Merge branch 'main' into tau-effective-power-sample

Author: LOCEANlloydizard

.ci_helpers/memory_usage/build_memory_summary.py

@@ -0,0 +1,101 @@
+import csv
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+
+root = Path("memory_artifacts")
+files = list(root.glob("**/memory_usage.csv"))
+
+groups = {
+    "integration": [],
+    "unit": [],
+    "windows": [],
+}
+
+linestyles = {
+    "3.11": "-",
+    "3.12": "--",
+    "3.13": ":",
+}
+
+colors = {
+    "integration": "orange",
+    "unit": "brown",
+    "windows": "purple",
+}
+
+
+def parse_label(name: str):
+    label = name.replace("memory-", "")
+
+    if label.startswith("integration-"):
+        group = "integration"
+        pyver = label.split("-")[1]
+    elif label.startswith("unit-"):
+        group = "unit"
+        pyver = label.split("-")[1]
+    elif label.startswith("windows-"):
+        group = "windows"
+        pyver = label.split("-")[1]
+    else:
+        return None, None
+
+    return group, pyver
+
+
+all_x = []
+
+for f in sorted(files):
+    label = f.parent.name
+    group, pyver = parse_label(label)
+    if group is None:
+        continue
+
+    times = []
+    used = []
+
+    with f.open() as fh:
+        reader = csv.DictReader(fh)
+        t0 = None
+        for row in reader:
+            t = float(row["timestamp"])
+            if t0 is None:
+                t0 = t
+            times.append((t - t0) / 60.0)
+            used.append(float(row["mem_used_mb"]))
+
+    if times:
+        all_x.extend(times)
+        groups[group].append((pyver, times, used))
+
+xmax = max(all_x) if all_x else 1
+
+fig, axes = plt.subplots(3, 1, figsize=(12, 10), sharex=True)
+
+subplot_order = [
+    ("integration", "Ubuntu integration"),
+    ("unit", "Ubuntu unit"),
+    ("windows", "Windows"),
+]
+
+for ax, (group, title) in zip(axes, subplot_order):
+    for pyver, times, used in sorted(groups[group], key=lambda x: x[0]):
+        ax.plot(
+            times,
+            used,
+            label=pyver,
+            color=colors[group],
+            linestyle=linestyles.get(pyver, "-"),
+            linewidth=2,
+        )
+
+    ax.set_title(title)
+    ax.set_ylabel("RAM used (MB)")
+    ax.set_xlim(0, xmax)
+    ax.legend(title="Python")
+
+axes[-1].set_xlabel("Time since job start (minutes)")
+
+fig.suptitle("CI memory usage by job", fontsize=16)
+fig.tight_layout()
+fig.savefig("memory_all_jobs.png", dpi=150)

.ci_helpers/memory_usage/monitor_memory_linux.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+mkdir -p ci_monitor
+echo "timestamp,mem_used_mb" > ci_monitor/memory_usage.csv
+
+while true; do
+  ts=$(date +%s)
+  used=$(free -m | awk '/^Mem:/ {print $3}')
+  echo "$ts,$used" >> ci_monitor/memory_usage.csv
+  sleep 5
+done

.ci_helpers/memory_usage/monitor_memory_windows.ps1

@@ -0,0 +1,15 @@
+New-Item -ItemType Directory -Force -Path ci_monitor | Out-Null
+"timestamp,mem_used_mb" | Out-File ci_monitor/memory_usage.csv -Encoding ascii
+
+while ($true) {
+    $ts = [DateTimeOffset]::UtcNow.ToUnixTimeSeconds()
+
+    $os = Get-CimInstance Win32_OperatingSystem
+    $total = $os.TotalVisibleMemorySize / 1024
+    $free = $os.FreePhysicalMemory / 1024
+    $used = [math]::Round($total - $free, 2)
+
+    "$ts,$used" | Out-File ci_monitor/memory_usage.csv -Append -Encoding ascii
+
+    Start-Sleep -Seconds 5
+}

.github/workflows/build.yaml

@@ -60,7 +60,7 @@ jobs:
             --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: ./coverage.xml
           flags: unit
@@ -205,7 +205,7 @@ jobs:
           --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: ./coverage.xml
           flags: integration

.github/workflows/docker.yaml

@@ -54,7 +54,7 @@ jobs:
         uses: docker/setup-qemu-action@v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
 
       - name: Login to DockerHub
         uses: docker/login-action@v4

.github/workflows/pr.yaml

@@ -59,13 +59,35 @@ jobs:
       - name: Install pooch (needed by conftest)
         run: python -m pip install pooch
 
+      - name: Start memory monitor
+        shell: bash
+        run: |
+          mkdir -p ci_monitor
+          nohup bash .ci_helpers/memory_usage/monitor_memory_linux.sh >/dev/null 2>&1 &
+          echo $! > ci_monitor/monitor.pid
+
       - name: Run unit tests
         run: |
           pytest -m unit -vvv -rx --numprocesses=auto \
             --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
 
+      - name: Stop memory monitor
+        if: always()
+        shell: bash
+        run: |
+          if [ -f ci_monitor/monitor.pid ]; then
+            kill "$(cat ci_monitor/monitor.pid)" || true
+          fi
+
+      - name: Upload memory CSV
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: memory-unit-${{ matrix.python-version }}-${{ matrix.runs-on }}
+          path: ci_monitor/memory_usage.csv
+
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: ./coverage.xml
           flags: unit
@@ -191,13 +213,35 @@ jobs:
           du -h -d 3 ${{ env.XDG_CACHE_HOME }} || true
           docker system df || true
 
+      - name: Start memory monitor
+        shell: bash
+        run: |
+          mkdir -p ci_monitor
+          nohup bash .ci_helpers/memory_usage/monitor_memory_linux.sh >/dev/null 2>&1 &
+          echo $! > ci_monitor/monitor.pid
+
       - name: Running integration tests
         run: |
           pytest -m integration -vvv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 \
           --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
 
+      - name: Stop memory monitor
+        if: always()
+        shell: bash
+        run: |
+          if [ -f ci_monitor/monitor.pid ]; then
+            kill "$(cat ci_monitor/monitor.pid)" || true
+          fi
+
+      - name: Upload memory CSV
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: memory-integration-${{ matrix.python-version }}-${{ matrix.runs-on }}
+          path: ci_monitor/memory_usage.csv
+
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: ./coverage.xml
           flags: integration
@@ -245,6 +289,13 @@ jobs:
       - name: Start local services
         run: python .ci_helpers/setup-services-windows.py start
 
+      - name: Start memory monitor
+        shell: pwsh
+        run: |
+          New-Item -ItemType Directory -Force -Path ci_monitor | Out-Null
+          $p = Start-Process pwsh -ArgumentList "-File", ".ci_helpers/memory_usage/monitor_memory_windows.ps1" -PassThru -WindowStyle Hidden
+          $p.Id | Out-File ci_monitor/monitor.pid -Encoding ascii
+
       - name: Running all tests
         shell: pwsh
         env:
@@ -255,8 +306,24 @@ jobs:
           --cov echopype --cov-report xml
           --log-cli-level WARNING --disable-warnings
 
+      - name: Stop memory monitor
+        if: always()
+        shell: pwsh
+        run: |
+          if (Test-Path ci_monitor/monitor.pid) {
+            $monitorPid = Get-Content ci_monitor/monitor.pid
+            Stop-Process -Id $monitorPid -Force -ErrorAction SilentlyContinue
+          }
+
+      - name: Upload memory CSV
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: memory-windows-${{ matrix.python-version }}
+          path: ci_monitor/memory_usage.csv
+
       - name: Upload code coverage
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: ./coverage.xml
           flags: unittests
@@ -267,3 +334,29 @@ jobs:
       - name: Teardown services
         if: always()
         run: python .ci_helpers/setup-services-windows.py stop
+
+  memory-summary:
+    name: memory-summary
+    runs-on: ubuntu-latest
+    needs: [unit-tests, integration-tests, test-windows]
+    if: always()
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Download all memory artifacts
+        uses: actions/download-artifact@v8
+        with:
+          path: memory_artifacts
+
+      - name: Install matplotlib
+        run: python -m pip install matplotlib
+
+      - name: Build memory summary
+        run: python .ci_helpers/memory_usage/build_memory_summary.py
+
+      - name: Upload combined memory plot
+        uses: actions/upload-artifact@v7
+        with:
+          name: memory-summary
+          path: memory_all_jobs.png

.github/workflows/pypi.yaml

@@ -28,8 +28,8 @@ jobs:
       with:
         python-version: 3.12
 
-    - name: Install dependencies
-      run: python -m pip install setuptools wheel
+    - name: Install build frontend
+      run: python -m pip install --upgrade pip build
 
     # This step is only necessary for testing purposes and for TestPyPI
     - name: Fix up version string for TestPyPI
@@ -42,7 +42,7 @@ jobs:
 
     - name: Build source and wheel distributions
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         echo ""
         echo "Generated files:"
         ls -lh dist/

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
         args: ["--profile", "black", "--filter-files"]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 26.3.0
+    rev: 26.3.1
     hooks:
       - id: black
 

.readthedocs.yml

@@ -19,10 +19,6 @@ build:
 sphinx:
    configuration: docs/source/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: []
 
@@ -34,6 +30,3 @@ python:
         path: .
         extra_requirements:
            - plot
-      - method: setuptools
-        path: .
-#   system_packages: true

MANIFEST.in

@@ -13,5 +13,4 @@ include *.txt
 # Ignore testing files and data
 prune echopype/test_data
 prune echopype/tests
-exclude echopype/testing.py
 exclude .gitattributes