ci: remove init, set tests to run on dev

.github/workflows/test_and_lint.yml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - main
+      - dev
 
 jobs:
   ci:

src/aind_qc_portal/projects/dataset.py

@@ -3,7 +3,11 @@
 import param
 
 from aind_qc_portal.docdb.database import get_project_data
-from aind_qc_portal.utils import format_link, qc_status_color_css, qc_status_link_html
+from aind_qc_portal.utils import (
+    format_link,
+    qc_status_color_css,
+    qc_status_link_html,
+)
 from aind_data_schema.core.quality_control import QualityControl, Status
 
 ALWAYS_COLUMNS = ["Subject ID", "Date"]
@@ -35,24 +39,24 @@ def __init__(self, project_name: str, **params):
         self.project_name = project_name
         self._df = pd.DataFrame(columns=["_id", "timestamp"])
 
-        self.subject_selector = pn.widgets.MultiChoice(
-            name="Subject ID"
-        )
-        self.columns_selector = pn.widgets.MultiChoice(
-            name="Columns"
-        )
-        self.derived_selector = pn.widgets.Select(name="Derived", options=["All", "Raw", "Derived"])
-        self.type_selector = pn.widgets.Select(
-            name="Type"
+        self.subject_selector = pn.widgets.MultiChoice(name="Subject ID")
+        self.columns_selector = pn.widgets.MultiChoice(name="Columns")
+        self.derived_selector = pn.widgets.Select(
+            name="Derived", options=["All", "Raw", "Derived"]
         )
+        self.type_selector = pn.widgets.Select(name="Type")
         self.status_selector = pn.widgets.Select(
             name="QC Status", options=QC_STATUS_OPTIONS
         )
 
         self._get_assets()
 
         self.subject_selector.options = self.subjects
-        self.columns_selector.options = [column for column in self.columns if column not in ALWAYS_COLUMNS + HIDDEN_COLUMNS]
+        self.columns_selector.options = [
+            column
+            for column in self.columns
+            if column not in ALWAYS_COLUMNS + HIDDEN_COLUMNS
+        ]
         self.type_selector.options = ["All"] + self.types
 
     def _get_assets(self):
@@ -102,7 +106,9 @@ def _get_assets(self):
 
             record_data = {
                 "_id": record.get("_id"),
-                "Raw Data": record.get("data_description", {}).get("data_level")
+                "Raw Data": record.get("data_description", {}).get(
+                    "data_level"
+                )
                 == "raw",
                 "project_name": record.get("data_description", {}).get(
                     "project_name"
@@ -141,11 +147,16 @@ def _get_assets(self):
             lambda x: ", ".join(x) if x else None
         )
         self._df["QC Status"] = self._df.apply(
-            lambda row: qc_status_link_html(row["QC Status"], row["qc_link"], row["QC Status"]), axis=1
+            lambda row: qc_status_link_html(
+                row["QC Status"], row["qc_link"], row["QC Status"]
+            ),
+            axis=1,
         )
         print(self._df["QC Status"].values[0])
 
-        self._df.drop(columns=["qc_link", "operator", "session_start_time", "location"])
+        self._df.drop(
+            columns=["qc_link", "operator", "session_start_time", "location"]
+        )
 
         # Sort dataframe by time and then by subject ID
         self._df.sort_values(by="timestamp", ascending=True, inplace=True)
@@ -168,13 +179,12 @@ def _data_filtered(self) -> pd.DataFrame:
 
         if self.derived_filter != "All":
             filtered_df = filtered_df[
-                filtered_df["Raw Data"] == (True if self.derived_filter == "Raw" else False)
+                filtered_df["Raw Data"]
+                == (True if self.derived_filter == "Raw" else False)
             ]
 
         if self.type_filter != "All":
-            filtered_df = filtered_df[
-                filtered_df["Type"] == self.type_filter
-            ]
+            filtered_df = filtered_df[filtered_df["Type"] == self.type_filter]
 
         if self.status_filter != "All":
             filtered_df = filtered_df[

src/aind_qc_portal/projects/project_view.py

@@ -41,12 +41,11 @@ def __init__(self, project_name: str, dataset: ProjectDataset):
         self.history_chart = self.history_panel()
         if hasattr(self.history_chart, "selection"):
             self.selection_history_chart = pn.bind(
-                self.selection_history_panel, self.history_chart.selection.param.brush
+                self.selection_history_panel,
+                self.history_chart.selection.param.brush,
             )
         else:
-            self.selection_history_chart = pn.widgets.StaticText(
-                value=""
-            )
+            self.selection_history_chart = pn.widgets.StaticText(value="")
 
     @property
     def has_data(self):
@@ -59,8 +58,7 @@ def get_asset_count(self):
         return len(self.dataset.data_filtered())
 
     def update_subject_selector(self, event):
-        """Update the subject selector based on the brush selection
-        """
+        """Update the subject selector based on the brush selection"""
         if event.new.get("Subject ID") is not None:
             self.dataset.subject_selector.value = event.new["Subject ID"]
         else:
@@ -76,8 +74,10 @@ def history_panel(self):
         data = self.dataset.data
 
         # Check that timestamp column has values
-        if data['timestamp'].isnull().all():
-            return pn.widgets.StaticText(value="Data processing error: project is missing timestamp data in some assets. Please reach out to scientific computing for help repairing your metadata.")
+        if data["timestamp"].isnull().all():
+            return pn.widgets.StaticText(
+                value="Data processing error: project is missing timestamp data in some assets. Please reach out to scientific computing for help repairing your metadata."
+            )
 
         # Calculate the time range to show on the x axis
         (min_range, max_range, range_unit, format) = df_timestamp_range(
@@ -102,7 +102,9 @@ def history_panel(self):
                     alt.Tooltip("Date:T", title="Date"),
                 ],
                 color=alt.condition(
-                    self.brush, alt.Color("Subject ID:N"), alt.value("lightgray")
+                    self.brush,
+                    alt.Color("Subject ID:N"),
+                    alt.value("lightgray"),
                 ),
                 href=alt.Href("qc_link:N"),
             )
@@ -125,7 +127,9 @@ def selection_history_panel(self, selection):
         data = self.dataset.data_filtered()
 
         if data.empty:
-            return pn.widgets.StaticText(value="No data found for the selected filters")
+            return pn.widgets.StaticText(
+                value="No data found for the selected filters"
+            )
 
         # Calculate the time range to show on the x axis
         (min_range, max_range, range_unit, format) = df_timestamp_range(
@@ -170,12 +174,14 @@ def selection_history_panel(self, selection):
 
         return pn.pane.Vega(chart, sizing_mode="stretch_width")
 
-    def _panel(self,
-               subject_filter,
-               derived_filter,
-               columns_filter,
-               type_filter,
-               status_filter) -> pn.Column:
+    def _panel(
+        self,
+        subject_filter,
+        derived_filter,
+        columns_filter,
+        type_filter,
+        status_filter,
+    ) -> pn.Column:
         """Return panel object"""
 
         self.dataset.subject_filter = subject_filter
@@ -192,11 +198,15 @@ def _panel(self,
 
     def panel(self):
 
-        return pn.Column(self.history_chart, pn.bind(
-            self._panel,
-            subject_filter=self.dataset.subject_selector,
-            derived_filter=self.dataset.derived_selector,
-            columns_filter=self.dataset.columns_selector,
-            type_filter=self.dataset.type_selector,
-            status_filter=self.dataset.status_selector,
-        ), styles=OUTER_STYLE)
+        return pn.Column(
+            self.history_chart,
+            pn.bind(
+                self._panel,
+                subject_filter=self.dataset.subject_selector,
+                derived_filter=self.dataset.derived_selector,
+                columns_filter=self.dataset.columns_selector,
+                type_filter=self.dataset.type_selector,
+                status_filter=self.dataset.status_selector,
+            ),
+            styles=OUTER_STYLE,
+        )

src/aind_qc_portal/qc_project_app.py

@@ -91,9 +91,7 @@ def panel(self):
 dataset.subject_selector.value = dataset.subject_filter
 dataset.derived_selector.value = dataset.derived_filter
 dataset.columns_selector.value = [
-    column
-    for column in dataset.columns_filter
-    if column not in ALWAYS_COLUMNS
+    column for column in dataset.columns_filter if column not in ALWAYS_COLUMNS
 ]
 dataset.type_selector.value = dataset.type_filter
 dataset.status_selector.value = dataset.status_filter

tests/test_utils.py

@@ -12,20 +12,35 @@
     df_timestamp_range,
     replace_markdown_with_html,
     qc_status_color_css,
-    bincount2D
+    bincount2D,
 )
 
 
 class TestUtils(unittest.TestCase):
 
     def test_format_link(self):
-        self.assertEqual(format_link("http://example.com"), '<a href="http://example.com" target="_blank">link</a>')
-        self.assertEqual(format_link("http://example.com", "Example"), '<a href="http://example.com" target="_blank">Example</a>')
+        self.assertEqual(
+            format_link("http://example.com"),
+            '<a href="http://example.com" target="_blank">link</a>',
+        )
+        self.assertEqual(
+            format_link("http://example.com", "Example"),
+            '<a href="http://example.com" target="_blank">Example</a>',
+        )
 
     def test_status_html(self):
-        self.assertEqual(qc_status_html(Status.PASS), '<span style="color:#1D8649;">Pass</span>')
-        self.assertEqual(qc_status_html(Status.PENDING), '<span style="color:#2A7DE1;">Pending</span>')
-        self.assertEqual(qc_status_html(Status.FAIL), '<span style="color:#FF5733;">Fail</span>')
+        self.assertEqual(
+            qc_status_html(Status.PASS),
+            '<span style="color:#1D8649;">Pass</span>',
+        )
+        self.assertEqual(
+            qc_status_html(Status.PENDING),
+            '<span style="color:#2A7DE1;">Pending</span>',
+        )
+        self.assertEqual(
+            qc_status_html(Status.FAIL),
+            '<span style="color:#FF5733;">Fail</span>',
+        )
 
     def test_df_timestamp_range(self):
         data = {
@@ -41,13 +56,24 @@ def test_df_timestamp_range(self):
         self.assertEqual(fmt, "%b %d")
 
     def test_md_style(self):
-        self.assertEqual(replace_markdown_with_html(12, "test"), '<span style="font-size:12pt">test</span>')
+        self.assertEqual(
+            replace_markdown_with_html(12, "test"),
+            '<span style="font-size:12pt">test</span>',
+        )
 
     def test_qc_color(self):
-        self.assertEqual(qc_status_color_css("No QC"), "background-color: #FFB71B")
-        self.assertEqual(qc_status_color_css("Pass"), "background-color: #1D8649")
-        self.assertEqual(qc_status_color_css("Fail"), "background-color: #FF5733")
-        self.assertEqual(qc_status_color_css("Pending"), "background-color: #2A7DE1")
+        self.assertEqual(
+            qc_status_color_css("No QC"), "background-color: #FFB71B"
+        )
+        self.assertEqual(
+            qc_status_color_css("Pass"), "background-color: #1D8649"
+        )
+        self.assertEqual(
+            qc_status_color_css("Fail"), "background-color: #FF5733"
+        )
+        self.assertEqual(
+            qc_status_color_css("Pending"), "background-color: #2A7DE1"
+        )
 
     def test_bincount2D(self):
         x = np.array([1, 2, 2, 3])
@@ -57,17 +83,25 @@ def test_bincount2D(self):
         self.assertTrue(np.array_equal(xscale, np.array([1, 2, 3])))
         self.assertTrue(np.array_equal(yscale, np.array([4, 5, 6])))
 
-    @patch('aind_qc_portal.utils.pn')
+    @patch("aind_qc_portal.utils.pn")
     def test_set_background(self, mock_pn):
         mock_pn.config.raw_css = []  # Mock raw_css to ensure a clean state
-        mock_pn.state.location.query_params = {}  # Mock query_params to ensure no background param
+        mock_pn.state.location.query_params = (
+            {}
+        )  # Mock query_params to ensure no background param
         format_css_background()
-        self.assertIn("background-color: #003057", mock_pn.config.raw_css[0])  # Default dark_blue color
+        self.assertIn(
+            "background-color: #003057", mock_pn.config.raw_css[0]
+        )  # Default dark_blue color
 
         mock_pn.config.raw_css = []  # Reset mock raw_css
-        mock_pn.state.location.query_params = {"background": "light_blue"}  # Mock query_params with light_blue
+        mock_pn.state.location.query_params = {
+            "background": "light_blue"
+        }  # Mock query_params with light_blue
         format_css_background()
-        self.assertIn("background-color: #2A7DE1", mock_pn.config.raw_css[0])  # light_blue color
+        self.assertIn(
+            "background-color: #2A7DE1", mock_pn.config.raw_css[0]
+        )  # light_blue color
 
 
 if __name__ == "__main__":