ProjectFlow: default tasks_to_skip to None; retire the _old_spec archive - #35
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jandrewjohnson wants to merge 37 commits into
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ProjectFlow: default tasks_to_skip to None; retire the _old_spec archive#35jandrewjohnson wants to merge 37 commits into
jandrewjohnson wants to merge 37 commits into
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Feature/test infra
feat: add release process documentation for Hazelbean, detailing auto…
Feat/removing emojis
fixed internet availability check
…ct_features_in_shapefile_by_attribute
…s (vector.py) General-purpose deck mechanics (add_slide_header/bullets/figure/caption/box) and an Overpass QL transport (read_overpass), parameterized with no project-specific content. python-pptx and requests are existing hazelbean deps, imported lazily inside the functions.
env1 runs pandas 3.0.1 (future.infer_string=True), so df[col].values yields Arrow-backed string arrays that break GEMPACK/harpy HAR I/O and other code passing .values into numpy-expecting APIs. Set future.infer_string=False at import, guarded to no-op on older pandas. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…lpers Add generic pptx slide primitives and read_overpass
Per-machine, never-committed settings (e.g. gtappy's solve-backend connection vars GTAP_VM_SSH_HOST / GTAP_GEMPACK_DIR) previously had to live in shell rc files — shell/OS-specific and invisible to IDE debug runs. hazelbean now loads KEY=value lines from ~/.config/hazelbean/machine.env at import, filling gaps in os.environ (setdefault semantics — a real env var always wins; missing file is a no-op). The parser tolerates 'export ' prefixes, quotes, and inline comments, so gtappy's modality_env.example.sh works verbatim as the file format and the same file can still be sourced from a shell. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Add per-machine env loader (~/.config/hazelbean/machine.env)
…rsion Refactor code structure for improved readability and maintainability
…re get_path - assign_to_object: the unified value grammar now resolves paths by NAME (columns/keys ending in _path) instead of by value heuristic, which wrongly get_path'd ssh targets (user@192.168.64.2 — trailing .2 matched the extension regex), backend-machine paths (C:\GP), and free text (Expansion/Loss). Blank/'skip' pass through, 'nan' -> None, cat-ears keep leave_ref_path_if_fail=True. The value heuristic survives as public looks_like_path for value-conditional columns (aoi, calibration_parameters_source), resolved at their consumers in seals. - project_flow: bare ProjectFlow() derives its default project dir git-aware (inside a repo -> <repo_parent>/projects/<stem>, logged); get_path is skip-aware (in a skipped task it publishes the would-be path instead of raising; consume contexts still fail fast). Pairs with same-named branches in seals, gtappy, gtap_invest, seals_cgebox_dev, earth_economy_devstack, ngfs_pnas. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ration Name-driven *_path hydration; git-aware project dir; skip-aware get_path
add_all_functions_from_script_to_task_tree silently turned every function in the calling script into a task, which confused newcomers and made helper functions into landmines. execute() on an empty tree now raises with the canonical fix (p.add_task / build_task_tree) spelled out. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ir inference
Single entry point for run_*.py files, replacing the boilerplate they all
repeated: run_mode validation ('check'/'fresh_intermediate'/'full'), the
'full' timestamp on project_name, project_dir composition, set_project_dir,
and the fresh_intermediate deletion of intermediate/ and outputs/ (input/ is
kept for per-machine parameters.csv values; guarded to project names
containing 'test').
extra_dirs is now optional: _infer_project_parent_dir walks up from the
calling script to its git repo and derives the projects dir — a stack
library repo maps to <repo_parent>/projects, a wrapped project repo (repo
nested inside a projects/ tree, e.g. ngfs_pnas) maps to its wrapper's
parent, so outputs land beside the checkout, never inside it.
_derive_default_project_dir now shares the same walk.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Run files on the caller-configured convention call p.skip_tasks(p.tasks_to_skip) after building the task tree. Initializing the attribute in __init__ means a run that skips nothing needs no guard, which removes the getattr(p, 'tasks_to_skip', None) fallback from every run file in the stack. Also adds the ProjectFlow project-dir resolution tests covering the merged hb.ProjectFlow(project_name=..., run_mode=...) API, and deletes project_flow_old_spec.py. Git history is the archive for pre-conversion forms. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Run files on the caller-configured convention call p.skip_tasks(p.tasks_to_skip) after building the task tree. Initializing the attribute in init means a run that skips nothing needs no guard, which removes the getattr(p, 'tasks_to_skip', None) fallback from every run file in the stack.
Also adds the ProjectFlow project-dir resolution tests covering the merged hb.ProjectFlow(project_name=..., run_mode=...) API, and deletes project_flow_old_spec.py. Git history is the archive for pre-conversion forms.