chore: update changelog for v0.3.11 [skip ci]

Reviewed-on: #85

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.3.10"
+current_version = "0.3.11"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

.gitea/workflows/ci.yml

@@ -28,9 +28,6 @@ jobs:
           echo "UV_LINK_MODE=copy" >> "$GITHUB_ENV"
       - run: uv sync --extra cpu --extra dev
       - run: uv run ruff check .
-      # The uv cache is a persistent volume shared by every job on this
-      # runner, so each job trims what it no longer needs before exiting.
-      - run: uv cache prune --ci
 
   ruff-format:
     name: Format (ruff format)
@@ -49,7 +46,6 @@ jobs:
           echo "UV_LINK_MODE=copy" >> "$GITHUB_ENV"
       - run: uv sync --extra cpu --extra dev
       - run: uv run ruff format --check .
-      - run: uv cache prune --ci
 
   type-check:
     name: Type check (ty)
@@ -68,7 +64,6 @@ jobs:
           echo "UV_LINK_MODE=copy" >> "$GITHUB_ENV"
       - run: uv sync --extra cpu --extra dev
       - run: uv run ty check .
-      - run: uv cache prune --ci
 
   test:
     name: Tests
@@ -92,7 +87,6 @@ jobs:
         with:
           name: coverage-report
           path: coverage.xml
-      - run: uv cache prune --ci
 
   bump-version:
     name: Bump version, tag, and update changelog on merge to master
@@ -179,10 +173,6 @@ jobs:
             git tag -a "$TAG" -m "$TAG"
             git push origin "refs/tags/$TAG"
           fi
-      # Same guard as every other step here: on a non-merge push uv was never
-      # set up, so there is nothing to prune.
-      - run: uv cache prune --ci
-        if: steps.merge_check.outputs.is_merge == 'true'
 
   sync-version-on-tag:
     name: Sync project version with tag
@@ -211,4 +201,3 @@ jobs:
           else
             echo "Tag version matches project version ($CURRENT_VERSION)"
           fi
-      - run: uv cache prune --ci

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.3.11] - 2026-08-26
+
+### Changed
+
+- Feat(analysis): per-step secondary multiplicity plots
+
 ## [0.3.10] - 2026-08-26
 
 ### Changed

CLAUDE.md

@@ -9,7 +9,6 @@ uv sync --extra cpu                # install dependencies with CPU-only torch (s
 uv sync --extra cuda               # install dependencies with CUDA 11.8 torch
 uv sync --extra cpu --extra dev    # add dev extras (pytest, ruff, ty, bump-my-version, git-cliff, + all runtime extras)
 uv sync --extra cpu --extra geometry  # add scikit-learn for the geometry oracle (giant rollout)
-uv sync --extra cpu --extra workflow  # add b2luigi for `giant workflow` pipeline orchestration
 pytest               # run tests
 giant new-run --hidden-dim 512 --lr 3e-4        # scaffold a config.toml + run dir ahead of training
 giant train path/to/steps.parquet               # train (defaults: stage 1 flow, stage 2 wgan + autoregressive)
@@ -19,9 +18,8 @@ giant train path/to/steps.parquet --router --router-type energy  # MoE routing t
 giant model summary --config config.toml         # build-only: parameter counts + which config keys actually bite
 giant predict path/to/steps.parquet --checkpoint ckpt/best.pt   # per-step predictions
 giant rollout path/to/steps.parquet --checkpoint ckpt/best.pt --geometry oracle.pkl  # full showers
-giant workflow run spec.toml --batch --workers 20          # whole pipeline (cache-warm -> train -> rollout -> analysis)
-giant analyze prep rollout.yaml --chunks 32                # lay out an analysis run dir (compute jobs come from the workflow)
-giant analyze render <run_dir> --gallery                   # render PDFs + HTML gallery (run_dir from prep)
+giant analyze submit rollout.yaml --accounting-group cms   # parallel rollout-vs-reference analysis on HTCondor
+giant analyze render <run_dir> --gallery                   # render PDFs + HTML gallery (run_dir from prep/submit)
 giant analyze metrics <train_run_dir>                      # training-progress plots from metrics.csv
 dwarf --help                                     # dataset/tooling CLI: convert, migrate, bump-gen,
                                                   # bump-schema, status, update-manifest, create-manifest,
@@ -53,7 +51,7 @@ Work on this repo happens across three kinds of machine:
 
 - **Local dev machines** (laptop + desktop, identical): repo at `~/Programming/giant`, no access to `/ceph` — datasets, training results, and models aren't reachable here.
 - **Portal machines** (`portal1`, `deepthought`, `deepthought2`, `bms1`, `bms2`, `bms3`): repo lives under `/work`, and `/ceph` holds ROOT/parquet files and trained models. **These are shared with other users** — stay strictly within `/work/lbogner` and `/ceph/lbogner`, and keep resource usage to roughly a quarter of CPU/RAM and a single GPU so as not to disturb other users' jobs.
-- **HTCondor worker nodes**: never run or SSH onto these directly — the only sanctioned path is `giant workflow run <spec.toml> --batch` (b2luigi, see the Workflow section), which submits and polls every job. `/ceph` is available there; `/work` is only sometimes mounted, depending on the node.
+- **HTCondor worker nodes**: never run or SSH onto these directly — the only sanctioned path is submitting jobs through condor (`giant analyze submit`, and the in-progress remote-GPU train/rollout submission on `condor-gpu-train-rollout`). `/ceph` is available there; `/work` is only sometimes mounted, depending on the node.
 
 ## Architecture
 
@@ -99,11 +97,9 @@ Secondary energies are a **stick-breaking partition of the `e_sec` budget** from
 
 **Validation** (`giant/validate.py`): step-level marginal + KL-divergence comparisons during training (`--validate-every`).
 
-**Analysis** (`giant/analysis/`, `giant analyze` CLI): a lean, streaming rollout-vs-reference plotting pipeline that compares one or more autoregressive `giant rollout` runs against a single held-out miniCaloSim reference steps file shared by all of them, and produces publication-styled PDFs assembled into an HTML gallery — one distinctly colored series per rollout, one reference line/panel. It exploits the fact that rollout output and a raw reference file share a world-frame physical column subset under identical names (`pre_*`/`post_*`/`edep`/`step_length`/`pdg`/`material`/`event_id`), so no ALR/local-frame decode is needed — everything is world-frame mm/MeV. Structure: `sources.py` (canonical LazyFrames + `RolloutSpec`/`Side` — a rollout's opened frames + per-checkpoint diagnostic inputs — + synthetic-termination-row filtering + the secondary view, which is `generation>0 & step_no==0` rollout tracks vs exploded `sec_*_list` reference columns), `variables.py` (the per-step value expressions shared by range sizing and the plot registry), `reduce.py` (the streaming primitives — a single `hist1d` `group_by([group,bin]).len()` pass, per-event scalars, edep-weighted depth/transverse profiles, species share, leakage), `grouping.py`/`context.py` (fixed bin edges + energy-quantile/pdg/material group sets resolved once by `prep` into `shared.json` over the union of the reference and every rollout, so every compute job is one pass with no range scan), `reduced.py` (`Partial`/`Reduced` — the compact self-describing JSON a compute job emits), `catalog.py` (the declarative `PlotSpec` registry — marginals × {overall,energy,pdg,material}, per-event totals, shower profiles/containment, species/leakage, secondaries, distance/confusion summaries, router and type-embedding diagnostics; `giant analyze list` prints every id), `runtime_estimate.py` (per-(plot, chunk) walltime estimates for the submit description), and `render.py` (the only module importing ETPlot's `plotstyle`/LaTeX; dispatches on `Reduced.kind`, writes PDFs + `metadata.yaml`; each rollout gets a stable `ps.get_color(i)` slot by its position in `series`, the reference always draws in one fixed dashed-ink style). `Bundle.rollouts` is a name-keyed dict of `Side`, and every `compute_partial`/`finalize` builds a `Reduced.payload["series"]` dict keyed the same way, with `payload["reference"]` as the one distinguished non-rollout entry. The heatmap-shaped specs (`marginal_distance_summary`, `n_sec_confusion`) and the checkpoint-bound diagnostics (`router_gating.py`, `type_embedding_distance.py`) are inherently one-matrix/one-checkpoint per rollout, so they render as one panel per rollout instead of one line/bar per rollout.
+**Analysis** (`giant/analysis/`, `giant analyze` CLI): a lean, streaming rollout-vs-reference plotting pipeline that compares one or more autoregressive `giant rollout` runs against a single held-out miniCaloSim reference steps file shared by all of them, and produces publication-styled PDFs assembled into an HTML gallery — one distinctly colored series per rollout, one reference line/panel. It exploits the fact that rollout output and a raw reference file share a world-frame physical column subset under identical names (`pre_*`/`post_*`/`edep`/`step_length`/`pdg`/`material`/`event_id`), so no ALR/local-frame decode is needed — everything is world-frame mm/MeV. Structure: `sources.py` (canonical LazyFrames + `RolloutSpec`/`Side` — a rollout's opened frames + per-checkpoint diagnostic inputs — + synthetic-termination-row filtering + the secondary view, which is `generation>0 & step_no==0` rollout tracks vs exploded `sec_*_list` reference columns), `variables.py` (the per-step value expressions shared by range sizing and the plot registry), `reduce.py` (the streaming primitives — a single `hist1d` `group_by([group,bin]).len()` pass, per-event scalars, edep-weighted depth/transverse profiles, species share, leakage), `grouping.py`/`context.py` (fixed bin edges + energy-quantile/pdg/material group sets resolved once by `prep` into `shared.json` over the union of the reference and every rollout, so every compute job is one pass with no range scan), `reduced.py` (`Partial`/`Reduced` — the compact self-describing JSON a compute job emits), `catalog.py` (the declarative `PlotSpec` registry — marginals × {overall,energy,pdg,material}, per-event totals, shower profiles/containment, species/leakage, secondaries, distance summaries, router and type-embedding diagnostics; `giant analyze list` prints every id), `runtime_estimate.py` (per-(plot, chunk) walltime estimates for the submit description), and `render.py` (the only module importing ETPlot's `plotstyle`/LaTeX; dispatches on `Reduced.kind`, writes PDFs + `metadata.yaml`; each rollout gets a stable `ps.get_color(i)` slot by its position in `series`, the reference always draws in one fixed dashed-ink style). `Bundle.rollouts` is a name-keyed dict of `Side`, and every `compute_partial`/`finalize` builds a `Reduced.payload["series"]` dict keyed the same way, with `payload["reference"]` as the one distinguished non-rollout entry. The heatmap-shaped specs (`marginal_distance_summary`, `sec_count_per_step_by_species` — the latter also drawing the reference as its own panel) and the checkpoint-bound diagnostics (`router_gating.py`, `type_embedding_distance.py`) are inherently one-matrix/one-checkpoint per rollout, so they render as one panel per rollout instead of one line/bar per rollout.
 
-**Input is one or more `giant rollout` YAML sidecars** (`run.py:load_rollout_yamls`): each YAML's `output`/`dataset` keys name its rollout parquet and seed file (= the reference truth); every supplied YAML must resolve to the same `dataset`, checked up front with a clear error otherwise (the premise is "N candidates vs one ground truth"). Each rollout's series name comes from a repeated `--label` CLI flag, else the YAML stem (N>1), else `"rollout"` (a single YAML). `prep` creates a **run directory** (`<cwd>/analysis_runs/analysis_<id>/` by default, `--run-dir` to override) holding `shared.json`, `run_meta.json` (`RunMeta.rollouts: list[{name,path,plot_meta}]`, insertion order = CLI order = every plot's series order), `reduced_partial/`, `reduced/`, `plots/`. **Compute/merge/render split:** `giant analyze prep a.yaml [b.yaml ...] --chunks N` records `N` in `run_meta.json`, and the workflow's `AnalysisComputeTask` runs one HTCondor job per (plot, chunk) pair (`compute-one --id --chunk --run-dir`, polars/numpy only — no LaTeX on workers), each streaming over an `event_id`-disjoint slice (`event_id % N == chunk`) of the reference **and every rollout** and writing a small `reduced_partial/<id>__<chunk>.json`; every `PlotSpec` splits into a `compute_partial`/`finalize` pair so chunks can be summed/concatenated back per rollout (`chunkable=False` specs — the checkpoint-bound diagnostics, already bounded/subsampled — always run as a single chunk). The local `giant analyze render <run_dir>` first joins every plot's chunk partials into `reduced/<id>.json` (`merge_all`, a no-op join when `N=1`; `merge-one` does a single plot for debugging), then turns those into the styled PDF/gallery tree. `giant analyze metrics <train_run_dir>` is a separate, unrelated entry point: training-progress plots straight from a run's `metrics.csv`.
-
-**Workflow orchestration** (`giant/workflow/`, `giant workflow run` CLI): b2luigi is the **only sanctioned way to run a multi-step pipeline**; `giant`/`dwarf` are single-step primitives the tasks invoke. One workflow TOML (`configs/workflow_example.toml`) parameterises a whole experiment — `[workflow]`/`[condor]`/`[dataset]`/`[geometry]` plus repeated `[[train]]`/`[[rollout]]`/`[[analysis]]` tables, each cross-referenced by name — and `spec.py` parses it into frozen dataclasses, rejecting unknown keys and dangling references. Every task's output directory is `<result_dir>/<kind>/name=<name>/spec_hash=<hash>/…`, where the 8-hex `spec_hash` covers that task's resolved sub-spec **and its transitive parents**, so an edited spec re-runs exactly the affected subtree instead of silently reusing stale outputs. The DAG (`tasks.py`): `DatasetTask` (external, fails fast if `/ceph` isn't mounted) → `WarmCacheTask` / `GeometryOracleTask` → `TrainEpochTask(name, milestone)` → `TrainTask` → `RolloutTask` → `AnalysisPrepTask` → `AnalysisComputeTask(name, plot_id, chunk)` → `AnalysisRenderTask` → `WorkflowTask`. Training is fanned out into **one short GPU job per epoch** (`epochs_per_job` trades queue waits back), chained by `--resume` on the previous job's `last.pt` — the loop already handles that unchanged — and `TrainTask` republishes `best.pt`/`last.pt`/a concatenated `metrics.csv` so nothing downstream sees the fan-out. `StreamingStepsDataset.set_epoch` and `config.epoch_seed` (both applied per epoch by `training/loop.py`) derive the batch order and the global RNG state from `(seed, epoch)`, so epoch *k* is bit-identical either way — verified by diffing a chained run's `metrics.csv` against a single 3-epoch `giant train`. `AnalysisRenderTask` is always local (the only step importing plotstyle/LaTeX); `htcondor.py` holds the CPU/GPU submit settings, with the GPU requirement strings (`TARGET.ProvidesEtpCeph` + device/memory pins) ported from the `condor-gpu-train-rollout` branch. `run.py` is the script b2luigi re-executes on workers (`--spec` forwarded via `task_cmd_additional_args`, so a worker resolves the identical graph); `giant workflow run` is a thin exec of it. Needs `uv sync --extra cpu --extra workflow`.
+**Input is one or more `giant rollout` YAML sidecars** (`condor.py:load_rollout_yamls`): each YAML's `output`/`dataset` keys name its rollout parquet and seed file (= the reference truth); every supplied YAML must resolve to the same `dataset`, checked up front with a clear error otherwise (the premise is "N candidates vs one ground truth"). Each rollout's series name comes from a repeated `--label` CLI flag, else the YAML stem (N>1), else `"rollout"` (a single YAML). `prep` creates a **run directory** (`<cwd>/analysis_runs/analysis_<id>/` by default, `--run-dir` to override) holding `shared.json`, `run_meta.json` (`RunMeta.rollouts: list[{name,path,plot_meta}]`, insertion order = CLI order = every plot's series order), `reduced_partial/`, `reduced/`, `plots/`. **Compute/merge/render split:** `giant analyze submit a.yaml [b.yaml ...] --chunks N` runs `prep` (recording `N` in `run_meta.json`) then submits one HTCondor job per (plot, chunk) pair (`compute-one --id --chunk --run-dir`, polars/numpy only — no LaTeX on workers), each streaming over an `event_id`-disjoint slice (`event_id % N == chunk`) of the reference **and every rollout** and writing a small `reduced_partial/<id>__<chunk>.json`; every `PlotSpec` splits into a `compute_partial`/`finalize` pair so chunks can be summed/concatenated back per rollout (`chunkable=False` specs — the checkpoint-bound diagnostics, already bounded/subsampled — always run as a single chunk). The local `giant analyze render <run_dir>` first joins every plot's chunk partials into `reduced/<id>.json` (`merge_all`, a no-op join when `N=1`; `merge-one` does a single plot for debugging), then turns those into the styled PDF/gallery tree. `giant analyze metrics <train_run_dir>` is a separate, unrelated entry point: training-progress plots straight from a run's `metrics.csv`.
 
 **Shower rollout** (`giant/rollout.py`, `giant rollout` CLI): autoregressively steps the two-stage model into a full shower, advancing tracks breadth-first (every sweep steps all active tracks once, in `batch_size` chunks, so many tracks share each forward pass). Each primary post-step becomes the next pre-step, secondaries are pushed as new tracks, and per-step `material`/`layer_id` come from a `GeometryOracle` (`giant/geometry.py`, built via `dwarf build-geometry-oracle`) that learns position → (material, layer_id) from data and flags detector escape by nearest-neighbour distance. Tracks terminate on one of the `TERM_*` reasons in `constants.py` (energy cutoff, max steps, escape, natural end, unknown pdg, max tracks); energy is deposited locally on every stop except escape (leakage), so showers conserve energy by construction. `giant/checkpoint_io.py` is the shared checkpoint → ready-to-run-models path used by both `predict` and `rollout`.
 
@@ -125,4 +121,4 @@ v0.2 configs and checkpoints are auto-migrated (`config.migrate_config`, `model.
 
 A sampling-calorimeter (multi-material) dataset track is still open and unblocked, not yet started. See the knowledge base (`/home/lars/knowledge-base/meta/roadmap.md`).
 
-**Condor-submitted GPU training/rollout (`condor-gpu-train-rollout` branch, superseded):** its goal — moving `giant train`/`giant rollout` off the shared portal GPU dev machines onto remote-GPU HTCondor submission — is now met by the b2luigi workflow above. Its `train-submit`/`rollout-submit` commands are deliberately **not** ported and must not be revived when that branch is eventually merged; the only part that survived is `_gpu_requirements`, which moved into `giant/workflow/htcondor.py`.
+**Condor-submitted GPU training/rollout (in progress, `condor-gpu-train-rollout` branch, not yet merged):** moves `giant train`/`giant rollout` off the shared portal GPU dev machines (see Compute environment) onto remote-GPU HTCondor submission on TOpAS/NEMO2. Partway between "needs major features" and feature-complete — not ready to merge yet.

README.md

@@ -110,15 +110,10 @@ giant/
 │   │   ├── reduced.py      #   Partial/Reduced — the compact JSON a compute job emits
 │   │   ├── catalog.py      #   declarative PlotSpec registry (`giant analyze list`)
 │   │   ├── router_gating.py / type_embedding_distance.py   # checkpoint-bound diagnostics
-│   │   ├── runtime_estimate.py  #   per-(plot, chunk) walltime estimates for the job requests
-│   │   ├── run.py          #   prep / compute-one / merge plumbing
+│   │   ├── runtime_estimate.py  #   per-(plot, chunk) walltime estimates for submit
+│   │   ├── condor.py       #   prep / compute-one / merge / submit-description plumbing
 │   │   └── render.py       #   PDFs + HTML gallery (only module importing plotstyle/LaTeX)
-│   ├── workflow/           # b2luigi pipeline orchestration (`giant workflow run spec.toml`)
-│   │   ├── spec.py         #   workflow TOML -> frozen dataclasses, validation, per-task spec hashes
-│   │   ├── htcondor.py     #   CPU/GPU submit settings (docker image, +RemoteJob, GPU requirements)
-│   │   ├── tasks.py        #   the task graph: cache-warm -> train (one job/epoch) -> rollout -> analysis
-│   │   └── run.py          #   the script b2luigi re-executes on every worker
-│   └── cli.py              # `giant train` / `new-run` / `model summary` / `predict` / `rollout` / `analyze` / `workflow`
+│   └── cli.py              # `giant train` / `new-run` / `model summary` / `predict` / `rollout` / `analyze`
 ├── giant/tools/                        # dataset/tooling logic, unified under the `dwarf` CLI (`dwarf --help`)
 │   ├── dwarf.py                        # Typer app: convert, migrate, bump-gen, bump-schema, status,
 │   │                                    #   update-manifest, create-manifest, make-root,
@@ -145,10 +140,9 @@ uv sync --extra cpu --extra geometry  # add scikit-learn, for `dwarf build-geome
 uv sync --extra cpu --extra analysis  # matplotlib/polars/plotstyle, for `giant analyze render`
 uv sync --extra cpu --extra convert   # uproot/awkward/polars, for `dwarf convert`
 uv sync --extra cpu --extra wandb     # W&B logging (`giant train --wandb`)
-uv sync --extra cpu --extra workflow  # b2luigi, for `giant workflow run`
 ```
 
-The `dev` extra pulls in `convert`, `analysis`, `geometry`, `wandb` and `workflow` as well.
+The `dev` extra pulls in `convert`, `analysis`, `geometry` and `wandb` as well.
 
 `cpu` and `cuda` are mutually exclusive — pick one to select the torch build (pinned to 2.3.x). Plain `uv sync` installs no torch at all. See `CLAUDE.md` for details.
 
@@ -185,29 +179,17 @@ Config-file-only knobs (no CLI flag — use `--config config.toml`): `stage2_mod
 - `giant analyze` — deeper rollout-vs-reference diagnostics (marginals by energy/pdg/material, per-event totals, shower profiles, species share, leakage, secondaries):
 
 ```bash
-giant analyze prep rollout.yaml --chunks 8                 # lay out the run directory
-giant analyze prep a.yaml b.yaml --label flow --label wgan  # N rollouts vs one shared reference
+giant analyze submit rollout.yaml --accounting-group cms   # prep + one HTCondor job per plot × chunk (compute only)
+giant analyze submit a.yaml b.yaml --accounting-group cms --label flow --label wgan  # N rollouts vs one shared reference
 giant analyze render <run_dir> --gallery                   # local: merge chunks, then styled PDFs + HTML gallery (needs LaTeX)
 
 giant analyze list                                         # every catalog plot id
+giant analyze prep rollout.yaml --chunks 8                 # just the run directory, no submission
 giant analyze compute-one --id marginal_edep --run-dir <run_dir> --chunk 0   # what a condor job runs
 giant analyze merge-one --id marginal_edep --run-dir <run_dir>               # merge one plot's chunks (debugging)
 ```
 
-The per-(plot, chunk) compute jobs themselves are submitted by the workflow (below), not by `giant analyze` — these commands are the single-step primitives it calls. `<run_dir>` defaults to `<cwd>/analysis_runs/analysis_<id>` (`--run-dir` overrides it; `prep` prints it). Multiple rollout YAMLs must all name the same reference (`dataset`) file; each renders as its own colored series against one reference line/panel. Compute jobs are polars/numpy only; only `render` needs LaTeX, so it always runs locally.
-
-## Workflow orchestration
-
-Multi-step pipelines run through [b2luigi](https://github.com/belle2/b2luigi) — one spec file describes a whole experiment, and every step's outputs are files on `/ceph` that are only recomputed when their spec (or an upstream one) changes:
-
-```bash
-uv sync --extra cpu --extra workflow
-giant workflow run configs/workflow_example.toml --mode dry-run   # what would run
-giant workflow run configs/workflow_example.toml --mode show-output  # where every output goes
-giant workflow run configs/workflow_example.toml --batch --workers 20  # submit to HTCondor and wait
-```
-
-The spec holds `[workflow]`/`[condor]`/`[dataset]`/`[geometry]` plus repeated `[[train]]`, `[[rollout]]` and `[[analysis]]` tables cross-referenced by name (see `configs/workflow_example.toml`). The task graph is `DatasetTask → WarmCacheTask/GeometryOracleTask → TrainEpochTask… → TrainTask → RolloutTask → AnalysisPrepTask → AnalysisComputeTask(plot, chunk) → AnalysisRenderTask`. Training is split into one short GPU job per epoch (chained by `--resume`), which schedules better on a busy farm and survives preemption; `TrainTask` then publishes one `best.pt`/`last.pt`/`metrics.csv` for everything downstream. Rendering always runs locally, since it is the only step that needs LaTeX.
+`<run_dir>` defaults to `<cwd>/analysis_runs/analysis_<id>` (`--run-dir` overrides it; `prep`/`submit` print it). Multiple rollout YAMLs must all name the same reference (`dataset`) file; each renders as its own colored series against one reference line/panel. Compute jobs are polars/numpy only; only `render` needs LaTeX, so it always runs locally.
 
 Separately, `giant analyze metrics <train_run_dir>` renders training-progress plots (loss/lr/accuracy/grad-norm/router/wgan/throughput) straight from a training run's `metrics.csv`.
 

configs/workflow_example.toml

@@ -1,68 +0,0 @@
-# Example GIANT workflow spec — `giant workflow run configs/workflow_example.toml`.
-#
-# One file parameterises a whole experiment: the datasets, the geometry oracle,
-# N trainings, N rollouts, and the analyses comparing them. Every task's output
-# directory carries a hash of its resolved sub-spec (plus its parents), so
-# editing anything here re-runs exactly the affected subtree and nothing else.
-#
-# result_dir/log_dir must be visible from both the submit host and the workers
-# (i.e. on /ceph) — there is deliberately no HTCondor file transfer.
-
-[workflow]
-name       = "baseline-vs-router"
-result_dir = "/ceph/lbogner/workflows/baseline-vs-router"
-log_dir    = "/ceph/lbogner/workflows/baseline-vs-router/logs"
-
-[condor]
-accounting_group = "cms"
-repo_dir         = "/work/lbogner/giant"   # also b2luigi's working_dir
-env_script       = "/work/lbogner/giant/condor_env.sh"
-docker_image_cpu = "cverstege/alma9-gridjob"
-docker_image_gpu = "mschnepf/slc7-condocker"
-remote           = true
-
-[dataset]
-steps     = "/ceph/lbogner/geant_steps/train/"     # training data
-reference = "/ceph/lbogner/geant_steps/holdout/"   # rollout seeds + analysis truth
-
-[geometry]
-method    = "slab"
-subsample = 500_000
-
-[[train]]
-name           = "baseline"
-config         = "configs/baseline.toml"
-epochs         = 200
-epochs_per_job = 1            # one short GPU job per epoch, chained
-request_gpus   = 1
-gpu_memory_mb  = 20000
-overrides      = { lr = 3e-4 }   # `giant train` flag names
-
-[[train]]
-name           = "router-balanced"
-config         = "configs/router.toml"
-epochs         = 200
-epochs_per_job = 1
-request_gpus   = 1
-gpu_memory_mb  = 20000
-
-[[rollout]]
-name          = "baseline"
-train         = "baseline"     # -> [[train]].name
-n_events      = 2000
-energy_cutoff = 0.1
-
-[[rollout]]
-name          = "router-balanced"
-train         = "router-balanced"
-n_events      = 2000
-energy_cutoff = 0.1
-
-[[analysis]]
-name        = "baseline-vs-router"
-rollouts    = ["baseline", "router-balanced"]
-chunks      = 32
-energy_bins = 4
-bins        = 50
-top_pdg     = 6
-gallery     = true

giant/analysis/__init__.py

@@ -4,7 +4,7 @@ Compares one or more autoregressive ``giant rollout`` runs against a single
 held-out miniCaloSim reference file shared by all of them, producing
 publication-styled comparison plots (one colored series per rollout, one
 reference line) generated in parallel on HTCondor (one job per plot x data
-chunk, compute/merge/render split) — orchestrated by ``giant/workflow``.
+chunk, compute/merge/render split).
 
 Only ``render`` (and the ``render`` CLI path) imports plotstyle/LaTeX; everything
 re-exported here is plotstyle-free so it runs on a compute worker. Import
@@ -12,9 +12,10 @@ re-exported here is plotstyle-free so it runs on a compute worker. Import
 """
 
 from giant.analysis.catalog import build_catalog, catalog_ids, get_spec
-from giant.analysis.run import (
+from giant.analysis.condor import (
     LoadedRollout,
     RunMeta,
+    SubmitConfig,
     compute_one,
     compute_reduced,
     derive_run_dir,
@@ -23,6 +24,7 @@ from giant.analysis.run import (
     merge_all,
     merge_one,
     prep,
+    write_submit,
 )
 from giant.analysis.context import Context, build_context
 from giant.analysis.reduced import Partial, Reduced
@@ -35,6 +37,7 @@ __all__ = [
     "get_spec",
     "LoadedRollout",
     "RunMeta",
+    "SubmitConfig",
     "compute_one",
     "compute_reduced",
     "derive_run_dir",
@@ -43,6 +46,7 @@ __all__ = [
     "merge_all",
     "merge_one",
     "prep",
+    "write_submit",
     "Context",
     "build_context",
     "Partial",

giant/analysis/catalog.py

@@ -22,9 +22,9 @@ which is the order rollouts were given on the CLI) plus the single reference.
 ``finalize`` merges each rollout's chunks independently and assembles a
 ``Reduced.payload`` keyed the same way: ``"series": {name: ...}`` for the
 rollouts, ``"reference": ...`` as one distinguished entry (omitted on
-rollout-only plots like ``leakage_fraction``). The two heatmap-shaped specs
-(``marginal_distance_summary``, ``n_sec_confusion``) and the router
-diagnostics are inherently one-matrix/one-checkpoint per rollout, so their
+rollout-only plots like ``leakage_fraction``). The heatmap-shaped specs
+(``marginal_distance_summary``, ``sec_count_per_step_by_species``) and the
+router diagnostics are inherently one-matrix/one-checkpoint per rollout, so their
 ``"series"`` entries are whole per-rollout artifacts (a matrix, a gating
 dict) rather than a single number/array — ``render.py`` draws those as one
 panel per rollout instead of one line/bar per rollout.
@@ -60,7 +60,6 @@ from giant.analysis.reduce import (
     leakage_fraction,
     profile_finalize,
     profile_partial,
-    sec_count_by_event,
     species_share,
     sum_merge,
     transverse_expr,
@@ -72,7 +71,15 @@ from giant.analysis.router_gating import (
     compute_router_share_by_process,
     compute_router_specialization,
 )
-from giant.analysis.sources import RolloutSide, RolloutSpec, Side, open_side, physical_steps, secondaries
+from giant.analysis.sources import (
+    RolloutSide,
+    RolloutSpec,
+    Side,
+    open_side,
+    physical_steps,
+    secondaries,
+    secondaries_by_step,
+)
 from giant.analysis.type_embedding_distance import compute_type_embedding_l1_distance
 from giant.analysis.variables import RANGED_VARS, cos_scatter_expr
 
@@ -211,31 +218,6 @@ def _ks_statistic(r_counts, t_counts) -> float:
     return float(np.max(np.abs(r_cdf - t_cdf)))
 
 
-def _integer_confusion(
-    t: np.ndarray, r: np.ndarray, max_bins: int = 21, cap: int | None = None
-) -> tuple[list[str], np.ndarray]:
-    """Confusion matrix of two paired small-integer arrays (e.g. secondary counts).
-
-    Bins are consecutive integers ``0..cap``, with the last bin an overflow
-    ``"cap+"`` bucket, so an occasional pathological count doesn't blow up the
-    heatmap. Returns ``(labels, matrix)`` with ``matrix[i, j]`` counting pairs
-    with ``t == i`` and ``r == j`` (both clipped into ``[0, cap]``).
-
-    ``cap``, if given, is used as-is instead of being derived from ``t``/``r``
-    — lets a multi-rollout caller fix one shared cap (and so one shared label
-    set) across every rollout's matrix rather than each panel picking its own.
-    """
-    if cap is None:
-        cap = min(max(int(t.max()) if len(t) else 0, int(r.max()) if len(r) else 0, 1), max_bins - 1)
-    t_c = np.clip(t.astype(np.int64), 0, cap)
-    r_c = np.clip(r.astype(np.int64), 0, cap)
-    n = cap + 1
-    mat = np.zeros((n, n), dtype=np.int64)
-    np.add.at(mat, (t_c, r_c), 1)
-    labels = [str(i) for i in range(cap)] + [f"{cap}+"]
-    return labels, mat
-
-
 def _containment_depths(mat: np.ndarray, edges: np.ndarray, quantile: float) -> np.ndarray:
     """Per-event depth containing ``quantile`` of that event's deposited energy.
 
@@ -802,6 +784,139 @@ def _sec_count_per_species_finalize(parts: list[dict], ctx: Context) -> Reduced:
     )
 
 
+# Per-step secondary multiplicity. Fixed integer edges (bin i == exactly i
+# secondaries, the top bin an overflow bucket) keep both plots sum-mergeable
+# across chunks — no shared-range pass needed. The species heatmap gets a
+# shorter row axis because a single step rarely emits many of *one* species.
+_N_SEC_STEP_CAP = 20
+_N_SEC_SPECIES_CAP = 10
+_OTHER_KEY = "other"
+
+
+def _n_sec_edges(cap: int) -> np.ndarray:
+    return np.arange(-0.5, cap + 1.5)
+
+
+def _sec_step_key_lf(lf: pl.LazyFrame, side: Side) -> pl.LazyFrame:
+    """Secondaries with their emitting-step key.
+
+    The rollout side reads *all* rows, not just physical ones: a secondary
+    whose very first row is a synthetic termination row (born, then immediately
+    escaped or cut) was still produced by its parent step, and dropping it would
+    undercount that step's multiplicity.
+    """
+    return secondaries_by_step(lf, side)
+
+
+def _n_steps(lf: pl.LazyFrame) -> int:
+    """Number of (physical) step rows — the denominator the zero rows come from."""
+    return int(lf.select(pl.len()).collect(engine="streaming").item())
+
+
+def _sec_count_per_step_partial(b: Bundle) -> dict:
+    edges = _n_sec_edges(_N_SEC_STEP_CAP)
+
+    def _side(sec_lf: pl.LazyFrame, steps_lf: pl.LazyFrame) -> dict:
+        per_step = sec_lf.group_by("step_key").agg(pl.len().alias("n"))
+        return {
+            "h": _partial_hist(per_step, pl.col("n").clip(0, _N_SEC_STEP_CAP), edges),
+            "n_steps": _n_steps(steps_lf),
+        }
+
+    return {
+        "r": _per_rollout(b, lambda rs: _side(_sec_step_key_lf(rs.all, Side.rollout), rs.phys)),
+        "t": _side(_sec_step_key_lf(b.t_all, Side.reference), b.t_phys),
+    }
+
+
+def _zero_filled(part_hists: list[dict], n_steps: int, key, nbins: int) -> list[int]:
+    """Merged counts for one series, with bin 0 (= steps that emitted none) filled in.
+
+    The reduction only ever sees steps that produced at least one secondary, so
+    the empty ones are recovered by subtraction from the total step count.
+    """
+    counts = _finalize_counts(sum_merge(part_hists), key, nbins)
+    counts[0] = max(n_steps - int(sum(counts)), 0)
+    return [int(c) for c in counts]
+
+
+def _sec_count_per_step_finalize(parts: list[dict], ctx: Context) -> Reduced:
+    edges = _n_sec_edges(_N_SEC_STEP_CAP)
+    nb = len(edges) - 1
+    names = list(parts[0]["r"])
+    series = {
+        name: _zero_filled([p["r"][name]["h"] for p in parts], sum(p["r"][name]["n_steps"] for p in parts), 0, nb)
+        for name in names
+    }
+    return Reduced(
+        id="sec_count_per_step",
+        family="secondaries",
+        kind="overlay_hist",
+        title="Number of secondaries per step",
+        xlabel="secondaries per step",
+        payload={
+            "edges": edges.tolist(),
+            "series": series,
+            "reference": _zero_filled([p["t"]["h"] for p in parts], sum(p["t"]["n_steps"] for p in parts), 0, nb),
+            "log_y": True,
+        },
+    )
+
+
+def _species_key_expr(top_pdgs: list[int]) -> pl.Expr:
+    """``pdg`` bucketed into the shared top-K columns plus one ``other`` bin."""
+    return pl.when(pl.col("pdg").is_in(list(top_pdgs))).then(pl.col("pdg").cast(pl.Utf8)).otherwise(pl.lit(_OTHER_KEY))
+
+
+def _sec_count_per_step_by_species_partial(b: Bundle) -> dict:
+    edges = _n_sec_edges(_N_SEC_SPECIES_CAP)
+    group = _species_key_expr(b.ctx.top_pdgs)
+
+    def _side(sec_lf: pl.LazyFrame, steps_lf: pl.LazyFrame) -> dict:
+        per_step_species = sec_lf.group_by("step_key", "pdg").agg(pl.len().alias("n"))
+        return {
+            "h": _partial_hist(per_step_species, pl.col("n").clip(0, _N_SEC_SPECIES_CAP), edges, group=group),
+            "n_steps": _n_steps(steps_lf),
+        }
+
+    return {
+        "r": _per_rollout(b, lambda rs: _side(_sec_step_key_lf(rs.all, Side.rollout), rs.phys)),
+        "t": _side(_sec_step_key_lf(b.t_all, Side.reference), b.t_phys),
+    }
+
+
+def _sec_count_per_step_by_species_finalize(parts: list[dict], ctx: Context) -> Reduced:
+    edges = _n_sec_edges(_N_SEC_SPECIES_CAP)
+    nb = len(edges) - 1
+    names = list(parts[0]["r"])
+    keys = [str(p) for p in ctx.top_pdgs] + [_OTHER_KEY]
+
+    def _matrix(hists: list[dict], n_steps: int) -> list[list[int]]:
+        # columns = species, rows = multiplicity; every species gets its own
+        # zero row (steps that produced none of *that* species).
+        cols = [_zero_filled(hists, n_steps, k, nb) for k in keys]
+        return [[cols[j][i] for j in range(len(keys))] for i in range(nb)]
+
+    return Reduced(
+        id="sec_count_per_step_by_species",
+        family="secondaries",
+        kind="heatmap",
+        title="Per-step secondary multiplicity by species",
+        xlabel="species",
+        payload={
+            "series": {
+                n: _matrix([p["r"][n]["h"] for p in parts], sum(p["r"][n]["n_steps"] for p in parts)) for n in names
+            },
+            "reference": _matrix([p["t"]["h"] for p in parts], sum(p["t"]["n_steps"] for p in parts)),
+            "row_labels": [str(i) for i in range(_N_SEC_SPECIES_CAP)] + [f"{_N_SEC_SPECIES_CAP}+"],
+            "col_labels": [pdg_label(k) for k in ctx.top_pdgs] + [_OTHER_KEY],
+            "ylabel": "secondaries of this species per step",
+            "cbar_label": "step count",
+            "log_color": True,
+        },
+    )
+
+
 def _sec_energy_partial(b: Bundle) -> dict:
     edges = np.linspace(*b.ctx.sec_energy_range, b.ctx.n_sec_bins + 1)
     return {
@@ -858,62 +973,6 @@ def _sec_cos_angle_finalize(parts: list[dict], ctx: Context) -> Reduced:
     )
 
 
-def _n_sec_confusion_partial(b: Bundle) -> dict:
-    t_ids, t_n = sec_count_by_event(b.t_all, _t_sec(b))
-
-    def _r(rs: RolloutSide) -> dict:
-        ids, n = sec_count_by_event(rs.phys, _r_sec(rs))
-        return {"ids": ids.tolist(), "n": n.tolist()}
-
-    return {"r": _per_rollout(b, _r), "t": {"ids": t_ids.tolist(), "n": t_n.tolist()}}
-
-
-def _n_sec_confusion_finalize(parts: list[dict], ctx: Context) -> Reduced:
-    names = list(parts[0]["r"])
-    # event-disjoint chunking (see Bundle.open) means each event_id appears in
-    # exactly one part on each side, so a plain dict build is a safe merge.
-    t_ids = np.concatenate([np.asarray(p["t"]["ids"], dtype=np.int64) for p in parts])
-    t_n = np.concatenate([np.asarray(p["t"]["n"], dtype=np.int64) for p in parts])
-    t_map = dict(zip(t_ids.tolist(), t_n.tolist()))
-
-    pairs: dict[str, tuple[np.ndarray, np.ndarray]] = {}
-    max_val = 0
-    for name in names:
-        r_ids = np.concatenate([np.asarray(p["r"][name]["ids"], dtype=np.int64) for p in parts])
-        r_n = np.concatenate([np.asarray(p["r"][name]["n"], dtype=np.int64) for p in parts])
-        r_map = dict(zip(r_ids.tolist(), r_n.tolist()))
-        common = sorted(set(r_map) & set(t_map))
-        true_n = np.array([t_map[e] for e in common], dtype=np.int64)
-        pred_n = np.array([r_map[e] for e in common], dtype=np.int64)
-        pairs[name] = (true_n, pred_n)
-        if len(true_n):
-            max_val = max(max_val, int(true_n.max()), int(pred_n.max()))
-
-    cap = min(max(max_val, 1), 20)
-    matrices: dict[str, list[list[int]]] = {}
-    labels: list[str] = []
-    for name in names:
-        true_n, pred_n = pairs[name]
-        labels, mat = _integer_confusion(true_n, pred_n, cap=cap)
-        matrices[name] = mat.tolist()
-
-    return Reduced(
-        id="n_sec_confusion",
-        family="secondaries",
-        kind="heatmap",
-        title="Predicted vs true secondary count per event",
-        xlabel="predicted secondaries (rollout)",
-        payload={
-            "series": matrices,
-            "row_labels": labels,
-            "col_labels": labels,
-            "ylabel": "true secondaries (reference)",
-            "cbar_label": "event count",
-            "vmin": 0.0,
-        },
-    )
-
-
 # ---------------------------------------------------------------------------
 # router diagnostics (not chunked — already bounded/subsampled)
 # ---------------------------------------------------------------------------
@@ -1077,6 +1136,18 @@ def build_catalog() -> list[PlotSpec]:
             compute_partial=_sec_count_per_species_partial,
             finalize=_sec_count_per_species_finalize,
         ),
+        PlotSpec(
+            "sec_count_per_step",
+            "secondaries",
+            compute_partial=_sec_count_per_step_partial,
+            finalize=_sec_count_per_step_finalize,
+        ),
+        PlotSpec(
+            "sec_count_per_step_by_species",
+            "secondaries",
+            compute_partial=_sec_count_per_step_by_species_partial,
+            finalize=_sec_count_per_step_by_species_finalize,
+        ),
         PlotSpec(
             "sec_energy",
             "secondaries",
@@ -1089,12 +1160,6 @@ def build_catalog() -> list[PlotSpec]:
             compute_partial=_sec_cos_angle_partial,
             finalize=_sec_cos_angle_finalize,
         ),
-        PlotSpec(
-            "n_sec_confusion",
-            "secondaries",
-            compute_partial=_n_sec_confusion_partial,
-            finalize=_n_sec_confusion_finalize,
-        ),
         PlotSpec(
             "router_gating",
             "model",

giant/analysis/condor.py

@@ -1,6 +1,4 @@
-"""Analysis run directories: prep, per-(plot, chunk) compute, and merge.
-
-Driven by one or more ``giant rollout`` YAML sidecars.
+"""HTCondor orchestration driven by one or more ``giant rollout`` YAML sidecars.
 
 A rollout writes a YAML sidecar (``giant/cli.py:_write_prediction_ref`` +
 rollout extras) that already names both files we need and carries the run's
@@ -24,16 +22,13 @@ everything out under it:
     <run_dir>/reduced/<id>.json   merged, per plot
     <run_dir>/plots/<family>/<id>.pdf   rendered locally
 
-Job model (one job per (plot, chunk), compute/merge/render split). Job
-submission itself is b2luigi's (``giant/workflow/tasks.py`` — ``AnalysisPrepTask``
-/ ``AnalysisComputeTask`` / ``AnalysisRenderTask``); this module only provides
-the three steps they call:
+Job model (one condor job per (plot, chunk), compute/merge/render split):
 
-1. ``prep`` runs once locally — reads the YAML, resolves the shared
+1. ``prep`` runs once on the submit node — reads the YAML, resolves the shared
    context from a subsample, writes ``shared.json`` + ``run_meta.json``
    (including the run's configured ``n_chunks``).
 2. one job per catalog id x chunk index runs ``giant analyze compute-one
-   --run-dir`` (or ``compute_one`` in-process) on a worker — a single streaming pass over that
+   --run-dir`` on a worker — a single streaming pass over that
    ``event_id``-disjoint chunk, writing ``reduced_partial/<id>__<chunk>.json``
    (polars/numpy only, no LaTeX). Specs marked ``chunkable=False``
    (``PlotSpec``, ``catalog.py``) always run as a single chunk.
@@ -43,15 +38,15 @@ the three steps they call:
    ``reduced/<id>.json``, then renders those into the styled PDF + gallery tree
    (that step imports plotstyle/LaTeX).
 
-Files on ``/ceph`` or ``/work`` are reached directly (see
-``giant/workflow/htcondor.py``); no HTCondor file transfer of the multi-GB
-inputs.
+Files on ``/ceph`` or ``/work`` are reached via ``ProvidesETPResources``; no
+HTCondor file transfer of the multi-GB inputs.
 """
 
 from __future__ import annotations
 
 import json
 import shutil
+import sys
 from collections.abc import Sequence
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -62,6 +57,7 @@ import yaml
 from giant.analysis.catalog import Bundle, catalog_ids, get_spec
 from giant.analysis.context import Context, build_context
 from giant.analysis.reduced import Partial
+from giant.analysis.runtime_estimate import estimate_runtime_s
 from giant.analysis.sources import RolloutSpec, Side, open_side
 
 # Keys copied verbatim from a rollout YAML into each plot's gallery metadata.
@@ -433,3 +429,136 @@ def merge_one(spec_id: str, run_dir: str | Path) -> Path:
 def merge_all(run_dir: str | Path) -> list[Path]:
     """Merge every catalog plot's chunk partials into ``reduced/<id>.json``."""
     return [merge_one(spec_id, run_dir) for spec_id in catalog_ids()]
+
+
+# ---------------------------------------------------------------------------
+# submit description
+# ---------------------------------------------------------------------------
+
+
+@dataclass
+class SubmitConfig:
+    run_dir: Path
+    accounting_group: str
+    repo_dir: Path
+    docker_image: str = "cverstege/alma9-gridjob"
+    request_memory_mb: int = 8192
+    request_cpus: int = 1
+    remote: bool = False  # +RemoteJob (grid I/O) vs ProvidesETPResources (local files)
+    n_chunks: int = 1  # per-plot data chunks; ignored for chunkable=False specs
+
+
+_WRAPPER = """#!/bin/bash
+set -euo pipefail
+cd {repo_dir}
+exec {giant_exe} analyze compute-one --id "$1" --chunk "$2" --run-dir {run_dir}
+"""
+
+
+def _submit_description(cfg: SubmitConfig, wrapper: Path, jobs_file: Path) -> str:
+    reqs_attrs = "+RemoteJob = True\n" if cfg.remote else "requirements = TARGET.ProvidesETPResources\n"
+    return (
+        "universe = docker\n"
+        f"docker_image = {cfg.docker_image}\n"
+        f"executable = {wrapper}\n"
+        "arguments = $(plotid) $(chunk)\n"
+        "should_transfer_files = YES\n"
+        "when_to_transfer_output = ON_EXIT\n"
+        f"request_memory = {cfg.request_memory_mb}\n"
+        f"request_cpus = {cfg.request_cpus}\n"
+        "+RequestWalltime = $(walltime)\n"
+        f"accounting_group = {cfg.accounting_group}\n"
+        f"{reqs_attrs}"
+        f"output = {cfg.run_dir}/logs/$(plotid)__$(chunk).out\n"
+        f"error = {cfg.run_dir}/logs/$(plotid)__$(chunk).err\n"
+        f"log = {cfg.run_dir}/logs/condor.log\n"
+        f"queue plotid,chunk,walltime from {jobs_file}\n"
+    )
+
+
+def _job_walltimes(run_dir: Path, ids: list[str], n_chunks: int) -> list[tuple[str, int, int]]:
+    """``(spec_id, chunk, walltime_s)`` for every job, sized from ``run_meta.json``.
+
+    Row counts come from ``prep``'s ``RunMeta.rows_per_chunk``/``total_rows``;
+    ``chunkable=False`` specs (router diagnostics) always use the dataset
+    total since they run as a single job regardless of ``n_chunks``.
+    """
+    meta = RunMeta.load(run_dir / "run_meta.json")
+    jobs: list[tuple[str, int, int]] = []
+    for spec_id in ids:
+        chunkable = get_spec(spec_id).chunkable
+        chunks = range(n_chunks) if chunkable else [0]
+        for chunk in chunks:
+            n_rows = meta.rows_per_chunk[chunk] if chunkable else meta.total_rows
+            jobs.append((spec_id, chunk, estimate_runtime_s(spec_id, n_rows)))
+    return jobs
+
+
+def _resolve_giant_executable(repo_dir: Path) -> Path:
+    """Path to the ``giant`` entry point to bake into the condor wrapper script.
+
+    Prefers the venv currently running this process (``sys.executable``'s
+    sibling ``giant``) so a submit from a non-default venv (e.g. ``--extra
+    cuda`` on a dev box) doesn't silently pick up a different one; falls back
+    to ``repo_dir/.venv/bin/giant`` for the case this is invoked from outside
+    any venv (e.g. a system Python).
+    """
+    active = Path(sys.executable).parent / "giant"
+    if active.exists():
+        return active
+    venv_giant = repo_dir / ".venv" / "bin" / "giant"
+    if not venv_giant.exists():
+        raise FileNotFoundError(
+            f"no `giant` executable found next to {sys.executable} or at "
+            f"{venv_giant} — condor jobs run it directly (no `uv` on the "
+            f"worker image), so run `uv sync --extra cpu` in {repo_dir} "
+            "before submitting."
+        )
+    return venv_giant
+
+
+def write_submit(cfg: SubmitConfig, ids: list[str] | None = None) -> Path:
+    """Write the wrapper script, (plot, chunk) job list, and HTCondor submit
+    description.
+
+    Each catalog id gets ``cfg.n_chunks`` jobs, except ``chunkable=False``
+    specs (the router diagnostics), which always get exactly one regardless of
+    ``cfg.n_chunks``. Every job's ``+RequestWalltime`` is estimated from its
+    chunk's row count (``runtime_estimate.estimate_runtime_s``, requires
+    ``run_meta.json`` from ``prep`` to already carry ``rows_per_chunk``).
+    Returns the submit description path (``<run_dir>/analyze.sub``). Does not
+    submit — call ``condor_submit`` on the returned file.
+
+    ``cfg.n_chunks`` and the run directory's own ``RunMeta.n_chunks`` (fixed by
+    ``prep``, and what ``RunMeta.rows_per_chunk`` was sized against) are two
+    independent values — checked equal up front so a mismatch is a clear error
+    here rather than an ``IndexError`` out of ``_job_walltimes``.
+    """
+    giant_exe = _resolve_giant_executable(cfg.repo_dir)
+
+    ids = ids or catalog_ids()
+    run_dir = cfg.run_dir
+    meta = RunMeta.load(run_dir / "run_meta.json")
+    if cfg.n_chunks != meta.n_chunks:
+        raise ValueError(
+            f"SubmitConfig.n_chunks={cfg.n_chunks} does not match the "
+            f"n_chunks this run directory was prepped with "
+            f"(RunMeta.n_chunks={meta.n_chunks} in {run_dir}/run_meta.json) — "
+            "re-run `prep` with the desired n_chunks, or fix cfg.n_chunks to "
+            "match it."
+        )
+    (run_dir / "logs").mkdir(parents=True, exist_ok=True)
+    (run_dir / "reduced").mkdir(parents=True, exist_ok=True)
+    (run_dir / "reduced_partial").mkdir(parents=True, exist_ok=True)
+
+    wrapper = run_dir / "run_compute.sh"
+    wrapper.write_text(_WRAPPER.format(repo_dir=cfg.repo_dir, giant_exe=giant_exe, run_dir=run_dir))
+    wrapper.chmod(0o755)
+
+    jobs = _job_walltimes(run_dir, ids, cfg.n_chunks)
+    jobs_file = run_dir / "jobs.txt"
+    jobs_file.write_text("\n".join(f"{i},{k},{w}" for i, k, w in jobs) + "\n")
+
+    sub = run_dir / "analyze.sub"
+    sub.write_text(_submit_description(cfg, wrapper, jobs_file))
+    return sub

giant/analysis/reduce.py

@@ -271,20 +271,3 @@ def leakage_fraction(lf: pl.LazyFrame) -> np.ndarray:
     escaped = per_event["escaped"].fill_null(0.0).to_numpy()
     total = deposited + escaped
     return np.where(total > 0, escaped / total, 0.0)
-
-
-def sec_count_by_event(lf_all: pl.LazyFrame, sec_lf: pl.LazyFrame) -> tuple[np.ndarray, np.ndarray]:
-    """Per-event secondary count, zero-filled for events that produced none.
-
-    Two bounded per-event ``group_by``s — the full event set (from ``lf_all``)
-    and the secondary counts (from ``sec_lf``, see ``sources.secondaries``) —
-    merged in Python via a dict. Both results are event-granularity (not
-    per-row), so this stays in the same bounded-memory budget as
-    ``event_scalars``; a plain ``group_by`` on ``sec_lf`` alone would silently
-    drop zero-secondary events instead of zero-filling them.
-    """
-    ev = lf_all.select("event_id").unique().collect(engine="streaming")["event_id"].to_numpy()
-    cnt_df = sec_lf.group_by("event_id").agg(pl.len().alias("n")).collect(engine="streaming")
-    cnt = dict(zip(cnt_df["event_id"].to_list(), cnt_df["n"].to_list()))
-    counts = np.array([cnt.get(int(e), 0) for e in ev], dtype=np.int64)
-    return ev, counts

giant/analysis/reduced.py

@@ -27,7 +27,7 @@ from pathlib import Path
 #   "router_specialization"  max gate weight vs energy (one scalar trend line
 #                    summarizing "router_gating"), per rollout with an enabled router
 #   "heatmap"        row x col matrix + colorbar, one panel per rollout (a
-#                    distance scorecard or a predicted-vs-true confusion matrix)
+#                    distance scorecard)
 #   "unavailable"    plot not applicable to this run (e.g. no MoE checkpoint)
 
 

giant/analysis/render.py

@@ -27,6 +27,7 @@ from pathlib import Path
 
 import numpy as np
 import plotstyle as ps
+from matplotlib.colors import LogNorm
 import yaml
 
 from giant.analysis.reduced import Reduced
@@ -376,10 +377,16 @@ def _render_router_specialization(r: Reduced, params: dict):
 
 
 def _render_heatmap(r: Reduced, params: dict):
-    series = r.payload["series"]
+    series = dict(r.payload["series"])
     row_labels = r.payload["row_labels"]
     col_labels = r.payload["col_labels"]
+    # A heatmap-shaped plot is one matrix per rollout, so the reference (when the
+    # comparison has one — the distance scorecard doesn't) becomes one more panel
+    # rather than another line.
+    if r.payload.get("reference") is not None:
+        series["reference"] = r.payload["reference"]
     names = list(series)
+    norm = LogNorm(vmin=1) if r.payload.get("log_color") else None
     fig, axes = ps.new_figure(
         "slide-16x9" if len(names) > 1 else "thesis-single",
         title=r.title,
@@ -397,8 +404,9 @@ def _render_heatmap(r: Reduced, params: dict):
             origin="upper",
             aspect="auto",
             cmap=r.payload.get("cmap", "viridis"),
-            vmin=r.payload.get("vmin"),
-            vmax=r.payload.get("vmax"),
+            norm=norm,
+            vmin=None if norm else r.payload.get("vmin"),
+            vmax=None if norm else r.payload.get("vmax"),
         )
         ax.set_xticks(range(len(col_labels)))
         ax.set_xticklabels(col_labels, rotation=45, ha="right")
@@ -535,7 +543,7 @@ def render_run(run_dir: str | Path, *, run_gallery: bool = False) -> list[Path]:
     (checkpoint, paths, cutoffs) from ``run_meta.json`` into every plot's
     gallery metadata and renders.
     """
-    from giant.analysis.run import RunMeta, merge_all
+    from giant.analysis.condor import RunMeta, merge_all
 
     run_dir = Path(run_dir)
     merge_all(run_dir)

giant/analysis/runtime_estimate.py

@@ -1,4 +1,4 @@
-"""Per-(plot, chunk) HTCondor walltime estimates for the analysis compute jobs.
+"""Per-(plot, chunk) HTCondor walltime estimates for `giant analyze submit`.
 
 Each catalog spec's compute cost is close to linear in the number of input
 rows a `compute-one` job streams over — every spec is one (or a couple of)

giant/analysis/sources.py

@@ -236,3 +236,34 @@ def secondaries(lf: pl.LazyFrame, side: Side) -> pl.LazyFrame:
             pl.col("sec_dz_list").alias("sdz"),
         )
     )
+
+
+def secondaries_by_step(lf: pl.LazyFrame, side: Side) -> pl.LazyFrame:
+    """One row per produced secondary, tagged with the step that produced it.
+
+    Canonical columns: ``step_key`` (an opaque struct identifying the emitting
+    step) and ``pdg``. ``secondaries`` deliberately drops that link; the
+    per-step multiplicity plots need it, so this is a separate view rather than
+    extra columns every other consumer would pay for.
+
+    - rollout: a secondary's birth row carries ``parent_id`` and a birth
+      position copied verbatim from the parent step's ``post_pos``, so
+      ``(event_id, parent_id, pre_pos)`` identifies the emitting step exactly —
+      no join against the (large) step frame is needed.
+    - reference: secondaries already live on their parent step's row, so the
+      row index *is* the step key. It is only ever used as a group key inside
+      one chunk's own aggregation, so indices repeating across chunks is
+      harmless.
+    """
+    if side is Side.rollout:
+        return lf.filter((pl.col("generation") > 0) & (pl.col("step_no") == 0)).select(
+            pl.struct("event_id", "parent_id", "pre_x", "pre_y", "pre_z").alias("step_key"),
+            "pdg",
+        )
+    return (
+        lf.select("sec_pdg_list")
+        .with_row_index("_row")
+        .explode("sec_pdg_list")
+        .drop_nulls("sec_pdg_list")
+        .select(pl.struct("_row").alias("step_key"), pl.col("sec_pdg_list").cast(pl.Int64).alias("pdg"))
+    )

giant/cli.py

@@ -4,7 +4,6 @@ from enum import Enum
 import math
 from pathlib import Path
 import re
-import sys
 from typing import Optional
 import uuid as uuid_mod
 
@@ -192,17 +191,8 @@ def _write_prediction_ref(
     out: Path,
     dataset_path: Path,
     comment: str | None = None,
-    explicit_out: bool = False,
 ) -> Path:
-    """Write the YAML sidecar and return its path.
-
-    With an explicit ``--out`` the sidecar sits next to the output file as
-    ``out.with_suffix(".yaml")`` — a *deterministic* path, which is what lets
-    a workflow task (``giant/workflow/tasks.py``) declare it as a target.
-    Without one, the historic uuid-named file under the checkpoint directory
-    is kept, so ad-hoc runs and the ``/ceph`` predictions convention are
-    unaffected.
-    """
+    """Write a YAML sidecar in the checkpoint directory and return its path."""
     ref = {
         "prediction_id": pred_uuid,
         "output": str(out),
@@ -212,7 +202,7 @@ def _write_prediction_ref(
     }
     if comment is not None:
         ref["comment"] = comment
-    ref_path = out.with_suffix(".yaml") if explicit_out else checkpoint.parent / f"{pred_uuid}.yaml"
+    ref_path = checkpoint.parent / f"{pred_uuid}.yaml"
     ref_path.write_text(yaml.dump(ref, default_flow_style=False, sort_keys=False))
     return ref_path
 
@@ -1086,7 +1076,6 @@ def predict(
     bs = batch_size_value
 
     # --- Output path ---
-    explicit_out = out is not None
     out, dataset_path, pred_uuid = _resolve_prediction_output(data, out)
     out.parent.mkdir(parents=True, exist_ok=True)
     typer.echo(f"output: {out}")
@@ -1306,7 +1295,7 @@ def predict(
     if writer is not None:
         writer.close()
 
-    ref_path = _write_prediction_ref(checkpoint, pred_uuid, out, dataset_path, comment, explicit_out=explicit_out)
+    ref_path = _write_prediction_ref(checkpoint, pred_uuid, out, dataset_path, comment)
     typer.echo(f"reference: {ref_path}")
 
     if skipped:
@@ -1454,7 +1443,6 @@ def rollout(
     seeds = _seed_from_data(files, n_events)
     typer.echo(f"seeded {len(seeds['event_id']):,} shower(s)")
 
-    explicit_out = out is not None
     out, dataset_path, pred_uuid = _resolve_prediction_output(data, out)
     out.parent.mkdir(parents=True, exist_ok=True)
 
@@ -1515,7 +1503,7 @@ def rollout(
 
     l1_summary = l1_dist_collector.summary()
 
-    ref_path = _write_prediction_ref(checkpoint, pred_uuid, out, dataset_path, explicit_out=explicit_out)
+    ref_path = _write_prediction_ref(checkpoint, pred_uuid, out, dataset_path)
     ref = yaml.safe_load(ref_path.read_text())
     ref.update(
         {
@@ -1559,49 +1547,6 @@ def rollout(
     typer.echo(f"reference: {ref_path}")
 
 
-workflow_app = typer.Typer(
-    no_args_is_help=True,
-    help="b2luigi pipeline orchestration: one spec file -> cache-warm, train, rollout, analysis.",
-)
-app.add_typer(workflow_app, name="workflow")
-
-
-@workflow_app.command("run")
-def workflow_run(
-    spec: Annotated[Path, typer.Argument(help="Workflow TOML (see configs/workflow_example.toml)")],
-    batch: Annotated[
-        bool,
-        typer.Option("--batch/--local", help="Submit batch-system tasks to HTCondor, or run everything locally"),
-    ] = False,
-    workers: Annotated[int, typer.Option("--workers", help="Concurrent luigi workers")] = 1,
-    mode: Annotated[
-        str,
-        typer.Option(
-            "--mode",
-            help="run | dry-run (print pending tasks) | show-output (print every target) | remove (delete outputs)",
-        ),
-    ] = "run",
-    scheduler_host: Annotated[Optional[str], typer.Option("--scheduler-host", help="luigid host")] = None,
-    scheduler_port: Annotated[Optional[int], typer.Option("--scheduler-port", help="luigid port")] = None,
-) -> None:
-    """Run a workflow spec end to end (the only sanctioned multi-step entry point).
-
-    A thin exec of `giant/workflow/run.py`, which b2luigi also re-executes on
-    every worker — so there is one documented entry point and one code path.
-    """
-    import subprocess
-
-    script = Path(__file__).resolve().parent / "workflow" / "run.py"
-    cmd = [sys.executable, str(script), "--spec", str(spec), "--workers", str(workers), "--mode", mode]
-    if batch:
-        cmd.append("--batch")
-    if scheduler_host:
-        cmd += ["--scheduler-host", scheduler_host]
-    if scheduler_port:
-        cmd += ["--scheduler-port", str(scheduler_port)]
-    raise typer.Exit(subprocess.run(cmd).returncode)
-
-
 analyze_app = typer.Typer(
     no_args_is_help=True,
     help="Rollout-vs-reference analysis: parallel compute on HTCondor + local render.",
@@ -1732,5 +1677,83 @@ def analyze_metrics(
     typer.echo(f"rendered {len(paths)} plots -> {paths[0].parent if paths else '(nothing to render)'}")
 
 
+@analyze_app.command("submit")
+def analyze_submit(
+    rollout_yamls: Annotated[
+        list[Path],
+        typer.Argument(
+            help="giant rollout YAML sidecar(s). Multiple compare N rollouts against one "
+            "shared reference — every YAML must name the same `dataset`."
+        ),
+    ],
+    accounting_group: Annotated[str, typer.Option("--accounting-group")],
+    label: Annotated[
+        Optional[list[str]],
+        typer.Option(
+            "--label",
+            help="Series name for a rollout YAML, positionally matched to it — give none, "
+            'or exactly one per YAML. Defaults to the YAML stem (or "rollout" for a '
+            "single YAML).",
+        ),
+    ] = None,
+    run_dir: Annotated[
+        Optional[Path],
+        typer.Option(
+            "--run-dir",
+            "-o",
+            help="Override the run directory (default: <cwd>/analysis_runs/analysis_<id>)",
+        ),
+    ] = None,
+    docker_image: Annotated[str, typer.Option("--docker-image")] = "cverstege/alma9-gridjob",
+    request_memory: Annotated[int, typer.Option("--request-memory", help="MB")] = 8192,
+    remote: Annotated[
+        bool,
+        typer.Option("--remote/--local", help="+RemoteJob vs ProvidesETPResources"),
+    ] = False,
+    chunks: Annotated[
+        int,
+        typer.Option(
+            "--chunks",
+            help="Split each plot's data into this many event_id chunks/jobs",
+        ),
+    ] = 1,
+    n_energy_bins: Annotated[int, typer.Option("--energy-bins")] = 4,
+    n_marginal_bins: Annotated[int, typer.Option("--bins")] = 50,
+    top_k_pdg: Annotated[int, typer.Option("--top-pdg")] = 6,
+    dry_run: Annotated[bool, typer.Option("--dry-run", help="Write files but don't condor_submit")] = False,
+) -> None:
+    """prep + write the HTCondor submit description (one job per plot x chunk), then submit."""
+    import subprocess
+
+    from giant.analysis import SubmitConfig, prep, write_submit
+
+    path = prep(
+        rollout_yamls,
+        run_dir,
+        n_chunks=chunks,
+        default_base=Path.cwd() / "analysis_runs",
+        labels=label,
+        n_energy_bins=n_energy_bins,
+        n_marginal_bins=n_marginal_bins,
+        top_k_pdg=top_k_pdg,
+    )
+    cfg = SubmitConfig(
+        run_dir=path,
+        accounting_group=accounting_group,
+        repo_dir=Path.cwd(),
+        docker_image=docker_image,
+        request_memory_mb=request_memory,
+        remote=remote,
+        n_chunks=chunks,
+    )
+    sub = write_submit(cfg)
+    typer.echo(f"run directory: {path}")
+    typer.echo(f"wrote submit description: {sub}")
+    if dry_run:
+        typer.echo("dry-run: not submitting")
+        return
+    subprocess.run(["condor_submit", str(sub)], check=True)
+
+
 if __name__ == "__main__":
     app()

giant/config.py

@@ -1769,19 +1769,6 @@ def resolve_default_out_dir(cfg: dict, base: Path = Path("checkpoints")) -> Path
     return out_dir
 
 
-def epoch_seed(seed: int, epoch: int) -> int:
-    """Per-epoch derivative of the run seed.
-
-    Reseeding the global RNGs from this at the top of every epoch makes epoch
-    *k* draw the same noise whether it runs inside one long `giant train` or
-    as its own resumed job in a per-epoch workflow chain
-    (`giant/workflow/tasks.py:TrainEpochTask`) — without it, a fresh process
-    would restart the stream at epoch 1's state. Mirrors what
-    `StreamingStepsDataset.set_epoch` does for the batch order.
-    """
-    return (int(seed) * 1_000_003 + int(epoch)) % (2**32)
-
-
 def seed_everything(seed: int) -> None:
     random.seed(seed)
     np.random.seed(seed)

giant/data/dataset.py

@@ -97,7 +97,6 @@ class StreamingStepsDataset(IterableDataset):
         mat_topn_map: dict[str, int] | None = None,
         sec_type_class_map: dict | None = None,
         k_max: int = K_MAX,
-        seed: int = 0,
     ) -> None:
         self.files = list(files)
         self._offsets = {path: event_id_offset(i) for i, path in enumerate(self.files)}
@@ -118,35 +117,16 @@ class StreamingStepsDataset(IterableDataset):
         self.mat_topn_map = mat_topn_map
         self.sec_type_class_map = sec_type_class_map
         self.k_max = k_max
-        self.seed = seed
-        self.epoch = 0
-        self._rng = np.random.default_rng()
-
-    def set_epoch(self, epoch: int) -> None:
-        """Select the shuffle stream for `epoch` (the DistributedSampler convention).
-
-        The training loop calls this at the top of every epoch. Shuffling is
-        seeded from `(seed, epoch, worker_id)` rather than the global numpy
-        state so epoch *k*'s batch order is the same whether it runs as epoch
-        *k* of one long `giant train`, or as its own resumed job in a
-        per-epoch workflow chain (`giant/workflow/tasks.py:TrainEpochTask`).
-        Workers are re-forked from this object each epoch (no
-        `persistent_workers`), so setting it here reaches them.
-        """
-        self.epoch = int(epoch)
 
     def __iter__(self):
         worker_info = torch.utils.data.get_worker_info()
         files = self.files
-        worker_id = worker_info.id if worker_info is not None else 0
         if worker_info is not None:
-            files = files[worker_id :: worker_info.num_workers]
-
-        self._rng = np.random.default_rng([self.seed, self.epoch, worker_id])
+            files = files[worker_info.id :: worker_info.num_workers]
 
         if self.shuffle:
             files = list(files)
-            self._rng.shuffle(files)
+            np.random.default_rng().shuffle(files)
 
         buf_cont: list[np.ndarray] = []
         buf_cat: list[np.ndarray] = []
@@ -242,7 +222,7 @@ class StreamingStepsDataset(IterableDataset):
         styp = np.concatenate(buf_type)
 
         if self.shuffle:
-            idx = self._rng.permutation(len(cont))
+            idx = np.random.permutation(len(cont))
             cont, cat, tgt = cont[idx], cat[idx], tgt[idx]
             nsec, sec, proc, styp = nsec[idx], sec[idx], proc[idx], styp[idx]
 

giant/pipeline.py

@@ -435,7 +435,6 @@ def run_train_job(
         mat_topn_map=cond_mat_topn,
         sec_type_class_map=sec_type_class_map,
         k_max=k_max,
-        seed=t["seed"],
     )
     val_ds = StreamingStepsDataset(
         files=files,

giant/tools/profile_analysis_costs.py

@@ -26,7 +26,7 @@ import numpy as np
 import polars as pl
 
 from giant.analysis.catalog import catalog_ids, get_spec
-from giant.analysis.run import compute_reduced
+from giant.analysis.condor import compute_reduced
 from giant.analysis.context import build_context
 from giant.analysis.sources import RolloutSpec
 

giant/training/loop.py

@@ -18,7 +18,6 @@ import torch
 from torch.utils.data import DataLoader
 from tqdm import tqdm
 
-from giant import config
 from giant.data.loader import TopNMap
 from giant.data.setup_cache import topnmap_to_json
 from giant.training.checkpoint import build_checkpoint, init_stages_from_checkpoints, load_checkpoint
@@ -185,17 +184,6 @@ def train(
             if device.type == "cuda":
                 torch.cuda.reset_peak_memory_stats(device)
             collector.start_epoch(epoch)
-            # Epoch-aware RNG: same noise (and, below, same batch order) for
-            # epoch k whether the run is one process or a chain of per-epoch
-            # jobs. See giant.config.epoch_seed.
-            config.seed_everything(config.epoch_seed(t["seed"], epoch))
-            # Epoch-aware shuffle stream (see StreamingStepsDataset.set_epoch):
-            # keeps epoch k's batch order identical whether it runs here or as
-            # its own resumed per-epoch job in a b2luigi workflow.
-            # (tests hand `train` a plain list of batches, which has neither)
-            set_epoch = getattr(getattr(train_loader, "dataset", None), "set_epoch", None)
-            if callable(set_epoch):
-                set_epoch(epoch)
             for trainer in trainers.values():
                 trainer.train_mode()
 

giant/training/plots.py

@@ -115,7 +115,7 @@ def derive_metrics_dir(
 
     Precedence: an explicit `out_dir` always wins. Otherwise
     `default_base / f"metrics_{run_dir.name}"` (the CLI passes the repo's
-    gitignored `analysis_runs/`, matching `giant.analysis.run.derive_run_dir`'s
+    gitignored `analysis_runs/`, matching `giant.analysis.condor.derive_run_dir`'s
     convention) — training-progress plots live alongside rollout-vs-reference
     analysis runs, not inside the training run directory itself.
     """

giant/workflow/__init__.py

@@ -1,40 +0,0 @@
-"""b2luigi orchestration of the full GIANT pipeline.
-
-One workflow TOML (``spec.py``) parameterises an entire experiment — dataset,
-geometry oracle, N trainings, N rollouts, N analyses — and ``giant workflow
-run <spec.toml>`` turns it into a b2luigi task graph (``tasks.py``) whose
-targets are files on ``/ceph``: nothing is recomputed that already exists,
-every step waits for its inputs, and HTCondor submission/polling is b2luigi's
-job rather than a hand-rolled submit-file generator.
-
-This is the only sanctioned way to run a multi-step pipeline; ``giant`` and
-``dwarf`` stay single-step primitives that these tasks invoke.
-
-``tasks``/``run`` import b2luigi, so they are *not* imported here — a plain
-``import giant.workflow`` (or ``giant.workflow.spec``) works without the
-``workflow`` extra installed.
-"""
-
-from giant.workflow.spec import (
-    AnalysisSpec,
-    CondorSpec,
-    DatasetSpec,
-    GeometrySpec,
-    RolloutSpec,
-    TrainSpec,
-    WorkflowSpec,
-    load_spec,
-    spec_hash,
-)
-
-__all__ = [
-    "AnalysisSpec",
-    "CondorSpec",
-    "DatasetSpec",
-    "GeometrySpec",
-    "RolloutSpec",
-    "TrainSpec",
-    "WorkflowSpec",
-    "load_spec",
-    "spec_hash",
-]

giant/workflow/htcondor.py

@@ -1,82 +0,0 @@
-"""HTCondor job descriptions for the workflow tasks.
-
-b2luigi writes every key of a task's ``htcondor_settings`` dict straight into
-that job's submit description, so these helpers are just the ETP-specific
-resource/requirement conventions in one place:
-
-* **CPU jobs** (setup cache, geometry oracle, analysis compute) keep what
-  the deleted ``giant analyze submit`` used: ``+RemoteJob`` for grid I/O, or
-  ``TARGET.ProvidesETPResources`` when the files are local to the cluster.
-* **GPU jobs** (training epochs, rollout) are remote-only, so they always
-  carry ``+RemoteJob`` and reach ``/ceph`` through
-  ``TARGET.ProvidesEtpCeph`` — the requirement strings are ported from the
-  ``condor-gpu-train-rollout`` branch's ``giant/condor.py`` rather than
-  rewritten, since they encode what the ETP HTCondor wiki documents for
-  TOpAS/NEMO2 GPU workers.
-"""
-
-from __future__ import annotations
-
-from giant.workflow.spec import CondorSpec
-
-__all__ = ["cpu_settings", "gpu_settings", "gpu_requirements"]
-
-
-def cpu_settings(
-    condor: CondorSpec,
-    *,
-    request_memory_mb: int | None = None,
-    request_cpus: int | None = None,
-    walltime_s: int | None = None,
-) -> dict:
-    settings: dict = {
-        "universe": "docker",
-        "docker_image": condor.docker_image_cpu,
-        "request_memory": request_memory_mb if request_memory_mb is not None else condor.request_memory_mb,
-        "request_cpus": request_cpus if request_cpus is not None else condor.request_cpus,
-        "accounting_group": condor.accounting_group,
-        "should_transfer_files": "YES",
-        "when_to_transfer_output": "ON_EXIT",
-    }
-    if condor.remote:
-        settings["+RemoteJob"] = "True"
-    else:
-        settings["requirements"] = "TARGET.ProvidesETPResources"
-    if walltime_s is not None:
-        settings["+RequestWalltime"] = int(walltime_s)
-    return settings
-
-
-def gpu_requirements(gpu_type: str | None = None, gpu_memory_mb: int | None = None) -> str:
-    """``TARGET.ProvidesEtpCeph`` (remote /ceph access) ANDed with any GPU pin."""
-    clauses = ["TARGET.ProvidesEtpCeph =?= True"]
-    if gpu_type is not None:
-        clauses.append(f'TARGET.GPUs_DeviceName =?= "{gpu_type}"')
-    if gpu_memory_mb is not None:
-        clauses.append(f"TARGET.GPUs_GlobalMemoryMb >= {gpu_memory_mb}")
-    return " && ".join(clauses)
-
-
-def gpu_settings(
-    condor: CondorSpec,
-    *,
-    request_gpus: int = 1,
-    gpu_type: str | None = None,
-    gpu_memory_mb: int | None = None,
-    request_memory_mb: int = 16384,
-    request_cpus: int = 4,
-    walltime_s: int = 86400,
-) -> dict:
-    return {
-        "universe": "docker",
-        "docker_image": condor.docker_image_gpu,
-        "request_memory": request_memory_mb,
-        "request_cpus": request_cpus,
-        "RequestGPUs": request_gpus,
-        "+RequestWalltime": int(walltime_s),
-        "accounting_group": condor.accounting_group,
-        "should_transfer_files": "YES",
-        "when_to_transfer_output": "ON_EXIT",
-        "+RemoteJob": "True",
-        "requirements": f"({gpu_requirements(gpu_type, gpu_memory_mb)})",
-    }

giant/workflow/run.py

@@ -1,103 +0,0 @@
-#!/usr/bin/env python
-"""Entry point b2luigi re-executes on every worker.
-
-Locally this is what ``giant workflow run <spec.toml>`` execs; on a batch
-worker it is what the generated wrapper script runs (after ``cd repo_dir`` and
-sourcing ``env_script``), with ``--spec`` forwarded via the
-``task_cmd_additional_args`` setting so the worker resolves exactly the same
-spec — and therefore the same task graph and output paths — as the submitter.
-
-b2luigi needs a real script path for that re-execution, which is why this is a
-script rather than a ``python -m`` module.
-"""
-
-from __future__ import annotations
-
-import argparse
-import sys
-from pathlib import Path
-
-# Allow `python giant/workflow/run.py` from a checkout that isn't installed.
-sys.path.insert(0, str(Path(__file__).resolve().parents[2]))
-
-import b2luigi  # noqa: E402
-
-from giant.workflow.spec import WorkflowSpec, load_spec  # noqa: E402
-from giant.workflow.tasks import WorkflowTask, set_spec  # noqa: E402
-
-
-def build_parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(description="Run a GIANT workflow spec with b2luigi.")
-    parser.add_argument("--spec", required=True, help="Workflow TOML (see configs/workflow_example.toml)")
-    parser.add_argument("--workers", type=int, default=1, help="Concurrent luigi workers")
-    parser.add_argument(
-        "--batch",
-        action="store_true",
-        help="Submit batch-system tasks to HTCondor (otherwise everything runs locally)",
-    )
-    parser.add_argument(
-        "--mode",
-        choices=("run", "dry-run", "show-output", "remove"),
-        default="run",
-        help="run (default), dry-run (print pending tasks), show-output (print every target), remove (delete outputs)",
-    )
-    parser.add_argument("--scheduler-host", default=None, help="luigid host (default: local scheduler)")
-    parser.add_argument("--scheduler-port", type=int, default=None, help="luigid port")
-    return parser
-
-
-def configure(spec: WorkflowSpec, spec_path: Path, batch: bool) -> None:
-    """Wire b2luigi's settings from the spec.
-
-    ``/ceph`` is shared between submit host and workers, so there is
-    deliberately no ``transfer_files``: ``result_dir``/``log_dir`` must live
-    somewhere both sides can see.
-    """
-    set_spec(spec)
-
-    b2luigi.set_setting("result_dir", spec.result_dir)
-    b2luigi.set_setting("log_dir", spec.log_dir)
-    b2luigi.set_setting("task_file_dir", str(Path(spec.result_dir) / "task_files"))
-    b2luigi.set_setting("use_parameter_name_in_output", True)
-    b2luigi.set_setting("batch_system", "htcondor" if batch else "local")
-    b2luigi.set_setting("working_dir", spec.condor.repo_dir)
-    b2luigi.set_setting("job_name", spec.name)
-    if spec.condor.env_script:
-        b2luigi.set_setting("env_script", spec.condor.env_script)
-    # The worker command is `<executable> [<basename of this file>] --batch-runner
-    # --task-id ...`, run after `cd working_dir`. Only the *basename* would be
-    # used, so the filename is dropped and the repo-relative script path is
-    # made part of the executable instead.
-    b2luigi.set_setting("add_filename_to_cmd", False)
-    b2luigi.set_setting("executable", [".venv/bin/python", "giant/workflow/run.py"])
-    b2luigi.set_setting("task_cmd_additional_args", ["--spec", str(spec_path)])
-
-
-def main(argv: list[str] | None = None) -> None:
-    args, _ = build_parser().parse_known_args(argv)
-    spec_path = Path(args.spec).resolve()
-    spec = load_spec(spec_path)
-    configure(spec, spec_path, batch=args.batch)
-
-    kwargs: dict = {}
-    if args.scheduler_host:
-        kwargs["scheduler_host"] = args.scheduler_host
-    if args.scheduler_port:
-        kwargs["scheduler_port"] = args.scheduler_port
-
-    b2luigi.process(
-        WorkflowTask(workflow_name=spec.name),
-        workers=args.workers,
-        batch=args.batch,
-        dry_run=args.mode == "dry-run",
-        show_output=args.mode == "show-output",
-        remove=args.mode == "remove",
-        auto_confirm=args.mode == "remove",
-        # run.py owns --spec/--mode/...; b2luigi must not choke on them.
-        ignore_additional_command_line_args=True,
-        **kwargs,
-    )
-
-
-if __name__ == "__main__":
-    main()

giant/workflow/spec.py

@@ -1,383 +0,0 @@
-"""Workflow TOML -> frozen dataclasses, validation, and per-task spec hashes.
-
-One spec file is the only place a pipeline is parameterised (see
-``configs/workflow_example.toml``):
-
-    [workflow]  name / result_dir / log_dir
-    [condor]    accounting group, repo dir, env script, docker images
-    [dataset]   steps (training) + reference (rollout seeds & analysis truth)
-    [geometry]  geometry-oracle build options
-    [[train]]   one per training run      (name, config, epochs, overrides, ...)
-    [[rollout]] one per rollout           (name, train = <a [[train]].name>, ...)
-    [[analysis]] one per comparison       (name, rollouts = [<[[rollout]].name>, ...])
-
-Every task carries its ``name`` plus a short ``spec_hash`` — 8 hex of the
-canonical JSON of its own resolved sub-spec **including its transitive
-parents**. That is what makes an edited spec produce a fresh result directory
-instead of silently reusing outputs computed under different settings: change
-the dataset and every hash downstream of it changes too.
-
-Unknown keys are rejected (with the valid ones listed), in the same spirit as
-``giant.config.validate_config_keys`` — a typo in a workflow spec would
-otherwise be a silently ignored setting on a multi-day pipeline.
-"""
-
-from __future__ import annotations
-
-import hashlib
-import json
-import tomllib
-from dataclasses import MISSING, dataclass, field, fields, is_dataclass
-from pathlib import Path
-from typing import Any
-
-__all__ = [
-    "AnalysisSpec",
-    "CondorSpec",
-    "DatasetSpec",
-    "GeometrySpec",
-    "RolloutSpec",
-    "TrainSpec",
-    "WorkflowSpec",
-    "load_spec",
-    "spec_hash",
-]
-
-
-class WorkflowSpecError(ValueError):
-    """Raised for any malformed workflow spec (unknown key, bad reference, ...)."""
-
-
-# ---------------------------------------------------------------------------
-# sub-specs
-# ---------------------------------------------------------------------------
-
-
-@dataclass(frozen=True)
-class CondorSpec:
-    """Where and how jobs run — the batch-system half of the spec.
-
-    ``repo_dir`` doubles as b2luigi's ``working_dir`` (jobs ``cd`` there before
-    running ``giant/workflow/run.py``), and ``env_script`` is sourced first,
-    since submit and worker machines don't share an environment.
-    """
-
-    accounting_group: str
-    repo_dir: str
-    env_script: str = ""
-    docker_image_cpu: str = "cverstege/alma9-gridjob"
-    docker_image_gpu: str = "mschnepf/slc7-condocker"
-    remote: bool = True
-    request_cpus: int = 1
-    request_memory_mb: int = 8192
-
-
-@dataclass(frozen=True)
-class DatasetSpec:
-    """The two datasets every pipeline needs.
-
-    ``steps`` is what training reads; ``reference`` is the held-out file
-    rollouts are seeded from and the analysis compares against (the "one
-    ground truth" premise of ``giant.analysis``).
-    """
-
-    steps: str
-    reference: str
-
-
-@dataclass(frozen=True)
-class GeometrySpec:
-    """``dwarf build-geometry-oracle`` options (see giant/tools/geometry_oracle.py)."""
-
-    method: str = "slab"
-    k: int = 1
-    subsample: int = 500_000
-    escape_factor: float = 5.0
-    seed: int = 0
-    depth_axis: int = 2
-    n_bins: int = 2000
-
-
-@dataclass(frozen=True)
-class TrainSpec:
-    """One training run, fanned out into ``ceil(epochs / epochs_per_job)`` jobs.
-
-    ``overrides`` are ``[train]``/model config keys merged on top of ``config``
-    exactly as ``giant train``'s flags are (``giant.config.merge_cli_overrides``),
-    so anything expressible on the CLI is expressible here.
-    """
-
-    name: str
-    config: str | None = None
-    epochs: int = 1
-    epochs_per_job: int = 1
-    overrides: dict[str, Any] = field(default_factory=dict)
-    request_gpus: int = 1
-    gpu_type: str | None = None
-    gpu_memory_mb: int | None = None
-    request_memory_mb: int = 16384
-    request_cpus: int = 4
-    walltime_s: int = 86400
-    num_workers: int = 4
-    shuffle_buffer: int = 65536
-    device: str | None = None
-
-
-@dataclass(frozen=True)
-class RolloutSpec:
-    """One ``giant rollout`` run against the checkpoint of ``train``."""
-
-    name: str
-    train: str
-    n_events: int | None = None
-    energy_cutoff: float = 0.1
-    max_steps: int = 1000
-    steps: int = 10
-    batch_size: int = 4096
-    max_tracks_per_event: int | None = None
-    escape_threshold: float | None = None
-    weights: str = "raw"
-    seed: int | None = None
-    request_gpus: int = 1
-    gpu_type: str | None = None
-    gpu_memory_mb: int | None = None
-    request_memory_mb: int = 16384
-    request_cpus: int = 2
-    walltime_s: int = 86400
-    device: str | None = None
-
-
-@dataclass(frozen=True)
-class AnalysisSpec:
-    """One rollout-vs-reference comparison (N rollout series, one reference)."""
-
-    name: str
-    rollouts: tuple[str, ...]
-    chunks: int = 1
-    energy_bins: int = 4
-    bins: int = 50
-    top_pdg: int = 6
-    gallery: bool = False
-    request_memory_mb: int = 8192
-    request_cpus: int = 1
-
-
-@dataclass(frozen=True)
-class WorkflowSpec:
-    """A whole pipeline: the parsed spec file plus name-keyed lookups."""
-
-    name: str
-    result_dir: str
-    log_dir: str
-    condor: CondorSpec
-    dataset: DatasetSpec
-    geometry: GeometrySpec
-    trains: tuple[TrainSpec, ...]
-    rollouts: tuple[RolloutSpec, ...]
-    analyses: tuple[AnalysisSpec, ...]
-    path: str = ""
-
-    # -- lookups ----------------------------------------------------------
-    def train(self, name: str) -> TrainSpec:
-        return _lookup(self.trains, name, "train")
-
-    def rollout(self, name: str) -> RolloutSpec:
-        return _lookup(self.rollouts, name, "rollout")
-
-    def analysis(self, name: str) -> AnalysisSpec:
-        return _lookup(self.analyses, name, "analysis")
-
-    # -- hashes -----------------------------------------------------------
-    # Each one folds in everything upstream of it, so a change anywhere in a
-    # task's ancestry moves its result directory (and only the affected
-    # subtree's).
-    def dataset_hash(self) -> str:
-        return spec_hash(self.dataset)
-
-    def warm_cache_hash(self, train_name: str) -> str:
-        # The setup cache depends on the dataset and on what this training's
-        # config asks of it (val split, conditioning, router) — not on how
-        # many epochs it runs for, so epochs/resources are deliberately left
-        # out and two trainings sharing a config share one warm-cache job.
-        t = self.train(train_name)
-        return spec_hash(self.dataset, t.config, t.overrides)
-
-    def geometry_hash(self) -> str:
-        return spec_hash(self.dataset, self.geometry)
-
-    def train_hash(self, name: str) -> str:
-        return spec_hash(self.dataset, self.train(name))
-
-    def rollout_hash(self, name: str) -> str:
-        ro = self.rollout(name)
-        return spec_hash(self.dataset, self.geometry, self.train(ro.train), ro)
-
-    def analysis_hash(self, name: str) -> str:
-        an = self.analysis(name)
-        parents = [self.rollout(r) for r in an.rollouts]
-        train_parents = [self.train(r.train) for r in parents]
-        return spec_hash(self.dataset, self.geometry, train_parents, parents, an)
-
-
-def _lookup(items, name: str, kind: str):
-    for item in items:
-        if item.name == name:
-            return item
-    known = ", ".join(sorted(i.name for i in items)) or "(none defined)"
-    raise WorkflowSpecError(f"no [[{kind}]] named {name!r} in this workflow — defined: {known}")
-
-
-# ---------------------------------------------------------------------------
-# hashing
-# ---------------------------------------------------------------------------
-
-
-def spec_hash(*parts: Any, length: int = 8) -> str:
-    """Short stable hash of one or more (sub-)specs.
-
-    Canonical JSON (sorted keys, dataclasses expanded) so the value depends
-    only on the resolved settings — not on key order in the TOML, nor on
-    which defaults were written out explicitly.
-    """
-    payload = json.dumps([_canonical(p) for p in parts], sort_keys=True, separators=(",", ":"))
-    return hashlib.sha256(payload.encode()).hexdigest()[:length]
-
-
-def _canonical(value: Any) -> Any:
-    if is_dataclass(value) and not isinstance(value, type):
-        return {f.name: _canonical(getattr(value, f.name)) for f in fields(value)}
-    if isinstance(value, dict):
-        return {str(k): _canonical(v) for k, v in value.items()}
-    if isinstance(value, (list, tuple)):
-        return [_canonical(v) for v in value]
-    if isinstance(value, Path):
-        return str(value)
-    return value
-
-
-# ---------------------------------------------------------------------------
-# parsing
-# ---------------------------------------------------------------------------
-
-
-def _build(cls, data: dict, where: str):
-    """Instantiate a frozen sub-spec, rejecting unknown/missing keys loudly."""
-    valid = {f.name for f in fields(cls)}
-    unknown = sorted(set(data) - valid)
-    if unknown:
-        raise WorkflowSpecError(f"{where}: unknown key(s) {unknown} — valid keys: {sorted(valid)}")
-    required = {f.name for f in fields(cls) if f.default is MISSING and f.default_factory is MISSING}
-    missing = sorted(required - set(data))
-    if missing:
-        raise WorkflowSpecError(f"{where}: missing required key(s) {missing}")
-    return cls(**data)
-
-
-def load_spec(path: str | Path) -> WorkflowSpec:
-    """Parse and validate a workflow TOML file."""
-    path = Path(path)
-    try:
-        raw = tomllib.loads(path.read_text())
-    except tomllib.TOMLDecodeError as exc:
-        raise WorkflowSpecError(f"{path}: not valid TOML — {exc}") from exc
-    return parse_spec(raw, path=path)
-
-
-def parse_spec(raw: dict, path: str | Path = "") -> WorkflowSpec:
-    """Validate an already-parsed workflow spec mapping."""
-    top_valid = {"workflow", "condor", "dataset", "geometry", "train", "rollout", "analysis"}
-    unknown = sorted(set(raw) - top_valid)
-    if unknown:
-        raise WorkflowSpecError(
-            f"{path or '<spec>'}: unknown top-level table(s) {unknown} — valid: {sorted(top_valid)}"
-        )
-
-    for required in ("workflow", "condor", "dataset"):
-        if required not in raw:
-            raise WorkflowSpecError(f"{path or '<spec>'}: missing required [{required}] table")
-
-    wf = dict(raw["workflow"])
-    wf_valid = {"name", "result_dir", "log_dir"}
-    wf_unknown = sorted(set(wf) - wf_valid)
-    if wf_unknown:
-        raise WorkflowSpecError(f"[workflow]: unknown key(s) {wf_unknown} — valid keys: {sorted(wf_valid)}")
-    if "name" not in wf or "result_dir" not in wf:
-        raise WorkflowSpecError("[workflow]: 'name' and 'result_dir' are required")
-    result_dir = str(Path(wf["result_dir"]).expanduser())
-    log_dir = str(Path(wf.get("log_dir", Path(result_dir) / "logs")).expanduser())
-
-    condor = _build(CondorSpec, dict(raw["condor"]), "[condor]")
-    dataset = _build(DatasetSpec, dict(raw["dataset"]), "[dataset]")
-    geometry = _build(GeometrySpec, dict(raw.get("geometry", {})), "[geometry]")
-
-    trains = tuple(_build(TrainSpec, dict(t), f"[[train]] #{i}") for i, t in enumerate(raw.get("train", [])))
-    rollouts = tuple(_build(RolloutSpec, dict(r), f"[[rollout]] #{i}") for i, r in enumerate(raw.get("rollout", [])))
-    analyses = tuple(
-        _build(AnalysisSpec, {**a, "rollouts": tuple(a.get("rollouts", ()))}, f"[[analysis]] #{i}")
-        for i, a in enumerate(raw.get("analysis", []))
-    )
-
-    _check_unique(trains, "train")
-    _check_unique(rollouts, "rollout")
-    _check_unique(analyses, "analysis")
-
-    train_names = {t.name for t in trains}
-    for ro in rollouts:
-        if ro.train not in train_names:
-            raise WorkflowSpecError(
-                f"[[rollout]] {ro.name!r}: train={ro.train!r} names no [[train]] — defined: {sorted(train_names)}"
-            )
-    rollout_names = {r.name for r in rollouts}
-    for an in analyses:
-        if not an.rollouts:
-            raise WorkflowSpecError(f"[[analysis]] {an.name!r}: 'rollouts' must name at least one [[rollout]]")
-        for r in an.rollouts:
-            if r not in rollout_names:
-                raise WorkflowSpecError(
-                    f"[[analysis]] {an.name!r}: rollout {r!r} is not defined — "
-                    f"defined: {sorted(rollout_names) or '(none)'}"
-                )
-        if len(set(an.rollouts)) != len(an.rollouts):
-            raise WorkflowSpecError(f"[[analysis]] {an.name!r}: repeated rollout name(s) in 'rollouts'")
-        if an.chunks < 1:
-            raise WorkflowSpecError(f"[[analysis]] {an.name!r}: chunks must be >= 1, got {an.chunks}")
-
-    for t in trains:
-        if t.epochs < 1:
-            raise WorkflowSpecError(f"[[train]] {t.name!r}: epochs must be >= 1, got {t.epochs}")
-        if t.epochs_per_job < 1:
-            raise WorkflowSpecError(f"[[train]] {t.name!r}: epochs_per_job must be >= 1, got {t.epochs_per_job}")
-
-    return WorkflowSpec(
-        name=wf["name"],
-        result_dir=result_dir,
-        log_dir=log_dir,
-        condor=condor,
-        dataset=dataset,
-        geometry=geometry,
-        trains=trains,
-        rollouts=rollouts,
-        analyses=analyses,
-        path=str(path),
-    )
-
-
-def _check_unique(items, kind: str) -> None:
-    names = [i.name for i in items]
-    dupes = sorted({n for n in names if names.count(n) > 1})
-    if dupes:
-        raise WorkflowSpecError(f"[[{kind}]] names must be unique — repeated: {dupes}")
-
-
-def epoch_milestones(train: TrainSpec) -> list[int]:
-    """Cumulative epoch counts, one per chained ``TrainEpochTask``.
-
-    ``epochs_per_job`` trades queue waits against job length: with
-    ``epochs=10, epochs_per_job=3`` this is ``[3, 6, 9, 10]``, i.e. job *k*
-    resumes job *k-1*'s ``last.pt`` and trains up to its own milestone.
-    """
-    step = train.epochs_per_job
-    milestones = list(range(step, train.epochs + 1, step))
-    if not milestones or milestones[-1] != train.epochs:
-        milestones.append(train.epochs)
-    return milestones

giant/workflow/tasks.py

@@ -1,647 +0,0 @@
-"""The b2luigi task graph: cache-warm -> train -> rollout -> analysis.
-
-    DatasetTask (external)  ─┬─> WarmCacheTask(train) ─> TrainEpochTask(train, 1..N) ─> TrainTask(train) ─┐
-                             └─> GeometryOracleTask ──┐                                                   │
-                                                      └──> RolloutTask(rollout) <────────────────────────┘
-                                                                       │
-    AnalysisPrepTask(analysis) ─> AnalysisComputeTask(analysis, plot, chunk) ─> AnalysisRenderTask(analysis)
-                                                                                        ^
-    WorkflowTask (wrapper) ─────────────────────────────────────────────────────────────┘
-
-Every task's output directory is ``<result_dir>/<kind>/name=<name>/spec_hash=
-<hash>/…`` — the hash covers the task's resolved sub-spec *and its transitive
-parents* (``giant/workflow/spec.py``), so editing the spec produces a fresh
-directory for exactly the affected subtree instead of silently reusing stale
-outputs.
-
-Task bodies never reimplement anything: they call the same entry points the
-CLIs do (``run_warm_setup_cache``, ``run_build_geometry_oracle``,
-``run_train_job``, ``giant.analysis.prep``/``compute_one``/``merge_all``,
-``render_run``), or shell out to ``giant rollout``, which has no library-level
-entry point of its own.
-
-Training is fanned out into **one short GPU job per epoch** (or per
-``epochs_per_job`` epochs): job *k* runs ``run_train_job`` with ``epochs = k``
-and ``resume = <job k-1>/last.pt``, which the training loop already handles
-(``giant/training/loop.py`` sets ``start_epoch = ckpt["epoch"] + 1`` and
-returns early when the checkpoint already covers ``epochs``). A 200-epoch run
-then becomes 200 schedulable jobs that survive preemption and give luigi a
-real progress signal, at the cost of one (cache-warmed) setup scan and one
-queue wait per job.
-"""
-
-from __future__ import annotations
-
-import json
-import shutil
-import subprocess
-import sys
-from pathlib import Path
-
-import b2luigi
-
-from giant.workflow.htcondor import cpu_settings, gpu_settings
-from giant.workflow.spec import WorkflowSpec, epoch_milestones
-
-__all__ = [
-    "AnalysisComputeTask",
-    "AnalysisPrepTask",
-    "AnalysisRenderTask",
-    "DatasetTask",
-    "GeometryOracleTask",
-    "RolloutTask",
-    "TrainEpochTask",
-    "TrainTask",
-    "WarmCacheTask",
-    "WorkflowTask",
-    "analysis_dir",
-    "analysis_jobs",
-    "get_spec",
-    "set_spec",
-]
-
-
-# ---------------------------------------------------------------------------
-# the active spec
-# ---------------------------------------------------------------------------
-# luigi parameters must be simple scalars, so tasks carry only `name` +
-# `spec_hash` and read the rest out of the one spec this process was started
-# with. Batch workers re-execute `run.py --spec <same file>` (see
-# `task_cmd_additional_args` there), so they resolve the identical spec.
-
-_SPEC: WorkflowSpec | None = None
-
-
-def set_spec(spec: WorkflowSpec) -> None:
-    global _SPEC
-    _SPEC = spec
-
-
-def get_spec() -> WorkflowSpec:
-    if _SPEC is None:
-        raise RuntimeError("no workflow spec loaded — call giant.workflow.tasks.set_spec() first")
-    return _SPEC
-
-
-def _result_dir(*parts: str) -> Path:
-    return Path(get_spec().result_dir).joinpath(*parts)
-
-
-def _task_dir(kind: str, name: str, spec_hash: str) -> Path:
-    """``<result_dir>/<kind>/name=<name>/spec_hash=<hash>``."""
-    return _result_dir(kind, f"name={name}", f"spec_hash={spec_hash}")
-
-
-def analysis_dir(spec: WorkflowSpec, name: str) -> Path:
-    """The analysis run directory — what ``prep`` lays out and every later step reads."""
-    return Path(spec.result_dir) / "analysis" / f"name={name}" / f"spec_hash={spec.analysis_hash(name)}"
-
-
-def analysis_jobs(spec: WorkflowSpec, name: str) -> list[tuple[str, int]]:
-    """Every ``(plot_id, chunk)`` compute job of one analysis.
-
-    ``chunkable=False`` specs (the checkpoint-bound diagnostics, already
-    bounded/subsampled) always run as a single chunk — the same rule the
-    deleted ``_job_walltimes`` applied.
-    """
-    from giant.analysis.catalog import catalog_ids, get_spec as get_plot_spec
-
-    chunks = spec.analysis(name).chunks
-    jobs: list[tuple[str, int]] = []
-    for plot_id in catalog_ids():
-        n = chunks if get_plot_spec(plot_id).chunkable else 1
-        jobs.extend((plot_id, chunk) for chunk in range(n))
-    return jobs
-
-
-def _giant_cmd() -> list[str]:
-    """How to invoke the ``giant`` CLI from inside a task (worker or locally)."""
-    return [sys.executable, "-m", "giant.cli"]
-
-
-# ---------------------------------------------------------------------------
-# inputs
-# ---------------------------------------------------------------------------
-
-
-class DatasetTask(b2luigi.ExternalTask):
-    """A steps parquet file or directory that must already exist.
-
-    Nothing produces it, so a missing path is a hard, immediate error rather
-    than a job that fails hours later — the usual cause being ``/ceph`` not
-    mounted on the machine the workflow was started from.
-    """
-
-    path = b2luigi.Parameter()
-
-    def output(self):
-        return b2luigi.LocalTarget(str(self.path))
-
-    def complete(self):
-        if not Path(str(self.path)).exists():
-            raise FileNotFoundError(
-                f"dataset {self.path!r} does not exist — is /ceph mounted on this machine? "
-                "(see CLAUDE.md's Compute environment section)"
-            )
-        return True
-
-
-# ---------------------------------------------------------------------------
-# setup stage
-# ---------------------------------------------------------------------------
-
-
-class WarmCacheTask(b2luigi.Task):
-    """Precompute one training's setup-stage sidecar (vocab maps, event split,
-    normalizer stats) so every per-epoch job is a cache hit instead of a
-    full rescan.
-
-    The real product (``<data>.giant_train_cache.json``) lives next to the
-    dataset, not under ``result_dir``, so the target here is a small stamp
-    recording that sidecar's path/mtime/size.
-    """
-
-    name = b2luigi.Parameter()
-    spec_hash = b2luigi.Parameter()
-
-    @property
-    def htcondor_settings(self):
-        spec = get_spec()
-        return cpu_settings(spec.condor, request_memory_mb=32768, request_cpus=4, walltime_s=21600)
-
-    def requires(self):
-        yield DatasetTask(path=get_spec().dataset.steps)
-
-    def output(self):
-        return b2luigi.LocalTarget(str(_task_dir("warm_cache", str(self.name), str(self.spec_hash)) / "stamp.json"))
-
-    def run(self):
-        from giant.data.setup_cache import sidecar_path
-        from giant.tools.warm_setup_cache import run_warm_setup_cache
-
-        spec = get_spec()
-        train = spec.train(str(self.name))
-        run_warm_setup_cache(
-            data=spec.dataset.steps,
-            config_path=Path(train.config) if train.config else None,
-        )
-        sidecar = Path(sidecar_path(spec.dataset.steps))
-        stamp = {
-            "sidecar": str(sidecar),
-            "mtime": sidecar.stat().st_mtime if sidecar.exists() else None,
-            "size": sidecar.stat().st_size if sidecar.exists() else None,
-        }
-        out = Path(self.output().path)
-        out.parent.mkdir(parents=True, exist_ok=True)
-        out.write_text(json.dumps(stamp, indent=2))
-
-
-class GeometryOracleTask(b2luigi.Task):
-    """Build the position -> (material, layer_id) oracle every rollout needs."""
-
-    spec_hash = b2luigi.Parameter()
-
-    @property
-    def htcondor_settings(self):
-        spec = get_spec()
-        return cpu_settings(spec.condor, request_memory_mb=32768, request_cpus=4, walltime_s=21600)
-
-    def requires(self):
-        yield DatasetTask(path=get_spec().dataset.steps)
-
-    def output(self):
-        return b2luigi.LocalTarget(
-            str(_result_dir("geometry", f"spec_hash={self.spec_hash}") / "oracle.pkl"),
-        )
-
-    def run(self):
-        from giant.tools.geometry_oracle import run_build_geometry_oracle
-
-        spec = get_spec()
-        g = spec.geometry
-        out = Path(self.output().path)
-        out.parent.mkdir(parents=True, exist_ok=True)
-        run_build_geometry_oracle(
-            data=Path(spec.dataset.steps),
-            out=out,
-            method=g.method,
-            k=g.k,
-            subsample=g.subsample,
-            escape_factor=g.escape_factor,
-            seed=g.seed,
-            depth_axis=g.depth_axis,
-            n_bins=g.n_bins,
-        )
-
-
-# ---------------------------------------------------------------------------
-# training
-# ---------------------------------------------------------------------------
-
-
-def _train_cfg(spec: WorkflowSpec, name: str, epochs: int) -> dict:
-    """The merged config one training job runs, resolved exactly as `giant train` does."""
-    from giant import config as gconfig
-
-    train = spec.train(name)
-    flags = {**train.overrides, "epochs": epochs}
-    overrides = gconfig.overrides_from_flags(flags)
-    cfg = gconfig.merge_cli_overrides(
-        gconfig.DEFAULT_CONFIG,
-        Path(train.config) if train.config else None,
-        overrides,
-    )
-    gconfig.validate_config(cfg, resume=True)
-    return cfg
-
-
-class TrainEpochTask(b2luigi.Task):
-    """Epochs up to ``milestone`` of one training, resuming the previous job.
-
-    Target is ``last.pt``. ``best.pt`` is written by the loop *only when that
-    epoch improved*, and ``best_val_loss`` travels inside the checkpoint, so
-    the global best comparison stays correct across jobs: "``best.pt`` exists
-    in milestone dir *k*" means exactly "one of that job's epochs was the best
-    so far".
-    """
-
-    name = b2luigi.Parameter()
-    spec_hash = b2luigi.Parameter()
-    milestone = b2luigi.IntParameter()
-
-    @property
-    def htcondor_settings(self):
-        spec = get_spec()
-        train = spec.train(str(self.name))
-        return gpu_settings(
-            spec.condor,
-            request_gpus=train.request_gpus,
-            gpu_type=train.gpu_type,
-            gpu_memory_mb=train.gpu_memory_mb,
-            request_memory_mb=train.request_memory_mb,
-            request_cpus=train.request_cpus,
-            walltime_s=train.walltime_s,
-        )
-
-    @property
-    def _dir(self) -> Path:
-        return _task_dir("train_epoch", str(self.name), str(self.spec_hash)) / f"epochs={int(self.milestone)}"
-
-    def _previous_milestone(self) -> int | None:
-        spec = get_spec()
-        milestones = epoch_milestones(spec.train(str(self.name)))
-        index = milestones.index(int(self.milestone))
-        return milestones[index - 1] if index > 0 else None
-
-    def requires(self):
-        previous = self._previous_milestone()
-        if previous is None:
-            yield WarmCacheTask(name=self.name, spec_hash=get_spec().warm_cache_hash(str(self.name)))
-        else:
-            yield TrainEpochTask(name=self.name, spec_hash=self.spec_hash, milestone=previous)
-
-    def output(self):
-        return b2luigi.LocalTarget(str(self._dir / "last.pt"))
-
-    def run(self):
-        import torch
-
-        from giant import config as gconfig
-        from giant.pipeline import run_train_job
-
-        spec = get_spec()
-        train = spec.train(str(self.name))
-        cfg = _train_cfg(spec, str(self.name), int(self.milestone))
-
-        previous = self._previous_milestone()
-        resume = None
-        if previous is not None:
-            resume = _task_dir("train_epoch", str(self.name), str(self.spec_hash)) / f"epochs={previous}" / "last.pt"
-
-        device = torch.device(train.device) if train.device else gconfig.auto_device()
-        out_dir = self._dir
-        out_dir.mkdir(parents=True, exist_ok=True)
-        run_train_job(
-            data=Path(spec.dataset.steps),
-            cfg=cfg,
-            out_dir=out_dir,
-            device=device,
-            shuffle_buffer=train.shuffle_buffer,
-            num_workers=train.num_workers,
-            resume=resume,
-            cache_setup=True,
-        )
-
-
-class TrainTask(b2luigi.Task):
-    """Publish one training's canonical outputs, hiding the epoch fan-out.
-
-    Everything downstream (``RolloutTask``, humans, ``giant analyze metrics``)
-    points here and never has to know which milestone directory happened to
-    hold the best checkpoint.
-    """
-
-    name = b2luigi.Parameter()
-    spec_hash = b2luigi.Parameter()
-    batch_system = "local"
-
-    @property
-    def _milestones(self) -> list[int]:
-        return epoch_milestones(get_spec().train(str(self.name)))
-
-    def requires(self):
-        yield TrainEpochTask(name=self.name, spec_hash=self.spec_hash, milestone=self._milestones[-1])
-
-    @property
-    def _dir(self) -> Path:
-        return _task_dir("train", str(self.name), str(self.spec_hash))
-
-    def output(self):
-        d = self._dir
-        return {
-            "best.pt": b2luigi.LocalTarget(str(d / "best.pt")),
-            "last.pt": b2luigi.LocalTarget(str(d / "last.pt")),
-            "metrics.csv": b2luigi.LocalTarget(str(d / "metrics.csv")),
-        }
-
-    def run(self):
-        epoch_base = _task_dir("train_epoch", str(self.name), str(self.spec_hash))
-        milestone_dirs = [epoch_base / f"epochs={m}" for m in self._milestones]
-
-        best_dirs = [d for d in milestone_dirs if (d / "best.pt").exists()]
-        if not best_dirs:
-            raise FileNotFoundError(
-                f"no best.pt in any milestone directory under {epoch_base} — "
-                "did every epoch job run with a validation split?"
-            )
-        out = self._dir
-        out.mkdir(parents=True, exist_ok=True)
-        shutil.copy2(best_dirs[-1] / "best.pt", out / "best.pt")
-        shutil.copy2(milestone_dirs[-1] / "last.pt", out / "last.pt")
-        for extra in ("config.toml", "run_meta.json"):
-            src = milestone_dirs[-1] / extra
-            if src.exists():
-                shutil.copy2(src, out / extra)
-
-        # One metrics.csv for the whole run: the first job's header, then
-        # every job's rows in epoch order, so `giant analyze metrics` sees a
-        # single continuous training curve.
-        lines: list[str] = []
-        header: str | None = None
-        for d in milestone_dirs:
-            csv = d / "metrics.csv"
-            if not csv.exists():
-                continue
-            rows = csv.read_text().splitlines()
-            if not rows:
-                continue
-            if header is None:
-                header = rows[0]
-            lines.extend(rows[1:])
-        (out / "metrics.csv").write_text("\n".join([header or ""] + lines) + "\n")
-
-
-# ---------------------------------------------------------------------------
-# rollout
-# ---------------------------------------------------------------------------
-
-
-class RolloutTask(b2luigi.Task):
-    """Roll one trained checkpoint forward into full showers.
-
-    ``giant rollout`` has no library-level entry point, so this shells out to
-    the CLI — with an explicit ``--out``, which puts the YAML sidecar at the
-    deterministic ``rollout.yaml`` next to the parquet (see
-    ``giant/cli.py:_write_prediction_ref``).
-    """
-
-    name = b2luigi.Parameter()
-    spec_hash = b2luigi.Parameter()
-
-    @property
-    def htcondor_settings(self):
-        spec = get_spec()
-        ro = spec.rollout(str(self.name))
-        return gpu_settings(
-            spec.condor,
-            request_gpus=ro.request_gpus,
-            gpu_type=ro.gpu_type,
-            gpu_memory_mb=ro.gpu_memory_mb,
-            request_memory_mb=ro.request_memory_mb,
-            request_cpus=ro.request_cpus,
-            walltime_s=ro.walltime_s,
-        )
-
-    @property
-    def _dir(self) -> Path:
-        return _task_dir("rollout", str(self.name), str(self.spec_hash))
-
-    def requires(self):
-        spec = get_spec()
-        ro = spec.rollout(str(self.name))
-        yield TrainTask(name=ro.train, spec_hash=spec.train_hash(ro.train))
-        yield GeometryOracleTask(spec_hash=spec.geometry_hash())
-        yield DatasetTask(path=spec.dataset.reference)
-
-    def output(self):
-        d = self._dir
-        return {
-            "rollout.parquet": b2luigi.LocalTarget(str(d / "rollout.parquet")),
-            "rollout.yaml": b2luigi.LocalTarget(str(d / "rollout.yaml")),
-        }
-
-    def run(self):
-        spec = get_spec()
-        ro = spec.rollout(str(self.name))
-        out = self._dir / "rollout.parquet"
-        out.parent.mkdir(parents=True, exist_ok=True)
-
-        checkpoint = _task_dir("train", ro.train, spec.train_hash(ro.train)) / "best.pt"
-        oracle = _result_dir("geometry", f"spec_hash={spec.geometry_hash()}") / "oracle.pkl"
-
-        cmd = [
-            *_giant_cmd(),
-            "rollout",
-            spec.dataset.reference,
-            "--checkpoint",
-            str(checkpoint),
-            "--geometry",
-            str(oracle),
-            "--out",
-            str(out),
-            "--energy-cutoff",
-            str(ro.energy_cutoff),
-            "--max-steps",
-            str(ro.max_steps),
-            "--steps",
-            str(ro.steps),
-            "--batch-size",
-            str(ro.batch_size),
-            "--weights",
-            ro.weights,
-        ]
-        for flag, value in (
-            ("--n-events", ro.n_events),
-            ("--max-tracks-per-event", ro.max_tracks_per_event),
-            ("--escape-threshold", ro.escape_threshold),
-            ("--seed", ro.seed),
-            ("--device", ro.device),
-        ):
-            if value is not None:
-                cmd += [flag, str(value)]
-        subprocess.run(cmd, check=True)
-
-
-# ---------------------------------------------------------------------------
-# analysis
-# ---------------------------------------------------------------------------
-
-
-class AnalysisPrepTask(b2luigi.Task):
-    """Resolve the shared bin edges/group sets once, for every compute job.
-
-    Cheap and streaming, so it runs locally: everything after it needs
-    ``shared.json``/``run_meta.json`` to already exist.
-    """
-
-    name = b2luigi.Parameter()
-    spec_hash = b2luigi.Parameter()
-    batch_system = "local"
-
-    def requires(self):
-        spec = get_spec()
-        for rollout_name in spec.analysis(str(self.name)).rollouts:
-            yield RolloutTask(name=rollout_name, spec_hash=spec.rollout_hash(rollout_name))
-
-    @property
-    def _dir(self) -> Path:
-        return analysis_dir(get_spec(), str(self.name))
-
-    def output(self):
-        d = self._dir
-        return {
-            "shared.json": b2luigi.LocalTarget(str(d / "shared.json")),
-            "run_meta.json": b2luigi.LocalTarget(str(d / "run_meta.json")),
-        }
-
-    def run(self):
-        from giant.analysis import prep
-
-        spec = get_spec()
-        an = spec.analysis(str(self.name))
-        yamls = [_task_dir("rollout", r, spec.rollout_hash(r)) / "rollout.yaml" for r in an.rollouts]
-        prep(
-            yamls,
-            run_dir=self._dir,
-            n_chunks=an.chunks,
-            labels=list(an.rollouts),
-            n_energy_bins=an.energy_bins,
-            n_marginal_bins=an.bins,
-            top_k_pdg=an.top_pdg,
-        )
-
-
-class AnalysisComputeTask(b2luigi.Task):
-    """One (plot, chunk) streaming reduction — the replaced ``jobs.txt`` row.
-
-    The output path is the on-disk contract ``compute-one``/``merge_one``
-    already share (``reduced_partial/<id>__<chunk>.json``), declared
-    explicitly rather than through b2luigi's own output naming so that
-    contract is untouched.
-    """
-
-    name = b2luigi.Parameter()
-    spec_hash = b2luigi.Parameter()
-    plot_id = b2luigi.Parameter()
-    chunk = b2luigi.IntParameter()
-
-    @property
-    def htcondor_settings(self):
-        # A property, so it is evaluated at submit time — i.e. after prep has
-        # written run_meta.json, whose row counts size the walltime request.
-        from giant.analysis import RunMeta
-        from giant.analysis.runtime_estimate import estimate_runtime_s
-
-        spec = get_spec()
-        an = spec.analysis(str(self.name))
-        walltime = None
-        meta_path = analysis_dir(spec, str(self.name)) / "run_meta.json"
-        if meta_path.exists():
-            from giant.analysis.catalog import get_spec as get_plot_spec
-
-            meta = RunMeta.load(meta_path)
-            chunkable = get_plot_spec(str(self.plot_id)).chunkable
-            n_rows = meta.rows_per_chunk[int(self.chunk)] if chunkable and meta.rows_per_chunk else meta.total_rows
-            walltime = estimate_runtime_s(str(self.plot_id), n_rows)
-        return cpu_settings(
-            spec.condor,
-            request_memory_mb=an.request_memory_mb,
-            request_cpus=an.request_cpus,
-            walltime_s=walltime,
-        )
-
-    def requires(self):
-        yield AnalysisPrepTask(name=self.name, spec_hash=self.spec_hash)
-
-    def output(self):
-        run_dir = analysis_dir(get_spec(), str(self.name))
-        return b2luigi.LocalTarget(str(run_dir / "reduced_partial" / f"{self.plot_id}__{int(self.chunk)}.json"))
-
-    def run(self):
-        from giant.analysis import compute_one
-
-        compute_one(str(self.plot_id), analysis_dir(get_spec(), str(self.name)), chunk_index=int(self.chunk))
-
-
-class AnalysisRenderTask(b2luigi.Task):
-    """Merge every plot's chunk partials, then render the PDFs + gallery.
-
-    Always local — this is the only step that imports plotstyle/LaTeX, which
-    the compute worker images don't have.
-    """
-
-    name = b2luigi.Parameter()
-    spec_hash = b2luigi.Parameter()
-    batch_system = "local"
-
-    def requires(self):
-        spec = get_spec()
-        for plot_id, chunk in analysis_jobs(spec, str(self.name)):
-            yield AnalysisComputeTask(
-                name=self.name,
-                spec_hash=self.spec_hash,
-                plot_id=plot_id,
-                chunk=chunk,
-            )
-
-    def output(self):
-        run_dir = analysis_dir(get_spec(), str(self.name))
-        return b2luigi.LocalTarget(str(run_dir / "plots" / "metadata.yaml"))
-
-    def run(self):
-        # render_run joins every plot's chunk partials (merge_all) before
-        # rendering, so this one call is the whole merge+render step.
-        from giant.analysis.render import render_run
-
-        spec = get_spec()
-        render_run(analysis_dir(spec, str(self.name)), run_gallery=spec.analysis(str(self.name)).gallery)
-
-
-class WorkflowTask(b2luigi.WrapperTask):
-    """The whole pipeline: every analysis in the spec, rendered."""
-
-    workflow_name = b2luigi.Parameter()
-
-    def requires(self):
-        spec = get_spec()
-        if not spec.analyses:
-            # A spec with no [[analysis]] still has work to do — fall back to
-            # the deepest tasks it does define.
-            for ro in spec.rollouts:
-                yield RolloutTask(name=ro.name, spec_hash=spec.rollout_hash(ro.name))
-            if not spec.rollouts:
-                for tr in spec.trains:
-                    yield TrainTask(name=tr.name, spec_hash=spec.train_hash(tr.name))
-            return
-        for an in spec.analyses:
-            yield AnalysisRenderTask(name=an.name, spec_hash=spec.analysis_hash(an.name))

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "giant"
-version = "0.3.10"
+version = "0.3.11"
 description = "Geant4 step-function surrogate via conditional flow matching"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -28,7 +28,7 @@ dev = [
     "ty>=0.0.50,<0.1",
     "bump-my-version>=1.2,<2",
     "git-cliff>=2,<3",
-    "giant[convert,analysis,geometry,wandb,workflow]",
+    "giant[convert,analysis,geometry,wandb]",
 ]
 geometry = [
     "scikit-learn>=1.4,<2",
@@ -49,11 +49,6 @@ analysis = [
     # `giant analyze render` step imports it; compute workers never do.
     "plotstyle>=1.0.0",
 ]
-# b2luigi pulls luigi + tenacity; the only sanctioned way to chain a
-# multi-step pipeline (see giant/workflow/).
-workflow = [
-    "b2luigi>=1.0,<2",
-]
 
 [project.scripts]
 giant = "giant.cli:app"
@@ -108,12 +103,3 @@ explicit = true
 name = "larsbogner"
 url = "https://git.larsbogner.de/api/packages/lars/pypi/simple/"
 explicit = true
-
-# luigi builds task constructors from class-level Parameter descriptors, so a
-# static checker sees no keyword parameters at all on `Task(name=..., ...)`.
-# The workflow code is written against that API; nothing else in the repo is.
-[[tool.ty.overrides]]
-include = ["giant/workflow/**", "tests/test_workflow_tasks.py"]
-
-[tool.ty.overrides.rules]
-unknown-argument = "ignore"

tests/test_analysis_reduce.py

@@ -13,6 +13,7 @@ from giant.analysis.sources import (
     open_side,
     physical_steps,
     secondaries,
+    secondaries_by_step,
 )
 from giant.data.loader import EVENT_ID_FILE_STRIDE
 
@@ -159,18 +160,17 @@ def test_secondaries_rollout_vs_reference_align():
     assert t["pdg"].to_list() == [22, 22]
 
 
-def test_sec_count_by_event_zero_fills_events_with_no_secondaries():
-    r_phys = physical_steps(_rollout_frame(), Side.rollout)
-    r_sec = secondaries(_rollout_frame(), Side.rollout)
-    ev, n = R.sec_count_by_event(r_phys, r_sec)
-    # event 1 has one secondary track; event 2 has none and must still appear (as 0),
-    # not silently drop out of a plain group_by on the secondaries frame alone.
-    assert dict(zip(ev.tolist(), n.tolist())) == {1: 1, 2: 0}
+def test_secondaries_by_step_keys_each_secondary_to_its_emitting_step():
+    r = secondaries_by_step(_rollout_frame(), Side.rollout).collect()
+    assert r["pdg"].to_list() == [22]
+    # the rollout key is (event_id, parent_id, birth position) — the parent
+    # step's post_pos, copied verbatim onto the child's birth row.
+    assert r["step_key"][0] == {"event_id": 1, "parent_id": 0, "pre_x": 0.0, "pre_y": 0.0, "pre_z": 1.0}
 
-    t_all = _reference_frame()
-    t_sec = secondaries(t_all, Side.reference)
-    ev, n = R.sec_count_by_event(t_all, t_sec)
-    assert dict(zip(ev.tolist(), n.tolist())) == {1: 1, 2: 1}
+    t = secondaries_by_step(_reference_frame(), Side.reference).collect()
+    assert t["pdg"].to_list() == [22, 22]
+    # one row per emitting step; the empty-list step drops out entirely
+    assert [k["_row"] for k in t["step_key"]] == [0, 2]
 
 
 def test_leakage_fraction():

tests/test_catalog.py

@@ -10,10 +10,10 @@ from giant.analysis.catalog import (
     Bundle,
     PlotSpec,
     _containment_depths,
-    _integer_confusion,
     _ks_statistic,
 )
 from giant.analysis.context import Context, build_context
+from giant.analysis.grouping import pdg_label
 from giant.analysis.sources import RolloutSpec
 from tests.test_analysis_reduce import _reference_frame, _rollout_frame
 
@@ -160,8 +160,9 @@ def _validate_payload(r, names: list[str]) -> None:
 # data-dependent edges (event_total_edep), concat-then-mean/std (shower_
 # longitudinal), concat-then-max-edge (leakage_fraction), pdg-keyed sum with a
 # ratio (species_edep_share), a chunkable=False passthrough (router_gating),
-# nested sum-merge into a scorecard (marginal_distance_summary), concat-then-
-# event-id-join (n_sec_confusion), and concat-then-per-event-derived-quantity
+# sum-mergeable-with-a-zero-fill-denominator (sec_count_per_step{,_by_species}),
+# nested sum-merge into a scorecard (marginal_distance_summary), and
+# concat-then-per-event-derived-quantity
 # (shower_containment_depth_90, reusing the profile matrix's own merge shape).
 _CHUNK_EQUIVALENCE_IDS = [
     "marginal_edep",
@@ -170,9 +171,10 @@ _CHUNK_EQUIVALENCE_IDS = [
     "shower_longitudinal",
     "leakage_fraction",
     "sec_count_per_species",
+    "sec_count_per_step",
+    "sec_count_per_step_by_species",
     "router_gating",
     "marginal_distance_summary",
-    "n_sec_confusion",
     "shower_containment_depth_90",
 ]
 
@@ -217,7 +219,7 @@ def test_chunked_matches_unchunked(two_ctx: Context, spec_id: str):
 
 
 # ---------------------------------------------------------------------------
-# new (gitea #76) reductions: KS distance, confusion matrix, containment depth
+# new (gitea #76) reductions: KS distance and containment depth
 # ---------------------------------------------------------------------------
 
 
@@ -228,28 +230,6 @@ def test_ks_statistic():
     assert _ks_statistic([10, 0], [0, 0]) == 1.0  # one side empty, other isn't -> maximal mismatch
 
 
-def test_integer_confusion_matches_event_pairing():
-    # true (reference) n_sec = [1, 1]; predicted (rollout) n_sec = [1, 0]
-    labels, mat = _integer_confusion(np.array([1, 1]), np.array([1, 0]))
-    assert labels == ["0", "1+"]
-    assert mat.tolist() == [[0, 0], [1, 1]]  # row=true, col=pred
-
-
-def test_integer_confusion_caps_pathological_outliers():
-    labels, mat = _integer_confusion(np.array([0, 500]), np.array([0, 0]), max_bins=5)
-    assert labels[-1] == "4+"
-    assert mat.shape == (5, 5)
-    assert mat.sum() == 2
-
-
-def test_integer_confusion_explicit_cap_overrides_local_range():
-    # Even though this pair's own max is 1, an explicit shared cap forces a
-    # wider (and so cross-rollout-consistent) label set.
-    labels, mat = _integer_confusion(np.array([1, 1]), np.array([0, 1]), cap=3)
-    assert labels == ["0", "1", "2", "3+"]
-    assert mat.shape == (4, 4)
-
-
 def test_containment_depths_simple_ramp():
     # one event, edep concentrated in the first bin -> 90%/95% containment
     # depth is the first bin's right edge; a zero-energy event is dropped.
@@ -259,17 +239,25 @@ def test_containment_depths_simple_ramp():
     assert depths.tolist() == [1.0]
 
 
-def test_n_sec_confusion_spec(bundle):
-    spec = get_spec("n_sec_confusion")
+def test_sec_count_per_step_counts_empty_steps(bundle):
+    spec = get_spec("sec_count_per_step")
     r = spec.finalize([spec.compute_partial(bundle)], bundle.ctx)
-    assert r.payload["row_labels"] == r.payload["col_labels"] == ["0", "1+"]
-    assert r.payload["series"]["rollout"] == [[0, 0], [1, 1]]
+    # reference: 3 steps, two of which emit exactly one secondary
+    assert r.payload["reference"][:2] == [1, 2]
+    # rollout: 4 physical steps, one of which emits a single secondary
+    assert r.payload["series"]["rollout"][:2] == [3, 1]
+    assert sum(r.payload["reference"]) == 3
 
 
-def test_n_sec_confusion_shares_one_cap_across_rollouts(two_bundle):
-    spec = get_spec("n_sec_confusion")
-    r = spec.finalize([spec.compute_partial(two_bundle)], two_bundle.ctx)
-    assert list(r.payload["series"]) == ["flow", "wgan"]
-    # both rollouts share the same fixture data here, so their matrices (and
-    # the shared label set) must be identical.
-    assert r.payload["series"]["flow"] == r.payload["series"]["wgan"]
+def test_sec_count_per_step_by_species_zero_row_is_per_species(bundle):
+    spec = get_spec("sec_count_per_step_by_species")
+    r = spec.finalize([spec.compute_partial(bundle)], bundle.ctx)
+    cols = r.payload["col_labels"]
+    ref = r.payload["reference"]
+    g = cols.index(pdg_label(22))
+    # two reference steps emit one photon each; the third emits none
+    assert [row[g] for row in ref][:2] == [1, 2]
+    # every other species column is "no such secondary" on all 3 steps
+    for j, _ in enumerate(cols):
+        if j != g:
+            assert ref[0][j] == 3 and sum(row[j] for row in ref[1:]) == 0

tests/test_condor.py

@@ -1,7 +1,8 @@
-"""Tests for the rollout-YAML(s) → run-directory flow, compute, and merge."""
+"""Tests for the rollout-YAML(s) → run-directory flow, compute, and submit."""
 
 from __future__ import annotations
 
+import sys
 from pathlib import Path
 
 import pyarrow.parquet as pq
@@ -10,6 +11,8 @@ import yaml
 
 from giant.analysis import (
     RunMeta,
+    SubmitConfig,
+    catalog_ids,
     compute_one,
     compute_reduced,
     derive_run_dir,
@@ -17,8 +20,10 @@ from giant.analysis import (
     load_rollout_yamls,
     merge_one,
     prep,
+    write_submit,
 )
-from giant.analysis.run import Context
+from giant.analysis.catalog import get_spec
+from giant.analysis.condor import Context
 from giant.analysis.reduced import Partial, Reduced
 from giant.constants import PREDICT_COORD_METADATA_KEY, ROLLOUT_COORD_VALUE
 from tests.test_analysis_reduce import _reference_frame, _rollout_frame
@@ -81,6 +86,14 @@ def _write_two_inputs(tmp_path: Path) -> tuple[Path, Path]:
     return paths[0], paths[1]
 
 
+def _fake_venv(repo_dir: Path) -> None:
+    """Stand in for a `uv sync`'d venv: write_submit checks `.venv/bin/giant` exists."""
+    giant = repo_dir / ".venv" / "bin" / "giant"
+    giant.parent.mkdir(parents=True, exist_ok=True)
+    giant.write_text("#!/bin/bash\n")
+    giant.chmod(0o755)
+
+
 def _prep(rollout_yamls, run_dir: str | Path | None = None, chunks: int = 1, labels=None) -> Path:
     """``prep`` with small test-sized context bins/sampling."""
     return prep(
@@ -300,6 +313,73 @@ def test_compute_reduced_rejects_out_of_range_chunk(tmp_path: Path):
         compute_one("marginal_edep", run_dir, chunk_index=1)
 
 
+def test_write_submit_description(tmp_path: Path):
+    run_dir = _prep([_write_inputs(tmp_path)])
+    _fake_venv(tmp_path)
+    cfg = SubmitConfig(run_dir=run_dir, accounting_group="cms", repo_dir=tmp_path)
+    txt = write_submit(cfg).read_text()
+    assert "universe = docker" in txt
+    assert "docker_image = cverstege/alma9-gridjob" in txt
+    assert "requirements = TARGET.ProvidesETPResources" in txt
+    assert "accounting_group = cms" in txt
+    assert "+RequestWalltime = $(walltime)" in txt
+    assert "queue plotid,chunk,walltime from" in txt
+    jobs = [line.split(",") for line in (run_dir / "jobs.txt").read_text().split()]
+    assert [i for i, _, _ in jobs] == catalog_ids()
+    assert all(k == "0" for _, k, _ in jobs)  # n_chunks=1 default
+    assert all(int(w) > 0 for _, _, w in jobs)
+    wrapper = run_dir / "run_compute.sh"
+    assert wrapper.exists() and (wrapper.stat().st_mode & 0o111)
+    body = wrapper.read_text()
+    assert "giant analyze compute-one --id" in body
+    assert "--chunk" in body and "--run-dir" in body
+
+
+def test_write_submit_requires_synced_venv(tmp_path: Path, monkeypatch: pytest.MonkeyPatch):
+    run_dir = _prep([_write_inputs(tmp_path)])
+    cfg = SubmitConfig(run_dir=run_dir, accounting_group="cms", repo_dir=tmp_path)
+    # No `giant` next to the (fake) active interpreter, so this falls through
+    # to repo_dir/.venv/bin/giant, which _write_inputs/_prep also didn't create.
+    monkeypatch.setattr(sys, "executable", str(tmp_path / "not-a-venv" / "bin" / "python"))
+    with pytest.raises(FileNotFoundError, match="uv sync"):
+        write_submit(cfg)
+
+
+def test_write_submit_remote_flag(tmp_path: Path):
+    run_dir = _prep([_write_inputs(tmp_path)])
+    _fake_venv(tmp_path)
+    cfg = SubmitConfig(run_dir=run_dir, accounting_group="cms", repo_dir=tmp_path, remote=True)
+    txt = write_submit(cfg).read_text()
+    assert "+RemoteJob = True" in txt
+    assert "ProvidesETPResources" not in txt
+
+
+def test_write_submit_chunks_respect_chunkable(tmp_path: Path):
+    assert get_spec("router_gating").chunkable is False
+    run_dir = _prep([_write_inputs(tmp_path)], chunks=4)
+    _fake_venv(tmp_path)
+    cfg = SubmitConfig(run_dir=run_dir, accounting_group="cms", repo_dir=tmp_path, n_chunks=4)
+    write_submit(cfg)
+    jobs = [line.split(",") for line in (run_dir / "jobs.txt").read_text().split()]
+    counts: dict[str, int] = {}
+    for spec_id, _, _ in jobs:
+        counts[spec_id] = counts.get(spec_id, 0) + 1
+    assert counts["marginal_edep"] == 4
+    assert counts["router_gating"] == 1  # chunkable=False, ignores n_chunks
+
+
+def test_write_submit_rejects_n_chunks_mismatch_with_run_meta(tmp_path: Path):
+    """cfg.n_chunks must match the n_chunks the run_dir was actually prepped
+    with — RunMeta.rows_per_chunk is sized to the prepped value, so a
+    mismatch would otherwise surface as a confusing IndexError deep inside
+    _job_walltimes instead of a clear error here."""
+    run_dir = _prep([_write_inputs(tmp_path)], chunks=2)
+    _fake_venv(tmp_path)
+    cfg = SubmitConfig(run_dir=run_dir, accounting_group="cms", repo_dir=tmp_path, n_chunks=4)
+    with pytest.raises(ValueError, match="n_chunks"):
+        write_submit(cfg)
+
+
 def test_estimate_runtime_s_scales_with_rows_and_margin():
     from giant.analysis import RUNTIME_SAFETY_MARGIN, estimate_runtime_s
     from giant.analysis.runtime_estimate import _FIXED_OVERHEAD_S
@@ -309,3 +389,18 @@ def test_estimate_runtime_s_scales_with_rows_and_margin():
     large = estimate_runtime_s("marginal_edep", 100_000_000)
     assert small >= (1 + RUNTIME_SAFETY_MARGIN) * _FIXED_OVERHEAD_S
     assert large > small  # bigger chunk -> longer estimate
+
+
+def test_write_submit_walltime_grows_with_chunk_rows(tmp_path: Path):
+    """A chunked run's later job walltimes track that chunk's row count."""
+    from giant.analysis.runtime_estimate import estimate_runtime_s
+
+    run_dir = _prep([_write_inputs(tmp_path)], chunks=2)
+    meta = RunMeta.load(run_dir / "run_meta.json")
+    _fake_venv(tmp_path)
+    cfg = SubmitConfig(run_dir=run_dir, accounting_group="cms", repo_dir=tmp_path, n_chunks=2)
+    write_submit(cfg)
+    jobs = {(i, int(k)): int(w) for i, k, w in (line.split(",") for line in (run_dir / "jobs.txt").read_text().split())}
+    for chunk in range(2):
+        expected = estimate_runtime_s("marginal_edep", meta.rows_per_chunk[chunk])
+        assert jobs[("marginal_edep", chunk)] == expected

tests/test_render.py

@@ -206,21 +206,21 @@ def test_render_all_run_gallery_invokes_subprocess(tmp_path: Path, monkeypatch):
     assert kwargs == {"check": True}
 
 
-def test_render_run_glues_run_meta_into_render_all(tmp_path: Path, monkeypatch):
-    from giant.analysis import run as run_mod
+def test_render_run_glues_condor_run_meta_into_render_all(tmp_path: Path, monkeypatch):
+    from giant.analysis import condor as condor_mod
 
     run_dir = tmp_path / "run"
     (run_dir / "reduced").mkdir(parents=True)
 
     merge_calls = []
-    monkeypatch.setattr(run_mod, "merge_all", lambda rd: merge_calls.append(Path(rd)))
-    meta = run_mod.RunMeta(
+    monkeypatch.setattr(condor_mod, "merge_all", lambda rd: merge_calls.append(Path(rd)))
+    meta = condor_mod.RunMeta(
         rollouts=[{"name": "rollout", "path": "rollout.parquet", "plot_meta": {"checkpoint": "ckpt/best.pt"}}],
         reference="reference.parquet",
         run_dir=str(run_dir),
         title="my-run",
     )
-    monkeypatch.setattr(run_mod.RunMeta, "load", classmethod(lambda cls, p: meta))
+    monkeypatch.setattr(condor_mod.RunMeta, "load", classmethod(lambda cls, p: meta))
 
     Reduced("s", "species", "single_hist", "Single", "x", {"edges": [0, 1], "series": {"rollout": [1]}}).save(
         run_dir / "reduced" / "s.json"
@@ -304,13 +304,15 @@ def test_render_one_of_each_kind(tmp_path: Path):
             "hm1",
             "secondaries",
             "heatmap",
-            "Confusion (single rollout)",
+            "Heatmap (single rollout)",
             "predicted",
             {
                 "series": {"flow": [[1, 0], [0, 1]]},
+                "reference": [[2, 0], [0, 1]],
                 "row_labels": ["0", "1+"],
                 "col_labels": ["0", "1+"],
                 "cbar_label": "count",
+                "log_color": True,
             },
         ),
     ]

tests/test_workflow_spec.py

@@ -1,148 +0,0 @@
-"""Workflow spec parsing, validation, and spec hashes (gitea #83)."""
-
-import pytest
-
-from giant.workflow.spec import (
-    WorkflowSpecError,
-    epoch_milestones,
-    load_spec,
-    parse_spec,
-    spec_hash,
-)
-
-MINIMAL = {
-    "workflow": {"name": "wf", "result_dir": "/tmp/wf"},
-    "condor": {"accounting_group": "cms", "repo_dir": "/work/lbogner/giant"},
-    "dataset": {"steps": "/data/train", "reference": "/data/holdout"},
-    "train": [{"name": "a", "epochs": 3}],
-    "rollout": [{"name": "a", "train": "a"}],
-    "analysis": [{"name": "cmp", "rollouts": ["a"], "chunks": 4}],
-}
-
-
-def _spec(**patch):
-    raw = {k: (v.copy() if isinstance(v, dict) else list(v)) for k, v in MINIMAL.items()}
-    raw.update(patch)
-    return parse_spec(raw)
-
-
-def test_parses_minimal_spec():
-    spec = _spec()
-    assert spec.name == "wf"
-    assert spec.log_dir == "/tmp/wf/logs"  # derived from result_dir
-    assert spec.train("a").epochs == 3
-    assert spec.rollout("a").train == "a"
-    assert spec.analysis("cmp").rollouts == ("a",)
-    # defaults come from the dataclasses, not the file
-    assert spec.geometry.method == "slab"
-    assert spec.condor.docker_image_gpu == "mschnepf/slc7-condocker"
-
-
-def test_example_config_is_valid():
-    spec = load_spec("configs/workflow_example.toml")
-    assert {t.name for t in spec.trains} == {"baseline", "router-balanced"}
-    assert spec.analysis("baseline-vs-router").rollouts == ("baseline", "router-balanced")
-
-
-@pytest.mark.parametrize(
-    "patch, message",
-    [
-        ({"train": [{"name": "a"}, {"name": "a"}]}, "unique"),
-        ({"rollout": [{"name": "r", "train": "nope"}]}, "names no"),
-        ({"analysis": [{"name": "c", "rollouts": ["nope"]}]}, "not defined"),
-        ({"analysis": [{"name": "c", "rollouts": []}]}, "at least one"),
-        ({"analysis": [{"name": "c", "rollouts": ["a"], "chunks": 0}]}, "chunks must be"),
-        ({"train": [{"name": "a", "epochs": 0}]}, "epochs must be"),
-        ({"train": [{"name": "a", "epchs": 3}]}, "unknown key"),
-        ({"geometry": {"methd": "slab"}}, "unknown key"),
-    ],
-)
-def test_validation_errors(patch, message):
-    with pytest.raises(WorkflowSpecError, match=message):
-        _spec(**patch)
-
-
-def test_unknown_top_level_table_rejected():
-    with pytest.raises(WorkflowSpecError, match="unknown top-level"):
-        _spec(nonsense={})
-
-
-def test_missing_required_table_rejected():
-    raw = {k: v for k, v in MINIMAL.items() if k != "dataset"}
-    with pytest.raises(WorkflowSpecError, match=r"missing required \[dataset\]"):
-        parse_spec(raw)
-
-
-def test_unknown_lookup_names_are_explicit():
-    spec = _spec()
-    with pytest.raises(WorkflowSpecError, match="no \\[\\[train\\]\\] named 'zzz'"):
-        spec.train("zzz")
-
-
-def test_hash_is_stable_and_order_independent():
-    a = _spec()
-    b = parse_spec(
-        {
-            "dataset": MINIMAL["dataset"],
-            "condor": MINIMAL["condor"],
-            "workflow": MINIMAL["workflow"],
-            "train": MINIMAL["train"],
-            "rollout": MINIMAL["rollout"],
-            "analysis": MINIMAL["analysis"],
-        }
-    )
-    assert a.train_hash("a") == b.train_hash("a")
-    assert a.analysis_hash("cmp") == b.analysis_hash("cmp")
-    assert len(a.train_hash("a")) == 8
-
-
-def test_hash_changes_with_own_settings():
-    base = _spec()
-    changed = _spec(train=[{"name": "a", "epochs": 4}])
-    assert base.train_hash("a") != changed.train_hash("a")
-
-
-def test_hash_propagates_from_parents():
-    """A dataset change must move every downstream task's directory."""
-    base = _spec()
-    changed = _spec(dataset={"steps": "/data/other", "reference": "/data/holdout"})
-    assert base.train_hash("a") != changed.train_hash("a")
-    assert base.rollout_hash("a") != changed.rollout_hash("a")
-    assert base.analysis_hash("cmp") != changed.analysis_hash("cmp")
-
-    # ... and so must a change to a training the analysis transitively uses.
-    retrained = _spec(train=[{"name": "a", "epochs": 9}])
-    assert retrained.analysis_hash("cmp") != base.analysis_hash("cmp")
-    # while an unrelated knob on the analysis leaves the training alone
-    rebinned = _spec(analysis=[{"name": "cmp", "rollouts": ["a"], "chunks": 4, "bins": 99}])
-    assert rebinned.train_hash("a") == base.train_hash("a")
-    assert rebinned.analysis_hash("cmp") != base.analysis_hash("cmp")
-
-
-def test_warm_cache_hash_ignores_epochs():
-    """Epoch count doesn't change the setup cache, so it must not re-warm it."""
-    base = _spec()
-    longer = _spec(train=[{"name": "a", "epochs": 50}])
-    assert base.warm_cache_hash("a") == longer.warm_cache_hash("a")
-    other_cfg = _spec(train=[{"name": "a", "epochs": 3, "config": "configs/router.toml"}])
-    assert base.warm_cache_hash("a") != other_cfg.warm_cache_hash("a")
-
-
-def test_spec_hash_expands_dataclasses():
-    spec = _spec()
-    assert spec_hash(spec.dataset) == spec_hash(spec.dataset)
-    assert spec_hash(spec.dataset) != spec_hash(spec.geometry)
-
-
-@pytest.mark.parametrize(
-    "epochs, per_job, expected",
-    [
-        (3, 1, [1, 2, 3]),
-        (10, 3, [3, 6, 9, 10]),
-        (9, 3, [3, 6, 9]),
-        (1, 5, [1]),
-    ],
-)
-def test_epoch_milestones(epochs, per_job, expected):
-    spec = _spec(train=[{"name": "a", "epochs": epochs, "epochs_per_job": per_job}])
-    assert epoch_milestones(spec.train("a")) == expected

tests/test_workflow_tasks.py

@@ -1,172 +0,0 @@
-"""Workflow task graph: dependencies, output paths, condor settings (gitea #83)."""
-
-import pytest
-
-from giant.analysis.catalog import catalog_ids, get_spec as get_plot_spec
-from giant.workflow import tasks
-from giant.workflow.spec import parse_spec
-
-CONDOR = {
-    "accounting_group": "cms",
-    "repo_dir": "/work/lbogner/giant",
-    "env_script": "/work/lbogner/giant/condor_env.sh",
-}
-
-RAW = {
-    "workflow": {"name": "wf", "result_dir": "/results/wf"},
-    "condor": CONDOR,
-    "dataset": {"steps": "/data/train", "reference": "/data/holdout"},
-    "train": [
-        {"name": "base", "epochs": 3, "gpu_memory_mb": 20000},
-        {"name": "router", "epochs": 2},
-    ],
-    "rollout": [
-        {"name": "base", "train": "base"},
-        {"name": "router", "train": "router"},
-    ],
-    "analysis": [{"name": "cmp", "rollouts": ["base", "router"], "chunks": 4}],
-}
-
-
-@pytest.fixture
-def spec():
-    s = parse_spec(RAW)
-    tasks.set_spec(s)
-    return s
-
-
-def _requires(task):
-    return list(task.requires() or [])
-
-
-def test_epoch_chain_is_linear_and_rooted_at_warm_cache(spec):
-    h = spec.train_hash("base")
-    third = tasks.TrainEpochTask(name="base", spec_hash=h, milestone=3)
-    second = _requires(third)
-    assert [type(t) for t in second] == [tasks.TrainEpochTask]
-    assert second[0].milestone == 2
-    first = _requires(second[0])[0]
-    assert first.milestone == 1
-    root = _requires(first)
-    assert [type(t) for t in root] == [tasks.WarmCacheTask]
-    # the warm cache is keyed by its own hash, not the training's
-    assert root[0].spec_hash == spec.warm_cache_hash("base")
-
-
-def test_epoch_task_outputs_last_pt_per_milestone(spec):
-    h = spec.train_hash("base")
-    path = tasks.TrainEpochTask(name="base", spec_hash=h, milestone=2).output().path
-    assert path == f"/results/wf/train_epoch/name=base/spec_hash={h}/epochs=2/last.pt"
-
-
-def test_train_task_requires_final_epoch_and_publishes_canonical_outputs(spec):
-    h = spec.train_hash("base")
-    train = tasks.TrainTask(name="base", spec_hash=h)
-    (dep,) = _requires(train)
-    assert isinstance(dep, tasks.TrainEpochTask) and dep.milestone == 3
-    out = train.output()
-    assert set(out) == {"best.pt", "last.pt", "metrics.csv"}
-    assert out["best.pt"].path == f"/results/wf/train/name=base/spec_hash={h}/best.pt"
-    # local: it only copies files around, no reason to queue a job for it
-    assert train.batch_system == "local"
-
-
-def test_rollout_requires_training_geometry_and_reference(spec):
-    ro = tasks.RolloutTask(name="base", spec_hash=spec.rollout_hash("base"))
-    deps = _requires(ro)
-    assert [type(d) for d in deps] == [tasks.TrainTask, tasks.GeometryOracleTask, tasks.DatasetTask]
-    assert deps[0].name == "base"
-    assert deps[2].path == "/data/holdout"
-    out = ro.output()
-    assert out["rollout.yaml"].path.endswith("rollout.yaml")
-    # the sidecar sits next to the parquet — the deterministic path
-    # `giant rollout --out` now produces
-    assert out["rollout.yaml"].path[: -len(".yaml")] == out["rollout.parquet"].path[: -len(".parquet")]
-
-
-def test_analysis_prep_requires_every_named_rollout(spec):
-    prep = tasks.AnalysisPrepTask(name="cmp", spec_hash=spec.analysis_hash("cmp"))
-    deps = _requires(prep)
-    assert [d.name for d in deps] == ["base", "router"]
-    assert all(isinstance(d, tasks.RolloutTask) for d in deps)
-    assert prep.batch_system == "local"
-
-
-def test_compute_job_enumeration_collapses_non_chunkable_specs(spec):
-    jobs = tasks.analysis_jobs(spec, "cmp")
-    non_chunkable = [i for i in catalog_ids() if not get_plot_spec(i).chunkable]
-    expected = (len(catalog_ids()) - len(non_chunkable)) * 4 + len(non_chunkable)
-    assert len(jobs) == expected
-    assert non_chunkable, "expected some chunkable=False specs in the catalog"
-    for spec_id in non_chunkable:
-        assert [c for i, c in jobs if i == spec_id] == [0]
-
-
-def test_compute_output_matches_the_on_disk_contract(spec):
-    h = spec.analysis_hash("cmp")
-    task = tasks.AnalysisComputeTask(name="cmp", spec_hash=h, plot_id="event_mean_length", chunk=2)
-    assert task.output().path == (
-        f"/results/wf/analysis/name=cmp/spec_hash={h}/reduced_partial/event_mean_length__2.json"
-    )
-    (dep,) = _requires(task)
-    assert isinstance(dep, tasks.AnalysisPrepTask)
-
-
-def test_render_requires_every_compute_job_and_runs_locally(spec):
-    render = tasks.AnalysisRenderTask(name="cmp", spec_hash=spec.analysis_hash("cmp"))
-    deps = _requires(render)
-    assert len(deps) == len(tasks.analysis_jobs(spec, "cmp"))
-    assert render.batch_system == "local"  # the only step importing plotstyle/LaTeX
-    assert render.output().path.endswith("/plots/metadata.yaml")
-
-
-def test_workflow_task_wraps_every_analysis(spec):
-    deps = _requires(tasks.WorkflowTask(workflow_name="wf"))
-    assert [(type(d), d.name) for d in deps] == [(tasks.AnalysisRenderTask, "cmp")]
-
-
-def test_workflow_without_analysis_falls_back_to_rollouts():
-    raw = {k: v for k, v in RAW.items() if k != "analysis"}
-    tasks.set_spec(parse_spec(raw))
-    deps = _requires(tasks.WorkflowTask(workflow_name="wf"))
-    assert [type(d) for d in deps] == [tasks.RolloutTask, tasks.RolloutTask]
-
-
-def test_gpu_settings_carry_remote_ceph_and_pins(spec):
-    settings = tasks.TrainEpochTask(name="base", spec_hash=spec.train_hash("base"), milestone=1).htcondor_settings
-    assert settings["+RemoteJob"] == "True"
-    assert settings["RequestGPUs"] == 1
-    assert "TARGET.ProvidesEtpCeph =?= True" in settings["requirements"]
-    assert "TARGET.GPUs_GlobalMemoryMb >= 20000" in settings["requirements"]
-    assert settings["accounting_group"] == "cms"
-    assert settings["docker_image"] == "mschnepf/slc7-condocker"
-
-
-def test_cpu_settings_used_for_analysis_compute(spec):
-    task = tasks.AnalysisComputeTask(
-        name="cmp", spec_hash=spec.analysis_hash("cmp"), plot_id="event_mean_length", chunk=0
-    )
-    settings = task.htcondor_settings
-    assert settings["docker_image"] == "cverstege/alma9-gridjob"
-    assert "RequestGPUs" not in settings
-    # no run_meta.json yet (prep hasn't run), so no walltime is claimed
-    assert "+RequestWalltime" not in settings
-
-
-def test_cpu_settings_local_files_use_provides_etp_resources():
-    raw = {**RAW, "condor": {**CONDOR, "remote": False}}
-    spec = parse_spec(raw)
-    tasks.set_spec(spec)
-    settings = tasks.GeometryOracleTask(spec_hash=spec.geometry_hash()).htcondor_settings
-    assert settings["requirements"] == "TARGET.ProvidesETPResources"
-    assert "+RemoteJob" not in settings
-
-
-def test_missing_dataset_fails_immediately(spec):
-    with pytest.raises(FileNotFoundError, match="/ceph"):
-        tasks.DatasetTask(path="/data/train").complete()
-
-
-def test_dataset_that_exists_is_complete(tmp_path, spec):
-    (tmp_path / "steps.parquet").write_text("")
-    assert tasks.DatasetTask(path=str(tmp_path / "steps.parquet")).complete()

uv.lock

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 version = "3.0.1"
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 name = "executing"
 version = "2.2.1"
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 [[package]]
 name = "giant"
-version = "0.3.10"
+version = "0.3.11"
 source = { editable = "." }
 dependencies = [
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@@ -766,14 +728,10 @@ geometry = [
 wandb = [
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-workflow = [
-    { name = "b2luigi" },
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 [package.metadata]
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-provides-extras = ["cpu", "cuda", "dev", "geometry", "wandb", "convert", "analysis", "workflow"]
+provides-extras = ["cpu", "cuda", "dev", "geometry", "wandb", "convert", "analysis"]
 
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