femic

Hello!

Documentation

Published docs (target URL): https://ubc-fresh.github.io/femic/

The docs are now split into:

• Guides: end-to-end workflow narrative recovered from legacy notebook text, with stage assumptions, QA interpretation, and troubleshooting playbooks.
• Reference: compact technical contracts plus CLI, API, and export/run-profile contracts.

If you want the shortest source-of-truth pages for repo invariants, instance roots, external data, stage boundaries, and restart behavior, start with:

• docs/reference/contracts/index.rst

Legacy notebook narrative provenance is preserved in:

• docs/guides/legacy-traceability.rst
• docs/guides/legacy_notebook_coverage.csv

New case onboarding starters:

• docs/guides/case-onboarding.rst
• instances/reference/config/run_profile.case_template.yaml
• instances/reference/config/tipsy/template.case.yaml

Developer Bootstrap (Fresh Clone)

For source-checkout development, use a repo-local virtual environment and editable install:

python -m venv .venv
. .venv/bin/activate
python -m pip install --upgrade pip setuptools wheel
python -m pip install -r requirements-dev.txt

This installs FEMIC in editable mode (-e .) plus development tools and DataLad (datalad[full]).

Then bootstrap annex-backed submodules and materialize real file content:

git submodule update --init --recursive
git annex version
datalad --version
git -C external/femic-public-data annex enableremote arbutus-s3
datalad get -r external/femic-public-data/data

Set the external data root for case preflight/runs:

export FEMIC_EXTERNAL_DATA_ROOT=$PWD/external/femic-public-data/data

Preflight before long runs:

femic prep validate-case --instance-root external/femic-k3z-instance --run-config config/run_profile.k3z.yaml
femic prep geospatial-preflight

If git annex version fails, install git-annex at the OS level and re-open the shell before retrying.

Full Scripted Bootstrap

Linux/macOS:

python -m venv .venv
. .venv/bin/activate
python -m pip install --upgrade pip setuptools wheel
python -m pip install -r requirements-dev.txt
python -m femic --help
ruff --version
mypy --version
pytest --version
pre-commit --version
sphinx-build --version
git annex version
datalad --version
git submodule update --init --recursive
git -C external/femic-public-data annex enableremote arbutus-s3
datalad get -r external/femic-public-data/data
export FEMIC_EXTERNAL_DATA_ROOT=$PWD/external/femic-public-data/data
femic prep validate-case --instance-root external/femic-k3z-instance --run-config config/run_profile.k3z.yaml
femic prep geospatial-preflight

Windows PowerShell:

python -m venv .venv
.venv\Scripts\Activate.ps1
python -m pip install --upgrade pip setuptools wheel
python -m pip install -r requirements-dev.txt
python -m femic --help
ruff --version
mypy --version
pytest --version
pre-commit --version
sphinx-build --version
git annex version
.venv\Scripts\datalad.exe --version
git submodule update --init --recursive
git -C external/femic-public-data annex enableremote arbutus-s3
.venv\Scripts\datalad.exe get -r external/femic-public-data/data
$env:FEMIC_EXTERNAL_DATA_ROOT="$PWD\external\femic-public-data\data"
femic prep validate-case --instance-root external/femic-k3z-instance --run-config config/run_profile.k3z.yaml
femic prep geospatial-preflight

If you are doing FEMIC work from VS Code/Cursor on Windows with a local Codex agent and assistant-rendered file links are opening in the browser instead of the editor, use the lab-maintained patch utility before fighting the IDE:

• https://github.com/UBC-FRESH/codex-local-file-link-patch

That repo includes agent-facing bootstrap notes plus a PowerShell patcher for the recurring Windows openai.chatgpt local-file-link regression.

The canonical guide version of this bootstrap ritual lives in docs/guides/developer-environment-bootstrap.rst. The compact companion contract page is docs/reference/contracts/repo-runtime-invariants.rst. For local VS Code/Codex workflow guidance, including this Windows recovery seam, see docs/guides/vscode-coding-agent-onboarding.rst. If you are creating or publishing a new DataLad-managed FEMIC instance dataset with an Arbutus special remote, use docs/guides/public-data-mirror-runbook.rst as the canonical maintainer runbook, especially on Windows.

Bundled Example Instances Under external/

This checkout carries the published example instances as git submodules:

• external/femic-k3z-instance
• external/femic-tsa29-instance

Use them as the bundled runtime roots when you want to run, amend, or rebuild the example cases from this FEMIC checkout.

Important rule of thumb:

• change FEMIC code/docs/tests in the parent repo;
• change example-instance configs, runbooks, and tracked case artifacts inside the submodule repo;
• if the bundled submodule should move to a new upstream commit, commit inside the submodule first, then commit the updated submodule pointer in FEMIC.

Typical amend/rebuild loop for K3Z from the FEMIC checkout:

Linux/macOS:

export FEMIC_EXTERNAL_DATA_ROOT=$PWD/external/femic-public-data/data
femic prep validate-case --instance-root external/femic-k3z-instance --run-config config/run_profile.k3z.yaml
femic prep geospatial-preflight
femic instance validate-spec --instance-root external/femic-k3z-instance --spec config/rebuild.spec.yaml
femic instance rebuild --instance-root external/femic-k3z-instance --spec config/rebuild.spec.yaml --baseline config/rebuild.baseline.json --allowlist config/rebuild.allowlist.yaml --run-config config/run_profile.k3z.yaml --run-id <run-id>

Windows PowerShell:

$env:FEMIC_EXTERNAL_DATA_ROOT="$PWD\external\femic-public-data\data"
femic prep validate-case --instance-root external/femic-k3z-instance --run-config config/run_profile.k3z.yaml
femic prep geospatial-preflight
femic instance validate-spec --instance-root external/femic-k3z-instance --spec config/rebuild.spec.yaml
femic instance rebuild --instance-root external/femic-k3z-instance --spec config/rebuild.spec.yaml --baseline config/rebuild.baseline.json --allowlist config/rebuild.allowlist.yaml --run-config config/run_profile.k3z.yaml --run-id <run-id>

Review the rebuild report at:

• external/femic-k3z-instance/vdyp_io/logs/instance_rebuild_report-<run-id>.json

Then commit in the correct repository:

• local experiment only: leave the submodule working tree dirty;
• persistent instance change: commit inside external/femic-k3z-instance or external/femic-tsa29-instance;
• parent FEMIC update to a new bundled instance revision: commit the submodule pointer change in FEMIC after the submodule commit exists.

The source-of-truth guide for this workflow is docs/guides/deployment-instances.rst.

BC Data Catalogue Discovery

FEMIC now includes a first-pass BC Data Catalogue resolver for turning likely TSR source-layer names into ranked catalogue matches, resource classifications, and optional direct downloads.

Resolve a likely BCDC object name:

& .\.venv\Scripts\python.exe -m femic data bcdc-resolve WHSE_FOREST_VEGETATION.F_OWN

Exercise the direct-download path when the top match exposes stable file resources:

& .\.venv\Scripts\python.exe -m femic data bcdc-resolve SITE_PROD_BC --download-direct --download-root data\downloads\bcdc --manifest-path runtime\logs\bcdc_site_prod_bc_manifest.json

For the fuller guide, classification buckets, and PowerShell quoting notes for multi-word queries, see docs/guides/bc-data-catalogue-discovery.rst.

CLI

Run the legacy pipeline through the FEMIC CLI:

femic run --tsa 08 --resume

femic run executes the legacy script in an isolated subprocess and filters known non-fatal shutdown noise lines from legacy stderr output. Each run writes a manifest at vdyp_io/logs/run_manifest-<run_id>.json and uses run-scoped VDYP log files (per TSA + run id). For each TSA, raw VDYP process streams are also captured to: vdyp_io/logs/vdyp_stdout-tsa<tsa>-<run_id>.log and vdyp_io/logs/vdyp_stderr-tsa<tsa>-<run_id>.log.

Quickstart (End-to-End)

1. Install package and initialize a deployment instance workspace:

python -m pip install femic
mkdir -p ~/femic-instance
cd ~/femic-instance
femic instance init

This scaffolds config/, data/, output/, and vdyp_io/logs/ under the current directory, and prompts to download standard BC VRI 2024 datasets. Use --no-download-bc-vri to skip dataset download during bootstrap.

2. Validate base install:

femic --help

3. Validate TIPSY config handoff files:

femic tipsy validate --config-dir config/tipsy --tsa 08

4. Run one TSA with resume enabled:

femic run --tsa 08 --resume

5. Summarize VDYP diagnostics:

femic vdyp report

6. After manual BatchTIPSY output is uploaded, run downstream stages only (01b + bundle):

femic tsa post-tipsy --tsa 29 -v

This command writes a run manifest to vdyp_io/logs/ (override with --log-dir and --run-id). When data/ria_vri_vclr1p_checkpoint8.feather is available, post-TIPSY bundle assembly also adds species-proportion curves for all top-6 VRI species present in the selected TSA(s): untreated_species_prop_<SPP> and treated_species_prop_<SPP> (single-point curves at x=1).

7. Export Patchworks starter package (ForestModel XML + fragments shapefile):

femic export patchworks --tsa k3z

By default this command reads bundle tables from data/model_input_bundle/ and stand geometry from data/ria_vri_vclr1p_checkpoint7.feather, then writes:

• output/patchworks/forestmodel.xml
• output/patchworks/fragments/fragments.shp

In the fragments shapefile, each row is one stand-fragment record. In the current exporter, BLOCK is one-to-one with these fragment rows.

Patchworks XML now includes species-wise yield attributes derived as TotalVolume(age) * SpeciesProportion(age) for unmanaged and managed tracks. CC treatment minimum age is now resolved per AU as CMAI(managed_total_curve)-20 (clamped to 0..--cc-max-age). ForestModel feature attributes also include old-growth indicators for each AU and totals:

• feature.Area.og1.<au_id> and feature.Area.og1.total
• feature.Area.og2.<au_id> and feature.Area.og2.total

og1 ramps linearly from 0 at unmanaged-curve CMAI age to 1 at unmanaged peak-yield age. og2 is a policy-step indicator that snaps from 0 at age 249 to 1 at age 250.

If your checkpoint carries continuous THLB signal values (for example thlb_raw in [0, 1]), you can tune managed/unmanaged assignment at export time:

femic export patchworks --tsa k3z --ifm-source-col thlb_raw --ifm-target-managed-share 0.8

To include seral-stage attributes in ForestModel output, provide a YAML config:

femic export patchworks --tsa k3z --seral-stage-config config/seral.k3z.yaml

With seral config enabled, export writes inventory-state accounts (feature.Seral.*) plus CC-treatment consequence area accounts with AU/stage specific labels (product.Seral.area.<stage>.<au_id>.CC).

8. (Optional) Run proprietary Patchworks Matrix Builder under Wine:

femic patchworks preflight --config config/patchworks.runtime.yaml
femic patchworks build-blocks --config config/patchworks.runtime.yaml
femic patchworks matrix-build --config config/patchworks.runtime.yaml

Runtime logs/manifests are written to vdyp_io/logs/ with run-scoped names: patchworks_matrixbuilder_stdout-<run_id>.log, patchworks_matrixbuilder_stderr-<run_id>.log, and patchworks_matrixbuilder_manifest-<run_id>.json. Set both SPS_LICENSE_SERVER and SPSHOME (or define patchworks.license_value and patchworks.spshome in config/patchworks.runtime.yaml). FEMIC preflight validates runtime/config state only; Patchworks performs license-server checks during launch. On native Windows hosts, femic patchworks launches Patchworks directly via the local java runtime (no Wine). Matrix-build completion is validated by expected tracks output artifacts and fatal-log signatures rather than JVM exit code alone. femic patchworks build-blocks creates a 1:1 stand:block dataset at <model>/blocks/blocks.shp (with BLOCK copied from FEATURE_ID/FRAGS_ID) and, by default, writes <model>/blocks/topology_blocks_200r.csv for PIN wiring. The tracked teaching prototype model now lives in-repo at models/k3z_patchworks_model/, and config/patchworks.runtime.windows.yaml points to this location.

9. Export Woodstock compatibility CSV package:

femic export woodstock --tsa k3z

This currently writes:

• output/woodstock/woodstock_yields.csv
• output/woodstock/woodstock_areas.csv
• output/woodstock/woodstock_actions.csv
• output/woodstock/woodstock_transitions.csv

Developer note: the preferred source-checkout path is editable install (python -m pip install -r requirements-dev.txt) so femic and python -m femic work without PYTHONPATH hacks. If you intentionally skip editable install, use PYTHONPATH=src python -m femic ....

Config-Driven Runs

Use a YAML/JSON profile to seed TSA selection and run modes:

PYTHONPATH=src python -m femic run --run-config instances/reference/config/run_profile.case_template.yaml

Profile schema and precedence are documented at docs/reference/run-config.rst. --run-config values are merged with CLI options; explicit CLI values still win for --tsa, --debug-rows, and --run-id.

Custom management-unit runs are also supported via run profile fields: selection.boundary_path, selection.boundary_layer, and selection.boundary_code. Example profile: config/run_profile.k3z.yaml (North Island Community Forest test case).

Validate case prerequisites before long runs:

PYTHONPATH=src python -m femic prep validate-case --run-config instances/reference/config/run_profile.<case>.yaml

Package Release Checks

Run package build/release-readiness checks locally:

python -m pip install build twine
scripts/release_package_checks.sh

For staged publication (TestPyPI then PyPI), use: docs/guides/pypi-release-runbook.rst.

Reproducibility Controls

Set deterministic VDYP sampling with:

export FEMIC_SAMPLING_SEED=42

Run manifests include:

• runtime_versions (tool/package versions)
• runtime_parameters (effective FEMIC env/runtime settings)
• config_provenance (run_config_path, run_config_sha256)
• outputs (output_root, version_tag, versioned_output_dir)

For faster debugging, limit the number of VRI rows processed (this disables cached checkpoints and output reuse):

femic run --tsa 08 --resume --debug-rows 1000

You can override run metadata/log routing:

femic run --tsa 08 --resume --run-id mytest01 --log-dir vdyp_io/logs

If --tsa is omitted, defaults are loaded from config/dev.toml ([run].default_tsa_list).

Note: In debug mode, some strata may lack VDYP curves. These are skipped with a warning. Rows whose strata do not map to an AU/curve (missing VDYP curves) are dropped with a warning summary. Debug mode also skips final TSA stand shapefile export by default; set FEMIC_SKIP_STANDS_SHP=0 to force shapefile output while debugging. ipyparallel is disabled by default (FEMIC_DISABLE_IPP=1) for stability; set FEMIC_DISABLE_IPP=0 to re-enable controller-backed execution. Row-wise operations default to pandas .apply(...); set FEMIC_USE_SWIFTER=1 to opt back into swifter acceleration.

VDYP diagnostics are written to vdyp_io/logs/ as JSONL files (e.g., vdyp_runs.jsonl, vdyp_curve_events.jsonl) to capture run status and curve-fit warnings. Summarize these logs with:

femic vdyp report

For regression checks in CI, apply warning-budget thresholds (command exits non-zero on breach):

femic vdyp report --max-curve-warnings 2 --max-first-point-mismatches 0 --min-curve-events 5 --min-run-events 6

Yield curves are anchored to a quasi-origin point (1, 1e-6) so downstream positive-value filters can remain unchanged while avoiding zero-age intercept issues.

Raw BC datasets are expected under ../data relative to your instance root (for example, if you run from instances/reference, this resolves to data/bc/vri/2019/VEG_COMP_LYR_R1_POLY.gdb at the workspace level). You can override this by setting FEMIC_EXTERNAL_DATA_ROOT to a different base path.

TIPSY Handoff Boundary

The TIPSY stage is currently a human-in-the-loop boundary:

1. Expert modeller derives TSA/AU-specific TIPSY parameter logic from TSR data packages.
2. FEMIC generates batch TIPSY input tables from that logic.
3. Batch TIPSY is run manually in Windows GUI.
4. Raw TIPSY output is copied back to Linux for automated downstream stages.

Draft config scaffolding for this handoff now lives in config/tipsy/:

• config/tipsy/README.md
• config/tipsy/template.tsa.yaml
• config/tipsy/tsa08.yaml and config/tipsy/tsa16.yaml (concrete TSA configs migrated from legacy logic)
• config/tipsy/tsa24.yaml (BEC-dependent branching migration from legacy logic)
• config/tipsy/tsa40.yaml and config/tipsy/tsa41.yaml (dynamic species-rank and forest-type-driven migrations)

If a TSA config file exists at config/tipsy/tsaXX.yaml (or .yml), the legacy run path now prefers that config for TIPSY parameter generation for that TSA. Override the config directory with FEMIC_TIPSY_CONFIG_DIR. If no config exists for a requested TSA, the run now fails fast unless FEMIC_TIPSY_USE_LEGACY=1 is set.

Validate TIPSY config handoff files before running:

femic tipsy validate --config-dir config/tipsy --tsa 08 --tsa 16

Config-driven TIPSY rules now also support deterministic weak-mapping controls:

• species_code_overrides (for example DR: FD, SX: SW)
• siteprod_si_fallback_by_species (species-specific SI fallback values when siteprod values are missing/invalid)

Patchworks Runtime Boundary

Patchworks software binaries are proprietary and must be supplied locally by users; the repository ignores reference/Patchworks/ by default and does not publish these runtime assets.

VDYP fit diagnostics also emit per-stratum L/M/H comparison overlays at: plots/vdyp_lmh_tsa<tsa>-<stratum>-<stratum_code>.png.