Merge pull request #16 from ACRLab/ci-test

Add github actions and fix manual peaks

Author: cdpaiva

.github/workflows/test.yaml

@@ -0,0 +1,59 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "windows-latest", "macos-latest"]
+
+    steps:
+      - name: Install Linux Qt deps
+        if: runner.os == 'Linux'
+        run: |
+            sudo apt install \
+            libgl1 \
+            libegl1 \
+            libdbus-1-3 \
+            libxkbcommon-x11-0 \
+            libxcb-icccm4 \
+            libxcb-image0 \
+            libxcb-keysyms1 \
+            libxcb-randr0 \
+            libxcb-render-util0 \
+            libxcb-xinerama0 \
+            libxcb-xfixes0 \
+            x11-utils && \
+            /sbin/start-stop-daemon --start --quiet \
+            --pidfile /tmp/custom_xvfb_99.pid \
+            --make-pidfile \
+            --background \
+            --exec /usr/bin/Xvfb -- \
+            :99 -screen 0 1920x1200x24 -ac +extension GLX
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: snazzy-env
+
+      - name: Install dependencies
+        run: conda env update -f environment.yml -n snazzy-env --quiet
+
+      - name: Test with pytest
+        run: conda run -n snazzy-env pytest
+        env:
+          QT_QPA_PLATFORM: offscreen
+          MPLBACKEND: Agg
+          HEADLESS: 1

environment.yml

@@ -30,3 +30,5 @@ dependencies:
     - statannotations==0.7.1
     - sphinx-book-theme==1.1.2
     - sphinx==7.3.7
+    - -e ./snazzy_analysis
+    - -e ./snazzy_processing

snazzy_analysis/snazzy_analysis/config.py

@@ -59,7 +59,7 @@ class PDParams(BaseModel):
 
 
 class EmbryoParams(BaseModel):
-    wlen: int = 30
+    wlen: int = 2
     manual_peaks: list[int] = Field(default_factory=list)
     manual_remove: list[int] = Field(default_factory=list)
     manual_widths: dict[str, Any] = Field(default_factory={})
@@ -175,7 +175,7 @@ def save_manual_peak_data(
 
         if not emb_name in self.data["embryos"]:
             self.data["embryos"][emb_name] = {
-                "wlen": 10,
+                "wlen": 2,
                 "manual_peaks": [],
                 "manual_remove": [],
                 "manual_widths": {},

snazzy_analysis/snazzy_analysis/gui/compare_plot_window.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+import os
 
 import matplotlib
 import matplotlib.axes
@@ -12,7 +13,10 @@
 from snazzy_analysis import FrequencyAnalysis, utils
 from snazzy_analysis.gui import GroupModel
 
-matplotlib.use("QtAgg")
+if os.environ.get("CI") or os.environ.get("HEADLESS"):
+    matplotlib.use("Agg")
+else:
+    matplotlib.use("QtAgg")
 
 
 class ComparePlotWindow(QWidget):

snazzy_analysis/snazzy_analysis/gui/model.py

@@ -225,7 +225,7 @@ def calc_peaks_all_embs(self, pd_params=None):
             {"pd_params": pd_params, "exp_params": {"to_remove": to_remove}}
         )
 
-    def add_peak(self, x, emb_name, trace, wlen=5):
+    def add_peak(self, x, emb_name, trace, wlen=2):
         # load corrected data to reconcile with the new add
         exp = self.selected_experiment
         corrected_peaks = exp.config.get_corrected_peaks(emb_name)
@@ -246,31 +246,31 @@ def add_peak(self, x, emb_name, trace, wlen=5):
         )
         return new_peak, new_peaks
 
-    def remove_peak(self, x, emb_name, trace, wlen=10):
+    def remove_peak(self, x, emb_name, trace, wlen=2):
         # load corrected data to reconcile with the new add
         exp = self.selected_experiment
         corrected_peaks = exp.config.get_corrected_peaks(emb_name)
         manual_add = [] if not corrected_peaks else corrected_peaks["manual_peaks"]
         manual_widths = (
             None if not corrected_peaks else corrected_peaks["manual_widths"]
         )
+        wlen = wlen if not corrected_peaks else corrected_peaks["wlen"]
 
-        removed, new_arr, added_peaks, peak_width_to_remove = self.pm.remove_peak(
-            x, trace, manual_add, manual_widths
+        removed, new_arr, added_peaks, filtered_peak_widths = self.pm.remove_peak(
+            x, trace, manual_add, manual_widths, wlen
         )
         # update corrected peaks
         if corrected_peaks:
             to_remove = corrected_peaks["manual_remove"]
             removed = list(set(to_remove + removed))
             corrected_peaks["manual_remove"] = removed
-        if manual_widths and peak_width_to_remove:
-            del manual_widths[str(peak_width_to_remove)]
+            corrected_peaks["manual_widths"] = filtered_peak_widths
 
         exp.config.save_manual_peak_data(
             emb_name,
             added_peaks=added_peaks,
             removed_peaks=removed,
-            manual_widths=manual_widths,
+            manual_widths=filtered_peak_widths,
         )
         return removed, new_arr
 

snazzy_analysis/snazzy_analysis/gui/peak_matcher.py

@@ -12,10 +12,11 @@ def local_peak_at(x, signal, wlen):
 
 
 class PeakMatcher:
-    def add_peak(self, x: int, trace: Trace, manual_remove: list[int], wlen: int = 5):
-        """Adds a new peak in the vicinity of `x`.
+    def add_peak(self, x: int, trace: Trace, manual_remove: list[int], wlen: int = 2):
+        """Add a new peak in the vicinity of `x`.
 
-        The new peak is calculated as the local maximum near `x`, in a window of 2*wlen points.
+        The new peak is calculated as the local maximum of a window centered at `x`,
+        that ranges `wlen` in each direction.
 
         Parameters:
             x (int):
@@ -37,19 +38,18 @@ def add_peak(self, x: int, trace: Trace, manual_remove: list[int], wlen: int = 5
         """
         window = slice(x - wlen, x + wlen)
         new_peak = local_peak_at(x, trace.dff[window], wlen)
+        if new_peak in trace.peak_idxes:
+            return new_peak, trace.peak_idxes, None
         new_arr = np.append(trace.peak_idxes, new_peak)
         new_arr.sort()
 
         # if we add a peak in a place where there's a manually removed peak,
         # that manually removed entry must be erased:
         to_remove = None
         if manual_remove:
-            try:
-                peak = next(p for p in manual_remove if x - wlen <= p <= x + wlen)
-                i = manual_remove.index(peak)
+            if new_peak in manual_remove:
+                i = manual_remove.index(new_peak)
                 to_remove = manual_remove[:i] + manual_remove[i + 1 :]
-            except StopIteration:
-                pass
 
         return new_peak, new_arr, to_remove
 
@@ -59,9 +59,9 @@ def remove_peak(
         trace: Trace,
         manual_add: list[int],
         manual_widths: dict[str, Any],
-        wlen=10,
+        wlen=2,
     ):
-        """Removes peaks that are within `wlen` of `x`.
+        """Remove all peaks that are within ±`wlen` of `x`.
 
         Parameters:
             x (int):
@@ -82,8 +82,8 @@ def remove_peak(
                 Updated list with all peaks.
             to_add (list[int]):
                 Updated list of manually added peaks.
-            peak_width_to_remove (int):
-                Key that should be removed from manual widths dict.
+            filtered_peak_widths (int):
+                Updated manual widhts dict without the peaks that were removed.
         """
         target = (trace.peak_idxes >= x - wlen) & (trace.peak_idxes <= x + wlen)
         removed = trace.peak_idxes[target].tolist()
@@ -93,20 +93,17 @@ def remove_peak(
         # that manually added peak entry must be erased
         to_add = None
         if manual_add:
-            try:
-                # FIXME: if you remove more than one element, this update method fails
-                peak = next(p for p in manual_add if x - wlen <= p <= x + wlen)
-                i = manual_add.index(peak)
-                to_add = manual_add[:i] + manual_add[i + 1 :]
-            except StopIteration:
-                pass
-        peak_width_to_remove = None
+            filtered_manual_add = [
+                p for p in manual_add if p < x - wlen or p > x + wlen
+            ]
+            to_add = filtered_manual_add
+
+        filtered_peak_widths = None
         if manual_widths:
-            try:
-                peak_width_to_remove = next(
-                    int(p) for p in manual_widths if x - wlen <= int(p) <= x + wlen
-                )
-            except StopIteration:
-                pass
-
-        return removed, new_arr, to_add, peak_width_to_remove
+            filtered_peak_widths = {
+                p: data
+                for p, data in manual_widths.items()
+                if int(p) < x - wlen or int(p) > x + wlen
+            }
+
+        return removed, new_arr, to_add, filtered_peak_widths

snazzy_analysis/snazzy_analysis/trace.py

@@ -344,21 +344,18 @@ def reconcile_manual_peaks(self, params):
         if corrected_peaks:
             to_add = corrected_peaks.get("manual_peaks", [])
             to_remove = corrected_peaks.get("manual_remove", [])
-            wlen = corrected_peaks.get("wlen", 10)
+            wlen = corrected_peaks.get("wlen", 2)
+
             filtered_peaks = [
                 p
                 for p in self._peak_idxes
                 if not any(abs(p - rp) < wlen for rp in to_remove)
             ]
-            filtered_add = [
-                ap
-                for ap in to_add
-                if not any(abs(p - ap) < wlen for p in filtered_peaks)
-            ]
+
             self.to_add = to_add
             self.to_remove = to_remove
             self._peak_idxes = np.array(
-                sorted(filtered_peaks + filtered_add), dtype=np.int64
+                sorted(list(set(filtered_peaks + to_add))), dtype=np.int64
             )
 
     def update_dsna_start(self, params):

snazzy_analysis/tests/test_gui.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+import sys
 
 import pytest
 from PyQt6.QtCore import Qt
@@ -14,6 +15,10 @@
 )
 from snazzy_analysis.gui.model import GroupModel, ExperimentModel
 
+pytestmark = pytest.mark.skipif(
+    not sys.platform.startswith("linux"), reason="Running headless tests on linux only."
+)
+
 VALID_DIR = Path(__file__).parent.joinpath("assets", "data", "20250210")