquisition/G_1/.zattrs +7 -0
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  612. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/specifications/hdmf-experimental/0.5.0/namespace/0 +1 -0
  613. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/specifications/hdmf-experimental/0.5.0/resources/.zarray +30 -0
  614. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/specifications/hdmf-experimental/0.5.0/resources/.zattrs +3 -0
  615. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/specifications/hdmf-experimental/0.5.0/resources/0 +1 -0
  616. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/stimulus/.zgroup +3 -0
  617. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/stimulus/presentation/.zgroup +3 -0
  618. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/stimulus/templates/.zgroup +3 -0
  619. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/timestamps_reference_time/.zarray +24 -0
  620. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/timestamps_reference_time/.zattrs +3 -0
  621. aind_dynamic_foraging_data_utils-0.1.0/tests/nwb/behavior_717531_2024-08-07_09-01-02.nwb/timestamps_reference_time/0 +0 -0
  622. aind_dynamic_foraging_data_utils-0.1.0/tests/test_aind_dynamic_foraging_data_utils.py +267 -0
  623. aind_dynamic_foraging_data_utils-0.1.0/tests/test_example.py +16 -0
@@ -0,0 +1,8 @@
1
+ [flake8]
2
+ extend-ignore = E203
3
+ exclude =
4
+ .git,
5
+ __pycache__,
6
+ build
7
+ max-complexity = 10
8
+ max-line-length = 100
@@ -0,0 +1,38 @@
1
+ ---
2
+ name: Bug report
3
+ about: Create a report to help us improve
4
+ title: ''
5
+ labels: ''
6
+ assignees: ''
7
+
8
+ ---
9
+
10
+ **Describe the bug**
11
+ A clear and concise description of what the bug is.
12
+
13
+ **To Reproduce**
14
+ Steps to reproduce the behavior:
15
+ 1. Go to '...'
16
+ 2. Click on '....'
17
+ 3. Scroll down to '....'
18
+ 4. See error
19
+
20
+ **Expected behavior**
21
+ A clear and concise description of what you expected to happen.
22
+
23
+ **Screenshots**
24
+ If applicable, add screenshots to help explain your problem.
25
+
26
+ **Desktop (please complete the following information):**
27
+ - OS: [e.g. iOS]
28
+ - Browser [e.g. chrome, safari]
29
+ - Version [e.g. 22]
30
+
31
+ **Smartphone (please complete the following information):**
32
+ - Device: [e.g. iPhone6]
33
+ - OS: [e.g. iOS8.1]
34
+ - Browser [e.g. stock browser, safari]
35
+ - Version [e.g. 22]
36
+
37
+ **Additional context**
38
+ Add any other context about the problem here.
@@ -0,0 +1,20 @@
1
+ ---
2
+ name: Feature request
3
+ about: Suggest an idea for this project
4
+ title: ''
5
+ labels: ''
6
+ assignees: ''
7
+
8
+ ---
9
+
10
+ **Is your feature request related to a problem? Please describe.**
11
+ A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
12
+
13
+ **Describe the solution you'd like**
14
+ A clear and concise description of what you want to happen.
15
+
16
+ **Describe alternatives you've considered**
17
+ A clear and concise description of any alternative solutions or features you've considered.
18
+
19
+ **Additional context**
20
+ 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
11
+ As a ..., I want to ..., so I can ...
12
+
13
+ *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
25
+
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
+ celerybeat.pid
100
+
101
+ # SageMath parsed files
102
+ *.sage.py
103
+
104
+ # Environments
105
+ .env
106
+ .venv
107
+ env/
108
+ venv/
109
+ ENV/
110
+ env.bak/
111
+ venv.bak/
112
+
113
+ # Spyder project settings
114
+ .spyderproject
115
+ .spyproject
116
+
117
+ # Rope project settings
118
+ .ropeproject
119
+
120
+ # mkdocs documentation
121
+ /site
122
+
123
+ # mypy
124
+ .mypy_cache/
125
+ .dmypy.json
126
+ dmypy.json
127
+
128
+ # Pyre type checker
129
+ .pyre/
130
+
131
+ # PyCharm
132
+ # JetBrains specific template is maintained in a separate JetBrains.gitignore that can
133
+ # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
134
+ # and can be added to the global gitignore or merged into this file. For a more nuclear
135
+ # option (not recommended) you can uncomment the following to ignore the entire idea folder.
136
+ .idea/
137
+
138
+ # MacOs
139
+ **/.DS_Store
@@ -0,0 +1,21 @@
1
+ MIT License
2
+
3
+ Copyright (c) 2022 Allen Institute for Neural Dynamics
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.
@@ -0,0 +1,125 @@
1
+ Metadata-Version: 2.1
2
+ Name: aind-dynamic-foraging-data-utils
3
+ Version: 0.1.0
4
+ Summary: Functions to help with postprocessing dynamic foraging data.
5
+ Author: Allen Institute for Neural Dynamics
6
+ License: MIT
7
+ Classifier: Programming Language :: Python :: 3
8
+ Requires-Python: >=3.7
9
+ Description-Content-Type: text/markdown
10
+ License-File: LICENSE
11
+ Requires-Dist: pandas
12
+ Requires-Dist: numpy
13
+ Requires-Dist: pynwb
14
+ Requires-Dist: hdmf_zarr
15
+ Provides-Extra: dev
16
+ Requires-Dist: black; extra == "dev"
17
+ Requires-Dist: coverage; extra == "dev"
18
+ Requires-Dist: flake8; extra == "dev"
19
+ Requires-Dist: interrogate; extra == "dev"
20
+ Requires-Dist: isort; extra == "dev"
21
+ Requires-Dist: Sphinx; extra == "dev"
22
+ Requires-Dist: furo; extra == "dev"
23
+
24
+ # aind-dynamic-foraging-data-utils
25
+
26
+
27
+ [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
28
+ ![Code Style](https://img.shields.io/badge/code%20style-black-black)
29
+ [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
30
+ ![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
31
+ ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
32
+ ![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python)
33
+
34
+
35
+
36
+ ## Scope
37
+ Purpose: Ingests NWB and spits out dataframes with the relevant information. Focused on dynamic foraging. Other tasks can branch and build task-specific utils.
38
+ Inputs are nwbs, outputs are dataframes (tidy and not)
39
+ Dependencies: xarray (includes numpy and pandas), scikit-learn (includes scipy), matplotlib
40
+
41
+
42
+
43
+
44
+ ## Installation
45
+ To use the software, in the root directory, run
46
+ ```bash
47
+ pip install -e .
48
+ ```
49
+
50
+ To develop the code, run
51
+ ```bash
52
+ pip install -e .[dev]
53
+ ```
54
+
55
+ ## Contributing
56
+
57
+ ### Linters and testing
58
+
59
+ There are several libraries used to run linters, check documentation, and run tests.
60
+
61
+ - 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
+ interrogate .
71
+ ```
72
+
73
+ - 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
100
+ - **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):
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+
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+ | Commit message | Release type |
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+ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
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+ | `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
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+ | `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
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+ | `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) |
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+
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+ ### Documentation
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+ To generate the rst files source files for documentation, run
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+ ```bash
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+ sphinx-apidoc -o doc_template/source/ src
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+ ```
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+ Then to create the documentation HTML files, run
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+ ```bash
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+ sphinx-build -b html doc_template/source/ doc_template/build/html
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+ ```
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+ More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
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+ # aind-dynamic-foraging-data-utils
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+
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+
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+ [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
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+ ![Code Style](https://img.shields.io/badge/code%20style-black-black)
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+ [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
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+ ![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
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+ ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
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+ ![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python)
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+
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+
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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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+
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+
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+
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+
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+ ## Installation
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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 .
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+ ```
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+
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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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+ ### Linters and testing
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+
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+ There are several libraries used to run linters, check documentation, and run tests.
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+
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+ - Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
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+
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+ ```bash
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+ coverage run -m unittest discover && coverage report
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+ ```
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+
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+ - Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
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+
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+ ```bash
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+ interrogate .
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+ ```
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+
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+ - Use **flake8** to check that code is up to standards (no unused imports, etc.):
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+ ```bash
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+ flake8 .
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+ ```
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+
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+ - Use **black** to automatically format the code into PEP standards:
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+ ```bash
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+ black .
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+ ```
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+
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+ - Use **isort** to automatically sort import statements:
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+ ```bash
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+ isort .
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+ ```
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+
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+ ### Pull requests
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+
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+ 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:
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+ ```text
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+ <type>(<scope>): <short summary>
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+ ```
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+
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+ where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
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+
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+ - **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
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+ - **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
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+ - **docs**: Documentation only changes
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+ - **feat**: A new feature
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+ - **fix**: A bugfix
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+ - **perf**: A code change that improves performance
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+ - **refactor**: A code change that neither fixes a bug nor adds a feature
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+ - **test**: Adding missing tests or correcting existing tests
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+
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+ ### Semantic Release
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+
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+ 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):
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+
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+ | Commit message | Release type |
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+ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
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+ | `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
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+ | `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
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+ | `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) |
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+
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+ ### Documentation
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+ To generate the rst files source files for documentation, run
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+ ```bash
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+ sphinx-apidoc -o doc_template/source/ src
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+ ```
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+ Then to create the documentation HTML files, run
99
+ ```bash
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+ sphinx-build -b html doc_template/source/ doc_template/build/html
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+ ```
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+ More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
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+ # Minimal makefile for Sphinx documentation
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+ #
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+
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+ # You can set these variables from the command line, and also
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+ # from the environment for the first two.
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+ SPHINXOPTS ?=
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+ SPHINXBUILD ?= sphinx-build
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+ SOURCEDIR = source
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+ BUILDDIR = build
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+
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+ # Put it first so that "make" without argument is like "make help".
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+ help:
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+ @$(SPHINXBUILD) -M help "$(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)