Release cycle, ? 2025 #449
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Removed the `picklable_lamda_alpha` and `picklable_lamda_sigma` methods from the `Parameters` class.
Created two files (`local-installation.md` and `local_install_or_update.sh`) that will likely make it easier for new flepiMoP users to install flepiMoP onto their machine.
* Added explicit exports, * Reordered imports, * Added general structure comments, and * Refactored all lines to be less than 92 characters.
Remvoed the `modinf` arg from the `_DataFrame2NumbaDict` internal utility and replaced it with the individual attributes from the `modinf` object that are needed.
Untangled the `Seeding` class from the `ModelInfo` class by adding a method to `ModelInfo` that interfaces with the `Seeding` class.
Updated remaining references in inactive code, notebooks and the `gempyor.dev` module.
Functionality to render jinja2 templates to make creating batch files easier. Also opens up the door to future use of templates like creating config files. Associated docs+tests included.
Attempt to fix Jinja2 lader issue by falling back to a file system loader if a package loader fails.
Added `gempyor.logging` module with `_get_logging_level`, `get_script_logger`, and `ClickHandler` along with corresponding documentation and unit tests.
Pytest hooks into the root logger, which breaks the use case here where we only want a single handler to emit a log record. Create a special carve out for pytest and put it in `get_script_logger` to make testing logging results of any function easy.
User local installation documentation and bash script
Added a helper to log the inputs given to a CLI tool when the verbosity is set to debug. Mostly for user/dev debugging. Also added corresponding docs and unit tests.
Added the `DurationParamType` for specifying custom durations in a user friendly way for CLI interfaces along with corresponding unit tests.
Also added unit tests, but still need to add documentation.
Fleshed out documentation for the `gempyor.shared_cli` module. Added the ability to optionally return the converted memory as an int instead of as a float to `MemoryParamType`. Removed pre-instantiated custom click param types.
Bug in `MemoryParamType.convert` was failing if a unit was not given with a value. Similar to `DurationParamType` it assumes that numbers without a unit are given in the default unit of the type.
TimothyWillard
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Per @pearsonca request: * Only use the `PackageLoader` for setting up the jinja environment. * Removed `gempyor._jinja._get_template/_render_template`.
* Per @pearsonca, @jcblemai suggestions call positional arguements with names. * Restyle call to `get_seeding_data` in `gempyor.seir.onerun_SEIR`.
* Added parameters to explicitly control the behavior of unitless values to both `DurationParamType` and `MemoryParamType`. * Fleshed out documentation for custom types.
Extracted `DurationParamType` and `MemoryParamType` out of `gempyor.shared_cli` into `gempyor._click`.
Initial Logging Infrastructure
Remove Dead Methods From `gempyor.parameters.Parameters`
Jinja2 Templating Infra
…-types Duration/Memory Convenience Click Types
…pendence-on-modinf Remove `gempyor.seeding` Dependence On `gempyor.model_info.ModelInfo`
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Description
This PR is a running accumulation of changes to merge from
devintomainthat will be merged at a to be decided release cycle.News
Breaking Changes
picklable_lamda_alpha/sigmamethods from thegempyor.parameters.Parametersclass, Remove Dead Methods Fromgempyor.parameters.Parameters#414.modinfargument toget_from_config/get_from_filemethods ofgempyor.seeding.Seedingclass with individual arguments pulled from model info, Removegempyor.seedingDependence Ongempyor.model_info.ModelInfo#422.New Features
conda, similar to HPC installs, is now the recommended and documented/scripted method, User local installation documentation and bash script #418.gempyor.loggingfor consistent output across CLI tools, Initial Logging Infrastructure #447.get_seeding_datamethod togempyor.model_info.ModelInfoclass, Removegempyor.seedingDependence Ongempyor.model_info.ModelInfo#422.Bug Fixes
Notes