Feature/libcbm optional dependency (#47)#48
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gparadis merged 1 commit intofeature/ems-paperfrom Sep 28, 2025
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* 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
gparadis
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Oct 12, 2025
* first branch commit. refactored `paper` directory to split into `joss` and `ems` subdirectories * solid start on implementing draft plan * kicked the can down the road several more steps. repo make script works. ems paper makefile compiles `paper.tex`. good progress. * Feature/libcbm optional dependency (#47) (#48) * 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 * expand introduction and contribution framing, and add spatial allocation example (to master examples library and then to ems paper repro script list) * added scalability tests (the logic is not quite right yet, but they run 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. * fix broken scaling model logic and rerun tests and update paper. * improve figure and table layout * more table and figure format tweaks. not perfect but much better now * fix neilson hack figure scaling * fixed broken Neilson hack example logic, and added Woodstock parity table and text (temp placeholder numbers for Woodstock but real WS3 numbers). * minor tweaks and cleanup. almost ready to declare manuscript draft submission-ready. * Trying to patch ws3 to revert back to "time is always defined in periods in Woodstock input and output files". Messy. Not quite there yet, but close now. * Update Woodstock TSA24 clipped model files 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 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 parity test) * Fixed inventory method logic to match woodstock logic (works now: exact match) * fix citation.cff (now points to up to date zenodo DOI) and fully integrate FAIR readiness table into repro artifacts and paper * ems paper basically done now. just have to fix the new OBO bug in libcbm linkage induced by recent inventory method behaviour tweak to ensure woodstock parity * Fixed minor OBO bug in Neilson hack example script logic induced by recent 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
gparadis
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Oct 18, 2025
* first branch commit. refactored `paper` directory to split into `joss` and `ems` subdirectories * solid start on implementing draft plan * kicked the can down the road several more steps. repo make script works. ems paper makefile compiles `paper.tex`. good progress. * Feature/libcbm optional dependency (#47) (#48) * 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 * expand introduction and contribution framing, and add spatial allocation example (to master examples library and then to ems paper repro script list) * added scalability tests (the logic is not quite right yet, but they run 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. * fix broken scaling model logic and rerun tests and update paper. * improve figure and table layout * more table and figure format tweaks. not perfect but much better now * fix neilson hack figure scaling * fixed broken Neilson hack example logic, and added Woodstock parity table and text (temp placeholder numbers for Woodstock but real WS3 numbers). * minor tweaks and cleanup. almost ready to declare manuscript draft submission-ready. * Trying to patch ws3 to revert back to "time is always defined in periods in Woodstock input and output files". Messy. Not quite there yet, but close now. * Update Woodstock TSA24 clipped model files 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 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 parity test) * Fixed inventory method logic to match woodstock logic (works now: exact match) * fix citation.cff (now points to up to date zenodo DOI) and fully integrate FAIR readiness table into repro artifacts and paper * ems paper basically done now. just have to fix the new OBO bug in libcbm linkage induced by recent inventory method behaviour tweak to ensure woodstock parity * Fixed minor OBO bug in Neilson hack example script logic induced by recent 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 * final tweak for eartharxiv preprint * add prisma latex sty file and graphical abstract image file * replace placeholder graphical abstract with proper image file, and swap out placeholder figure 1 workflow diagram with new prisma-based version * final tweaks applied. should be ready for ems submission now * save initial reference validation script output * add reference validation script and document use in README * rebuild pdf one last time to make sure that all is well
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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