gazeaudit 0.1.0__tar.gz

gazeaudit-0.1.0/.github/workflows/distribution.yml

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+name: distribution
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  build-and-verify:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 20
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v7
+
+      - name: Set up Python 3.12.14
+        uses: actions/setup-python@v7
+        with:
+          python-version: '3.12.14'
+          cache: pip
+
+      - name: Install build validators
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip install --upgrade pip
+          python -m pip install build twine
+
+      - name: Build clean sdist and wheel
+        shell: bash
+        run: |
+          set -euo pipefail
+          rm -rf build dist
+          python -m build
+          test "$(find dist -maxdepth 1 -type f | wc -l)" -eq 2
+
+      - name: Validate package metadata
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m twine check dist/*
+          python tools/verify_distribution.py dist
+
+      - name: Install wheel in fresh environment
+        shell: bash
+        run: |
+          set -euo pipefail
+          wheel="$(find dist -maxdepth 1 -name '*.whl' -print -quit)"
+          test -n "$wheel"
+          python -m venv .wheel-smoke
+          .wheel-smoke/bin/python -m pip install --upgrade pip
+          .wheel-smoke/bin/python -m pip install "$wheel"
+          .wheel-smoke/bin/python - <<'PY'
+          import tomllib
+          from importlib import metadata, resources
+          from pathlib import Path
+
+          import gazeaudit
+
+          project = tomllib.loads(Path("pyproject.toml").read_text(encoding="utf-8"))
+          expected = project["project"]["version"]
+          if metadata.version("gazeaudit") != expected:
+              raise SystemExit("installed wheel version differs from pyproject.toml")
+          if not hasattr(gazeaudit, "GazeStudy"):
+              raise SystemExit("installed wheel does not expose GazeStudy")
+          resource = resources.files("gazeaudit.data").joinpath(
+              "pedrotti2023_sampling_missingness_v1.json"
+          )
+          if not resource.is_file():
+              raise SystemExit("installed wheel is missing frozen scientific package data")
+          PY
+
+      - name: Archive qualified distributions
+        uses: actions/upload-artifact@v7
+        with:
+          name: gazeaudit-distribution-${{ github.sha }}
+          path: dist/
+          if-no-files-found: error
+          retention-days: 30
+          compression-level: 0

gazeaudit-0.1.0/.github/workflows/interop.yml

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+name: interoperability
+
+on:
+  push:
+    branches: [main, "dev/**"]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.head_ref || github.ref_name }}
+  cancel-in-progress: true
+
+jobs:
+  live-contracts:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install interoperability dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[test,interop]"
+
+      - name: Verify upstream versions
+        run: |
+          python - <<'PY'
+          import peyes
+          import pymovements
+          print("pEYES", peyes.__version__)
+          print("pymovements", pymovements.__version__)
+          PY
+
+      - name: Run live interoperability contract tests
+        run: pytest -q tests/test_optional_interop.py

gazeaudit-0.1.0/.github/workflows/korthals-scientific-execution.yml

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+name: korthals-scientific-execution
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: korthals-scientific-execution-v2
+  cancel-in-progress: false
+
+jobs:
+  scientific-execution:
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-24.04
+    timeout-minutes: 180
+    steps:
+      - name: Checkout exact GazeAudit commit
+        uses: actions/checkout@v4
+
+      - name: Set up exact Python 3.12.14
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12.14'
+          cache: pip
+
+      - name: Verify exact main execution identity
+        shell: bash
+        run: |
+          set -euo pipefail
+          test "$GITHUB_REF" = "refs/heads/main"
+          test "$(git rev-parse HEAD)" = "$GITHUB_SHA"
+
+      - name: Checkout frozen companion implementation
+        shell: bash
+        run: |
+          set -euo pipefail
+          git clone https://github.com/lukekorthals/pursuing-smooth-pursuits-data companion
+          git -C companion checkout 1d7ebec23e3fe20f6db952eefda1a0dd58ae09da
+          test "$(git -C companion rev-parse HEAD)" = \
+            "1d7ebec23e3fe20f6db952eefda1a0dd58ae09da"
+
+      - name: Install source-freeze-matched critical execution stack
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip install --upgrade pip
+          python -m pip install \
+            "numpy==2.5.3" \
+            "pandas==2.3.3" \
+            "scipy==1.18.1"
+          python -m pip install -e .
+          python -m pip install ./companion
+          python - <<'PY'
+          import platform
+          import numpy as np
+          import pandas as pd
+          import scipy
+
+          expected = {
+              "python": "3.12.14",
+              "numpy": "2.5.3",
+              "pandas": "2.3.3",
+              "scipy": "1.18.1",
+          }
+          observed = {
+              "python": platform.python_version(),
+              "numpy": np.__version__,
+              "pandas": pd.__version__,
+              "scipy": scipy.__version__,
+          }
+          if observed != expected:
+              raise SystemExit(f"execution environment differs from source freeze: {observed}")
+          PY
+
+      - name: Download complete published OSF source
+        shell: bash
+        run: |
+          set -euo pipefail
+          python - <<'PY'
+          from gazeaudit.korthals_osf import fetch_korthals_osf_resumable
+
+          summary = fetch_korthals_osf_resumable(
+              max_attempts=6,
+              initial_backoff_seconds=15.0,
+          )
+          print(
+              "verified endpoint-blind OSF transfer: "
+              f"files={summary['file_count']} attempts={summary['attempts']} "
+              f"retained={summary['retained_verified_files']} "
+              f"removed_partials={summary['removed_partial_files']}"
+          )
+          PY
+
+      - name: Verify locked public-source bytes before preprocessing
+        shell: bash
+        run: |
+          set -euo pipefail
+          python - <<'PY'
+          from gazeaudit.korthals_source_lock import verify_korthals_locked_source_manifest
+          from gazeaudit.korthals_v2 import build_korthals_source_manifest_v2
+
+          manifest = build_korthals_source_manifest_v2("data")
+          verify_korthals_locked_source_manifest(manifest)
+          PY
+
+      - name: Capture exact dependency environment before scientific execution
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip freeze | LC_ALL=C sort > pip-freeze.txt
+          test -s pip-freeze.txt
+          grep -Fx 'numpy==2.5.3' pip-freeze.txt
+          grep -Fx 'pandas==2.3.3' pip-freeze.txt
+          grep -Fx 'scipy==1.18.1' pip-freeze.txt
+
+      - name: Execute locked protocol v2 without revealing scientific results
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m gazeaudit.korthals_execution_v2_cli \
+            --data-root data \
+            --output-dir korthals-scientific-execution \
+            --environment-file pip-freeze.txt \
+            --execution-commit "$GITHUB_SHA" \
+            --run-id "$GITHUB_RUN_ID" \
+            --runner-os "$RUNNER_OS" \
+            --runner-arch "$RUNNER_ARCH"
+
+      - name: Verify locked scientific archive before upload
+        shell: bash
+        run: |
+          set -euo pipefail
+          python - <<'PY'
+          from gazeaudit.korthals_execution_archive_v2 import (
+              verify_korthals_locked_execution_artifacts_v2,
+          )
+
+          if not verify_korthals_locked_execution_artifacts_v2(
+              "korthals-scientific-execution"
+          ):
+              raise SystemExit("locked Korthals protocol-v2 archive verification failed")
+          PY
+
+      - name: Archive scientific execution before reveal
+        uses: actions/upload-artifact@v4
+        with:
+          name: korthals-scientific-v2-${{ github.sha }}
+          path: korthals-scientific-execution/
+          if-no-files-found: error
+          retention-days: 90
+          compression-level: 0
+
+      - name: Reveal archived scientific result
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m gazeaudit.korthals_reveal_v2_cli \
+            --artifact-dir korthals-scientific-execution

gazeaudit-0.1.0/.github/workflows/korthals-source-freeze.yml

@@ -0,0 +1,139 @@
+name: korthals-source-freeze
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: korthals-source-freeze-v2
+  cancel-in-progress: false
+
+jobs:
+  source-freeze:
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-24.04
+    timeout-minutes: 180
+    steps:
+      - name: Checkout exact GazeAudit commit
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: pip
+
+      - name: Verify exact main execution identity
+        shell: bash
+        run: |
+          set -euo pipefail
+          test "$GITHUB_REF" = "refs/heads/main"
+          test "$(git rev-parse HEAD)" = "$GITHUB_SHA"
+          printf '%s\n' "$GITHUB_SHA" > execution-commit.txt
+
+      - name: Checkout frozen companion implementation
+        shell: bash
+        run: |
+          set -euo pipefail
+          git clone https://github.com/lukekorthals/pursuing-smooth-pursuits-data companion
+          git -C companion checkout 1d7ebec23e3fe20f6db952eefda1a0dd58ae09da
+          test "$(git -C companion rev-parse HEAD)" = "1d7ebec23e3fe20f6db952eefda1a0dd58ae09da"
+
+      - name: Install exact execution stack
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip install --upgrade pip
+          # The frozen companion relies on pandas 2.x DataFrameGroupBy.apply retaining
+          # the grouping column. pandas 3.x drops it by default, which removes
+          # trial_number before the companion's blink-masking step.
+          python -m pip install "pandas==2.3.3"
+          python -m pip install -e .
+          python -m pip install ./companion
+          python - <<'PY'
+          import pandas as pd
+
+          if pd.__version__ != "2.3.3":
+              raise SystemExit(f"unexpected pandas version: {pd.__version__}")
+          PY
+
+      - name: Download complete published OSF source
+        shell: bash
+        run: |
+          set -euo pipefail
+          # Frozen companion selection remains exactly:
+          # raw_clean="both", train_test="both", participants="all", overwrite=False.
+          python - <<'PY'
+          from gazeaudit.korthals_osf import fetch_korthals_osf_resumable
+
+          summary = fetch_korthals_osf_resumable(
+              max_attempts=6,
+              initial_backoff_seconds=15.0,
+          )
+          print(
+              "verified endpoint-blind OSF transfer: "
+              f"files={summary['file_count']} attempts={summary['attempts']} "
+              f"retained={summary['retained_verified_files']} "
+              f"removed_partials={summary['removed_partial_files']}"
+          )
+          PY
+
+      - name: Build endpoint-blind protocol-v2 source intake
+        shell: bash
+        run: |
+          set -euo pipefail
+          gazeaudit-korthals-source-intake-v2 \
+            --data-root data \
+            --output-dir source-intake \
+            > source-intake-status.txt
+
+      - name: Capture dependency environment
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip freeze | LC_ALL=C sort > pip-freeze.txt
+          test -s pip-freeze.txt
+
+      - name: Build protocol-v2 source-freeze envelope
+        shell: bash
+        run: |
+          set -euo pipefail
+          gazeaudit-korthals-source-freeze-v2 \
+            --intake-dir source-intake \
+            --output-dir korthals-source-freeze \
+            --environment-file pip-freeze.txt \
+            --execution-commit "$GITHUB_SHA" \
+            --run-id "$GITHUB_RUN_ID" \
+            --runner-os "$RUNNER_OS" \
+            --runner-arch "$RUNNER_ARCH" \
+            > source-freeze-status.json
+
+      - name: Verify protocol-v2 frozen source envelope before archive
+        shell: bash
+        run: |
+          set -euo pipefail
+          python - <<'PY'
+          from gazeaudit.korthals_freeze_v2 import (
+              verify_korthals_source_freeze_artifacts_v2,
+          )
+
+          if not verify_korthals_source_freeze_artifacts_v2("korthals-source-freeze"):
+              raise SystemExit("Korthals protocol-v2 source-freeze verification failed")
+          PY
+
+      - name: Archive source freeze before reveal
+        uses: actions/upload-artifact@v4
+        with:
+          name: korthals-source-freeze-v2-${{ github.sha }}
+          path: korthals-source-freeze/
+          if-no-files-found: error
+          retention-days: 90
+          compression-level: 0
+
+      - name: Reveal archived source identity
+        shell: bash
+        run: |
+          set -euo pipefail
+          cat source-freeze-status.json

gazeaudit-0.1.0/.github/workflows/pedrotti-scientific-execution.yml

@@ -0,0 +1,159 @@
+name: pedrotti-scientific-execution
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: pedrotti-scientific-execution-v1
+  cancel-in-progress: false
+
+jobs:
+  scientific-execution:
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-24.04
+    timeout-minutes: 180
+    steps:
+      - name: Checkout exact GazeAudit commit
+        uses: actions/checkout@v7
+
+      - name: Set up Python 3.12.14
+        uses: actions/setup-python@v7
+        with:
+          python-version: '3.12.14'
+          cache: pip
+
+      - name: Verify exact main execution identity
+        shell: bash
+        run: |
+          set -euo pipefail
+          test "$GITHUB_REF" = "refs/heads/main"
+          test "$(git rev-parse HEAD)" = "$GITHUB_SHA"
+
+      - name: Install frozen scientific stack
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip install --upgrade pip
+          python -m pip install "numpy==2.5.3" "pandas==2.3.3"
+          python -m pip install -e .
+          python - <<'PY'
+          import platform
+          import numpy as np
+          import pandas as pd
+
+          if platform.python_version() != "3.12.14":
+              raise SystemExit(f"unexpected Python version: {platform.python_version()}")
+          if np.__version__ != "2.5.3":
+              raise SystemExit(f"unexpected NumPy version: {np.__version__}")
+          if pd.__version__ != "2.3.3":
+              raise SystemExit(f"unexpected pandas version: {pd.__version__}")
+          PY
+
+      - name: Download exact checksum-locked Zenodo source
+        shell: bash
+        run: |
+          set -euo pipefail
+          python - <<'PY'
+          from gazeaudit.pedrotti_fetch import fetch_pedrotti_zenodo_source
+          from gazeaudit.pedrotti_prefetch import prefetch_pedrotti_source_bytes
+
+          prefetch = prefetch_pedrotti_source_bytes(
+              "pedrotti-source",
+              max_attempts=6,
+              initial_backoff_seconds=15.0,
+              timeout_seconds=180.0,
+          )
+          print(
+              "checksum-locked redundant byte prefetch: "
+              f"files={prefetch['file_count']} "
+              f"request_attempts={prefetch['request_attempts']} "
+              f"retained={prefetch['retained_verified_files']} "
+              f"removed_mismatches={prefetch['removed_mismatched_files']}"
+          )
+          summary = fetch_pedrotti_zenodo_source(
+              "pedrotti-source",
+              max_attempts=6,
+              initial_backoff_seconds=15.0,
+              timeout_seconds=180.0,
+              metadata_max_attempts=2,
+              metadata_timeout_seconds=30.0,
+          )
+          print(
+              "verified endpoint-blind Zenodo transfer: "
+              f"files={summary['file_count']} "
+              f"metadata_source={summary['metadata_source']} "
+              f"retained={summary['retained_verified_files']} "
+              f"removed_mismatches={summary['removed_mismatched_files']}"
+          )
+          PY
+
+      - name: Verify locked endpoint-blind intake before scientific execution
+        shell: bash
+        run: |
+          set -euo pipefail
+          python - <<'PY'
+          from gazeaudit.pedrotti_source import inspect_pedrotti_source
+          from gazeaudit.pedrotti_source_lock import (
+              verify_pedrotti_locked_intake,
+              verify_pedrotti_source_lock,
+          )
+
+          verify_pedrotti_source_lock()
+          intake = inspect_pedrotti_source("pedrotti-source")
+          verify_pedrotti_locked_intake(intake)
+          print("Pedrotti endpoint-blind source lock: verified")
+          PY
+
+      - name: Capture frozen dependency environment
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip freeze | LC_ALL=C sort > pip-freeze.txt
+          test -s pip-freeze.txt
+
+      - name: Execute frozen protocol and build hidden scientific archive
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m gazeaudit.pedrotti_execution_cli \
+            --source-dir pedrotti-source \
+            --output-dir pedrotti-scientific-archive \
+            --environment-file pip-freeze.txt \
+            --execution-commit "$GITHUB_SHA" \
+            --run-id "$GITHUB_RUN_ID" \
+            --runner-os "$RUNNER_OS" \
+            --runner-arch "$RUNNER_ARCH"
+
+      - name: Verify scientific archive before upload
+        shell: bash
+        run: |
+          set -euo pipefail
+          python - <<'PY'
+          from gazeaudit.pedrotti_execution import (
+              verify_pedrotti_locked_execution_artifacts,
+          )
+
+          if not verify_pedrotti_locked_execution_artifacts(
+              "pedrotti-scientific-archive"
+          ):
+              raise SystemExit("Pedrotti scientific archive verification failed")
+          PY
+
+      - name: Archive scientific result before reveal
+        uses: actions/upload-artifact@v7
+        with:
+          name: pedrotti-scientific-execution-v1-${{ github.sha }}
+          path: pedrotti-scientific-archive/
+          if-no-files-found: error
+          retention-days: 90
+          compression-level: 0
+
+      - name: Reveal archived scientific result
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m gazeaudit.pedrotti_reveal_cli \
+            --archive-dir pedrotti-scientific-archive