Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / hopkinsidd/flepimop issues and pull requests

#486 - Manifest JSON Writing Utility

Pull Request - State: open - Opened by TimothyWillard 15 days ago
Labels: enhancement, gempyor, batch, high priority, quick issue, next release

#485 - [Bug]: The `environment.yml` File Formatting

Issue - State: open - Opened by TimothyWillard 16 days ago
Labels: bug, low priority, quick issue, meta/workflow, installation, dependency

#484 - [Feature request]: Clear Warning From `gempyor.statistics.Statistic.llik` When Any Entries Are Not Finite

Issue - State: open - Opened by TimothyWillard 16 days ago - 3 comments
Labels: enhancement, gempyor, high priority, quick issue, inference

#483 - [Feature request]: Subset Statistics By Subpopulation/Date in `gempyor.statistics.Statistic`

Issue - State: open - Opened by TimothyWillard 16 days ago
Labels: enhancement, gempyor, config, medium priority, quick issue, inference

#483 - [Feature request]: Subset Statistics By Subpopulation/Date in `gempyor.statistics.Statistic`

Issue - State: open - Opened by TimothyWillard 16 days ago
Labels: enhancement, gempyor, config, medium priority, quick issue, inference

#482 - [Feature request]: NaN Handling Options For `gempyor.statistics.Statistics` For Ground Truth And Model Data

Issue - State: open - Opened by TimothyWillard 16 days ago
Labels: enhancement, gempyor, config, medium priority, inference

#482 - [Feature request]: NaN Handling Options For `gempyor.statistics.Statistics` For Ground Truth And Model Data

Issue - State: open - Opened by TimothyWillard 16 days ago
Labels: enhancement, gempyor, config, medium priority, inference

#481 - Consistent Xarray NaN To Int Coersion

Pull Request - State: closed - Opened by TimothyWillard 16 days ago - 3 comments
Labels: bug, gempyor, high priority, quick issue, inference

#480 - Purging `data_path` from flepiMoP

Pull Request - State: open - Opened by emprzy 16 days ago - 1 comment
Labels: documentation, medium priority, next release, cli

#479 - [Bug]: R CLI no longer consistent with config files

Issue - State: open - Opened by emprzy 16 days ago
Labels: bug, medium priority, cli

#478 - Expand Scalar Likelihoods Manually In `Statistics.llik`

Pull Request - State: closed - Opened by TimothyWillard 17 days ago - 3 comments
Labels: bug, gempyor, high priority, quick issue, inference

#477 - [Bug]: 'rmse' And 'absolute_error' Likelihoods Produce Scalars Instead Of Arrays In `Statistics.llik`

Issue - State: open - Opened by TimothyWillard 17 days ago
Labels: bug, gempyor, medium priority, inference

#476 - [Refactor]: regularize approach to relative path resolution

Issue - State: open - Opened by pearsonca 17 days ago
Labels: documentation, enhancement, medium priority, cli

#475 - [Feature request]: Install `flepiMoP` In GitHub Actions Using Install Scripts

Issue - State: open - Opened by TimothyWillard 17 days ago - 1 comment
Labels: low priority, meta/workflow, installation

#474 - [Feature request]: Run Unit Test CIs Against `main` (And `dev`) On A Crontab

Issue - State: open - Opened by TimothyWillard 17 days ago
Labels: low priority, quick issue, meta/workflow

#473 - [Bug]: gitbook initial conditions documentation

Issue - State: open - Opened by pearsonca 17 days ago
Labels: documentation, low priority

#472 - [Refactor]: purge deprecated configuration option `data_path`

Issue - State: open - Opened by pearsonca 18 days ago - 7 comments
Labels: documentation, config, high priority, docstring

#471 - Fix R CI Actions With Ubuntu 22 To 24 Update

Pull Request - State: closed - Opened by TimothyWillard 22 days ago - 1 comment
Labels: r-inference, high priority, meta/workflow, r-flepicommon

#470 - [Feature request]: Add Standardized Dry Run And Verbose Flags To All `flepimop` CLI Actions

Issue - State: open - Opened by TimothyWillard 23 days ago
Labels: enhancement, medium priority, cli

#469 - [Feature request]: Deprecate `gempyor.parameters.Parameters` Class In Favor Of Individual Parameter Classes

Issue - State: open - Opened by TimothyWillard 23 days ago - 1 comment
Labels: enhancement, gempyor, medium priority

#468 - `gempyor` API docstring refurbishment

Pull Request - State: open - Opened by emprzy 24 days ago - 1 comment
Labels: gempyor, high priority, quick issue, docstring, next release

#467 - [Feature request]: Split `gempyor.parameters.Parameters` Class Into Two

Issue - State: closed - Opened by TimothyWillard 24 days ago - 3 comments
Labels: enhancement, gempyor, medium priority

#462 - [Feature request]: Ensure docstring documentation exists in major sub-modules of `gempyor`

Issue - State: open - Opened by emprzy 29 days ago - 4 comments
Labels: documentation, gempyor, high priority, quick issue

#460 - flepimop.org documentation updates for information pertaining to new users

Pull Request - State: open - Opened by emprzy about 1 month ago - 4 comments
Labels: documentation, medium priority

#455 - Cluster Info

Pull Request - State: open - Opened by TimothyWillard about 1 month ago - 9 comments
Labels: enhancement, gempyor, batch, high priority, next release

#450 - [Feature request]: `flepimop sync` CLI Tool

Issue - State: open - Opened by TimothyWillard about 1 month ago
Labels: enhancement, low priority, cli

#449 - Release cycle, ? 2025

Pull Request - State: open - Opened by TimothyWillard about 1 month ago
Labels: low priority, next release

#429 - Random Draws For SEIR Parameters Per Slot

Pull Request - State: open - Opened by TimothyWillard about 2 months ago - 8 comments
Labels: bug, gempyor, medium priority

#428 - Adding `check_parameter_positivity()` function to `seir.py`

Pull Request - State: open - Opened by emprzy about 2 months ago - 5 comments
Labels: enhancement, gempyor, low priority, quick issue, next release

#410 - [Feature request]: Rewrite `examples/simple_usa_statelevel/inference_benchmark.ipynb` To Use Only Data In `flepiMoP`

Issue - State: open - Opened by TimothyWillard 2 months ago - 3 comments
Labels: documentation, gempyor, low priority

#401 - [Feature request]: User Local Install Documentation

Issue - State: open - Opened by TimothyWillard 3 months ago - 4 comments
Labels: documentation, high priority, installation, cli

#380 - [Bug]: Parsing error in modifiers/inference parameter (checking in bounds?)

Issue - State: closed - Opened by saraloo 3 months ago - 14 comments
Labels: bug, gempyor, low priority, quick issue, inference

#355 - [Feature request]: incorporate update / init capabilities into flepimop CLI

Issue - State: open - Opened by pearsonca 4 months ago - 1 comment
Labels: enhancement, batch, operations, cli

#355 - [Feature request]: incorporate update / init capabilities into flepimop CLI

Issue - State: open - Opened by pearsonca 4 months ago - 1 comment
Labels: enhancement, batch, operations, cli

#354 - [Feature request]: GitHub Action To Alert On Stale Branches

Issue - State: open - Opened by TimothyWillard 4 months ago
Labels: low priority, meta/workflow

#354 - [Feature request]: GitHub Action To Alert On Stale Branches

Issue - State: open - Opened by TimothyWillard 4 months ago
Labels: low priority, meta/workflow

#343 - [Feature request]: YAML Linting

Issue - State: open - Opened by TimothyWillard 4 months ago - 3 comments
Labels: enhancement, low priority, meta/workflow

#343 - [Feature request]: YAML Linting

Issue - State: open - Opened by TimothyWillard 4 months ago - 3 comments
Labels: enhancement, low priority, meta/workflow

#342 - [Feature request]: Generic Cluster Config

Issue - State: open - Opened by TimothyWillard 4 months ago - 2 comments
Labels: enhancement, good first issue, batch, low priority

#342 - [Feature request]: Generic Cluster Config

Issue - State: open - Opened by TimothyWillard 4 months ago - 2 comments
Labels: enhancement, good first issue, batch, low priority

#341 - [Feature request]: Add `set_zero_to` Field To Individual Statistics Entries In Config

Issue - State: open - Opened by TimothyWillard 4 months ago
Labels: enhancement, gempyor, r-inference, low priority, quick issue

#341 - [Feature request]: Add `set_zero_to` Field To Individual Statistics Entries In Config

Issue - State: open - Opened by TimothyWillard 4 months ago
Labels: enhancement, gempyor, r-inference, low priority, quick issue

#335 - [Bug]: gitbook usage

Issue - State: open - Opened by pearsonca 4 months ago
Labels: bug, documentation, low priority, meta/workflow

#335 - [Bug]: gitbook usage

Issue - State: open - Opened by pearsonca 4 months ago
Labels: bug, documentation, low priority, meta/workflow

#332 - [Bug]: Upgrade `flepicommon`'s `covidcast` Dependency To `epidatr`

Issue - State: open - Opened by TimothyWillard 4 months ago - 3 comments
Labels: bug, medium priority, quick issue, dependency

#332 - [Bug]: Upgrade `flepicommon`'s `covidcast` Dependency To `epidatr`

Issue - State: open - Opened by TimothyWillard 4 months ago - 3 comments
Labels: bug, medium priority, quick issue, dependency

#322 - [Feature request]: Harmonize EMCEE files saved to be exactly similar that classical inference

Issue - State: open - Opened by jcblemai 5 months ago - 1 comment
Labels: enhancement, gempyor, r-inference, high priority, inference

#322 - [Feature request]: Harmonize EMCEE files saved to be exactly similar that classical inference

Issue - State: open - Opened by jcblemai 5 months ago - 1 comment
Labels: enhancement, gempyor, r-inference, high priority, inference

#290 - Convert `as_random_distribution` To Use `scipy.stats` Distributions

Issue - State: open - Opened by TimothyWillard 6 months ago - 2 comments
Labels: enhancement, gempyor, medium priority

#275 - Remove `path_prefix` Argument From `Parameters` Class

Issue - State: open - Opened by TimothyWillard 6 months ago - 2 comments
Labels: gempyor, low priority

#274 - Support Xarray In `gempyor.parameters.Parameters`

Issue - State: open - Opened by TimothyWillard 6 months ago
Labels: enhancement, gempyor, low priority

#265 - Mobility model only applied if more than one disease state in `proportional_to`

Issue - State: open - Opened by twallema 7 months ago - 1 comment
Labels: enhancement, gempyor, medium priority

#265 - Mobility model only applied if more than one disease state in `proportional_to`

Issue - State: open - Opened by twallema 7 months ago - 1 comment
Labels: enhancement, gempyor, medium priority

#263 - Website upgrades

Issue - State: open - Opened by jcblemai 7 months ago
Labels: medium priority, meta/workflow

#257 - Model Output File Management Class For `gempyor`

Issue - State: open - Opened by TimothyWillard 7 months ago - 6 comments
Labels: enhancement, gempyor, low priority

#256 - Move hardcoded `percent_day_away=0.5` to config file

Issue - State: open - Opened by twallema 7 months ago - 2 comments
Labels: enhancement, gempyor, medium priority

#236 - Reintroduce Dual Likelihood (Chimeric/Global) Parameter Inference To `gempyor`

Issue - State: open - Opened by TimothyWillard 8 months ago
Labels: enhancement, gempyor, r-inference, low priority

#213 - sunset calls to create_seeding.R within inference

Issue - State: open - Opened by alsnhll 10 months ago - 1 comment
Labels: r-inference, low priority

#196 - Write Unit Tests for inference_slot.R and inference_main.R

Issue - State: open - Opened by shauntruelove 11 months ago - 2 comments
Labels: bug, good first issue, r-inference, low priority

#192 - Split-up the batchs scripts in commands

Issue - State: open - Opened by jcblemai 11 months ago - 1 comment
Labels: enhancement, good first issue, batch, cli

#191 - make the batch submisson cluster agnostic

Issue - State: open - Opened by jcblemai 11 months ago - 5 comments
Labels: batch, high priority

#183 - Inference: File writing with all initial conditions options

Issue - State: open - Opened by saraloo 11 months ago - 4 comments
Labels: r-inference, high priority

#183 - Inference: File writing with all initial conditions options

Issue - State: open - Opened by saraloo 11 months ago - 4 comments
Labels: r-inference, high priority

#171 - Explore addition of Explicit Contact Matrices

Issue - State: open - Opened by shauntruelove 12 months ago - 3 comments
Labels: enhancement, gempyor, config, medium priority

#163 - Revise R tests to make the breaking ones work once we merge.

Issue - State: open - Opened by shauntruelove about 1 year ago
Labels: bug, high priority

#160 - Change `VALIDATION_DATE` to `FORECAST_DATE`

Issue - State: open - Opened by jcblemai about 1 year ago
Labels: gempyor, r-inference, config, low priority

#150 - Config fails when there are no parameters

Issue - State: open - Opened by saraloo about 1 year ago
Labels: bug, gempyor, low priority

#146 - Add functionality to run subpops fully independently in same config

Issue - State: open - Opened by shauntruelove about 1 year ago - 1 comment
Labels: enhancement, r-inference, low priority

#145 - Gempyor check for unused config arguments

Issue - State: open - Opened by jcblemai about 1 year ago - 1 comment
Labels: enhancement, gempyor, config, medium priority

#144 - Consistent behaviour for seeding when the source is zero

Issue - State: open - Opened by jcblemai about 1 year ago - 1 comment
Labels: bug, gempyor, high priority, seeding

#139 - remove time column from hosp model_output - already have date

Issue - State: open - Opened by alsnhll about 1 year ago
Labels: enhancement, low priority

#138 - add more checks/warnings on inference, re likelihoods + data aggregation

Issue - State: open - Opened by alsnhll about 1 year ago - 1 comment
Labels: enhancement, r-inference, low priority

#138 - add more checks/warnings on inference, re likelihoods + data aggregation

Issue - State: open - Opened by alsnhll about 1 year ago - 1 comment
Labels: enhancement, r-inference, low priority

#134 - Need to strip inference and flepimop in general of all US/COVID specific references

Issue - State: open - Opened by alsnhll about 1 year ago - 1 comment
Labels: documentation, good first issue, config, low priority

#134 - Need to strip inference and flepimop in general of all US/COVID specific references

Issue - State: open - Opened by alsnhll about 1 year ago - 1 comment
Labels: documentation, good first issue, config, low priority

#133 - inference:simulations_per_slot config option never used

Issue - State: open - Opened by alsnhll about 1 year ago
Labels: bug, r-inference, medium priority

#132 - inference does not work unless seeding perturbations are specified

Issue - State: open - Opened by alsnhll about 1 year ago - 1 comment
Labels: bug, r-inference, low priority, quick issue

#131 - add config option in header to run scripts before any aspect of model run

Issue - State: open - Opened by alsnhll about 1 year ago - 2 comments
Labels: enhancement, good first issue, low priority, quick issue

#125 - Multiple problems with timeseries parameters

Issue - State: open - Opened by alsnhll over 1 year ago - 1 comment
Labels: bug, medium priority

#124 - gempyor is creating snpi director in model_output even when there is no seir_modifier section in the config

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: enhancement, good first issue, low priority

#120 - Clarify form of "Force of Infection" and general higher-order transitions in flepimop

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: documentation, medium priority

#120 - Clarify form of "Force of Infection" and general higher-order transitions in flepimop

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: documentation, medium priority

#117 - change seeding options in config and writer - flu and breaking_improvements

Issue - State: open - Opened by shauntruelove over 1 year ago - 1 comment
Labels: bug, medium priority

#110 - Add ability to simulate stochastic/individual outcomes

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: enhancement, medium priority

#110 - Add ability to simulate stochastic/individual outcomes

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: enhancement, medium priority

#108 - Documentation: explain compartments structure

Issue - State: open - Opened by jcblemai over 1 year ago - 1 comment
Labels: documentation, low priority

#108 - Documentation: explain compartments structure

Issue - State: open - Opened by jcblemai over 1 year ago - 1 comment
Labels: documentation, low priority

#104 - Document and streamline the continuation workflow

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: documentation, batch, medium priority

#104 - Document and streamline the continuation workflow

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: documentation, batch, medium priority

#103 - Document simplified parameters

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: documentation, low priority

#102 - Gempyor handle file handling propagation for inference run:

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: gempyor, batch, medium priority

#101 - Allow post and pre-computation plug-in

Issue - State: closed - Opened by jcblemai over 1 year ago - 5 comments
Labels: gempyor, medium priority

#101 - Allow post and pre-computation plug-in

Issue - State: closed - Opened by jcblemai over 1 year ago - 5 comments
Labels: gempyor, medium priority

#100 - Phase out outcomes subclasses

Issue - State: closed - Opened by jcblemai over 1 year ago - 2 comments
Labels: good first issue, gempyor, low priority

#100 - Phase out outcomes subclasses

Issue - State: closed - Opened by jcblemai over 1 year ago - 2 comments
Labels: good first issue, gempyor, low priority

#99 - Stochastic subpopulation movement

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: enhancement, gempyor, medium priority

#98 - Standardize the management of credentials

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: batch, low priority

#97 - Remove mentions of `incidI`

Issue - State: closed - Opened by jcblemai over 1 year ago - 1 comment
Labels: gempyor, low priority, quick issue

#97 - Remove mentions of `incidI`

Issue - State: closed - Opened by jcblemai over 1 year ago - 1 comment
Labels: gempyor, low priority, quick issue

#96 - Outcomes: allow `param_from_file` to be omitted

Issue - State: closed - Opened by jcblemai over 1 year ago - 1 comment
Labels: gempyor, medium priority, quick issue