Feature/ems paper by gparadis · Pull Request #49 · UBC-FRESH/ws3

gparadis · 2025-10-12T06:52:45Z

EMS manuscript package and Woodstock/libCBM parity improvements

Split publications into papers/joss and papers/ems, author the full EMS manuscript, and wire LaTeX assets (figures, tables, FAIR checklist, citations) with deterministic repro scripts.
Refresh the examples suite: expand sequential/spatial/libCBM notebooks, add scaling and parallel-scheduling studies, and update TSA24 clipped Woodstock inputs plus growing-stock outputs to support new figures.
Harden Woodstock parity: rework ForestModel.inventory semantics, regenerate parity tables/figures (incl. Neilson hack assets), and add optional ws3[cbm] dependency path for libCBM linkage.
Polish project metadata (README, CHANGELOG, CONTRIBUTING, CITATION.cff) and bump the package version to 1.0.5 in preparation for release/Zenodo archiving.

…` and `ems` subdirectories

…ks. ems paper makefile compiles `paper.tex`. good progress.

* remove libcbm from pyproject.toml required deps list and move to optional deps list (so does not block publication on conda-forge) * increment version to 1.0.3 * move gurobi and pulp deps to to optional, bump version to 1.0.4

…ion example (to master examples library and then to ems paper repro script list)

…un without errors and give mostly sane results) and integrated these into the text. updated readiness checklist and are basically at a soft "full green light" status (but weak). first complete draft now (no missing pieces). about to start a first round of critical review and improvements.

…able and text (temp placeholder numbers for Woodstock but real WS3 numbers).

…bmission-ready.

…ods in Woodstock input and output files". Messy. Not quite there yet, but close now.

Added everything.txt and tsa24_clipped.rep report files. Updated .act, .are, .run, and .seq files with new parameters, corrected values, and revised scheduling and reporting outputs for the TSA24 clipped model.

Uncommented and configured growing stock output in tsa24_clipped.out, added growing_stock values to everything.txt, and updated file timestamps. This change allows tracking of growing stock across periods in the TSA24 clipped model.

…rity test)

…ct match)

…grate FAIR readiness table into repro artifacts and paper

…cbm linkage induced by recent inventory method behaviour tweak to ensure woodstock parity

…ecent tweak to inventory compile logic (needed to ensure woodstock logic parity). Good to go now to PR and lock in!

gparadis and others added 23 commits September 28, 2025 15:45

first branch commit. refactored paper directory to split into `joss…

7d871c6

…` and `ems` subdirectories

solid start on implementing draft plan

3920db7

kicked the can down the road several more steps. repo make script wor…

4fcf624

…ks. ems paper makefile compiles `paper.tex`. good progress.

Feature/libcbm optional dependency (#47) (#48)

0b0ed0e

* remove libcbm from pyproject.toml required deps list and move to optional deps list (so does not block publication on conda-forge) * increment version to 1.0.3 * move gurobi and pulp deps to to optional, bump version to 1.0.4

expanding repro example scope

b1e119e

expand introduction and contribution framing, and add spatial allocat…

27d8ebe

…ion example (to master examples library and then to ems paper repro script list)

fix broken scaling model logic and rerun tests and update paper.

fa95706

improve figure and table layout

b30a237

more table and figure format tweaks. not perfect but much better now

e93e6dc

fix neilson hack figure scaling

1cf2057

fixed broken Neilson hack example logic, and added Woodstock parity t…

2100aca

…able and text (temp placeholder numbers for Woodstock but real WS3 numbers).

minor tweaks and cleanup. almost ready to declare manuscript draft su…

ff238b4

…bmission-ready.

Trying to patch ws3 to revert back to "time is always defined in peri…

44096a0

…ods in Woodstock input and output files". Messy. Not quite there yet, but close now.

Update Woodstock TSA24 clipped model files

24b883e

Added everything.txt and tsa24_clipped.rep report files. Updated .act, .are, .run, and .seq files with new parameters, corrected values, and revised scheduling and reporting outputs for the TSA24 clipped model.

Enable growing stock output in Woodstock model files

109944a

Uncommented and configured growing stock output in tsa24_clipped.out, added growing_stock values to everything.txt, and updated file timestamps. This change allows tracking of growing stock across periods in the TSA24 clipped model.

Fix inventory method logic to match woodstock logic (for ems paper pa…

d3d129d

…rity test)

Fixed inventory method logic to match woodstock logic (works now: exa…

350b96f

…ct match)

fix citation.cff (now points to up to date zenodo DOI) and fully inte…

2b20386

…grate FAIR readiness table into repro artifacts and paper

ems paper basically done now. just have to fix the new OBO bug in lib…

fd0ca3d

…cbm linkage induced by recent inventory method behaviour tweak to ensure woodstock parity

Fixed minor OBO bug in Neilson hack example script logic induced by r…

aabe570

…ecent tweak to inventory compile logic (needed to ensure woodstock logic parity). Good to go now to PR and lock in!

bump version to 1.0.5

da5caa4

Merge branch 'dev' into feature/ems-paper

687f452

gparadis merged commit 2032d8b into dev Oct 12, 2025
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Feature/ems paper#49

Feature/ems paper#49
gparadis merged 23 commits intodevfrom
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gparadis commented Oct 12, 2025

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gparadis commented Oct 12, 2025

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