https://github.com/alleninstitute/dynamic_routing_analysis
Tools for accessing, processing and presenting data from Dynamic Routing experiments.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 5 committers (40.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Keywords from Contributors
Repository
Tools for accessing, processing and presenting data from Dynamic Routing experiments.
Basic Info
Statistics
- Stars: 2
- Watchers: 5
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
dynamicroutinganalysis
installation
- clone the dynamicroutinganalysis repo
- create a new environment with python=3.11.5
bash conda create -n dr_analysis python=3.11.5 - navigate to the folder where you cloned the repo
- activate your new environment
bash conda activate dr_analysis - Optional: if you want to plot on the CCF, install allensdk (not necessary for other analyses; workaround to override some of allensdk's deps with dynamicroutinganalysis deps)
bash pip install allensdk - install remaining dependencies from requirements.txt file
bash pip install -r requirements.txt - install dynamicroutinganalysis in editable mode
bash pip install -e .
contributing
first-time capsule use
- duplicate the dev capsule https://codeocean.allenneuraldynamics.org/capsule/3127916
- attach AWS and GitHub credentials (requires an access token)
- fire up VSCode
- pull from origin/main, activate and update the dev venv outside of conda:
bash conda deactivate source install.sh - verify that the venv is activated in VSCode
- `Ctrl+Shift+P` and start typing any part of `Python: Select Interpreter`
- the interpreter should be set to `Python 3.9.12 ('.venv': venv) ./.venv/bin/python`
- if that's not an option, hit the refresh button
- if it still doesn't appear, hit `Enter interpreter path...` and enter `./.venv/bin/python`
verify that the venv is activated in a new terminal
[Ctrl+Shift+`]the folder name and Python version should be indicated on the command line (e.g.
dra-3.9):shell (dra-3.9) root@c5876abdc7b5:/code/dra# |
capsule re-use
- Make sure to check for updates in the source control tab in VSCode
[Ctrl+Shift+G]and pull where appropriate - Update the venv in a terminal with
shell pdm update
adding/removing dependencies
when adding, this method will find a compatible version of the dependency, based on the package's Python version requirement and other existing dependencies
the dependency will be added/removed from:
- pyproject.toml, which specifies required dependencies
- the currently-activated dev venv
- if removed, all of its sub-dependencies will also be removed
- pdm.lock, which specifies the dev venv
- commit any changes to the
pdm.lockto signal updates to the common dev venv - if you're unsure if your lock file is correct, run
pdm update- this will add add the most up-to-date versions of dependencies specifed in pyproject.toml - if your venv is broken, delete the
.venvfolder and re-install
- commit any changes to the
For dependencies of the package itself (ie. needed for code within dynamic_routing_analysis):
shell
pdm add numpy pandas
pdm remove numpy pandas
For dependencies needed for development of the package (ie. testing, linting, formatting, static type-analysis):
shell
pdm add -G dev mypy pytest
pdm remove -G dev mypy pytest
updating dependencies
If we specify only a lower bound on a dependency (e.g. pandas >= 2.0), any new install of dynamic_routing_analysis will also install the latest version of pandas.
To make sure that the latest versions of dependencies don't introduce breaking changes, we should update the dev venv periodically by running pdm update and running any tests, then committing pdm.lock.
More info on pdm and the lock file: https://pdm.fming.dev/latest/usage/dependency/#install-the-packages-pinned-in-lock-file
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Watch event: 1
- Push event: 228
- Create event: 1
Last Year
- Watch event: 1
- Push event: 228
- Create event: 1
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| egmcbride | e****e@g****m | 182 |
| Shailaja Akella | s****3@u****u | 138 |
| bjhardcastle | b****e@a****g | 110 |
| shawn | 3****n | 2 |
| github-actions | 4****] | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 0
- Total pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: about 6 hours
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- bjhardcastle (3)
- arjunsridhar12345 (1)