refactor(config): replace hydra/omegaconf with typed pydantic+tyro

.github/workflows/build.yml

@@ -9,6 +9,19 @@ on:
       - main
 
 jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install ruff
+      - name: Ruff check
+        run: ruff check .
+      - name: Ruff format
+        run: ruff format --check .
+
   build:
     runs-on: ubuntu-latest
     steps:
@@ -23,33 +36,104 @@ jobs:
       - name: build
         run: pip wheel --no-deps -w dist .
 
+  test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: pip install -e ".[test]"
+      - name: Run tests with coverage
+        run: python -m pytest -m "not benchmark" --timeout=60 --cov=gigaevo --cov-report=term-missing --cov-report=xml:coverage.xml tests/
+      - name: Smoke-test typed CLI on every shipped experiment
+        env:
+          OPENAI_API_KEY: test-key-for-ci-dry-run
+        run: |
+          set -eo pipefail
+          for exp in experiments/*.py; do
+            echo "--- smoke: $exp"
+            if ! timeout 30s python run.py "$exp" --dry-run; then
+              echo "::error file=$exp::dry-run failed or exceeded 30s timeout"
+              exit 1
+            fi
+          done
+          echo "All experiments validated successfully."
+      - name: Upload coverage report
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: coverage.xml
+      - name: Extract coverage percentage
+        if: always()
+        id: coverage
+        run: |
+          TOTAL=$(python -c "
+          import xml.etree.ElementTree as ET
+          tree = ET.parse('coverage.xml')
+          print(round(float(tree.getroot().attrib['line-rate']) * 100))
+          ")
+          echo "total=$TOTAL" >> "$GITHUB_OUTPUT"
+          echo "Coverage: $TOTAL%"
+      - name: Update coverage badge in README
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        run: |
+          TOTAL=${{ steps.coverage.outputs.total }}
+          if [ "$TOTAL" -ge 80 ]; then COLOR="brightgreen"
+          elif [ "$TOTAL" -ge 60 ]; then COLOR="yellow"
+          elif [ "$TOTAL" -ge 40 ]; then COLOR="orange"
+          else COLOR="red"; fi
+          ENCODED_PCT="${TOTAL}%25"
+          sed -i "s|!\[Coverage\](https://img.shields.io/badge/coverage-[^)]*)|![Coverage](https://img.shields.io/badge/coverage-${ENCODED_PCT}-${COLOR})|" README.md
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add README.md
+          git diff --cached --quiet && exit 0
+          git commit -m "chore: update coverage badge to ${TOTAL}% [skip ci]"
+          git push origin HEAD:main
+
   release:
-    needs: build
+    needs: [lint, build, test]
     permissions:
       contents: write
       id-token: write
-    if: github.event_name == 'push' && github.ref == 'refs/heads/main' && !contains(github.event.head_commit.message, 'chore(release):')
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main' && !startsWith(github.event.head_commit.message, 'Automatically generated by python-semantic-release')
     runs-on: ubuntu-latest
     concurrency: release
     steps:
+      # Checkout on the actual branch (not detached HEAD) so that
+      # python-semantic-release can push the version commit back to main.
+      # Fetch the latest origin/main (which may include the coverage badge
+      # commit pushed by the test job) so semantic-release doesn't fail
+      # with an "upstream has changed" error.
       - uses: actions/checkout@v4
         with:
+          ref: ${{ github.ref_name }}
           fetch-depth: 0
+      - name: Sync with latest origin/main
+        run: |
+          git fetch origin main
+          git reset --hard origin/main
       - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
       - name: Install dependencies
         run: pip install build
       - name: Semantic Release
         id: release
-        uses: python-semantic-release/python-semantic-release@v10.4.1
+        uses: python-semantic-release/python-semantic-release@v10.5.3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
       - name: Build package
         run: python -m build
         if: steps.release.outputs.released == 'true'
       - name: Publish package distributions to GitHub Releases
-        uses: python-semantic-release/publish-action@main
+        uses: python-semantic-release/publish-action@v10.5.3
         if: steps.release.outputs.released == 'true'
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,6 +1,9 @@
 # GigaEvo .gitignore
 # Comprehensive ignore patterns for evolutionary computation project
 
+# MkDocs build output
+site/
+
 # =============================================================================
 # Python
 # =============================================================================
@@ -11,7 +14,7 @@ __pycache__/
 *$py.class
 
 # C extensions
-*.so
+# *.so
 
 # Distribution / packaging
 .Python
@@ -32,13 +35,14 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
-
+*top_programs
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 *.spec
-
+*results*
+!experiments/**/05_results.md
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
@@ -339,6 +343,16 @@ outputs
 ehthumbs.db
 Thumbs.db
 
+# =============================================================================
+# Memory
+# =============================================================================
+
+evo_memory_agent/evo_test/
+evo_memory_agent/memory_usage_store/
+insights_appearence/
+selected_ideas/
+redis_commands.txt
+
 # =============================================================================
 # Development and Testing
 # =============================================================================
@@ -364,11 +378,13 @@ coverage.xml
 # Large data files
 *.csv
 *.json
+*.jsonl
 *.pickle
 *.pkl
 *.h5
 *.hdf5
 *.parquet
+.nltk_data/
 
 # Model files
 *.model
@@ -459,6 +475,7 @@ benchmark
 # Program archives
 program_archive/
 archive_*/
+archives/
 
 # Fitness data
 fitness_*.csv
@@ -578,3 +595,64 @@ problems/*/*.json
 !docs/**/*.txt
 !tools/**/*.ipynb
 !demos/**/*.svg
+
+# Runtime data directories (binary artifacts, not for VCS)
+data/
+outcmaes/
+wandb/
+runs/
+tb_logs/
+tensorboard/
+
+# Numpy compressed arrays
+*.npz
+
+# Experiment runtime artifacts (plots, test evals, archives, pids, cfg dumps)
+experiments/**/plots/
+experiments/**/test_evals/
+experiments/**/archives/
+experiments/**/*.yaml.tmp
+experiments/**/*.yaml.lock
+experiments/**/pids.txt
+experiments/**/cfg_run_*.txt
+
+# Dataset indexes (large binary files — rebuild locally with build_*_index.py)
+problems/chains/hotpotqa/dataset/bm25s_index/
+problems/chains/hotpotqa/dataset/colbert_index/
+
+# LiteLLM proxy (generated config, DB, logs, pidfile)
+tools/.litellm_config.yaml
+tools/.litellm.db
+tools/.litellm.log
+tools/.litellm.pid
+
+# Claude Code (machine-specific memory and indexes — not for sharing)
+.claude/projects/
+.claude/agent-memory/
+.claude/perf-sprint-*.md
+AGENTS.md
+snapshots/
+
+# Large dataset files (downloaded by dataset scripts)
+problems/chains/hover/dataset/*.gz
+problems/chains/hover/dataset/*.pkl
+problems/chains/hover/dataset/*.tar.bz2
+problems/chains/hover/dataset/bm25s_index/
+problems/chains/hover/dataset/*.jsonl
+gigaevo/llm/ideas_tracker/utils/it_logger_description.md
+
+gigaevo.memory/
+mut_dmp/
+.codex
+evo_memory_agent/
+insights_appearence/
+selected_ideas/
+redis_commands.txt
+gigaevo/memory/memory_usage_store/
+bm25s_index/
+wiki17_abstracts.jsonl.gz
+task_bm25s_index
+check_openrouter_key.py
+experiments.txt
+AlgoTune-main/
+.env

.pre-commit-config.yaml

@@ -1,4 +1,5 @@
 exclude: '^problems/'
+default_stages: [pre-push]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks