Fix bug and test large scale for lwg

.dockerignore

@@ -0,0 +1,8 @@
+# The image is built from the wheel. Keep large benchmark and documentation
+# corpora out of the Docker build context.
+*
+!pyproject.toml
+!README.md
+!LICENSE
+!synkit/
+!synkit/**

.gitattributes

@@ -0,0 +1 @@
+*.json text eol=lf

.github/workflows/docker-publish.yml

@@ -3,12 +3,8 @@ name: Publish SynKit Docker Package
 
 on:
   push:
-    # Fire on semver tags for real releases…
     tags:
       - 'v*.*.*'
-    # …and on any push to the refractor branch for testing
-    branches:
-      - 'staging'
 
 jobs:
   build-and-push:

.github/workflows/publish-package.yml

@@ -1,9 +1,11 @@
 name: PyPI publish
 
 on:
-  release:
-    types:
-      - published
+  push:
+    branches:
+      - stereo
+    paths:
+      - .github/workflows/publish-package.yml
 
 permissions:
   contents: read
@@ -78,7 +80,7 @@ jobs:
   publish:
     name: Publish package to PyPI
     needs: build
-    if: github.event_name == 'release'
+    if: github.event_name == 'push' && github.ref == 'refs/heads/stereo'
     runs-on: ubuntu-latest
 
     environment:

.github/workflows/test-and-lint.yml

@@ -2,7 +2,7 @@ name: Test & Lint
 
 on:
   push:
-    branches: [ "main", "staging", "mech", "stereo" ]
+    branches: [ "main", "staging", "mech", "stereo", "lwg" ]
   pull_request:
     branches: [ "main" ]
 
@@ -44,20 +44,20 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate synkit-env
-          bash lint.sh
+          bash scripts/lint.sh
 
       # 3b) Lint on Windows
       - name: Lint (Windows)
         if: matrix.os == 'windows-latest'
         shell: bash -l {0}
         run: |
           conda activate synkit-env
-          bash lint.sh
+          bash scripts/lint.sh
 
 
       # 4) Test
       - name: Test
         shell: bash -l {0}
         run: |
           conda activate synkit-env
-          bash pytest.sh
+          bash scripts/pytest.sh

.gitignore

@@ -1,6 +1,11 @@
 *.pyc
 *cachedir
 *.csv
+!Experiment/Lewis/Data/all.csv
+!Experiment/Lewis/Data/combinatorial_all.csv
+!Experiment/Lewis/mech_path/Data/reconstruction_audit/polar-failures.csv
+!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-failures.csv
+!Experiment/Lewis/mech_path/Data/reconstruction_audit/radical-arrow-review.csv
 */catboost_info/*
 
 
@@ -9,12 +14,6 @@
 
 .coverage
 dev/*
-# Local development, audit, and debugging helpers.
-/tools/
-!/tools/
-/tools/*
-!/tools/stereo_conformance.py
-!/tools/check_python_file_size.py
 /debug/
 /Test/Conformance/
 *.rdf
@@ -30,6 +29,7 @@ Data/Benchmark/mech/*
 !Data/Benchmark/mech/polar-failures.csv
 !Data/Benchmark/mech/radical-failures.csv
 *.json.gz
+!Experiment/Lewis/Data/benchmark.json.gz
 # *.png
 
 run.sh
@@ -46,12 +46,31 @@ Data/Study/CRN/case_formose/*
 synkit/Graph/dev/*
 *.ipynb
 *.json
+# Stereo benchmark inputs are versioned for reproducible fresh-clone runs.
+# Generated reports stay Git-visible so completed results can be committed
+# explicitly, including reports created by the long raw stress stages.
+!Experiment/Stereo/Data/**/*.csv
+!Experiment/Stereo/Data/**/*.json
 !Data/Schema/
 !Data/Schema/attribute_propagation_v1_5.json
 !/tools/python_file_size_baseline.json
 !Data/Mech/polar.json
 !Data/Mech/radical.json
 !Data/Mech/stereo.json
+!Experiment/Lewis/Data/hydrogen.pkl.gz
+# Canonical reviewed MechanismBench partitions are executable test data.
+!Experiment/Lewis/mech_path/Data/MechanismBench/polar.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/radical.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/stereo.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/electrocyclic_machinery.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/stereo_branch_coverage.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/stereo_couplings.json
+!Experiment/Lewis/mech_path/Data/MechanismBench/evidence/mechanismbench_evidence.json
+!Experiment/Lewis/rule_replay/Data/bidirectional-replay/results.json
+!Experiment/Lewis/rule_replay/Data/relative-lone-pair/results.json
+!Experiment/Stereo/Data/manifest.json
+!Experiment/Stereo/Data/Perception/perception_conformance_cases.json
+!Experiment/Stereo/Data/Perception/full_detection_report.json
 !Test/Synthesis/Reactor/fixtures/small_rewrite_conformance.json
 !Data/Conformance/stereomolgraph_graph_conformance.json
 !Data/Benchmark/Stereo/
@@ -67,6 +86,22 @@ test_syn.py
 measure_candidate_stages.py
 run_valid_bug_cases.py
 paper/*
+# Nested standalone Git repository.
+/paper/og_paper/
+
+# Fresh benchmark runs are reproducible and can be large. Retained reference
+# outputs live inside each experiment's Data directory.
+Experiment/Lewis/Runs/
+
+# Generated FLOWER intermediates and long-run evidence. The portable
+# full-reaction batch payload is intentionally retained in Git.
+Experiment/Lewis/FLOWER/batches/
+Experiment/Lewis/FLOWER/full_reactions/
+Experiment/Lewis/FLOWER/replay-debug/
+Experiment/Lewis/FLOWER/replay-runs/
+Experiment/Lewis/FLOWER/replay-results*/
+!Experiment/Lewis/FLOWER/full-reaction-batches/manifest.json
+!Experiment/Lewis/FLOWER/full-reaction-replay-summary.json
 
 # Keep generated Python bytecode ignored after directory re-inclusions above.
 **/__pycache__/