New Structure, regions & parallelization by jnnsbrr · Pull Request #15 · pik-copan/inseeds

jnnsbrr · 2026-02-10T14:28:18Z

Implementation of regions (countries) into InSEEDS and parallelization based on countries

Structural changes in InSEEDS structure:

realisations folder instead of models
component.py has been moved entirely to each realisation for more explicit control of model wiring
flat (no nested) structure of each component (farming, etc.)

Copilot

Pull request overview

This PR restructures InSEEDS “models” into “realisations”, introduces a country/region (3-level) hierarchy intended to enable country-level parallelization, and updates tests + CI to match the new structure and output collection approach.

Changes:

Added new regenerative_tillage_regions realisation (Model/main/config) with country-level entities and parallelization settings.
Migrated regenerative_tillage to the new realisations/ structure and adjusted model update/output collection flow.
Expanded/rewrote tests + pytest fixtures, and enhanced CI workflows (coverage, build checks) plus a new release workflow.

Reviewed changes

Copilot reviewed 44 out of 48 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
`inseeds/realisations/regenerative_tillage_regions/model.py`	New regions-aware model wiring (World/Country/Cell/Farmer) and per-year update flow
`inseeds/realisations/regenerative_tillage_regions/main.py`	New entry point using `pycopanlpjml.run.run_simulation`
`inseeds/realisations/regenerative_tillage_regions/config.yaml`	Adds parallelization/output configuration for regions run
`inseeds/realisations/regenerative_tillage/model.py`	Updates model to use `lpjml.Model`, new init/update/output collection behavior
`inseeds/realisations/regenerative_tillage/main.py`	Updates imports to the new realisations location
`inseeds/components/farming/*`	Adds `Region/Country` mixins, updates `World.update`, refactors tillage farmer base class usage
`inseeds/components/base/*`	Removes local output-writing logic; migrates to `pycopanlpjml` output mixins/classes
`tests/conftest.py`	Reworks fixtures to cache LPJmL pickles and create/run models once per session
`tests/test_regenerative_tillage.py`	Updates tests for new structure/output comparison approach
`tests/test_regenerative_tillage_regions.py`	New test suite for 3-level hierarchy and compatibility checks
`tests/test_components_base.py` / `tests/test_components_farming.py` / `tests/test_main.py`	Adds unit/import/entry-point tests
`.github/workflows/check.yml`	Updates CI: newer setup-python, coverage scope, build + twine checks
`.github/workflows/release.yml`	Adds automated release pipeline (tests, lint, build, PyPI publish, GH release)
`CITATION.cff`	Updates cited version metadata
`README.md`	Updates documentation to refer to `realisations/` structure
`scripts/*` and `tests/data/write_testdata.py`	Updates script paths and LPJmL run helper usage for new layout

Comments suppressed due to low confidence (1)

inseeds/realisations/regenerative_tillage/model.py:121

has_crops is an xarray DataArray comparison, so if not has_crops: will raise (DataArray has no truth value). Convert to a Python bool/scalar first (e.g., use .item() / .values.item() after the reduction) before using it in the if condition.

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Copilot · 2026-02-10T14:32:53Z

+    # 'mpi' = reuse LPJmL's MPI processes (recommended if LPJmL uses MPI)
+    # 'serial' = force serial execution
+    mode: 'dask' # 'auto'
+


This config hard-codes parallelization mode: 'dask'. If Dask isn't installed/available in the target environment, runs will fail even though auto/serial would work. Consider defaulting to auto (as in the non-regions config) and documenting how to opt into Dask explicitly.

Copilot · 2026-02-10T14:32:53Z

 type: software
 title: 'Model of integrated social-ecological resilient land systems (InSEEDS)'
-version: 0.2.8
+version: 1.2.0


pyproject.toml still declares the package version as 0.2.8, but CITATION.cff is updated to 1.2.0. Align these versions (or document why they intentionally differ) so packaging, releases, and citation metadata stay consistent.

Suggested change

version: 1.2.0

version: 0.2.8

Copilot · 2026-02-10T14:32:53Z

+            self.countries = []
+            print(
+                "Warning: No country data available. "
+                "Running without country-level structure."
+            )


Library code prints a warning directly during model initialization. This is hard to control for downstream users and test runners; prefer warnings.warn(...) or the project logger so callers can filter/redirect it.

Copilot · 2026-02-10T14:32:54Z

+    # @property
+    # def farmers(self):
+    #     """Return the set of all farmers."""
+    #     farmers = {
+    #         farmer
+    #         for farmer in self.individuals
+    #         if farmer.__class__.__name__ == "Farmer"  # noqa
+    #     }
+    #     return farmers

-    @property
-    def farmer(self):
-        """Return the first farmer."""
-        farmers = self.farmers
-        if len(farmers) == 0:
-            return None
-        return list(farmers)[0]
+    # @property
+    # def farmer(self):
+    #     """Return the first farmer."""
+    #     farmers = self.farmers
+    #     if len(farmers) == 0:
+    #         return None
+    #     return list(farmers)[0]


This file comments out the farmers/farmer properties rather than removing them or keeping them implemented. Consider deleting the dead commented code (or reintroducing the properties if still part of the public API) to keep the module clean and avoid confusion.

Copilot · 2026-02-10T14:32:54Z

+            has_crops = cell.from_earth.cftfrac.sum("band") > 0
+            if not has_crops:
+                continue


has_crops is an xarray DataArray comparison, so if not has_crops: will raise (DataArray has no truth value). Convert to a Python bool/scalar first (e.g., use .item() / .values.item() after the reduction) before using it in the if condition.

Copilot · 2026-02-10T14:32:54Z

  build:
    runs-on: ubuntu-latest
+    permissions:
+      contents: write


This workflow grants contents: write, but it only checks out code, runs tests/lint/build, and uploads coverage. Reduce to least-privilege (typically contents: read) to avoid unnecessarily broad repository write permissions for PRs.

Suggested change

contents: write

contents: read

jnnsbrr added 8 commits June 5, 2025 09:05

draft for regions support

3ac6289

control run fix and improve data writing

492bc46

Merge branch 'fix_update' into regions

eeeff4b

add new model for both region and without region compatibility

75c9c18

implement working regions and parallelization

70c913c

add tests, restructure and update to new workflow

2bed079

Version 1.2.0

3861b9f

fix linter errors

5c1fc77

jnnsbrr requested a review from Copilot February 10, 2026 14:28

Copilot started reviewing on behalf of jnnsbrr February 10, 2026 14:28 View session

jnnsbrr requested a review from hannah-pra February 10, 2026 14:29

Copilot AI reviewed Feb 10, 2026

View reviewed changes

jnnsbrr added 2 commits February 10, 2026 16:13

fix version

0a67dbd

Version 0.3.0

e0536e1

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New Structure, regions & parallelization - #15

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jnnsbrr commented Feb 10, 2026

Implementation of regions (countries) into InSEEDS and parallelization based on countries

Structural changes in InSEEDS structure:

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