From 6c09acc4b0eaa1f0cab48a3c56308daeef5de46e Mon Sep 17 00:00:00 2001 From: Kristan Reed Date: Tue, 24 Feb 2026 14:38:31 -0500 Subject: [PATCH 1/6] corrects typos in changelog --- changelog.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/changelog.md b/changelog.md index 5c892adf6f..b45d0d7fef 100644 --- a/changelog.md +++ b/changelog.md @@ -282,11 +282,11 @@ v0.9.2 - [2655](https://github.com/RuminantFarmSystems/MASM/pull/2655) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated RationManager class to allow for more flexibility in user inputs in Feed input file. - [2670](https://github.com/RuminantFarmSystems/MASM/pull/2670) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated Animal module unit testing to 100% coverage. - [2673](https://github.com/RuminantFarmSystems/MASM/pull/2673) - [minor change] [Feed] [InputChange] [NoOutputChange] Adds a default for purchased feed buffer of 0.15. -- [2678](https://github.com/RuminantFarmSystems/MASM/pull/2678) - [minor change] [Feed] [InputChange] [OutputChange] Removes default reporting 0.0s for FGFs that aren't grown during a simulation. + - [2675](https://github.com/RuminantFarmSystems/MASM/pull/2675) - [minor change] [DataValidator] [NoInputChange] [NoOutputChange] Fixes and clarifies data fixing error messaging for IM. -- [2676](https://github.com/RuminantFarmSystems/MASM/pull/2673) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Corrects a bug in Separators and adds a check to prevent a bug in Slurry Storage Outdoor, Slurry Storage Underfloor, and Anaerobic Lagoon. - [2674](https://github.com/RuminantFarmSystems/MASM/pull/2674) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Prevent simulation fails when metadata blobs for fields/manure/harvest does not exist. -- [2676](https://github.com/RuminantFarmSystems/MASM/pull/2676) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Corrects a bug in Separators and adds a check to prevent a bug in Slurry Storage Outdoor, Slurry Storage Underfloor, and Anaerobic Lagoon. +- [2678](https://github.com/RuminantFarmSystems/MASM/pull/2678) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Corrects a bug in Separators and adds a check to prevent a bug in Slurry Storage Outdoor, Slurry Storage Underfloor, and Anaerobic Lagoon. +- [2679](https://github.com/RuminantFarmSystems/MASM/pull/2678) - [minor change] [Feed] [NoInputChange] [OutputChange] Removes default reporting 0.0s for FGFs that aren't grown during a simulation - [2688](https://github.com/RuminantFarmSystems/MASM/pull/2688) - [minor change] [InputManager] [NoInputChange] [NoOutputChange] Hot fix to correct the missing part of 2640. - [2689](https://github.com/RuminantFarmSystems/MASM/pull/2689) - [minor change] [InputManager] [InputChange] [NoOutputChange] Add support for multiple properties files. - [2701](https://github.com/RuminantFarmSystems/MASM/pull/2701) - [minor change] [EEEManager] [NoInputChange] [NoOutputChange] Hot fix to correct the failure in EEEManager.. From 99517902fae1dda1ba034ef00d8bd270208ff4bf Mon Sep 17 00:00:00 2001 From: Pooya Hekmati Date: Wed, 4 Mar 2026 12:22:07 -0500 Subject: [PATCH 2/6] update MASM to RuFaS --- changelog.md | 538 +++++++++++++++++++++++++-------------------------- 1 file changed, 269 insertions(+), 269 deletions(-) diff --git a/changelog.md b/changelog.md index b45d0d7fef..dac453c7bc 100644 --- a/changelog.md +++ b/changelog.md @@ -13,7 +13,7 @@ A **changelog** is a structured record of changes made to the codebase over time ### Example Entry -- [123](https://github.com/RuminantFarmSystems/MASM/pull/123) - [Major change/ minor change] [Impact Area] Short description of the change or feature. +- [123](https://github.com/RuminantFarmSystems/RuFaS/pull/123) - [Major change/ minor change] [Impact Area] Short description of the change or feature. --- @@ -24,157 +24,157 @@ A **changelog** is a structured record of changes made to the codebase over time v0.9.2 ### Next Version Updates -- [2081](https://github.com/RuminantFarmSystems/MASM/pull/2081) - [minor change] [Crop & Soil] Break down the `_setup_field()` function in `FieldManager`. -- [2011](https://github.com/RuminantFarmSystems/MASM/pull/2011) - [minor change] [Animal] Implements the Animal Growth submodule logic and tests. -- [2021](https://github.com/RuminantFarmSystems/MASM/pull/2021) - [minor change] [Animal] **Adds dependency**. Creates a new `MilkProduction` submodule and several support submodules to calculate milk production. -- [2022](https://github.com/RuminantFarmSystems/MASM/pull/2022) - [minor change] [Manure] Removes DefaultEnum class and all references to it in the Manure module. -- [2006](https://github.com/RuminantFarmSystems/MASM/pull/2006) - [minor change] [Manure] Adds a method to determine storage manure temperature based on outdoor air temperature for use in calculations of emissions associated with Manure Storages. -- [2023](https://github.com/RuminantFarmSystems/MASM/pull/2023) - [minor change] [Manure] Fixes calculation of organic bedding dry solids added to manure in manure handler. -- [2025](https://github.com/RuminantFarmSystems/MASM/pull/2025) - [minor change] [Formatting] Sorts import statements in codebase. -- [2004](https://github.com/RuminantFarmSystems/MASM/pull/2004) - [minor change] [Animal] Implement the animal digestive system in the biophysical folder. -- [2017](https://github.com/RuminantFarmSystems/MASM/pull/2017) - [minor change] [Animal] Deduplicates references to lactation parameters in the `LactationCurve` submodule and reorganizes structure to be consistent with other animal submodules. -- [1985](https://github.com/RuminantFarmSystems/MASM/pull/1985) - [minor change] [TaskManager] extracts all the input data values (for all input variables from JSON input files) for each task and combines them into a single CSV file for side-by-side comparison. -- [2029](https://github.com/RuminantFarmSystems/MASM/pull/2029) - [minor change] [EEE] Adding tests for emission.py (2/2) -- [2031](https://github.com/RuminantFarmSystems/MASM/pull/2031) - [minor change] [Formatting] Changes all relative import statements that import from higher-level modules to be absolute import statements. -- [2032](https://github.com/RuminantFarmSystems/MASM/pull/2032) - [minor change] [Soil] Change the daily routine sequence to prevent unrealistic decomposition. -- [2033](https://github.com/RuminantFarmSystems/MASM/pull/2033) - [minor change] [InputManager] Consolidate methods for adding data to the Input Manager at runtime. -- [2039](https://github.com/RuminantFarmSystems/MASM/pull/2039) - [minor change] [Animal][Testing] Renames AnimalNutrients to Nutrients and adds full unit testing coverage for this class. -- [2014](https://github.com/RuminantFarmSystems/MASM/pull/2014) - [minor change] [Feed Storage] Fixes the Feed Storage mass degradation routines to properly account for mass and moisture loss, and updates E2E test suite to test these changes. -- [2054](https://github.com/RuminantFarmSystems/MASM/pull/2054) - [minor change] [e2e Testing] Adding end-to-end testing coverage for the Crop and Soil module. -- [1575](https://github.com/RuminantFarmSystems/MASM/pull/1575) - [minor change] [OutputManager] Adds options to periodically dump variables pool to a JSON file to help manage the size of the pool during a simulation. -- [2047](https://github.com/RuminantFarmSystems/MASM/pull/2047) - [minor change] [Soil and Crop] Break down methods in the fields_data_reporter into smaller and more specific methods. -- [1945](https://github.com/RuminantFarmSystems/MASM/pull/1945) - [minor change] [Animal] Implements Animal Genetics submodule. -- [2048](https://github.com/RuminantFarmSystems/MASM/pull/2048) - [minor change] [Animal][Testing] Adds end to end testing for Animal domain. -- [1809](https://github.com/RuminantFarmSystems/MASM/pull/1809) - [minor change] [InputManager] Extract the validation methods from InputManager. -- [2045](https://github.com/RuminantFarmSystems/MASM/pull/2045) - [minor change] [Documentation] Regenerates the Sphinx HTML documentation. -- [2050](https://github.com/RuminantFarmSystems/MASM/pull/2050) - [minor change] [Crop & Soil][Feed Storage] Disentangle the Crop & Soil and Feed Storage modules. -- [2061](https://github.com/RuminantFarmSystems/MASM/pull/2061) - [minor change] [DataValidator] Removed the usage of OutputManager in DataValidator. -- [2057](https://github.com/RuminantFarmSystems/MASM/pull/2057) - [minor change] [Crop & Soil][Manure] Disentangle the Crop & Soil and Manure modules. -- [2059](https://github.com/RuminantFarmSystems/MASM/pull/2059) - [minor change] [Crop & Soil][GeneralConstants] Update references to constants in Crop and Soil module to use GeneralConstants. -- [1866](https://github.com/RuminantFarmSystems/MASM/pull/1866) - [minor change] [Metadata] Adds minimums for some Animal module inputs in metadata. -- [2066](https://github.com/RuminantFarmSystems/MASM/pull/2066) - [minor change] [OutputManager] Handles data origins info and enables user control over reporting detail levels. -- [2069](https://github.com/RuminantFarmSystems/MASM/pull/2069) - [minor change] [Crop & Soil] Flatten the units in SC module. -- [2076](https://github.com/RuminantFarmSystems/MASM/pull/2076) - [minor change] [Crop & Soil] Removes TODOs from the Crop & Soil module. -- [1785](https://github.com/RuminantFarmSystems/MASM/pull/1785) - [minor change] [TaskManager] Adds sobol and morris samplers, updates argument names. -- [2093](https://github.com/RuminantFarmSystems/MASM/pull/2093) - [minor change] [Testing] Increases tolerance level for comparing values changed in E2E testing results comparisons. -- [2091](https://github.com/RuminantFarmSystems/MASM/pull/2091) - [minor change] [Crop and Soil] Adding LAI errors to OM before throwing errors. -- [2070](https://github.com/RuminantFarmSystems/MASM/pull/2070) - [minor change] [Crop & Soil] Restructure schedule class in the crop and soil module. -- [2086](https://github.com/RuminantFarmSystems/MASM/pull/2086) - [minor change] [Animal] Updates default parity fraction. -- [2118](https://github.com/RuminantFarmSystems/MASM/pull/2118) - [minor change] [Crop and Soil] Removed the usage of input validation methods in HeatUnits. -- [2090](https://github.com/RuminantFarmSystems/MASM/pull/2090) - [minor change] [Crop & Soil] Restructures CropData class. -- [1836](https://github.com/RuminantFarmSystems/MASM/pull/1836) - [minor change] [Feed] Updates default prices in default_feed.json using average prices sourced by Kristan (detailed in sheet in PR). -- [2119](https://github.com/RuminantFarmSystems/MASM/pull/2119) - [minor change] [OutputManager] Make the log routing usable by other modules. -- [2046](https://github.com/RuminantFarmSystems/MASM/pull/2046) - [major change] [Data Collection App] Integrates the Data Collection App into the RuFaS repository and adds a RuFaS task type to update it. -- [2132](https://github.com/RuminantFarmSystems/MASM/pull/2132) - [major change] [Feed Storage] Fixing the nutrient loss of crude protein in hay during end-to-end testing -- [2075](https://github.com/RuminantFarmSystems/MASM/pull/2075) - [minor change] [Readme] Adds project goals for RuFaS year 2024 - 2025 -- [2067](https://github.com/RuminantFarmSystems/MASM/pull/2067) - [minor change] [EEE] Adds updated feeds emissions sheets, which replaces 0s with the average of neighboring FIPS codes. -- [2150](https://github.com/RuminantFarmSystems/MASM/pull/2150) - [minor change] [Manure] Allow users to have more control over whether how synthetic fertilizers are used. -- [2120](https://github.com/RuminantFarmSystems/MASM/pull/2120) - [minor change] [Crop and Soil] Log errors to OM before throwing errors in NitrogenIncorporation. -- [2143](https://github.com/RuminantFarmSystems/MASM/pull/2143) - [minor change] [GraphGenerator] Add user option to set time on x-axis for graphs. -- [2133](https://github.com/RuminantFarmSystems/MASM/pull/2133) - [minor change] [Animal] Use closest available genetic data for animals entering the herd or being initialized as calves. -- [2149](https://github.com/RuminantFarmSystems/MASM/pull/2149) - [minor change] [Crop and Soil] Relocates TillageImplements to data structures dir. -- [2137](https://github.com/RuminantFarmSystems/MASM/pull/2137) - [minor change] [Feed] Make post_wilting_moisture_percentage and user input. -- [2155](https://github.com/RuminantFarmSystems/MASM/pull/2155) - [minor change] [Git Actions] Added default data paths tp the protected list. -- [2156](https://github.com/RuminantFarmSystems/MASM/pull/2156) - [minor change] [Feed] Fixed test_process_degradations in test_silage.py. -- [2134](https://github.com/RuminantFarmSystems/MASM/pull/2134) - [minor change] [Crop & Soil] Adds ammonium fraction to fertilizer mixes input. -- [2136](https://github.com/RuminantFarmSystems/MASM/pull/2136) - [minor change] [Animal] Adds data structures to support calculation of animal nutrient requirements and supply. -- [2138](https://github.com/RuminantFarmSystems/MASM/pull/2138) - [minor change] [Animal] Refreshes module which calculates the nutrients supplied to an animal by a ration. -- [2128](https://github.com/RuminantFarmSystems/MASM/pull/2128) - [minor change] [Animal] Updates culling-related metadata descriptions -- [2162](https://github.com/RuminantFarmSystems/MASM/pull/2162) - [minor change] [Data Collection App] Replace the usage of PROPERTIES_TO_CREATE_SCHEMA_FOR with property's boolean field "data_collection_app_compatible". -- [2164](https://github.com/RuminantFarmSystems/MASM/pull/2128) - [minor change] [GraphGenerator] Aligns graphs with alphabetized, user-customized GG legend. -- [2141](https://github.com/RuminantFarmSystems/MASM/pull/2141) - [minor change] [Animal] Refreshes module which calculates the nutrition requirements of an animal with the NASEM (2021) methodology. -- [2142](https://github.com/RuminantFarmSystems/MASM/pull/2142) - [minor change] [Animal] Refreshes module which calculates the nutrition requirements of an animal with the NRC (2001) methodology. -- [2144](https://github.com/RuminantFarmSystems/MASM/pull/2144) - [minor change] [Animal] Refreshes module which evaluates if the nutrition supply of a ration satisfies the demand of animal or the average demand of a group of animals. -- [2165](https://github.com/RuminantFarmSystems/MASM/pull/2165) - [minor change] [Crop and Soil] Reorganize logic of crop's nutrient uptake routines. -- [2161](https://github.com/RuminantFarmSystems/MASM/pull/2161) - [minor change] [Animal] Refreshes calf nutrition intake and requirement routines. -- [2171](https://github.com/RuminantFarmSystems/MASM/pull/2171) - [minor change] [Animal] Allows users to supplement manure NutrientRequest shortfalls with external manure. -- [2172](https://github.com/RuminantFarmSystems/MASM/pull/2172) - [minor change] [Data Collection App] Makes TaskManager Tasks a type of input that can be collected with the Data Collection App. -- [2180](https://github.com/RuminantFarmSystems/MASM/pull/2180) - [minor change] [Github][TaskManager] Updates Github Actions to use Python 3.12 and checks Python version with which the user is running the model. -- [2189](https://github.com/RuminantFarmSystems/MASM/pull/2189) - [minor change] [Testing] Sets up a new task to automatically regenerate E2E testing expected-results. -- [2187](https://github.com/RuminantFarmSystems/MASM/pull/2187) - [minor change] [Manure] Implements the refreshed manure stream. -- [2196](https://github.com/RuminantFarmSystems/MASM/pull/2196) - [minor change] [Inputs][Crop & Soil] Adds new input file for crop configurations and metadata properties for validating these configurations. Also includes the new file in existing metadata files. -- [2201](https://github.com/RuminantFarmSystems/MASM/pull/2201) - [minor change] [Inputs] Remove deprecated input files. -- [2179](https://github.com/RuminantFarmSystems/MASM/pull/2179) - [major change] [Crop] Makes crops configured entirely with user input. -- [2203](https://github.com/RuminantFarmSystems/MASM/pull/2203) - [minor change] [Time] Changed units of "Time.day" from "simulation day" to "julian day". -- [2206](https://github.com/RuminantFarmSystems/MASM/pull/2206) - [minor change] [Manure][Animal] Establishes PenManureData class and StreamType enum for Manure refresh. -- [2209](https://github.com/RuminantFarmSystems/MASM/pull/2209) - [minor change] [Manure] Fixes error found when attempting to record an empty ManureNutrientRequestResults. -- [2210](https://github.com/RuminantFarmSystems/MASM/pull/2210) - [minor change] [OutputManager] Refactor tests in test_output_manager.py to all use pytest-mock. -- [2205](https://github.com/RuminantFarmSystems/MASM/pull/2205) - [minor change] [Manure] Implements base manure Processor class. -- [2212](https://github.com/RuminantFarmSystems/MASM/pull/2212) - [minor change] [E2E Testing] Updates Feed Storage E2E Testing expected results. -- [2223](https://github.com/RuminantFarmSystems/MASM/pull/2223) - [minor change] [Weather] Updates weather metadata to add missing boundaries on some inputs. -- [2191](https://github.com/RuminantFarmSystems/MASM/pull/2191) - [minor change] [Documentation] Regenerate code documentation and structure. -- [2221](https://github.com/RuminantFarmSystems/MASM/pull/2221) - [minor change] [DCA] Added dropdowns for feed storage options. -- [2225](https://github.com/RuminantFarmSystems/MASM/pull/2225) - [minor change] [OutputManager] Adds ability for user to control significant digits of output. -- [2211](https://github.com/RuminantFarmSystems/MASM/pull/2211) - [minor change] [Data Collection App] Makes error messages specific and detailed when invalid input is entered into the Data Collection App. -- [2229](https://github.com/RuminantFarmSystems/MASM/pull/2229) - [minor change] [Emissions] Bug fix for date comparisons in emissions.py. -- [2230](https://github.com/RuminantFarmSystems/MASM/pull/2230) - [minor change] [Manure] Updates Manure metadata descriptions and ranges. -- [2237](https://github.com/RuminantFarmSystems/MASM/pull/2237) - [minor change] [Manure] Implemented base class for handler. -- [2234](https://github.com/RuminantFarmSystems/MASM/pull/2234) - [minor change] [Manure] Implements base manure Separator class. -- [2236](https://github.com/RuminantFarmSystems/MASM/pull/2236) - [minor change] [Testing] Changes E2E expected results update task to automatically update all expected results regardless of whether the old and new expected results differ. -- [2233](https://github.com/RuminantFarmSystems/MASM/pull/2233) - [minor change] [Manure] Adds a base manure Digester class. -- [2247](https://github.com/RuminantFarmSystems/MASM/pull/2247) - [minor change] [Crop & Soil] Fix the ZeroDivisionError for surface machine manure application. -- [2255](https://github.com/RuminantFarmSystems/MASM/pull/2255) - [minor change] [OutputManager] Fix the error reporting units properly to CSV OM files. -- [2269](https://github.com/RuminantFarmSystems/MASM/pull/2269) - [minor change] [Animal][Testing] Adds unit tests for Animal Repro. -- [2214](https://github.com/RuminantFarmSystems/MASM/pull/2214) - [minor change] [Manure] Adds a base manure Storage class. -- [2272](https://github.com/RuminantFarmSystems/MASM/pull/2272) - [minor change] [Animal][Testing] Adds test coverage for refreshed Ration and Nutrition modules. -- [2273](https://github.com/RuminantFarmSystems/MASM/pull/2273) - [minor change] [Manure] Re-implements the logic for Anaerobic Digestion. -- [2279](https://github.com/RuminantFarmSystems/MASM/pull/2279) - [minor change] [Animal][Testing] Adds test coverage for refreshed animal datatypes files. -- [2278](https://github.com/RuminantFarmSystems/MASM/pull/2278) - [minor change] [GraphGenerator] Adds Graph Generator logs mapping original variable name to how it appears in the graph legend -- [2280](https://github.com/RuminantFarmSystems/MASM/pull/2280) - [minor change] [Manure] Updates input configs for refreshed Separator class. -- [2298](https://github.com/RuminantFarmSystems/MASM/pull/2298) - [minor change] [Manure] Fixed failing tests in handler. -- [2235](https://github.com/RuminantFarmSystems/MASM/pull/2235) - [major change] [Animal] Refresh the Animal module. -- [2297](https://github.com/RuminantFarmSystems/MASM/pull/2297) - [minor change] [Animal] Fix the flake8 errors in the refreshed animal module and modify "HerdManager._gather_pen_history()" to optimize run time. -- [2308](https://github.com/RuminantFarmSystems/MASM/pull/2308) - [minor change] [Manure] Re-implement open lot storage. -- [2194](https://github.com/RuminantFarmSystems/MASM/pull/2194) - [minor change] [E2E Testing] Implement the functionality to convert the previous variable names to match the new variable name. -- [2310](https://github.com/RuminantFarmSystems/MASM/pull/2310) - [minor change] [Bug fix] Quick fix for errors introduced by PR #2194. -- [2306](https://github.com/RuminantFarmSystems/MASM/pull/2306) - [minor change] [Manure] Implement patches to manure refresh after the dev team discussion. -- [2302](https://github.com/RuminantFarmSystems/MASM/pull/2302) - [minor change] [Manure] Rename the ammonia emission output in Handler from "housing_ammonia_emissions" to "housing_ammonia_N_emissions". -- [2253](https://github.com/RuminantFarmSystems/MASM/pull/2253) - [minor change] [Manure] Implement parlor cleaning handler. -- [2311](https://github.com/RuminantFarmSystems/MASM/pull/2311) - [minor change] [Manure] Rename the ammonia emission output in Handler from "housing_ammonia_emissions" to "housing_ammonia_N_emissions". -- [2313](https://github.com/RuminantFarmSystems/MASM/pull/2313) - [minor change] [Manure] Reimplements Composting for Manure refresh. -- [2291](https://github.com/RuminantFarmSystems/MASM/pull/2291) - [minor change] [GraphGenerator] Expand the support datetime format options for GraphGenerator X-axis. -- [2285](https://github.com/RuminantFarmSystems/MASM/pull/2285) - [minor change] [Manure] Re-implements the logic for SlurryStorageOutdoor and SlurryStorageUnderfloor. -- [2282](https://github.com/RuminantFarmSystems/MASM/pull/2282) - [minor change] [Manure] Establishes manure Processor enum class. -- [2320](https://github.com/RuminantFarmSystems/MASM/pull/2320) - [minor change] [Manure] Fix determine_handler_cleaning_water_volume to be static. -- [2316](https://github.com/RuminantFarmSystems/MASM/pull/2316) - [minor change] [Animal][HerdFactory] Create User-defined directory for saving generated herd if not already exists. -- [2311](https://github.com/RuminantFarmSystems/MASM/pull/2311) - [minor change] [Project Build][Dependencies] Set the minimum required versions for all RuFaS dependencies specified in requirements.txt. -- [2315](https://github.com/RuminantFarmSystems/MASM/pull/2315) - [minor change] [Time] Rename `Time` to `RufasTime`. -- [2325](https://github.com/RuminantFarmSystems/MASM/pull/2325) - [minor change] [OutputManager] Fix class-name-reporting to Output Manager for a handful of variables. -- [2321](https://github.com/RuminantFarmSystems/MASM/pull/2321) - [minor change] [Animal] Fix ZeroDivision Error when No Calf in Pen . -- [2183](https://github.com/RuminantFarmSystems/MASM/pull/2183) - [minor change] [helpful_scripts] Removes now-deprecated files used to help develop sensitivity analysis methodology. Files archived and relevant info/graphics moved to scientific documentation. -- [2322](https://github.com/RuminantFarmSystems/MASM/pull/2322) - [minor change] [Github action] Make unauthorized files change check to log and trigger exit at the end of the second step. -- [2331](https://github.com/RuminantFarmSystems/MASM/pull/2331) - [minor change] [Github action] Fixing failed final check. -- [2333](https://github.com/RuminantFarmSystems/MASM/pull/2333) - [minor change] [Github action] Fixing failing final test by saving current branch name to a variable. -- [2314](https://github.com/RuminantFarmSystems/MASM/pull/2314) - [minor change] [Animal] Report Herd Summary Statistics for Starting Animal Population. -- [2332](https://github.com/RuminantFarmSystems/MASM/pull/2332) - [minor change] [Crop & Soil] Refactor `Field._execute_manure_application()` and increase test coverage of field.py to 100%. -- [2327](https://github.com/RuminantFarmSystems/MASM/pull/2327) - [minor change] [Animal] Reduces the number of warnings during a default simulation run. -- [2318](https://github.com/RuminantFarmSystems/MASM/pull/2318) - [minor change] [Manure] Step 1/3 for implementing the refreshed ManureManager: initialization process including input validation, creating processor instances, and populating the adjacency matrix. -- [2328](https://github.com/RuminantFarmSystems/MASM/pull/2318) - [minor change] [Manure] Re-implements the logic for compost bedded pack barn.. -- [2323](https://github.com/RuminantFarmSystems/MASM/pull/2323) - [minor change] [Animal] Removes day offset in report_sold_animal_information_sort_by_sell_day. -- [2342](https://github.com/RuminantFarmSystems/MASM/pull/2342) - [minor change] [Manure] Clean up shared constants across processor subclasses. -- [2292](https://github.com/RuminantFarmSystems/MASM/pull/2292) - [minor change] [Animal] Updates NASEM equations in calculation of gravid uterine weight and protein requirement in cases of negative uterine weight. -- [2335](https://github.com/RuminantFarmSystems/MASM/pull/2335) - [minor change] [OutputManager] Increase packaging of data sent to Output Manager. -- [2350](https://github.com/RuminantFarmSystems/MASM/pull/2350) - [minor change] [Testing] Updates end-to-end testing expected results. -- [2343](https://github.com/RuminantFarmSystems/MASM/pull/2343) - [minor change] [Manure Manager] Validate and traverse the adjacency matrix. -- [2338](https://github.com/RuminantFarmSystems/MASM/pull/2338) - [minor change] [Manure] Remove Unused Calculations in AnaerobicDigester. -- [2355](https://github.com/RuminantFarmSystems/MASM/pull/2355) - [minor change] [Manure] Fix Methane Leakage Calculation in ContinuousMix. -- [2336](https://github.com/RuminantFarmSystems/MASM/pull/2336) - [minor change] [Animal] Removes ability to add extra pens during simulation. Pens now overstock based on previous allocation algorithm and log warning. -- [2334](https://github.com/RuminantFarmSystems/MASM/pull/2334) - [minor change] [OutputManager] Add option to specify landscape or portrait layouts for CSVs. -- [2344](https://github.com/RuminantFarmSystems/MASM/pull/2344) - [minor change] [Soil and Crop] Update all the `add_variable()` calls in `FieldDataReporter` to include the data origins of each variable in its info_map. -- [2354](https://github.com/RuminantFarmSystems/MASM/pull/2354) - [minor change] [Soil and Crop] Debug Soil N Cycling and Field N2O emissions. -- [2351](https://github.com/RuminantFarmSystems/MASM/pull/2351) - [minor change] [Output Manager] Adds validations to report filter contents. -- [2370](https://github.com/RuminantFarmSystems/MASM/pull/2370) - [minor change] [Animal] Added console warning when using sexed semen for her initialization. -- [2371](https://github.com/RuminantFarmSystems/MASM/pull/2371) - [minor change] [ReportGenerator] Allow for RG aggregation of np.float()s -- [2340](https://github.com/RuminantFarmSystems/MASM/pull/2340) - [minor change] [Animal] Updates the structure of the Mitscherlich Model 3 to calculate enteric CH4 emissions. -- [2252](https://github.com/RuminantFarmSystems/MASM/pull/2252) - [minor change] [Animal] Adds logic to initialize herds using specific parity distributions. -- [2391](https://github.com/RuminantFarmSystems/MASM/pull/2391) - [minor change] [Crop and Soil] Ensures harvesting continues even if the crop is not used for feed. +- [2081](https://github.com/RuminantFarmSystems/RuFaS/pull/2081) - [minor change] [Crop & Soil] Break down the `_setup_field()` function in `FieldManager`. +- [2011](https://github.com/RuminantFarmSystems/RuFaS/pull/2011) - [minor change] [Animal] Implements the Animal Growth submodule logic and tests. +- [2021](https://github.com/RuminantFarmSystems/RuFaS/pull/2021) - [minor change] [Animal] **Adds dependency**. Creates a new `MilkProduction` submodule and several support submodules to calculate milk production. +- [2022](https://github.com/RuminantFarmSystems/RuFaS/pull/2022) - [minor change] [Manure] Removes DefaultEnum class and all references to it in the Manure module. +- [2006](https://github.com/RuminantFarmSystems/RuFaS/pull/2006) - [minor change] [Manure] Adds a method to determine storage manure temperature based on outdoor air temperature for use in calculations of emissions associated with Manure Storages. +- [2023](https://github.com/RuminantFarmSystems/RuFaS/pull/2023) - [minor change] [Manure] Fixes calculation of organic bedding dry solids added to manure in manure handler. +- [2025](https://github.com/RuminantFarmSystems/RuFaS/pull/2025) - [minor change] [Formatting] Sorts import statements in codebase. +- [2004](https://github.com/RuminantFarmSystems/RuFaS/pull/2004) - [minor change] [Animal] Implement the animal digestive system in the biophysical folder. +- [2017](https://github.com/RuminantFarmSystems/RuFaS/pull/2017) - [minor change] [Animal] Deduplicates references to lactation parameters in the `LactationCurve` submodule and reorganizes structure to be consistent with other animal submodules. +- [1985](https://github.com/RuminantFarmSystems/RuFaS/pull/1985) - [minor change] [TaskManager] extracts all the input data values (for all input variables from JSON input files) for each task and combines them into a single CSV file for side-by-side comparison. +- [2029](https://github.com/RuminantFarmSystems/RuFaS/pull/2029) - [minor change] [EEE] Adding tests for emission.py (2/2) +- [2031](https://github.com/RuminantFarmSystems/RuFaS/pull/2031) - [minor change] [Formatting] Changes all relative import statements that import from higher-level modules to be absolute import statements. +- [2032](https://github.com/RuminantFarmSystems/RuFaS/pull/2032) - [minor change] [Soil] Change the daily routine sequence to prevent unrealistic decomposition. +- [2033](https://github.com/RuminantFarmSystems/RuFaS/pull/2033) - [minor change] [InputManager] Consolidate methods for adding data to the Input Manager at runtime. +- [2039](https://github.com/RuminantFarmSystems/RuFaS/pull/2039) - [minor change] [Animal][Testing] Renames AnimalNutrients to Nutrients and adds full unit testing coverage for this class. +- [2014](https://github.com/RuminantFarmSystems/RuFaS/pull/2014) - [minor change] [Feed Storage] Fixes the Feed Storage mass degradation routines to properly account for mass and moisture loss, and updates E2E test suite to test these changes. +- [2054](https://github.com/RuminantFarmSystems/RuFaS/pull/2054) - [minor change] [e2e Testing] Adding end-to-end testing coverage for the Crop and Soil module. +- [1575](https://github.com/RuminantFarmSystems/RuFaS/pull/1575) - [minor change] [OutputManager] Adds options to periodically dump variables pool to a JSON file to help manage the size of the pool during a simulation. +- [2047](https://github.com/RuminantFarmSystems/RuFaS/pull/2047) - [minor change] [Soil and Crop] Break down methods in the fields_data_reporter into smaller and more specific methods. +- [1945](https://github.com/RuminantFarmSystems/RuFaS/pull/1945) - [minor change] [Animal] Implements Animal Genetics submodule. +- [2048](https://github.com/RuminantFarmSystems/RuFaS/pull/2048) - [minor change] [Animal][Testing] Adds end to end testing for Animal domain. +- [1809](https://github.com/RuminantFarmSystems/RuFaS/pull/1809) - [minor change] [InputManager] Extract the validation methods from InputManager. +- [2045](https://github.com/RuminantFarmSystems/RuFaS/pull/2045) - [minor change] [Documentation] Regenerates the Sphinx HTML documentation. +- [2050](https://github.com/RuminantFarmSystems/RuFaS/pull/2050) - [minor change] [Crop & Soil][Feed Storage] Disentangle the Crop & Soil and Feed Storage modules. +- [2061](https://github.com/RuminantFarmSystems/RuFaS/pull/2061) - [minor change] [DataValidator] Removed the usage of OutputManager in DataValidator. +- [2057](https://github.com/RuminantFarmSystems/RuFaS/pull/2057) - [minor change] [Crop & Soil][Manure] Disentangle the Crop & Soil and Manure modules. +- [2059](https://github.com/RuminantFarmSystems/RuFaS/pull/2059) - [minor change] [Crop & Soil][GeneralConstants] Update references to constants in Crop and Soil module to use GeneralConstants. +- [1866](https://github.com/RuminantFarmSystems/RuFaS/pull/1866) - [minor change] [Metadata] Adds minimums for some Animal module inputs in metadata. +- [2066](https://github.com/RuminantFarmSystems/RuFaS/pull/2066) - [minor change] [OutputManager] Handles data origins info and enables user control over reporting detail levels. +- [2069](https://github.com/RuminantFarmSystems/RuFaS/pull/2069) - [minor change] [Crop & Soil] Flatten the units in SC module. +- [2076](https://github.com/RuminantFarmSystems/RuFaS/pull/2076) - [minor change] [Crop & Soil] Removes TODOs from the Crop & Soil module. +- [1785](https://github.com/RuminantFarmSystems/RuFaS/pull/1785) - [minor change] [TaskManager] Adds sobol and morris samplers, updates argument names. +- [2093](https://github.com/RuminantFarmSystems/RuFaS/pull/2093) - [minor change] [Testing] Increases tolerance level for comparing values changed in E2E testing results comparisons. +- [2091](https://github.com/RuminantFarmSystems/RuFaS/pull/2091) - [minor change] [Crop and Soil] Adding LAI errors to OM before throwing errors. +- [2070](https://github.com/RuminantFarmSystems/RuFaS/pull/2070) - [minor change] [Crop & Soil] Restructure schedule class in the crop and soil module. +- [2086](https://github.com/RuminantFarmSystems/RuFaS/pull/2086) - [minor change] [Animal] Updates default parity fraction. +- [2118](https://github.com/RuminantFarmSystems/RuFaS/pull/2118) - [minor change] [Crop and Soil] Removed the usage of input validation methods in HeatUnits. +- [2090](https://github.com/RuminantFarmSystems/RuFaS/pull/2090) - [minor change] [Crop & Soil] Restructures CropData class. +- [1836](https://github.com/RuminantFarmSystems/RuFaS/pull/1836) - [minor change] [Feed] Updates default prices in default_feed.json using average prices sourced by Kristan (detailed in sheet in PR). +- [2119](https://github.com/RuminantFarmSystems/RuFaS/pull/2119) - [minor change] [OutputManager] Make the log routing usable by other modules. +- [2046](https://github.com/RuminantFarmSystems/RuFaS/pull/2046) - [major change] [Data Collection App] Integrates the Data Collection App into the RuFaS repository and adds a RuFaS task type to update it. +- [2132](https://github.com/RuminantFarmSystems/RuFaS/pull/2132) - [major change] [Feed Storage] Fixing the nutrient loss of crude protein in hay during end-to-end testing +- [2075](https://github.com/RuminantFarmSystems/RuFaS/pull/2075) - [minor change] [Readme] Adds project goals for RuFaS year 2024 - 2025 +- [2067](https://github.com/RuminantFarmSystems/RuFaS/pull/2067) - [minor change] [EEE] Adds updated feeds emissions sheets, which replaces 0s with the average of neighboring FIPS codes. +- [2150](https://github.com/RuminantFarmSystems/RuFaS/pull/2150) - [minor change] [Manure] Allow users to have more control over whether how synthetic fertilizers are used. +- [2120](https://github.com/RuminantFarmSystems/RuFaS/pull/2120) - [minor change] [Crop and Soil] Log errors to OM before throwing errors in NitrogenIncorporation. +- [2143](https://github.com/RuminantFarmSystems/RuFaS/pull/2143) - [minor change] [GraphGenerator] Add user option to set time on x-axis for graphs. +- [2133](https://github.com/RuminantFarmSystems/RuFaS/pull/2133) - [minor change] [Animal] Use closest available genetic data for animals entering the herd or being initialized as calves. +- [2149](https://github.com/RuminantFarmSystems/RuFaS/pull/2149) - [minor change] [Crop and Soil] Relocates TillageImplements to data structures dir. +- [2137](https://github.com/RuminantFarmSystems/RuFaS/pull/2137) - [minor change] [Feed] Make post_wilting_moisture_percentage and user input. +- [2155](https://github.com/RuminantFarmSystems/RuFaS/pull/2155) - [minor change] [Git Actions] Added default data paths tp the protected list. +- [2156](https://github.com/RuminantFarmSystems/RuFaS/pull/2156) - [minor change] [Feed] Fixed test_process_degradations in test_silage.py. +- [2134](https://github.com/RuminantFarmSystems/RuFaS/pull/2134) - [minor change] [Crop & Soil] Adds ammonium fraction to fertilizer mixes input. +- [2136](https://github.com/RuminantFarmSystems/RuFaS/pull/2136) - [minor change] [Animal] Adds data structures to support calculation of animal nutrient requirements and supply. +- [2138](https://github.com/RuminantFarmSystems/RuFaS/pull/2138) - [minor change] [Animal] Refreshes module which calculates the nutrients supplied to an animal by a ration. +- [2128](https://github.com/RuminantFarmSystems/RuFaS/pull/2128) - [minor change] [Animal] Updates culling-related metadata descriptions +- [2162](https://github.com/RuminantFarmSystems/RuFaS/pull/2162) - [minor change] [Data Collection App] Replace the usage of PROPERTIES_TO_CREATE_SCHEMA_FOR with property's boolean field "data_collection_app_compatible". +- [2164](https://github.com/RuminantFarmSystems/RuFaS/pull/2128) - [minor change] [GraphGenerator] Aligns graphs with alphabetized, user-customized GG legend. +- [2141](https://github.com/RuminantFarmSystems/RuFaS/pull/2141) - [minor change] [Animal] Refreshes module which calculates the nutrition requirements of an animal with the NASEM (2021) methodology. +- [2142](https://github.com/RuminantFarmSystems/RuFaS/pull/2142) - [minor change] [Animal] Refreshes module which calculates the nutrition requirements of an animal with the NRC (2001) methodology. +- [2144](https://github.com/RuminantFarmSystems/RuFaS/pull/2144) - [minor change] [Animal] Refreshes module which evaluates if the nutrition supply of a ration satisfies the demand of animal or the average demand of a group of animals. +- [2165](https://github.com/RuminantFarmSystems/RuFaS/pull/2165) - [minor change] [Crop and Soil] Reorganize logic of crop's nutrient uptake routines. +- [2161](https://github.com/RuminantFarmSystems/RuFaS/pull/2161) - [minor change] [Animal] Refreshes calf nutrition intake and requirement routines. +- [2171](https://github.com/RuminantFarmSystems/RuFaS/pull/2171) - [minor change] [Animal] Allows users to supplement manure NutrientRequest shortfalls with external manure. +- [2172](https://github.com/RuminantFarmSystems/RuFaS/pull/2172) - [minor change] [Data Collection App] Makes TaskManager Tasks a type of input that can be collected with the Data Collection App. +- [2180](https://github.com/RuminantFarmSystems/RuFaS/pull/2180) - [minor change] [Github][TaskManager] Updates Github Actions to use Python 3.12 and checks Python version with which the user is running the model. +- [2189](https://github.com/RuminantFarmSystems/RuFaS/pull/2189) - [minor change] [Testing] Sets up a new task to automatically regenerate E2E testing expected-results. +- [2187](https://github.com/RuminantFarmSystems/RuFaS/pull/2187) - [minor change] [Manure] Implements the refreshed manure stream. +- [2196](https://github.com/RuminantFarmSystems/RuFaS/pull/2196) - [minor change] [Inputs][Crop & Soil] Adds new input file for crop configurations and metadata properties for validating these configurations. Also includes the new file in existing metadata files. +- [2201](https://github.com/RuminantFarmSystems/RuFaS/pull/2201) - [minor change] [Inputs] Remove deprecated input files. +- [2179](https://github.com/RuminantFarmSystems/RuFaS/pull/2179) - [major change] [Crop] Makes crops configured entirely with user input. +- [2203](https://github.com/RuminantFarmSystems/RuFaS/pull/2203) - [minor change] [Time] Changed units of "Time.day" from "simulation day" to "julian day". +- [2206](https://github.com/RuminantFarmSystems/RuFaS/pull/2206) - [minor change] [Manure][Animal] Establishes PenManureData class and StreamType enum for Manure refresh. +- [2209](https://github.com/RuminantFarmSystems/RuFaS/pull/2209) - [minor change] [Manure] Fixes error found when attempting to record an empty ManureNutrientRequestResults. +- [2210](https://github.com/RuminantFarmSystems/RuFaS/pull/2210) - [minor change] [OutputManager] Refactor tests in test_output_manager.py to all use pytest-mock. +- [2205](https://github.com/RuminantFarmSystems/RuFaS/pull/2205) - [minor change] [Manure] Implements base manure Processor class. +- [2212](https://github.com/RuminantFarmSystems/RuFaS/pull/2212) - [minor change] [E2E Testing] Updates Feed Storage E2E Testing expected results. +- [2223](https://github.com/RuminantFarmSystems/RuFaS/pull/2223) - [minor change] [Weather] Updates weather metadata to add missing boundaries on some inputs. +- [2191](https://github.com/RuminantFarmSystems/RuFaS/pull/2191) - [minor change] [Documentation] Regenerate code documentation and structure. +- [2221](https://github.com/RuminantFarmSystems/RuFaS/pull/2221) - [minor change] [DCA] Added dropdowns for feed storage options. +- [2225](https://github.com/RuminantFarmSystems/RuFaS/pull/2225) - [minor change] [OutputManager] Adds ability for user to control significant digits of output. +- [2211](https://github.com/RuminantFarmSystems/RuFaS/pull/2211) - [minor change] [Data Collection App] Makes error messages specific and detailed when invalid input is entered into the Data Collection App. +- [2229](https://github.com/RuminantFarmSystems/RuFaS/pull/2229) - [minor change] [Emissions] Bug fix for date comparisons in emissions.py. +- [2230](https://github.com/RuminantFarmSystems/RuFaS/pull/2230) - [minor change] [Manure] Updates Manure metadata descriptions and ranges. +- [2237](https://github.com/RuminantFarmSystems/RuFaS/pull/2237) - [minor change] [Manure] Implemented base class for handler. +- [2234](https://github.com/RuminantFarmSystems/RuFaS/pull/2234) - [minor change] [Manure] Implements base manure Separator class. +- [2236](https://github.com/RuminantFarmSystems/RuFaS/pull/2236) - [minor change] [Testing] Changes E2E expected results update task to automatically update all expected results regardless of whether the old and new expected results differ. +- [2233](https://github.com/RuminantFarmSystems/RuFaS/pull/2233) - [minor change] [Manure] Adds a base manure Digester class. +- [2247](https://github.com/RuminantFarmSystems/RuFaS/pull/2247) - [minor change] [Crop & Soil] Fix the ZeroDivisionError for surface machine manure application. +- [2255](https://github.com/RuminantFarmSystems/RuFaS/pull/2255) - [minor change] [OutputManager] Fix the error reporting units properly to CSV OM files. +- [2269](https://github.com/RuminantFarmSystems/RuFaS/pull/2269) - [minor change] [Animal][Testing] Adds unit tests for Animal Repro. +- [2214](https://github.com/RuminantFarmSystems/RuFaS/pull/2214) - [minor change] [Manure] Adds a base manure Storage class. +- [2272](https://github.com/RuminantFarmSystems/RuFaS/pull/2272) - [minor change] [Animal][Testing] Adds test coverage for refreshed Ration and Nutrition modules. +- [2273](https://github.com/RuminantFarmSystems/RuFaS/pull/2273) - [minor change] [Manure] Re-implements the logic for Anaerobic Digestion. +- [2279](https://github.com/RuminantFarmSystems/RuFaS/pull/2279) - [minor change] [Animal][Testing] Adds test coverage for refreshed animal datatypes files. +- [2278](https://github.com/RuminantFarmSystems/RuFaS/pull/2278) - [minor change] [GraphGenerator] Adds Graph Generator logs mapping original variable name to how it appears in the graph legend +- [2280](https://github.com/RuminantFarmSystems/RuFaS/pull/2280) - [minor change] [Manure] Updates input configs for refreshed Separator class. +- [2298](https://github.com/RuminantFarmSystems/RuFaS/pull/2298) - [minor change] [Manure] Fixed failing tests in handler. +- [2235](https://github.com/RuminantFarmSystems/RuFaS/pull/2235) - [major change] [Animal] Refresh the Animal module. +- [2297](https://github.com/RuminantFarmSystems/RuFaS/pull/2297) - [minor change] [Animal] Fix the flake8 errors in the refreshed animal module and modify "HerdManager._gather_pen_history()" to optimize run time. +- [2308](https://github.com/RuminantFarmSystems/RuFaS/pull/2308) - [minor change] [Manure] Re-implement open lot storage. +- [2194](https://github.com/RuminantFarmSystems/RuFaS/pull/2194) - [minor change] [E2E Testing] Implement the functionality to convert the previous variable names to match the new variable name. +- [2310](https://github.com/RuminantFarmSystems/RuFaS/pull/2310) - [minor change] [Bug fix] Quick fix for errors introduced by PR #2194. +- [2306](https://github.com/RuminantFarmSystems/RuFaS/pull/2306) - [minor change] [Manure] Implement patches to manure refresh after the dev team discussion. +- [2302](https://github.com/RuminantFarmSystems/RuFaS/pull/2302) - [minor change] [Manure] Rename the ammonia emission output in Handler from "housing_ammonia_emissions" to "housing_ammonia_N_emissions". +- [2253](https://github.com/RuminantFarmSystems/RuFaS/pull/2253) - [minor change] [Manure] Implement parlor cleaning handler. +- [2311](https://github.com/RuminantFarmSystems/RuFaS/pull/2311) - [minor change] [Manure] Rename the ammonia emission output in Handler from "housing_ammonia_emissions" to "housing_ammonia_N_emissions". +- [2313](https://github.com/RuminantFarmSystems/RuFaS/pull/2313) - [minor change] [Manure] Reimplements Composting for Manure refresh. +- [2291](https://github.com/RuminantFarmSystems/RuFaS/pull/2291) - [minor change] [GraphGenerator] Expand the support datetime format options for GraphGenerator X-axis. +- [2285](https://github.com/RuminantFarmSystems/RuFaS/pull/2285) - [minor change] [Manure] Re-implements the logic for SlurryStorageOutdoor and SlurryStorageUnderfloor. +- [2282](https://github.com/RuminantFarmSystems/RuFaS/pull/2282) - [minor change] [Manure] Establishes manure Processor enum class. +- [2320](https://github.com/RuminantFarmSystems/RuFaS/pull/2320) - [minor change] [Manure] Fix determine_handler_cleaning_water_volume to be static. +- [2316](https://github.com/RuminantFarmSystems/RuFaS/pull/2316) - [minor change] [Animal][HerdFactory] Create User-defined directory for saving generated herd if not already exists. +- [2311](https://github.com/RuminantFarmSystems/RuFaS/pull/2311) - [minor change] [Project Build][Dependencies] Set the minimum required versions for all RuFaS dependencies specified in requirements.txt. +- [2315](https://github.com/RuminantFarmSystems/RuFaS/pull/2315) - [minor change] [Time] Rename `Time` to `RufasTime`. +- [2325](https://github.com/RuminantFarmSystems/RuFaS/pull/2325) - [minor change] [OutputManager] Fix class-name-reporting to Output Manager for a handful of variables. +- [2321](https://github.com/RuminantFarmSystems/RuFaS/pull/2321) - [minor change] [Animal] Fix ZeroDivision Error when No Calf in Pen . +- [2183](https://github.com/RuminantFarmSystems/RuFaS/pull/2183) - [minor change] [helpful_scripts] Removes now-deprecated files used to help develop sensitivity analysis methodology. Files archived and relevant info/graphics moved to scientific documentation. +- [2322](https://github.com/RuminantFarmSystems/RuFaS/pull/2322) - [minor change] [Github action] Make unauthorized files change check to log and trigger exit at the end of the second step. +- [2331](https://github.com/RuminantFarmSystems/RuFaS/pull/2331) - [minor change] [Github action] Fixing failed final check. +- [2333](https://github.com/RuminantFarmSystems/RuFaS/pull/2333) - [minor change] [Github action] Fixing failing final test by saving current branch name to a variable. +- [2314](https://github.com/RuminantFarmSystems/RuFaS/pull/2314) - [minor change] [Animal] Report Herd Summary Statistics for Starting Animal Population. +- [2332](https://github.com/RuminantFarmSystems/RuFaS/pull/2332) - [minor change] [Crop & Soil] Refactor `Field._execute_manure_application()` and increase test coverage of field.py to 100%. +- [2327](https://github.com/RuminantFarmSystems/RuFaS/pull/2327) - [minor change] [Animal] Reduces the number of warnings during a default simulation run. +- [2318](https://github.com/RuminantFarmSystems/RuFaS/pull/2318) - [minor change] [Manure] Step 1/3 for implementing the refreshed ManureManager: initialization process including input validation, creating processor instances, and populating the adjacency matrix. +- [2328](https://github.com/RuminantFarmSystems/RuFaS/pull/2318) - [minor change] [Manure] Re-implements the logic for compost bedded pack barn.. +- [2323](https://github.com/RuminantFarmSystems/RuFaS/pull/2323) - [minor change] [Animal] Removes day offset in report_sold_animal_information_sort_by_sell_day. +- [2342](https://github.com/RuminantFarmSystems/RuFaS/pull/2342) - [minor change] [Manure] Clean up shared constants across processor subclasses. +- [2292](https://github.com/RuminantFarmSystems/RuFaS/pull/2292) - [minor change] [Animal] Updates NASEM equations in calculation of gravid uterine weight and protein requirement in cases of negative uterine weight. +- [2335](https://github.com/RuminantFarmSystems/RuFaS/pull/2335) - [minor change] [OutputManager] Increase packaging of data sent to Output Manager. +- [2350](https://github.com/RuminantFarmSystems/RuFaS/pull/2350) - [minor change] [Testing] Updates end-to-end testing expected results. +- [2343](https://github.com/RuminantFarmSystems/RuFaS/pull/2343) - [minor change] [Manure Manager] Validate and traverse the adjacency matrix. +- [2338](https://github.com/RuminantFarmSystems/RuFaS/pull/2338) - [minor change] [Manure] Remove Unused Calculations in AnaerobicDigester. +- [2355](https://github.com/RuminantFarmSystems/RuFaS/pull/2355) - [minor change] [Manure] Fix Methane Leakage Calculation in ContinuousMix. +- [2336](https://github.com/RuminantFarmSystems/RuFaS/pull/2336) - [minor change] [Animal] Removes ability to add extra pens during simulation. Pens now overstock based on previous allocation algorithm and log warning. +- [2334](https://github.com/RuminantFarmSystems/RuFaS/pull/2334) - [minor change] [OutputManager] Add option to specify landscape or portrait layouts for CSVs. +- [2344](https://github.com/RuminantFarmSystems/RuFaS/pull/2344) - [minor change] [Soil and Crop] Update all the `add_variable()` calls in `FieldDataReporter` to include the data origins of each variable in its info_map. +- [2354](https://github.com/RuminantFarmSystems/RuFaS/pull/2354) - [minor change] [Soil and Crop] Debug Soil N Cycling and Field N2O emissions. +- [2351](https://github.com/RuminantFarmSystems/RuFaS/pull/2351) - [minor change] [Output Manager] Adds validations to report filter contents. +- [2370](https://github.com/RuminantFarmSystems/RuFaS/pull/2370) - [minor change] [Animal] Added console warning when using sexed semen for her initialization. +- [2371](https://github.com/RuminantFarmSystems/RuFaS/pull/2371) - [minor change] [ReportGenerator] Allow for RG aggregation of np.float()s +- [2340](https://github.com/RuminantFarmSystems/RuFaS/pull/2340) - [minor change] [Animal] Updates the structure of the Mitscherlich Model 3 to calculate enteric CH4 emissions. +- [2252](https://github.com/RuminantFarmSystems/RuFaS/pull/2252) - [minor change] [Animal] Adds logic to initialize herds using specific parity distributions. +- [2391](https://github.com/RuminantFarmSystems/RuFaS/pull/2391) - [minor change] [Crop and Soil] Ensures harvesting continues even if the crop is not used for feed. - [2382](https://github.com/RuminantFarmSystems/RuFaS/pull/2382) - [minor change] [Animal] Fixes the bug in heifer reproduction ED bug when insemination is unsuccessful. -- [2383](https://github.com/RuminantFarmSystems/MASM/pull/2383) - [minor change] [Code of Conduct] Added contributor code of conduct. -- [2326](https://github.com/RuminantFarmSystems/MASM/pull/2326) - [minor change] [Animal] Added automated ration formulation methodology using refresh methods. +- [2383](https://github.com/RuminantFarmSystems/RuFaS/pull/2383) - [minor change] [Code of Conduct] Added contributor code of conduct. +- [2326](https://github.com/RuminantFarmSystems/RuFaS/pull/2326) - [minor change] [Animal] Added automated ration formulation methodology using refresh methods. - [2399](https://github.com/RuminantFarmSystems/RuFaS/pull/2399) - [minor change] [Crop and Soil] Change infiltration value in ManureApplication to default of 0.4. - [2400](https://github.com/RuminantFarmSystems/RuFaS/pull/2400) - [minor change] [Animal] Fixes the bug in heifer first estrus day calculation. - [2409](https://github.com/RuminantFarmSystems/RuFaS/pull/2409) - [minor change] [Animal] Adds back code we did not want removed in #2404 and implements original fix in #2404 - fixes incorrect attribute reference in heifer enteric methane calculation and updates references to MilkProduction class attributes. -- [2374](https://github.com/RuminantFarmSystems/MASM/pull/2374) - [minor change] [Report Generator] Validate and overwrite the constants in report filter. +- [2374](https://github.com/RuminantFarmSystems/RuFaS/pull/2374) - [minor change] [Report Generator] Validate and overwrite the constants in report filter. - [2412](https://github.com/RuminantFarmSystems/RuFaS/pull/2412) - [minor change] [Crop and Soil] Update docstrings in cut_crop - [2414](https://github.com/RuminantFarmSystems/RuFaS/pull/2414) - [minor change] [Animal] Uses utf-8 encoding for saving CSVs from OutputManager. - [2415](https://github.com/RuminantFarmSystems/RuFaS/pull/2415) - [minor change] [Animal] Add "None" as valid cow repro sub methods. @@ -183,11 +183,11 @@ v0.9.2 - [2414](https://github.com/RuminantFarmSystems/RuFaS/pull/2414) - [minor change] [GitHub Actions] Fixes Sphinx Github Action so that it fully updates the website to also reflect new/removed/renamed file; change the theme to sphinx-awesome; added logo. - [2435](https://github.com/RuminantFarmSystems/RuFaS/pull/2414) - [minor change] [GitHub Actions] Adds scientific documentation equation IDs to Animal Module - [2442](https://github.com/RuminantFarmSystems/RuFaS/pull/2442) - [minor change] [FeedManager][FeedStorage] Finishes up version 1 of the Feed Storage/Manager modules. -- [2317](https://github.com/RuminantFarmSystems/MASM/pull/2317) - [minor change] [Animal][Manure] Moves the bedding calculations into the Animal module. -- [2388](https://github.com/RuminantFarmSystems/MASM/pull/2388) - [minor change] [Manure] Enacts and incorporates refreshed daily manure processing functionality. -- [2348](https://github.com/RuminantFarmSystems/MASM/pull/2348) - [minor change] [Animal][Metadata][Manure] Metadata Update for Animal Manure Connection. +- [2317](https://github.com/RuminantFarmSystems/RuFaS/pull/2317) - [minor change] [Animal][Manure] Moves the bedding calculations into the Animal module. +- [2388](https://github.com/RuminantFarmSystems/RuFaS/pull/2388) - [minor change] [Manure] Enacts and incorporates refreshed daily manure processing functionality. +- [2348](https://github.com/RuminantFarmSystems/RuFaS/pull/2348) - [minor change] [Animal][Metadata][Manure] Metadata Update for Animal Manure Connection. - [2451](https://github.com/RuminantFarmSystems/RuFaS/pull/2451) - [minor change] [Sphinx] Updates favicon for the sphinx website; Updates the wiki for TaskManager about detail Herd Generation info. -- [2452](https://github.com/RuminantFarmSystems/MASM/pull/2452) - [minor change] [Wiki]Updated external documents. +- [2452](https://github.com/RuminantFarmSystems/RuFaS/pull/2452) - [minor change] [Wiki]Updated external documents. - [2438](https://github.com/RuminantFarmSystems/RuFaS/pull/2438) - [minor change] [GitHub Actions] Updates the Sphinx documentation workflow to deploy to GitHub Pages via the gh-pages branch and removes build artifacts from the main branch. - [2443](https://github.com/RuminantFarmSystems/RuFaS/pull/2443) - [minor change] [metadata] Moves input/metadata/task_manager_metadata.json to input/task_manager_metadata.json and updates the corresponding entries in the code. - [2453](https://github.com/RuminantFarmSystems/RuFaS/pull/2453) - [minor change] [Code Owners] Create CODEOWNERS file. @@ -198,109 +198,109 @@ v0.9.2 - [2459](https://github.com/RuminantFarmSystems/RuFaS/pull/2459) - [minor change] [Readme] Updated links in readme. - [2457](https://github.com/RuminantFarmSystems/RuFaS/pull/2457) - [minor change] [Documentation] Added scientific documentation folder with first PDFs. - [2426](https://github.com/RuminantFarmSystems/RuFaS/pull/2426) - [minor change] [Animal] Adds a warning when the days_in_preg_when_dry is set to less than or equal to the 3rd preg check day. -- [2369](https://github.com/RuminantFarmSystems/MASM/pull/2369) - [minor change] [Licensing] Addition of licensing documents to repository. -- [2462](https://github.com/RuminantFarmSystems/MASM/pull/2462) - [minor change] [Feed] Bug fix to prevent rounding error in feed inventory tracking -- [2381](https://github.com/RuminantFarmSystems/MASM/pull/2381) - [minor change] [Animal] Refactor ration formulation. -- [2462](https://github.com/RuminantFarmSystems/MASM/pull/2462) - [minor change] [Feed] Bug fix to prevent rounding error in feed inventory tracking. -- [2472](https://github.com/RuminantFarmSystems/MASM/pull/2472) - [minor change] [Animal] Removed duplicate logics to filter animals. -- [2464](https://github.com/RuminantFarmSystems/MASM/pull/2464) - [minor change] [E2E] Removes temporary Feed/Storage E2E testing setup files and functions. -- [2392](https://github.com/RuminantFarmSystems/MASM/pull/2392) - [minor change] [Animal] Tracks rate related to each life stage's deaths. -- [2473](https://github.com/RuminantFarmSystems/MASM/pull/2473) - [minor change] [E2E] Removes TODOs related to temporary Feed/Storage E2E testing setup files and functions. -- [2474](https://github.com/RuminantFarmSystems/MASM/pull/2474) - [minor change] [Manure] Fixes a bug in manure handlers that interfered with flushing functionality. -- [2486](https://github.com/RuminantFarmSystems/MASM/pull/2486) - [minor change] [Input Manager] Add data deletion function in input manager. -- [2470](https://github.com/RuminantFarmSystems/MASM/pull/2470) - [minor change] [Feed] Adds shrink factor, buffer inputs and buffer usage logic in feed manager. -- [2293](https://github.com/RuminantFarmSystems/MASM/pull/2293) - [minor change] [Animal] Adds behavior in an animal reporter method to create an empty output variable in case where there are no sold animals for a given AnimalCombination. -- [2497](https://github.com/RuminantFarmSystems/MASM/pull/2497) - [minor change] Establishes a FeedManager balance reporting system. -- [2479](https://github.com/RuminantFarmSystems/MASM/pull/2479) - [minor change] Removes `errors.py`. -- [2492](https://github.com/RuminantFarmSystems/MASM/pull/2492) - [minor change] [Manure] Use annual mean temperature and redo MCF factor calculation in bedded pack. -- [2504](https://github.com/RuminantFarmSystems/MASM/pull/2504) - [minor change] [Data Validator] Raise helpful error messages when object level data validations failed. -- [2499](https://github.com/RuminantFarmSystems/MASM/pull/2499) - [minor change] Updates `pyproject.toml` and added check for user meeting dependency requirements. -- [2500](https://github.com/RuminantFarmSystems/MASM/pull/2500) - [minor change] Moves `AnimalCombination`, `AnimalManureExcretions`, and removes the old `PenManureData`. -- [2518](https://github.com/RuminantFarmSystems/MASM/pull/2518) - [minor change] Cleanup all TODOs in the codebase. -- [2502](https://github.com/RuminantFarmSystems/MASM/pull/2502) - [minor change] [Manure] Implement Manure Methane Potential Tracking. -- [2524](https://github.com/RuminantFarmSystems/MASM/pull/2502) - [minor change] [EEE][FeedManager] Updates calculation method for purchased feed emissions. -- [2513](https://github.com/RuminantFarmSystems/MASM/pull/2502) - [minor change] [Manure] Add type to separator. -- [2491](https://github.com/RuminantFarmSystems/MASM/pull/2491) - [minor change] [Manure] Fixes a bug in manure request management when trying to supplement a request from a farm that has no on-farm manure. -- [2461](https://github.com/RuminantFarmSystems/MASM/pull/2461) [Input] Create Example Input files. -- [2526](https://github.com/RuminantFarmSystems/MASM/pull/2526) - [minor change] Update expected e2e results and fix flake8 error. -- [2505](https://github.com/RuminantFarmSystems/MASM/pull/2505) - [minor change] Update the wiki pages .rst files and the onboarding doc. -- [2521](https://github.com/RuminantFarmSystems/MASM/pull/2521) - [minor change] Separate `UserConstants` from `GeneralConstants`. -- [2534](https://github.com/RuminantFarmSystems/MASM/pull/2534) - [minor change][docs] Update rufas logo. -- [2529](https://github.com/RuminantFarmSystems/MASM/pull/2529) - [minor change] E2E Testing for No Animal C&S Run. -- [2552](https://github.com/RuminantFarmSystems/MASM/pull/2552) - [minor change] Reduce example run warning count. -- [2551](https://github.com/RuminantFarmSystems/MASM/pull/2551) - [minor change] Raises error in main.py to direct user to errors file for debugging. -- [2547](https://github.com/RuminantFarmSystems/MASM/pull/2547) - [minor change] [Input Manager] 1/5 Cross Validation basic setup. -- [2559](https://github.com/RuminantFarmSystems/MASM/pull/2559) - [minor change] [Manure] Implement daily spread processor. -- [2482](https://github.com/RuminantFarmSystems/MASM/pull/2554) - [minor change] [Animal] Restructure newborn calf status categorization and reporting. -- [2550](https://github.com/RuminantFarmSystems/MASM/pull/2550) - [minor change] Create metadata for no animal scenario. -- [2553](https://github.com/RuminantFarmSystems/MASM/pull/2553) - [minor change] [Input Manager] 3/5 Cross Validation: implement expression block. -- [2567](https://github.com/RuminantFarmSystems/MASM/pull/2567) - [minor change] Creates and prints e2e testing results summary for all metadata e2e testing runs. -- [2571](https://github.com/RuminantFarmSystems/MASM/pull/2571) - [minor change] Revert manure and animal input changes from PR2552. -- [2572](https://github.com/RuminantFarmSystems/MASM/pull/2572) - [minor change] [Feed][FeedStorage] Switches duplicate crop storage data warning to log. -- [2563](https://github.com/RuminantFarmSystems/MASM/pull/2563) - [minor change] Changed calculations to support multi method calculations and update inputs. -- [2582](https://github.com/RuminantFarmSystems/MASM/pull/2582) - [minor change] Reverts the support for multi prediction model usage and replace it with single model selection usage for each animal type. -- [2574](https://github.com/RuminantFarmSystems/MASM/pull/2574) - [minor change] [Cross Validation] Implement alias pool functions in the cross validator. -- [2575](https://github.com/RuminantFarmSystems/MASM/pull/2575) - [minor change] Updates feed storage inputs. -- [2573](https://github.com/RuminantFarmSystems/MASM/pull/2573) - [minor change][Manure] Additional solids calculation changes for manure handler -- [2581](https://github.com/RuminantFarmSystems/MASM/pull/2581) - [minor change] [Inputs] Update inputs files from default to example metadata and prefixes. -- [2324](https://github.com/RuminantFarmSystems/MASM/pull/2324) - [minor change] [Manure] Caps total manure excreted by total solids for dry cows and heifers. Also changes calculation of final solids wet mass from using bedding density to manure density. -- [2413](https://github.com/RuminantFarmSystems/MASM/pull/2413) - [minor change] [Animal] Updates default user defined ration behavior with improved methods. -- [2598](https://github.com/RuminantFarmSystems/MASM/pull/2598) - [minor change] [FeedManager][Feed Storage] Adjust feed deduction logic to gather and remove available feeds by storage rather than crop. -- [2587](https://github.com/RuminantFarmSystems/MASM/pull/2587) - [major change] [Output Manager] Add cross-scenario aggregation and running EEE to post processing task. -- [2583](https://github.com/RuminantFarmSystems/MASM/pull/2583) - [minor change] [Github Action] Fix the GitHub Action for forked branches. -- [2579](https://github.com/RuminantFarmSystems/MASM/pull/2563) - [minor change] [Animal] Changed location of milking cow fraction to main animal input file. -- [2594](https://github.com/RuminantFarmSystems/MASM/pull/2594) - [minor change] [Manure] Fixed splitting-logic for manure_deposition_surface_area based on stream type. -- [2586](https://github.com/RuminantFarmSystems/MASM/pull/2586) - [minor change] Make `max_daily_feed_recalculations_per_year` an User Input -- [2584](https://github.com/RuminantFarmSystems/MASM/pull/2584) - [minor change] [Manure] Implement unit test for Processor.check_manure_stream_compatibility(). -- [2597](https://github.com/RuminantFarmSystems/MASM/pull/2597) - [minor change] [Cross Validation] Implement conditional clause functions. -- [2393](https://github.com/RuminantFarmSystems/MASM/pull/2393) - [minor change] Cleans up the AnimalModuleReporter. -- [2603](https://github.com/RuminantFarmSystems/MASM/pull/2603) - [minor change] Revert pen emission reporting deleted by PR 2393. -- [2605](https://github.com/RuminantFarmSystems/MASM/pull/2605) - [minor change] Adds E2E testing for Feed and Feed Storage modules. -- [2606](https://github.com/RuminantFarmSystems/MASM/pull/2606) - [minor change] Moves Field/Crop/Soil module to `biophysical` and removes `routines` directory. -- [2599](https://github.com/RuminantFarmSystems/MASM/pull/2599) - [minor change] Implement separate tracking of bedding manure in manure module. -- [2612](https://github.com/RuminantFarmSystems/MASM/pull/2612) - [minor change] Remove the generation of `dummy_path` when running unit tests. -- [2613](https://github.com/RuminantFarmSystems/MASM/pull/2613) - [minor change] Added new image and adjust phrasing on a step in rufas onboarding documentation. -- [2628](https://github.com/RuminantFarmSystems/MASM/pull/2628) - [minor change] [CrossValidation] Implement entry function to CrossValidator. -- [2618](https://github.com/RuminantFarmSystems/MASM/pull/2618) - [minor change] Removes outdated example regional feed inputs. -- [2624](https://github.com/RuminantFarmSystems/MASM/pull/2624) - [minor change] [NoInputChange][NoOutputChange] Updates the PR template and changelog to reflect IO changes. -- [1299](https://github.com/RuminantFarmSystems/MASM/pull/1299) - [minor change] [InputChange][OutputChange] Implements the Energy submodule of the EEE module with diesel consumption calculation. -- [2629](https://github.com/RuminantFarmSystems/MASM/pull/2629) - [minor change] [NoInputChange][NoOutputChange][Units][Reporting] Updates a couple units mappings that were incorrect/misspelled. -- [2635](https://github.com/RuminantFarmSystems/MASM/pull/2635) - [minor change] [NoInputChange][NoOutputChange] Updates the ReadMe `Getting Started` section to be more straightforward about how to get RUFAS running. -- [2634](https://github.com/RuminantFarmSystems/MASM/pull/2634) - [minor change] [NoInputChange][NoOutputChange][Animal] Reinstates functionality of report_daily_herd_total_ration method. -- [2639](https://github.com/RuminantFarmSystems/MASM/pull/2639) - [minor change] [InputChange][NoOutputChange][EEE] Add Economics prices dataset. -- [2640](https://github.com/RuminantFarmSystems/MASM/pull/2640) - [minor change] [InputChange][NoOutputChange][Input Manager] Add functionality to load data anad metadata lazily. -- [2643](https://github.com/RuminantFarmSystems/MASM/pull/2643) - [minor change] [NoInputChange][NoOutputChange][Animal] Reinstates functionality of report_daily_herd_total_ration method. -- [2638](https://github.com/RuminantFarmSystems/MASM/pull/2638) - [minor change] [NoInputChange][OutputChange] Institutes 25% manure retention for anaerobic lagoon. -- [2641](https://github.com/RuminantFarmSystems/MASM/pull/2641) - [minor change] [NoInputChange][NoOutputChange][ReadMe] Fix Readme badges. -- [2644](https://github.com/RuminantFarmSystems/MASM/pull/2644) - [minor change] [NoInputChange][NoOutputChange] Ensures a particular crop-field pair can only match one particular storage. -- [2643](https://github.com/RuminantFarmSystems/MASM/pull/2643) - [minor change] [InputChange][NoOutputChange] Expand task file and dir regex pattern matching. -- [2633](https://github.com/RuminantFarmSystems/MASM/pull/2633) - [minor change] [NoInputChange][OutputChange][EEE] Refactors the Farmgrown Feed Emissions calculation and reporting. -- [2600](https://github.com/RuminantFarmSystems/MASM/pull/2600) - [major change] [Animal] [InputChange] [NoOutputChange] Updates energy supply calculations and ration formulation to NASEM standards. -- [2636](https://github.com/RuminantFarmSystems/MASM/pull/2636) - [minor change] [Manure] [NoInputChange] [OutputChange] Improve temperature estimation of slurry of liquid manure in storage. -- [2660](https://github.com/RuminantFarmSystems/MASM/pull/2660) - [minor change] [InputChange][NoOutputChange][Input][Properties] Adds task property to allow running simulations using inputs from external repos. -- [2653](https://github.com/RuminantFarmSystems/MASM/pull/2653) - [minor change] [NoInputChange][NoOutputChange][Unit Test] Separate Unit Tests for `photosynthesize()` and `partition_biomass()` in `allocate_biomass()`. -- [2655](https://github.com/RuminantFarmSystems/MASM/pull/2655) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated RationManager class to allow for more flexibility in user inputs in Feed input file. -- [2670](https://github.com/RuminantFarmSystems/MASM/pull/2670) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated Animal module unit testing to 100% coverage. -- [2673](https://github.com/RuminantFarmSystems/MASM/pull/2673) - [minor change] [Feed] [InputChange] [NoOutputChange] Adds a default for purchased feed buffer of 0.15. +- [2369](https://github.com/RuminantFarmSystems/RuFaS/pull/2369) - [minor change] [Licensing] Addition of licensing documents to repository. +- [2462](https://github.com/RuminantFarmSystems/RuFaS/pull/2462) - [minor change] [Feed] Bug fix to prevent rounding error in feed inventory tracking +- [2381](https://github.com/RuminantFarmSystems/RuFaS/pull/2381) - [minor change] [Animal] Refactor ration formulation. +- [2462](https://github.com/RuminantFarmSystems/RuFaS/pull/2462) - [minor change] [Feed] Bug fix to prevent rounding error in feed inventory tracking. +- [2472](https://github.com/RuminantFarmSystems/RuFaS/pull/2472) - [minor change] [Animal] Removed duplicate logics to filter animals. +- [2464](https://github.com/RuminantFarmSystems/RuFaS/pull/2464) - [minor change] [E2E] Removes temporary Feed/Storage E2E testing setup files and functions. +- [2392](https://github.com/RuminantFarmSystems/RuFaS/pull/2392) - [minor change] [Animal] Tracks rate related to each life stage's deaths. +- [2473](https://github.com/RuminantFarmSystems/RuFaS/pull/2473) - [minor change] [E2E] Removes TODOs related to temporary Feed/Storage E2E testing setup files and functions. +- [2474](https://github.com/RuminantFarmSystems/RuFaS/pull/2474) - [minor change] [Manure] Fixes a bug in manure handlers that interfered with flushing functionality. +- [2486](https://github.com/RuminantFarmSystems/RuFaS/pull/2486) - [minor change] [Input Manager] Add data deletion function in input manager. +- [2470](https://github.com/RuminantFarmSystems/RuFaS/pull/2470) - [minor change] [Feed] Adds shrink factor, buffer inputs and buffer usage logic in feed manager. +- [2293](https://github.com/RuminantFarmSystems/RuFaS/pull/2293) - [minor change] [Animal] Adds behavior in an animal reporter method to create an empty output variable in case where there are no sold animals for a given AnimalCombination. +- [2497](https://github.com/RuminantFarmSystems/RuFaS/pull/2497) - [minor change] Establishes a FeedManager balance reporting system. +- [2479](https://github.com/RuminantFarmSystems/RuFaS/pull/2479) - [minor change] Removes `errors.py`. +- [2492](https://github.com/RuminantFarmSystems/RuFaS/pull/2492) - [minor change] [Manure] Use annual mean temperature and redo MCF factor calculation in bedded pack. +- [2504](https://github.com/RuminantFarmSystems/RuFaS/pull/2504) - [minor change] [Data Validator] Raise helpful error messages when object level data validations failed. +- [2499](https://github.com/RuminantFarmSystems/RuFaS/pull/2499) - [minor change] Updates `pyproject.toml` and added check for user meeting dependency requirements. +- [2500](https://github.com/RuminantFarmSystems/RuFaS/pull/2500) - [minor change] Moves `AnimalCombination`, `AnimalManureExcretions`, and removes the old `PenManureData`. +- [2518](https://github.com/RuminantFarmSystems/RuFaS/pull/2518) - [minor change] Cleanup all TODOs in the codebase. +- [2502](https://github.com/RuminantFarmSystems/RuFaS/pull/2502) - [minor change] [Manure] Implement Manure Methane Potential Tracking. +- [2524](https://github.com/RuminantFarmSystems/RuFaS/pull/2502) - [minor change] [EEE][FeedManager] Updates calculation method for purchased feed emissions. +- [2513](https://github.com/RuminantFarmSystems/RuFaS/pull/2502) - [minor change] [Manure] Add type to separator. +- [2491](https://github.com/RuminantFarmSystems/RuFaS/pull/2491) - [minor change] [Manure] Fixes a bug in manure request management when trying to supplement a request from a farm that has no on-farm manure. +- [2461](https://github.com/RuminantFarmSystems/RuFaS/pull/2461) [Input] Create Example Input files. +- [2526](https://github.com/RuminantFarmSystems/RuFaS/pull/2526) - [minor change] Update expected e2e results and fix flake8 error. +- [2505](https://github.com/RuminantFarmSystems/RuFaS/pull/2505) - [minor change] Update the wiki pages .rst files and the onboarding doc. +- [2521](https://github.com/RuminantFarmSystems/RuFaS/pull/2521) - [minor change] Separate `UserConstants` from `GeneralConstants`. +- [2534](https://github.com/RuminantFarmSystems/RuFaS/pull/2534) - [minor change][docs] Update rufas logo. +- [2529](https://github.com/RuminantFarmSystems/RuFaS/pull/2529) - [minor change] E2E Testing for No Animal C&S Run. +- [2552](https://github.com/RuminantFarmSystems/RuFaS/pull/2552) - [minor change] Reduce example run warning count. +- [2551](https://github.com/RuminantFarmSystems/RuFaS/pull/2551) - [minor change] Raises error in main.py to direct user to errors file for debugging. +- [2547](https://github.com/RuminantFarmSystems/RuFaS/pull/2547) - [minor change] [Input Manager] 1/5 Cross Validation basic setup. +- [2559](https://github.com/RuminantFarmSystems/RuFaS/pull/2559) - [minor change] [Manure] Implement daily spread processor. +- [2482](https://github.com/RuminantFarmSystems/RuFaS/pull/2554) - [minor change] [Animal] Restructure newborn calf status categorization and reporting. +- [2550](https://github.com/RuminantFarmSystems/RuFaS/pull/2550) - [minor change] Create metadata for no animal scenario. +- [2553](https://github.com/RuminantFarmSystems/RuFaS/pull/2553) - [minor change] [Input Manager] 3/5 Cross Validation: implement expression block. +- [2567](https://github.com/RuminantFarmSystems/RuFaS/pull/2567) - [minor change] Creates and prints e2e testing results summary for all metadata e2e testing runs. +- [2571](https://github.com/RuminantFarmSystems/RuFaS/pull/2571) - [minor change] Revert manure and animal input changes from PR2552. +- [2572](https://github.com/RuminantFarmSystems/RuFaS/pull/2572) - [minor change] [Feed][FeedStorage] Switches duplicate crop storage data warning to log. +- [2563](https://github.com/RuminantFarmSystems/RuFaS/pull/2563) - [minor change] Changed calculations to support multi method calculations and update inputs. +- [2582](https://github.com/RuminantFarmSystems/RuFaS/pull/2582) - [minor change] Reverts the support for multi prediction model usage and replace it with single model selection usage for each animal type. +- [2574](https://github.com/RuminantFarmSystems/RuFaS/pull/2574) - [minor change] [Cross Validation] Implement alias pool functions in the cross validator. +- [2575](https://github.com/RuminantFarmSystems/RuFaS/pull/2575) - [minor change] Updates feed storage inputs. +- [2573](https://github.com/RuminantFarmSystems/RuFaS/pull/2573) - [minor change][Manure] Additional solids calculation changes for manure handler +- [2581](https://github.com/RuminantFarmSystems/RuFaS/pull/2581) - [minor change] [Inputs] Update inputs files from default to example metadata and prefixes. +- [2324](https://github.com/RuminantFarmSystems/RuFaS/pull/2324) - [minor change] [Manure] Caps total manure excreted by total solids for dry cows and heifers. Also changes calculation of final solids wet mass from using bedding density to manure density. +- [2413](https://github.com/RuminantFarmSystems/RuFaS/pull/2413) - [minor change] [Animal] Updates default user defined ration behavior with improved methods. +- [2598](https://github.com/RuminantFarmSystems/RuFaS/pull/2598) - [minor change] [FeedManager][Feed Storage] Adjust feed deduction logic to gather and remove available feeds by storage rather than crop. +- [2587](https://github.com/RuminantFarmSystems/RuFaS/pull/2587) - [major change] [Output Manager] Add cross-scenario aggregation and running EEE to post processing task. +- [2583](https://github.com/RuminantFarmSystems/RuFaS/pull/2583) - [minor change] [Github Action] Fix the GitHub Action for forked branches. +- [2579](https://github.com/RuminantFarmSystems/RuFaS/pull/2563) - [minor change] [Animal] Changed location of milking cow fraction to main animal input file. +- [2594](https://github.com/RuminantFarmSystems/RuFaS/pull/2594) - [minor change] [Manure] Fixed splitting-logic for manure_deposition_surface_area based on stream type. +- [2586](https://github.com/RuminantFarmSystems/RuFaS/pull/2586) - [minor change] Make `max_daily_feed_recalculations_per_year` an User Input +- [2584](https://github.com/RuminantFarmSystems/RuFaS/pull/2584) - [minor change] [Manure] Implement unit test for Processor.check_manure_stream_compatibility(). +- [2597](https://github.com/RuminantFarmSystems/RuFaS/pull/2597) - [minor change] [Cross Validation] Implement conditional clause functions. +- [2393](https://github.com/RuminantFarmSystems/RuFaS/pull/2393) - [minor change] Cleans up the AnimalModuleReporter. +- [2603](https://github.com/RuminantFarmSystems/RuFaS/pull/2603) - [minor change] Revert pen emission reporting deleted by PR 2393. +- [2605](https://github.com/RuminantFarmSystems/RuFaS/pull/2605) - [minor change] Adds E2E testing for Feed and Feed Storage modules. +- [2606](https://github.com/RuminantFarmSystems/RuFaS/pull/2606) - [minor change] Moves Field/Crop/Soil module to `biophysical` and removes `routines` directory. +- [2599](https://github.com/RuminantFarmSystems/RuFaS/pull/2599) - [minor change] Implement separate tracking of bedding manure in manure module. +- [2612](https://github.com/RuminantFarmSystems/RuFaS/pull/2612) - [minor change] Remove the generation of `dummy_path` when running unit tests. +- [2613](https://github.com/RuminantFarmSystems/RuFaS/pull/2613) - [minor change] Added new image and adjust phrasing on a step in rufas onboarding documentation. +- [2628](https://github.com/RuminantFarmSystems/RuFaS/pull/2628) - [minor change] [CrossValidation] Implement entry function to CrossValidator. +- [2618](https://github.com/RuminantFarmSystems/RuFaS/pull/2618) - [minor change] Removes outdated example regional feed inputs. +- [2624](https://github.com/RuminantFarmSystems/RuFaS/pull/2624) - [minor change] [NoInputChange][NoOutputChange] Updates the PR template and changelog to reflect IO changes. +- [1299](https://github.com/RuminantFarmSystems/RuFaS/pull/1299) - [minor change] [InputChange][OutputChange] Implements the Energy submodule of the EEE module with diesel consumption calculation. +- [2629](https://github.com/RuminantFarmSystems/RuFaS/pull/2629) - [minor change] [NoInputChange][NoOutputChange][Units][Reporting] Updates a couple units mappings that were incorrect/misspelled. +- [2635](https://github.com/RuminantFarmSystems/RuFaS/pull/2635) - [minor change] [NoInputChange][NoOutputChange] Updates the ReadMe `Getting Started` section to be more straightforward about how to get RUFAS running. +- [2634](https://github.com/RuminantFarmSystems/RuFaS/pull/2634) - [minor change] [NoInputChange][NoOutputChange][Animal] Reinstates functionality of report_daily_herd_total_ration method. +- [2639](https://github.com/RuminantFarmSystems/RuFaS/pull/2639) - [minor change] [InputChange][NoOutputChange][EEE] Add Economics prices dataset. +- [2640](https://github.com/RuminantFarmSystems/RuFaS/pull/2640) - [minor change] [InputChange][NoOutputChange][Input Manager] Add functionality to load data anad metadata lazily. +- [2643](https://github.com/RuminantFarmSystems/RuFaS/pull/2643) - [minor change] [NoInputChange][NoOutputChange][Animal] Reinstates functionality of report_daily_herd_total_ration method. +- [2638](https://github.com/RuminantFarmSystems/RuFaS/pull/2638) - [minor change] [NoInputChange][OutputChange] Institutes 25% manure retention for anaerobic lagoon. +- [2641](https://github.com/RuminantFarmSystems/RuFaS/pull/2641) - [minor change] [NoInputChange][NoOutputChange][ReadMe] Fix Readme badges. +- [2644](https://github.com/RuminantFarmSystems/RuFaS/pull/2644) - [minor change] [NoInputChange][NoOutputChange] Ensures a particular crop-field pair can only match one particular storage. +- [2643](https://github.com/RuminantFarmSystems/RuFaS/pull/2643) - [minor change] [InputChange][NoOutputChange] Expand task file and dir regex pattern matching. +- [2633](https://github.com/RuminantFarmSystems/RuFaS/pull/2633) - [minor change] [NoInputChange][OutputChange][EEE] Refactors the Farmgrown Feed Emissions calculation and reporting. +- [2600](https://github.com/RuminantFarmSystems/RuFaS/pull/2600) - [major change] [Animal] [InputChange] [NoOutputChange] Updates energy supply calculations and ration formulation to NASEM standards. +- [2636](https://github.com/RuminantFarmSystems/RuFaS/pull/2636) - [minor change] [Manure] [NoInputChange] [OutputChange] Improve temperature estimation of slurry of liquid manure in storage. +- [2660](https://github.com/RuminantFarmSystems/RuFaS/pull/2660) - [minor change] [InputChange][NoOutputChange][Input][Properties] Adds task property to allow running simulations using inputs from external repos. +- [2653](https://github.com/RuminantFarmSystems/RuFaS/pull/2653) - [minor change] [NoInputChange][NoOutputChange][Unit Test] Separate Unit Tests for `photosynthesize()` and `partition_biomass()` in `allocate_biomass()`. +- [2655](https://github.com/RuminantFarmSystems/RuFaS/pull/2655) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated RationManager class to allow for more flexibility in user inputs in Feed input file. +- [2670](https://github.com/RuminantFarmSystems/RuFaS/pull/2670) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated Animal module unit testing to 100% coverage. +- [2673](https://github.com/RuminantFarmSystems/RuFaS/pull/2673) - [minor change] [Feed] [InputChange] [NoOutputChange] Adds a default for purchased feed buffer of 0.15. -- [2675](https://github.com/RuminantFarmSystems/MASM/pull/2675) - [minor change] [DataValidator] [NoInputChange] [NoOutputChange] Fixes and clarifies data fixing error messaging for IM. -- [2674](https://github.com/RuminantFarmSystems/MASM/pull/2674) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Prevent simulation fails when metadata blobs for fields/manure/harvest does not exist. -- [2678](https://github.com/RuminantFarmSystems/MASM/pull/2678) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Corrects a bug in Separators and adds a check to prevent a bug in Slurry Storage Outdoor, Slurry Storage Underfloor, and Anaerobic Lagoon. -- [2679](https://github.com/RuminantFarmSystems/MASM/pull/2678) - [minor change] [Feed] [NoInputChange] [OutputChange] Removes default reporting 0.0s for FGFs that aren't grown during a simulation -- [2688](https://github.com/RuminantFarmSystems/MASM/pull/2688) - [minor change] [InputManager] [NoInputChange] [NoOutputChange] Hot fix to correct the missing part of 2640. -- [2689](https://github.com/RuminantFarmSystems/MASM/pull/2689) - [minor change] [InputManager] [InputChange] [NoOutputChange] Add support for multiple properties files. -- [2701](https://github.com/RuminantFarmSystems/MASM/pull/2701) - [minor change] [EEEManager] [NoInputChange] [NoOutputChange] Hot fix to correct the failure in EEEManager.. -- [2672](https://github.com/RuminantFarmSystems/MASM/pull/2672) - [minor change] [EEE] [NoInputChange] [NoOutputChange] Allow multiple crop-field combos to map to the same feed storage. +- [2675](https://github.com/RuminantFarmSystems/RuFaS/pull/2675) - [minor change] [DataValidator] [NoInputChange] [NoOutputChange] Fixes and clarifies data fixing error messaging for IM. +- [2674](https://github.com/RuminantFarmSystems/RuFaS/pull/2674) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Prevent simulation fails when metadata blobs for fields/manure/harvest does not exist. +- [2678](https://github.com/RuminantFarmSystems/RuFaS/pull/2678) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Corrects a bug in Separators and adds a check to prevent a bug in Slurry Storage Outdoor, Slurry Storage Underfloor, and Anaerobic Lagoon. +- [2679](https://github.com/RuminantFarmSystems/RuFaS/pull/2678) - [minor change] [Feed] [NoInputChange] [OutputChange] Removes default reporting 0.0s for FGFs that aren't grown during a simulation +- [2688](https://github.com/RuminantFarmSystems/RuFaS/pull/2688) - [minor change] [InputManager] [NoInputChange] [NoOutputChange] Hot fix to correct the missing part of 2640. +- [2689](https://github.com/RuminantFarmSystems/RuFaS/pull/2689) - [minor change] [InputManager] [InputChange] [NoOutputChange] Add support for multiple properties files. +- [2701](https://github.com/RuminantFarmSystems/RuFaS/pull/2701) - [minor change] [EEEManager] [NoInputChange] [NoOutputChange] Hot fix to correct the failure in EEEManager.. +- [2672](https://github.com/RuminantFarmSystems/RuFaS/pull/2672) - [minor change] [EEE] [NoInputChange] [NoOutputChange] Allow multiple crop-field combos to map to the same feed storage. - [2677](https://github.com/RuminantFarmSystems/RuFaS/pull/2677) - [minor change] [Animal] [NoInputChange] [NoOutputChange] Removes possibility of infinite loop in ration formulation. - [2708](https://github.com/RuminantFarmSystems/RuFaS/pull/2708) - [minor change] [FeedStorage] [NoInputChange] [NoOutputChange] Eases restriction on type for feed storage config inputs. - [2709](https://github.com/RuminantFarmSystems/RuFaS/pull/2709) - [minor change] [OutputManager] [NoInputChange] [NoOutputChange] Updates use-name to allow for exact regex match var name use in outputs. - [2710](https://github.com/RuminantFarmSystems/RuFaS/pull/2710) - [minor change] [Pilot testing] [NoInputChange] [NoOutputChange] Quick fix for farm 4 failure in pilot testing. -- [2711](https://github.com/RuminantFarmSystems/MASM/pull/2711) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Updates damping factor and Arrhenius constant values -- [2721](https://github.com/RuminantFarmSystems/MASM/pull/2721) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Adds error for instances of negative liquid manure water, and adds protection against division by 0 errors in digesters. -- [2726](https://github.com/RuminantFarmSystems/MASM/pull/2726) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Report the Farm Grown Feed Emissions on a daily basis. -- [2731](https://github.com/RuminantFarmSystems/MASM/pull/2726) - [minor change] [Scientific Documentation] [NoInputChange] [NoOutputChange] Adds scientific documentation latex files to docs folder. -- [2608](https://github.com/RuminantFarmSystems/MASM/pull/2608) - [minor change] [InputChange][OutputChange][Animal] Implements the Genetics submodule. -- [2705](https://github.com/RuminantFarmSystems/MASM/pull/2705) - [minor change] [InputChange][OutputChange][e2e-testing] Fix end to end testing for the new emission files. +- [2711](https://github.com/RuminantFarmSystems/RuFaS/pull/2711) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Updates damping factor and Arrhenius constant values +- [2721](https://github.com/RuminantFarmSystems/RuFaS/pull/2721) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Adds error for instances of negative liquid manure water, and adds protection against division by 0 errors in digesters. +- [2726](https://github.com/RuminantFarmSystems/RuFaS/pull/2726) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Report the Farm Grown Feed Emissions on a daily basis. +- [2731](https://github.com/RuminantFarmSystems/RuFaS/pull/2726) - [minor change] [Scientific Documentation] [NoInputChange] [NoOutputChange] Adds scientific documentation latex files to docs folder. +- [2608](https://github.com/RuminantFarmSystems/RuFaS/pull/2608) - [minor change] [InputChange][OutputChange][Animal] Implements the Genetics submodule. +- [2705](https://github.com/RuminantFarmSystems/RuFaS/pull/2705) - [minor change] [InputChange][OutputChange][e2e-testing] Fix end to end testing for the new emission files. - [2732](https://github.com/RuminantFarmSystems/RuFaS/pull/2732) - [minor change] [NoInputChange] [NoOutputChange] Skip Animal module and Manure module if no animals are present in simulation. - [2739](https://github.com/RuminantFarmSystems/RuFaS/pull/2739) - [minor change] [NoInputChange] [NoOutputChange] Fixes manure outputs and updates E2E expected results accordingly. - [2763](https://github.com/RuminantFarmSystems/RuFaS/pull/2763) - [minor change] [NoInputChange] [NoOutputChange] Fixes feed order issue by sorting user feed inputs. @@ -308,22 +308,22 @@ v0.9.2 - [2760](https://github.com/RuminantFarmSystems/RuFaS/pull/2760) - [minor change] [NoInputChange] [OutputChange] [Feed][Emission] Implement dictionary reporting structure for feed deduction data ### v0.9.2 -- [1968](https://github.com/RuminantFarmSystems/MASM/pull/1968) - [minor change] [Changelog] Move the changelog from a Google sheet into a markdown document in the repository. -- [1976](https://github.com/RuminantFarmSystems/MASM/pull/1976) - [minor change] [EEE] Add unit tests for the Emission module. -- [1977](https://github.com/RuminantFarmSystems/MASM/pull/1977) - [minor change] [EEE] Improve emission.py codebase and clarity. -- [1948](https://github.com/RuminantFarmSystems/MASM/pull/1948) - [minor change] [Soil and Crop] Utilize a residue tracker property method in the layer data pool that sums structural and metabolic litter. -- [1980](https://github.com/RuminantFarmSystems/MASM/pull/1980) - [minor change] [Soil and Crop] Set return value and add warning when silt and clay are zero. -- [1973](https://github.com/RuminantFarmSystems/MASM/pull/1973) - [minor change] [OutputManager] Avoid global variable usage of output manager [2/2]. -- [1870](https://github.com/RuminantFarmSystems/MASM/pull/1870) - [minor change] [Soil and Crop] Partition denitrified nitrates between nitrous oxide emissions and dinitrogen emissions, -- [1974](https://github.com/RuminantFarmSystems/MASM/pull/1974) - [minor change] [Animal] Establishes the AnimalPhosphorusStatus calculator class and the AnimalPhosphorus class to perform the daily phosphorus update for each animal for eventual incorporation into the newly refreshed Animal module. -- [1944](https://github.com/RuminantFarmSystems/MASM/pull/1944) - [minor change] [GitHub Actions] Updates the Sphinx GitHub Action so that it can be triggered manually on specific branches and modifies it to not remove any .rst files. -- [1986](https://github.com/RuminantFarmSystems/MASM/pull/1986) - [minor change] [Animal] Creates the biophysical folder, and necessary files with empty class and folders for the redesigned animal module. -- [1979](https://github.com/RuminantFarmSystems/MASM/pull/1979) - [minor change] [EEE] Updates synthetic fertilizer emissions to be partitioned by crop schedule instead of by dry yield. -- [1784](https://github.com/RuminantFarmSystems/MASM/pull/1784) - [minor change] [Task Manager][Feed Storage] Adds end-to-end testing routine for the Feed Storage module which can be extended to test other parts of RuFaS. -- [1998](https://github.com/RuminantFarmSystems/MASM/pull/1998) - [minor change] [GitHub Actions] Adds if statement to make sure there is a PR to comment on before attempting to post a comment. -- [2000](https://github.com/RuminantFarmSystems/MASM/pull/2000) - [minor change] [CurrentWeatherConditions] Removed optional type hints. -- [1989](https://github.com/RuminantFarmSystems/MASM/pull/1989) - [minor change] [Animal] Method formulate_ration now correctly returns pen.ration_per_animal instead of pen.ration. -- [2001](https://github.com/RuminantFarmSystems/MASM/pull/2001) - [minor change] [E2E Testing] Changes E2ETestResultsComparer so that it constructs file paths properly on Windows machines. -- [2010](https://github.com/RuminantFarmSystems/MASM/pull/2010) - [minor change] Updates liquid manure nitrogen input source used to calculate N2O emissions for manure storages. -- [2002](https://github.com/RuminantFarmSystems/MASM/pull/2002) - [minor change] [Manure] Adds a method to determine the ambient inside barn temperature based on the outdoor air temperature for use in calculations of emissions associated with Manure Handlers. -- [2009](https://github.com/RuminantFarmSystems/MASM/pull/2009) - [minor change] [Time][Feed Storage] Modifies the init of Time so that a time object can be created without needing config from IM. This in turn allows us to avoid deep copies used for time management. +- [1968](https://github.com/RuminantFarmSystems/RuFaS/pull/1968) - [minor change] [Changelog] Move the changelog from a Google sheet into a markdown document in the repository. +- [1976](https://github.com/RuminantFarmSystems/RuFaS/pull/1976) - [minor change] [EEE] Add unit tests for the Emission module. +- [1977](https://github.com/RuminantFarmSystems/RuFaS/pull/1977) - [minor change] [EEE] Improve emission.py codebase and clarity. +- [1948](https://github.com/RuminantFarmSystems/RuFaS/pull/1948) - [minor change] [Soil and Crop] Utilize a residue tracker property method in the layer data pool that sums structural and metabolic litter. +- [1980](https://github.com/RuminantFarmSystems/RuFaS/pull/1980) - [minor change] [Soil and Crop] Set return value and add warning when silt and clay are zero. +- [1973](https://github.com/RuminantFarmSystems/RuFaS/pull/1973) - [minor change] [OutputManager] Avoid global variable usage of output manager [2/2]. +- [1870](https://github.com/RuminantFarmSystems/RuFaS/pull/1870) - [minor change] [Soil and Crop] Partition denitrified nitrates between nitrous oxide emissions and dinitrogen emissions, +- [1974](https://github.com/RuminantFarmSystems/RuFaS/pull/1974) - [minor change] [Animal] Establishes the AnimalPhosphorusStatus calculator class and the AnimalPhosphorus class to perform the daily phosphorus update for each animal for eventual incorporation into the newly refreshed Animal module. +- [1944](https://github.com/RuminantFarmSystems/RuFaS/pull/1944) - [minor change] [GitHub Actions] Updates the Sphinx GitHub Action so that it can be triggered manually on specific branches and modifies it to not remove any .rst files. +- [1986](https://github.com/RuminantFarmSystems/RuFaS/pull/1986) - [minor change] [Animal] Creates the biophysical folder, and necessary files with empty class and folders for the redesigned animal module. +- [1979](https://github.com/RuminantFarmSystems/RuFaS/pull/1979) - [minor change] [EEE] Updates synthetic fertilizer emissions to be partitioned by crop schedule instead of by dry yield. +- [1784](https://github.com/RuminantFarmSystems/RuFaS/pull/1784) - [minor change] [Task Manager][Feed Storage] Adds end-to-end testing routine for the Feed Storage module which can be extended to test other parts of RuFaS. +- [1998](https://github.com/RuminantFarmSystems/RuFaS/pull/1998) - [minor change] [GitHub Actions] Adds if statement to make sure there is a PR to comment on before attempting to post a comment. +- [2000](https://github.com/RuminantFarmSystems/RuFaS/pull/2000) - [minor change] [CurrentWeatherConditions] Removed optional type hints. +- [1989](https://github.com/RuminantFarmSystems/RuFaS/pull/1989) - [minor change] [Animal] Method formulate_ration now correctly returns pen.ration_per_animal instead of pen.ration. +- [2001](https://github.com/RuminantFarmSystems/RuFaS/pull/2001) - [minor change] [E2E Testing] Changes E2ETestResultsComparer so that it constructs file paths properly on Windows machines. +- [2010](https://github.com/RuminantFarmSystems/RuFaS/pull/2010) - [minor change] Updates liquid manure nitrogen input source used to calculate N2O emissions for manure storages. +- [2002](https://github.com/RuminantFarmSystems/RuFaS/pull/2002) - [minor change] [Manure] Adds a method to determine the ambient inside barn temperature based on the outdoor air temperature for use in calculations of emissions associated with Manure Handlers. +- [2009](https://github.com/RuminantFarmSystems/RuFaS/pull/2009) - [minor change] [Time][Feed Storage] Modifies the init of Time so that a time object can be created without needing config from IM. This in turn allows us to avoid deep copies used for time management. From a1221a941f04ab19652a77691dba16fdacae6f0c Mon Sep 17 00:00:00 2001 From: Kristan <41019131+KFosterReed@users.noreply.github.com> Date: Wed, 4 Mar 2026 15:52:47 -0500 Subject: [PATCH 3/6] Update changelog.md Co-authored-by: JoeWaddell <109082924+JoeWaddell@users.noreply.github.com> --- changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/changelog.md b/changelog.md index dac453c7bc..e47e22e35a 100644 --- a/changelog.md +++ b/changelog.md @@ -298,7 +298,7 @@ v0.9.2 - [2711](https://github.com/RuminantFarmSystems/RuFaS/pull/2711) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Updates damping factor and Arrhenius constant values - [2721](https://github.com/RuminantFarmSystems/RuFaS/pull/2721) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Adds error for instances of negative liquid manure water, and adds protection against division by 0 errors in digesters. - [2726](https://github.com/RuminantFarmSystems/RuFaS/pull/2726) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Report the Farm Grown Feed Emissions on a daily basis. -- [2731](https://github.com/RuminantFarmSystems/RuFaS/pull/2726) - [minor change] [Scientific Documentation] [NoInputChange] [NoOutputChange] Adds scientific documentation latex files to docs folder. +- [2731](https://github.com/RuminantFarmSystems/RuFaS/pull/2731) - [minor change] [Scientific Documentation] [NoInputChange] [NoOutputChange] Adds scientific documentation latex files to docs folder. - [2608](https://github.com/RuminantFarmSystems/RuFaS/pull/2608) - [minor change] [InputChange][OutputChange][Animal] Implements the Genetics submodule. - [2705](https://github.com/RuminantFarmSystems/RuFaS/pull/2705) - [minor change] [InputChange][OutputChange][e2e-testing] Fix end to end testing for the new emission files. - [2732](https://github.com/RuminantFarmSystems/RuFaS/pull/2732) - [minor change] [NoInputChange] [NoOutputChange] Skip Animal module and Manure module if no animals are present in simulation. From 1c3cb10dd8bc6525904388df4299be05cd1ffeea Mon Sep 17 00:00:00 2001 From: Kristan <41019131+KFosterReed@users.noreply.github.com> Date: Wed, 4 Mar 2026 15:53:46 -0500 Subject: [PATCH 4/6] Apply suggestion from @JoeWaddell Co-authored-by: JoeWaddell <109082924+JoeWaddell@users.noreply.github.com> --- changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/changelog.md b/changelog.md index e47e22e35a..e7a6b4b561 100644 --- a/changelog.md +++ b/changelog.md @@ -181,7 +181,7 @@ v0.9.2 - [2421](https://github.com/RuminantFarmSystems/RuFaS/pull/2421) - [minor change] [Soil and Crop] Update Canopy Water handling. - [2420](https://github.com/RuminantFarmSystems/RuFaS/pull/2420) - [minor change] [Crop and Soil] Update Root Depth for Perennial Crops in Establishment Year. - [2414](https://github.com/RuminantFarmSystems/RuFaS/pull/2414) - [minor change] [GitHub Actions] Fixes Sphinx Github Action so that it fully updates the website to also reflect new/removed/renamed file; change the theme to sphinx-awesome; added logo. -- [2435](https://github.com/RuminantFarmSystems/RuFaS/pull/2414) - [minor change] [GitHub Actions] Adds scientific documentation equation IDs to Animal Module +- [2435](https://github.com/RuminantFarmSystems/RuFaS/pull/2435) - [minor change] [GitHub Actions] Adds scientific documentation equation IDs to Animal Module - [2442](https://github.com/RuminantFarmSystems/RuFaS/pull/2442) - [minor change] [FeedManager][FeedStorage] Finishes up version 1 of the Feed Storage/Manager modules. - [2317](https://github.com/RuminantFarmSystems/RuFaS/pull/2317) - [minor change] [Animal][Manure] Moves the bedding calculations into the Animal module. - [2388](https://github.com/RuminantFarmSystems/RuFaS/pull/2388) - [minor change] [Manure] Enacts and incorporates refreshed daily manure processing functionality. From 841e94afceb3ab10af1caf79acc8e7095dec750f Mon Sep 17 00:00:00 2001 From: Kristan <41019131+KFosterReed@users.noreply.github.com> Date: Wed, 4 Mar 2026 15:54:51 -0500 Subject: [PATCH 5/6] Apply suggestions from code review Co-authored-by: JoeWaddell <109082924+JoeWaddell@users.noreply.github.com> --- changelog.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/changelog.md b/changelog.md index e7a6b4b561..93ce05778c 100644 --- a/changelog.md +++ b/changelog.md @@ -218,7 +218,7 @@ v0.9.2 - [2500](https://github.com/RuminantFarmSystems/RuFaS/pull/2500) - [minor change] Moves `AnimalCombination`, `AnimalManureExcretions`, and removes the old `PenManureData`. - [2518](https://github.com/RuminantFarmSystems/RuFaS/pull/2518) - [minor change] Cleanup all TODOs in the codebase. - [2502](https://github.com/RuminantFarmSystems/RuFaS/pull/2502) - [minor change] [Manure] Implement Manure Methane Potential Tracking. -- [2524](https://github.com/RuminantFarmSystems/RuFaS/pull/2502) - [minor change] [EEE][FeedManager] Updates calculation method for purchased feed emissions. +- [2524](https://github.com/RuminantFarmSystems/RuFaS/pull/2524) - [minor change] [EEE][FeedManager] Updates calculation method for purchased feed emissions. - [2513](https://github.com/RuminantFarmSystems/RuFaS/pull/2502) - [minor change] [Manure] Add type to separator. - [2491](https://github.com/RuminantFarmSystems/RuFaS/pull/2491) - [minor change] [Manure] Fixes a bug in manure request management when trying to supplement a request from a farm that has no on-farm manure. - [2461](https://github.com/RuminantFarmSystems/RuFaS/pull/2461) [Input] Create Example Input files. @@ -231,7 +231,7 @@ v0.9.2 - [2551](https://github.com/RuminantFarmSystems/RuFaS/pull/2551) - [minor change] Raises error in main.py to direct user to errors file for debugging. - [2547](https://github.com/RuminantFarmSystems/RuFaS/pull/2547) - [minor change] [Input Manager] 1/5 Cross Validation basic setup. - [2559](https://github.com/RuminantFarmSystems/RuFaS/pull/2559) - [minor change] [Manure] Implement daily spread processor. -- [2482](https://github.com/RuminantFarmSystems/RuFaS/pull/2554) - [minor change] [Animal] Restructure newborn calf status categorization and reporting. +- [2482](https://github.com/RuminantFarmSystems/RuFaS/pull/2482) - [minor change] [Animal] Restructure newborn calf status categorization and reporting. - [2550](https://github.com/RuminantFarmSystems/RuFaS/pull/2550) - [minor change] Create metadata for no animal scenario. - [2553](https://github.com/RuminantFarmSystems/RuFaS/pull/2553) - [minor change] [Input Manager] 3/5 Cross Validation: implement expression block. - [2567](https://github.com/RuminantFarmSystems/RuFaS/pull/2567) - [minor change] Creates and prints e2e testing results summary for all metadata e2e testing runs. @@ -248,7 +248,7 @@ v0.9.2 - [2598](https://github.com/RuminantFarmSystems/RuFaS/pull/2598) - [minor change] [FeedManager][Feed Storage] Adjust feed deduction logic to gather and remove available feeds by storage rather than crop. - [2587](https://github.com/RuminantFarmSystems/RuFaS/pull/2587) - [major change] [Output Manager] Add cross-scenario aggregation and running EEE to post processing task. - [2583](https://github.com/RuminantFarmSystems/RuFaS/pull/2583) - [minor change] [Github Action] Fix the GitHub Action for forked branches. -- [2579](https://github.com/RuminantFarmSystems/RuFaS/pull/2563) - [minor change] [Animal] Changed location of milking cow fraction to main animal input file. +- [2579](https://github.com/RuminantFarmSystems/RuFaS/pull/2579) - [minor change] [Animal] Changed location of milking cow fraction to main animal input file. - [2594](https://github.com/RuminantFarmSystems/RuFaS/pull/2594) - [minor change] [Manure] Fixed splitting-logic for manure_deposition_surface_area based on stream type. - [2586](https://github.com/RuminantFarmSystems/RuFaS/pull/2586) - [minor change] Make `max_daily_feed_recalculations_per_year` an User Input - [2584](https://github.com/RuminantFarmSystems/RuFaS/pull/2584) - [minor change] [Manure] Implement unit test for Processor.check_manure_stream_compatibility(). @@ -286,7 +286,7 @@ v0.9.2 - [2675](https://github.com/RuminantFarmSystems/RuFaS/pull/2675) - [minor change] [DataValidator] [NoInputChange] [NoOutputChange] Fixes and clarifies data fixing error messaging for IM. - [2674](https://github.com/RuminantFarmSystems/RuFaS/pull/2674) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Prevent simulation fails when metadata blobs for fields/manure/harvest does not exist. - [2678](https://github.com/RuminantFarmSystems/RuFaS/pull/2678) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Corrects a bug in Separators and adds a check to prevent a bug in Slurry Storage Outdoor, Slurry Storage Underfloor, and Anaerobic Lagoon. -- [2679](https://github.com/RuminantFarmSystems/RuFaS/pull/2678) - [minor change] [Feed] [NoInputChange] [OutputChange] Removes default reporting 0.0s for FGFs that aren't grown during a simulation +- [2679](https://github.com/RuminantFarmSystems/RuFaS/pull/2679) - [minor change] [Feed] [NoInputChange] [OutputChange] Removes default reporting 0.0s for FGFs that aren't grown during a simulation - [2688](https://github.com/RuminantFarmSystems/RuFaS/pull/2688) - [minor change] [InputManager] [NoInputChange] [NoOutputChange] Hot fix to correct the missing part of 2640. - [2689](https://github.com/RuminantFarmSystems/RuFaS/pull/2689) - [minor change] [InputManager] [InputChange] [NoOutputChange] Add support for multiple properties files. - [2701](https://github.com/RuminantFarmSystems/RuFaS/pull/2701) - [minor change] [EEEManager] [NoInputChange] [NoOutputChange] Hot fix to correct the failure in EEEManager.. From cf874c4a625d8faf08c10c9fac20cba282450f51 Mon Sep 17 00:00:00 2001 From: Kristan <41019131+KFosterReed@users.noreply.github.com> Date: Wed, 4 Mar 2026 15:55:55 -0500 Subject: [PATCH 6/6] Update changelog with recent minor changes --- changelog.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/changelog.md b/changelog.md index 93ce05778c..08c34e885f 100644 --- a/changelog.md +++ b/changelog.md @@ -282,7 +282,6 @@ v0.9.2 - [2655](https://github.com/RuminantFarmSystems/RuFaS/pull/2655) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated RationManager class to allow for more flexibility in user inputs in Feed input file. - [2670](https://github.com/RuminantFarmSystems/RuFaS/pull/2670) - [minor change] [Animal] [InputChange] [NoOutputChange] Updated Animal module unit testing to 100% coverage. - [2673](https://github.com/RuminantFarmSystems/RuFaS/pull/2673) - [minor change] [Feed] [InputChange] [NoOutputChange] Adds a default for purchased feed buffer of 0.15. - - [2675](https://github.com/RuminantFarmSystems/RuFaS/pull/2675) - [minor change] [DataValidator] [NoInputChange] [NoOutputChange] Fixes and clarifies data fixing error messaging for IM. - [2674](https://github.com/RuminantFarmSystems/RuFaS/pull/2674) - [minor change] [Feed] [NoInputChange] [NoOutputChange] Prevent simulation fails when metadata blobs for fields/manure/harvest does not exist. - [2678](https://github.com/RuminantFarmSystems/RuFaS/pull/2678) - [minor change] [Manure] [NoInputChange] [NoOutputChange] Corrects a bug in Separators and adds a check to prevent a bug in Slurry Storage Outdoor, Slurry Storage Underfloor, and Anaerobic Lagoon. @@ -304,10 +303,8 @@ v0.9.2 - [2732](https://github.com/RuminantFarmSystems/RuFaS/pull/2732) - [minor change] [NoInputChange] [NoOutputChange] Skip Animal module and Manure module if no animals are present in simulation. - [2739](https://github.com/RuminantFarmSystems/RuFaS/pull/2739) - [minor change] [NoInputChange] [NoOutputChange] Fixes manure outputs and updates E2E expected results accordingly. - [2763](https://github.com/RuminantFarmSystems/RuFaS/pull/2763) - [minor change] [NoInputChange] [NoOutputChange] Fixes feed order issue by sorting user feed inputs. - - [2760](https://github.com/RuminantFarmSystems/RuFaS/pull/2760) - [minor change] [NoInputChange] [OutputChange] [Feed][Emission] Implement dictionary reporting structure for feed deduction data ### v0.9.2 - - [1968](https://github.com/RuminantFarmSystems/RuFaS/pull/1968) - [minor change] [Changelog] Move the changelog from a Google sheet into a markdown document in the repository. - [1976](https://github.com/RuminantFarmSystems/RuFaS/pull/1976) - [minor change] [EEE] Add unit tests for the Emission module. - [1977](https://github.com/RuminantFarmSystems/RuFaS/pull/1977) - [minor change] [EEE] Improve emission.py codebase and clarity.