From 0762c16e2234dcbdd705917cc0de7da04c7da537 Mon Sep 17 00:00:00 2001
From: "Richard J. Reyes" <reyes.ricky30@gmail.com>
Date: Thu, 9 Jul 2026 19:13:36 -0700
Subject: [PATCH 1/4] Add photodiode analysis dependency manifest

---
 requirements.txt | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 requirements.txt

diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..1e833d3
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,6 @@
+numpy>=1.24,<3
+pandas>=2.0,<3
+scipy>=1.10,<2
+matplotlib>=3.7,<4
+python-dotenv>=1.0,<2
+pytest>=7,<9

From ad5f60c00bb97e4e94ce20ff32b996812bb71e79 Mon Sep 17 00:00:00 2001
From: "Richard J. Reyes" <reyes.ricky30@gmail.com>
Date: Thu, 9 Jul 2026 19:13:42 -0700
Subject: [PATCH 2/4] Add analysis-only photodiode container

---
 Dockerfile | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..ccb5db9
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,21 @@
+FROM python:3.12-slim
+
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    MPLBACKEND=Agg \
+    PIP_NO_CACHE_DIR=1
+
+WORKDIR /app
+
+COPY requirements.txt ./
+RUN python -m pip install --upgrade pip \
+    && python -m pip install --requirement requirements.txt
+
+COPY . /app
+
+RUN mkdir -p /work/outputs_npy_logcos
+WORKDIR /work
+
+VOLUME ["/work/outputs_npy_logcos"]
+
+CMD ["python", "/app/scan_npy_logcos.py", "--input", "/app/captures/20260309_010802/waveform_raw.npy", "--sample-rate", "20000", "--fmin", "20", "--fmax", "1000", "--nperm", "100", "--cpu"]

From c989d34dab81d858896000469c74f40911f384c0 Mon Sep 17 00:00:00 2001
From: "Richard J. Reyes" <reyes.ricky30@gmail.com>
Date: Thu, 9 Jul 2026 19:13:58 -0700
Subject: [PATCH 3/4] Add photodiode Docker build exclusions

---
 .dockerignore | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 .dockerignore

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..2f5fdaa
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,14 @@
+.git
+.github
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.venv/
+venv/
+.env
+outputs_npy_logcos/
+proof_runs/
+proof/
+csv/
+control/
+pic/

From 81cd534cfa26292eb01bec110500b45b7e25ba6b Mon Sep 17 00:00:00 2001
From: "Richard J. Reyes" <reyes.ricky30@gmail.com>
Date: Thu, 9 Jul 2026 19:14:10 -0700
Subject: [PATCH 4/4] Add photodiode analysis and container CI

---
 .github/workflows/container-ci.yml | 73 ++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 .github/workflows/container-ci.yml

diff --git a/.github/workflows/container-ci.yml b/.github/workflows/container-ci.yml
new file mode 100644
index 0000000..ced9100
--- /dev/null
+++ b/.github/workflows/container-ci.yml
@@ -0,0 +1,73 @@
+name: Analysis and container CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: container-ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  analysis-smoke:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+      - name: Install analysis dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --requirement requirements.txt
+      - name: Compile Python sources
+        run: python -m compileall -q .
+      - name: Reproduce a fast CPU analysis in an isolated directory
+        run: |
+          mkdir -p /tmp/photodiode-ci
+          cd /tmp/photodiode-ci
+          python "$GITHUB_WORKSPACE/scan_npy_logcos.py" \
+            --input "$GITHUB_WORKSPACE/captures/20260309_010802/waveform_raw.npy" \
+            --sample-rate 20000 \
+            --fmin 20 \
+            --fmax 1000 \
+            --nk 200 \
+            --no-null \
+            --cpu
+      - name: Validate generated summary
+        run: |
+          python - <<'PY'
+          import json
+          from pathlib import Path
+
+          path = Path('/tmp/photodiode-ci/outputs_npy_logcos/summary.json')
+          data = json.loads(path.read_text(encoding='utf-8'))
+          assert data['samples'] == 10000
+          assert data['sample_rate_Hz'] == 20000.0
+          assert data['best_logcos']['k'] > 0
+          PY
+
+  container:
+    runs-on: ubuntu-24.04
+    needs: analysis-smoke
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build analysis image
+        run: docker build --tag photodiode-ci .
+      - name: Run fast container analysis
+        run: |
+          docker run --rm photodiode-ci \
+            python /app/scan_npy_logcos.py \
+            --input /app/captures/20260309_010802/waveform_raw.npy \
+            --sample-rate 20000 \
+            --fmin 20 \
+            --fmax 1000 \
+            --nk 200 \
+            --no-null \
+            --cpu