Output formatting (#84)

* Refactor model configuration to use frozen dataclasses instead of dicts

Introduce strongly-typed dataclasses for model configuration:
- Dimensions, Labels, Anchoring, EstimationOptions, TransitionInfo
- FactorEndogenousInfo, EndogenousFactorsInfo

This improves type safety and enables IDE autocompletion while keeping
user-facing model_dict as a plain dictionary.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Use frozendict for immutable dict fields in dataclasses

Replace dict fields with frozendict in frozen dataclasses to ensure
true immutability:
- Labels.aug_periods_to_periods
- Labels.aug_stages_to_stages
- Anchoring.outcomes
- TransitionInfo.param_names, individual_functions, function_names
- EndogenousFactorsInfo.aug_periods_to_aug_period_meas_types, factor_info

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Ignore ty false positive.

* Return ProcessedModel dataclass from process_model() instead of dict

Update process_model() to return a ProcessedModel frozen dataclass
and update all consumers to use attribute access instead of dict access.

This provides:
- Better type safety with explicit typed fields
- Immutability via frozen dataclass
- IDE autocomplete support
- Clear documentation of the model structure

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Rename FactorEndogenousInfo to FactorInfo

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Ensure complete typing in src/skillmodels.

* Require Python 3.14 before fixing type annotations.

* Move TESTS_DIR -> TEST_DATA_DIR, which points to a subdirectory of src so that config.TEST_DATA_DIR is valid also for skillmodels the package (as opposed to the project).

* Fix more linting issues.

* Make ruff rules much stricter.

* Further tighten type annotations. Fix a missing run-time annotation of NDArray.

* Move unsafe_fixes = false from .pre-commit config to pyproject.

* Fix query in data simulation.

* More fixes to imports, add test.

* Use more tuples in place of lists to prevent errors.

* Fix typing.

* Dataclasses for user input.

* Simplify.

* Use modern rng everywhere.

* Update CLAUDE.md

* Get rid of if TYPE_CHECKING blocks

* Update hooks and clean up

* Call by name throughout.

* Autogenerated docs, harmonised hooks / project configuration.

* Get rid of model_dict.

* Replace yaml model specifications by ModelSpec-s.

* Next shot at fixing pickling.

* Add improved output formatting.

* Add variance decompositions.

* Fix variance decomposition to use aug_period instead of period.

The filtered_states DataFrame and params index both use aug_period as the
period identifier, not period. This fixes KeyError when calling
decompose_measurement_variance.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix diagnostic_plots double-processing of debug data.

debug_loglike already returns processed debug data (it calls
process_debug_data internally). Remove the redundant second call
to process_debug_data which was causing AttributeError when trying
to iterate over already-processed DataFrames.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Review comments 1: single EstimationOptions; improved dataclasses with all defaults set right there; get rid of remaining mutable types being passed around.

* Review comments on docs; tighten typing of Mapping to MappingProxyType where we could do so.

* Back to general implementation of ensure_containers_are_immutable.

* Small fixes.

* Latest boilerplate version.

* Make optimagic a package dependency.

* Latest boilerplate.

* Make jupyterbook and pytask required deps.

* Use dags 0.5.0 dev branch.

* Update CLAUDE.md with complete API docs and actual application usage

Document all 14 public exports, get_maximization_inputs return dict,
ProcessedModel attributes, frequently used internal APIs, all 7
transition functions, and ModelSpec builder methods — based on how
the package is actually used in skane-struct-bw and health-cognition.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Increase test coverage to close to 100%.

* Fix bugs caught by review agent.

* Call ty environment 'type-checking'.

* Require dags 0.5, bump pandas, numpy and hooks, fix resulting issues.

* Remove suppression of deprecation warning, which is unnecessary in Pandas 3.0

* Make ruff stricter.

* Update boilerplate.

* Update ty and remove a couple of unused-ignores.

* Rename _sel to select_by_loc; fix stale docstring

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* Allow passing states directly to get_transition_plots (health-cognition use case).

* Fix aug_period/period bug in transition equation visualization

The viz code assumed states DataFrames always have `aug_period` as a
column, but pre-computed states (e.g. from health-cognition) may carry
`period` in the index instead. Add `_normalize_states_columns` to
promote index levels and rename `period` → `aug_period` when needed.

Also document the period vs aug_period convention in CLAUDE.md.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* Remove aug_periods from public-facing functions.

* Previous commit was too greedy.

* Use pixi 0.66 in CI; prek autoupdate.

* CHORE: Approximation-tolerant floating point comparisons, remove pandas in-place operations.

* Get rid of unnecessary block-comments.

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

Author: hmgaudecker

.ai-instructions

@@ -23,27 +23,42 @@ jobs:
           - macos-latest
           - windows-latest
         python-version:
-          - '3.13'
+          - '3.14'
     steps:
       - uses: actions/checkout@v6
-      - uses: prefix-dev/setup-pixi@v0.9.3
+      - uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          pixi-version: v0.62.2
+          pixi-version: v0.66.0
           cache: true
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
-          environments: test-cpu
+          environments: tests-cpu
           activate-environment: true
           frozen: true
       - name: Run pytest
-        if: runner.os != 'Linux' || matrix.python-version != '3.13'
+        if: runner.os != 'Linux' || matrix.python-version != '3.14'
         shell: bash -l {0}
-        run: pixi run -e test-cpu tests
+        run: pixi run -e tests-cpu tests
       - name: Run pytest with coverage
-        if: runner.os == 'Linux' && matrix.python-version == '3.13'
+        if: runner.os == 'Linux' && matrix.python-version == '3.14'
         shell: bash -l {0}
-        run: pixi run -e test-cpu tests-with-cov
+        run: pixi run -e tests-cpu tests-with-cov
       - name: Upload coverage report
-        if: runner.os == 'Linux' && matrix.python-version == '3.13'
+        if: runner.os == 'Linux' && matrix.python-version == '3.14'
         uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  run-ty:
+    name: Run ty
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          pixi-version: v0.66.0
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+          frozen: true
+          environments: type-checking
+      - name: Run ty
+        run: pixi run -e type-checking ty
+        shell: bash -el {0}

.github/workflows/main.yml

@@ -1,3 +1,6 @@
+# Claude Code
+.claude/
+
 # Distribution / packaging
 *.egg
 *.egg-info/
@@ -13,7 +16,6 @@ wheels/
 
 # Documentation
 docs/_build/
-_build/
 
 # IDE
 .idea/
@@ -27,6 +29,7 @@ _build/
 
 # pixi
 .pixi/
+node_modules/
 
 # Python
 __pycache__/
@@ -48,5 +51,3 @@ htmlcov/
 
 # Version file (generated by hatch-vcs)
 src/*/_version.py
-
-.claude

.gitignore

@@ -0,0 +1,4 @@
+[submodule ".ai-instructions"]
+	path = .ai-instructions
+	url = git@github.com:OpenSourceEconomics/ai-instructions.git
+	branch = make-submodule

.gitmodules

@@ -4,10 +4,10 @@ repos:
     hooks:
       - id: check-hooks-apply
       - id: check-useless-excludes
-  - repo: https://github.com/tox-dev/tox-toml-fmt
-    rev: v1.2.2
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.19.0
     hooks:
-      - id: tox-toml-fmt
+      - id: pyproject-fmt
   - repo: https://github.com/lyz-code/yamlfix
     rev: 1.19.1
     hooks:
@@ -17,7 +17,7 @@ repos:
     hooks:
       - id: check-added-large-files
         args:
-          - --maxkb=50000
+          - --maxkb=10000
       - id: check-ast
       - id: check-case-conflict
       - id: check-docstring-first
@@ -47,7 +47,7 @@ repos:
     hooks:
       - id: yamllint
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.15.6
     hooks:
       - id: ruff-check
         args:
@@ -62,7 +62,7 @@ repos:
           - pyi
           - python
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.9.0
+    rev: 0.9.1
     hooks:
       - id: nbstripout
         args:
@@ -79,6 +79,6 @@ repos:
         args:
           - --wrap
           - '88'
-        files: (CLAUDE\.md|README\.md)
+        files: (AGENTS\.md|CLAUDE\.md|README\.md|modules/.*\.md|profiles/.*\.md)
 ci:
   autoupdate_schedule: monthly

.pre-commit-config.yaml

@@ -16,5 +16,7 @@ build:
       # Jupyter Book 2.0 builds site content to _build/html.
       # For ReadTheDocs, we build and then copy to the expected output location.
       - mkdir --parents $READTHEDOCS_OUTPUT/html/
-      - BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" pixi run -e docs docs
+      - >-
+        BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION"
+        pixi run -e docs build-docs
       - cp -a docs/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r docs/_build

.readthedocs.yaml

@@ -29,11 +29,8 @@ rules:
   quoted-strings: disable
   trailing-spaces: enable
   truthy:
-    check-keys: false
     level: warning
 yaml-files:
   - '*.yaml'
   - '*.yml'
   - .yamllint
-ignore:
-  - src/skillmodels/test_data/simplest_augmented_model.yaml