WIP Run Launcher widget

pyproject.toml

@@ -25,6 +25,7 @@ dependencies = [
     "ipywidgets",
     "jupyter-app-launcher",
     "matplotlib",
+    "papermill",
     "pandas",
     "photutils >=1.9",
     "pydantic >=2",
@@ -178,4 +179,6 @@ filterwarnings = [
     'ignore:RADECSYS=:',
     # photutils changed the name of a function again
     'ignore:The make_gaussian_sources_image function is deprecated',
+    # papermill is using deprecated jupyter paths
+    'ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning',
 ]

stellarphot/notebooks/run-launcher.ipynb

@@ -2,80 +2,38 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "e5f2fc8f-b893-400e-8fb7-4dd8e871334f",
    "metadata": {},
    "outputs": [],
    "source": [
     "import ipywidgets as ipw\n",
-    "import papermill as pm\n",
-    "\n",
-    "from ipyautoui.custom import FileChooser\n",
     "\n",
-    "from stellarphot.gui_tools import FitsOpener\n",
-    "from stellarphot.settings.custom_widgets import Confirm\n",
-    "from stellarphot.settings import PhotometryRunSettings"
+    "from stellarphot.settings.custom_widgets import Kaboodle"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "2389ff77-c8ac-4bad-afb7-79cdd5c0f365",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "class Kaboodle(ipw.VBox):\n",
-    "    def __init__(self, *args, **kwargs):\n",
-    "        super().__init__(*args, **kwargs)\n",
-    "        self.fo = FitsOpener(title=\"Choose any image in the folder of images to do photometry on that contains the object of interest\")\n",
-    "        self.info_box = ipw.HTML()\n",
-    "        self.run_output = ipw.Output()\n",
-    "        self.confirm = Confirm(message=\"Is this correct?\")\n",
-    "        self.children = (self.fo.file_chooser, self.info_box, self.confirm, self.run_output)\n",
-    "        self.fo.file_chooser.observe(self._file_chosen, \"_value\")\n",
-    "        self.confirm.observe(self._confirmation, \"value\")\n",
-    "        self.run_settings = None\n",
-    "\n",
-    "    def _file_chosen(self, change=None):\n",
-    "        self.run_settings = PhotometryRunSettings(\n",
-    "            directory_with_images=self.fo.path.parent, \n",
-    "            object_of_interest=self.fo.header['object']\n",
-    "        )\n",
-    "        self.info_box.value = \"<h2>\" + self.info_message + \"</br>Is this correct?\" + \"</h2>\"\n",
-    "        self.confirm.show()\n",
-    "\n",
-    "    @property\n",
-    "    def info_message(self):\n",
-    "        return (f\"Photomery will be done on all images of the object \"\n",
-    "                f\"'<code>{self.run_settings.object_of_interest}</code>' in the \"\n",
-    "                f\"folder '<code>{self.run_settings.directory_with_images}</code>'\")\n",
-    "        \n",
-    "    def _confirmation(self, change=None):\n",
-    "        if change[\"new\"]:\n",
-    "            # User said yes\n",
-    "\n",
-    "            # Update informational message\n",
-    "            self.info_box.value = \"<h2>\" + self.info_message + \"</br>Photometry is running...\" + \"</h2>\"\n",
-    "            with self.run_output:\n",
-    "                pm.execute_notebook(\n",
-    "                    \"stellarphot/notebooks/photometry_runner.ipynb\",\n",
-    "                    \"MEEEPhonk.ipynb\",\n",
-    "                    parameters=self.run_settings.model_dump(mode=\"json\")\n",
-    "                )\n",
-    "        else:\n",
-    "            # User said no, so reset to initial state.\n",
-    "            self.fo.file_chooser.reset()\n",
-    "            self.info_box.value = \"\"\n",
-    "            self.run_settings = None\n",
-    "    "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "c5eed8a2-7533-4411-8f6e-303b854f4e3e",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "415ea731dc1d42279fcce2ff8a718672",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Kaboodle(children=(FileChooser(path='/Users/mattcraig/development/astronomy/stellarphot/stellarphot/notebooks'…"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "kab = Kaboodle()\n",
     "kab"

stellarphot/settings/custom_widgets.py

@@ -14,7 +14,9 @@ class StrEnum(str, Enum):
 
 
 import ipywidgets as ipw
+import papermill as pm
 import traitlets as tr
+from astropy.utils.data import get_pkg_data_filename
 from camel_converter import to_snake
 from ipyautoui.autoobject import AutoObject
 from ipyautoui.custom.iterable import ItemBox
@@ -25,10 +27,12 @@ class StrEnum(str, Enum):
     Observatory,
     PartialPhotometrySettings,
     PassbandMap,
+    PhotometryRunSettings,
     PhotometryWorkingDirSettings,
     SavedSettings,
     ui_generator,
 )
+from stellarphot.settings.fits_opener import FitsOpener
 
 __all__ = ["ChooseOrMakeNew", "Confirm", "SettingWithTitle"]
 
@@ -987,3 +991,71 @@ def save_wd(_=None):
         raise ValueError(
             f"The widget {setting_widget} is not a recognized type of widget."
         )
+
+
+class PhotometryRunner(ipw.VBox):
+    def __init__(
+        self, photometry_notebook_name="photometry_run.ipynb", *args, **kwargs
+    ):
+        super().__init__(*args, **kwargs)
+        self.photometry_notebook_name = photometry_notebook_name
+        self.fo = FitsOpener(
+            title=(
+                "Choose any image in the folder of images to do photometry on that "
+                "contains the object of interest"
+            )
+        )
+        self.info_box = ipw.HTML()
+        self.run_output = ipw.Output()
+        self.confirm = Confirm(message="Is this correct?")
+        self.children = (
+            self.fo.file_chooser,
+            self.info_box,
+            self.confirm,
+            self.run_output,
+        )
+        self.fo.file_chooser.observe(self._file_chosen, "_value")
+        self.confirm.observe(self._confirmation, "value")
+        self.run_settings = None
+
+    def _file_chosen(self, _):
+        self.run_settings = PhotometryRunSettings(
+            directory_with_images=self.fo.path.parent,
+            object_of_interest=self.fo.header["object"],
+        )
+        self.info_box.value = (
+            "<h2>" + self.info_message + "</br>Is this correct?" + "</h2>"
+        )
+        self.confirm.show()
+
+    @property
+    def info_message(self):
+        return (
+            f"Photometry will be done on all images of the object "
+            f"'<code>{self.run_settings.object_of_interest}</code>' in the "
+            f"folder '<code>{self.run_settings.directory_with_images}</code>'"
+        )
+
+    def _confirmation(self, change=None):
+        if change["new"]:
+            # User said yes
+
+            # Update informational message
+            self.info_box.value = (
+                "<h2>" + self.info_message + "</br>Photometry is running..." + "</h2>"
+            )
+            template_nb = get_pkg_data_filename(
+                "photometry_runner.ipynb", package="stellarphot.notebooks"
+            )
+            print(template_nb)
+            with self.run_output:
+                pm.execute_notebook(
+                    template_nb,
+                    self.photometry_notebook_name,
+                    parameters=self.run_settings.model_dump(mode="json"),
+                )
+        else:
+            # User said no, so reset to initial state.
+            self.fo.file_chooser.reset()
+            self.info_box.value = ""
+            self.run_settings = None

stellarphot/settings/tests/test_photometry_runner.py

@@ -0,0 +1,100 @@
+import os
+from pathlib import Path
+
+import ipywidgets as ipw
+import pytest
+from astropy.io import fits
+
+from stellarphot.settings import (
+    PhotometrySettings,
+    PhotometryWorkingDirSettings,
+    settings_files,
+)
+from stellarphot.settings.custom_widgets import PhotometryRunner
+from stellarphot.settings.tests.test_models import DEFAULT_PHOTOMETRY_SETTINGS
+
+
+# See test_settings_file.TestSavedSettings for a detailed description of what the
+# following fixture does. In brief, it patches the settings_files.PlatformDirs class
+# so that the user_data_dir method returns the temporary directory.
+@pytest.fixture(autouse=True)
+def fake_settings_dir(mocker, tmp_path):
+    mocker.patch.object(
+        settings_files.PlatformDirs, "user_data_dir", tmp_path / "stellarphot"
+    )
+
+
+class TestPhotometryRunner:
+
+    # This auto-used fixture changes the working directory to the temporary directory
+    # and then changes back to the original directory after the test is done.
+    @pytest.fixture(autouse=True)
+    def change_to_tmp_dir(self, tmp_path):
+        original_dir = os.getcwd()
+        os.chdir(tmp_path)
+        # Yielding here is important. It means that when the test is done, the remainder
+        # of the function will be executed. This is important because the test is run in
+        # a temporary directory and we want to change back to the original directory
+        # when the test is done.
+        yield
+        os.chdir(original_dir)
+
+    def test_photometry_runner_creation(self):
+        # This test simply makes sure we can create the object
+        photometry_runner = PhotometryRunner()
+        assert isinstance(photometry_runner, ipw.Box)
+
+    @pytest.mark.parametrize("do_photometry", [True, False])
+    def test_photometry_runner_with_valid_settings(self, do_photometry):
+        # This test makes sure that the PhotometryRunner widget can be used
+        # to *start* a photometry run. It does not check the actual photometry
+        # or the results of the photometry run, except to ensure that the expected
+        # files are created.
+        # Make a settings
+        phot_settings = PhotometrySettings.model_validate(DEFAULT_PHOTOMETRY_SETTINGS)
+
+        # Save a copy to the working directory
+        wd_settings = PhotometryWorkingDirSettings()
+        wd_settings.save(phot_settings)
+
+        # Make sure a source list file exists
+        sources = Path(phot_settings.source_location_settings.source_list_file)
+        sources.touch()
+
+        # Make sure a fake fits file exists
+        fake_fits = Path("fake.fits")
+        fits_data = fits.PrimaryHDU(data=[[1, 2], [3, 4]])
+        object_name = "Fake Object"
+        fits_data.header["object"] = object_name
+        fits_data.writeto(fake_fits)
+
+        photometry_runner = PhotometryRunner()
+        # Select a fits file
+        photometry_runner.fo.file_chooser.reset(".", fake_fits.name)
+        photometry_runner.fo.file_chooser._apply_selection()
+        photometry_runner.fo.file_chooser.value = fake_fits
+
+        # Check that the message in the information box is as expected
+        assert "Photometry will be done" in photometry_runner.info_box.value
+        assert object_name in photometry_runner.info_box.value
+
+        if do_photometry:
+            # Run the photometry
+            photometry_runner.confirm._yes.click()
+            assert "Photometry is running" in photometry_runner.info_box.value
+
+            # Check that the expected file was created, in this case just the notebook.
+            # No photometry is actually done because the source is empty and the "image"
+            # has no stars.
+            assert Path(photometry_runner.photometry_notebook_name).exists()
+
+            # Make sure we do get the error we expect, which is generated when
+            # the source list is read. It is an empty file, not actually an ecsv.
+            with open(photometry_runner.photometry_notebook_name) as f:
+                notebook_text = f.read()
+                assert "InconsistentTableError" in notebook_text
+        else:
+            # Cancel the photometry
+            photometry_runner.confirm._no.click()
+
+            assert photometry_runner.info_box.value == ""