update scripts + add CI workflow

.github/workflows/example-scripts.yml

@@ -0,0 +1,39 @@
+name: Example scripts
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  run-examples:
+    runs-on: ubuntu-latest
+
+    env:
+      MPLBACKEND: Agg
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        python-version: "3.11"
+
+    - name: Setup venv
+      run: uv python install
+
+    - name: Install dependencies
+      run: uv sync --all-extras --dev
+
+    - name: Run example scripts
+      run: |
+        for f in examples/*.py; do
+          echo "Running $f"
+          uv run python "$f" || exit 1
+        done
+
+    - name: Run example notebooks
+      run: |
+        uv run --with nbconvert jupyter nbconvert --to notebook --execute --inplace examples/*.ipynb

README.md

@@ -1,6 +1,7 @@
 # Rascal: RANSAC Assisted Spectral CALibration
 
 [![Python package](https://github.com/jveitchmichaelis/rascal/actions/workflows/python-package.yml/badge.svg)](https://github.com/jveitchmichaelis/rascal/actions/workflows/python-package.yml)
+[![Example scripts](https://github.com/jveitchmichaelis/rascal/actions/workflows/example-scripts.yml/badge.svg)](https://github.com/jveitchmichaelis/rascal/actions/workflows/example-scripts.yml)
 [![Coverage Status](https://coveralls.io/repos/github/jveitchmichaelis/rascal/badge.svg?branch=main)](https://coveralls.io/github/jveitchmichaelis/rascal?branch=main)
 [![Readthedocs Status](https://readthedocs.org/projects/rascal/badge/?version=latest\&style=flat)](https://rascal.readthedocs.io/en/latest/)
 [![PyPI version](https://badge.fury.io/py/rascal.svg)](https://badge.fury.io/py/rascal)

examples/example_gemini_gmos_longslit.py

@@ -12,7 +12,11 @@
 
 sys.path.append("../../bhtomspec/GMOS")
 
-from gmos_fieldflattening import create_pixel_array
+try:
+    from gmos_fieldflattening import create_pixel_array
+except ImportError:
+    print("Skipping: gmos_fieldflattening module not available")
+    sys.exit(0)
 
 pixels = create_pixel_array("north", 2)
 rawpix_to_pix_itp = interpolate.interp1d(np.arange(len(pixels)), pixels)

examples/example_gemini_gmos_longslit_manual_atlas.py

@@ -13,7 +13,11 @@
 
 sys.path.append("../../bhtomspec/GMOS")
 
-from gmos_fieldflattening import create_pixel_array
+try:
+    from gmos_fieldflattening import create_pixel_array
+except ImportError:
+    print("Skipping: gmos_fieldflattening module not available")
+    sys.exit(0)
 
 pixels = create_pixel_array("north", 2)
 rawpix_to_pix_itp = interpolate.interp1d(np.arange(len(pixels)), pixels)

examples/example_gtc_osiris.py

@@ -83,7 +83,7 @@
 
 c.do_hough_transform()
 
-c.plot_arc(save_fig="png", filename="output/gtc-osiris-arc-spectrum")
+c.plot_arc(save_fig="png", filename=os.path.join(base_dir, "output", "gtc-osiris-arc-spectrum"))
 
 c.do_hough_transform()
 
@@ -105,7 +105,7 @@
     log_spectrum=False,
     tolerance=5.0,
     save_fig="png",
-    filename="output/gtc-osiris-wavelength-calibration",
+    filename=os.path.join(base_dir, "output", "gtc-osiris-wavelength-calibration"),
 )
 
 # Show the parameter space for searching possible solution
@@ -114,4 +114,4 @@
 print("Peaks utilisation rate: {}%".format(peak_utilisation * 100))
 print("Atlas utilisation rate: {}%".format(atlas_utilisation * 100))
 
-c.plot_search_space(save_fig="png", filename="output/gtc-osiris-search-space")
+c.plot_search_space(save_fig="png", filename=os.path.join(base_dir, "output", "gtc-osiris-search-space"))

examples/example_keck_deimos_830g.py

@@ -1,4 +1,5 @@
 import json
+import os
 
 import numpy as np
 from scipy.signal import find_peaks
@@ -8,15 +9,17 @@
 from rascal.util import refine_peaks
 
 # Load the 1D Spectrum from Pypeit
-spectrum_json = json.load(open("data_keck_deimos/keck_deimos_830g_l_PYPIT.json"))
+base_dir = os.path.dirname(__file__)
+os.makedirs(os.path.join(base_dir, "output"), exist_ok=True)
+spectrum_json = json.load(open(os.path.join(base_dir, "data_keck_deimos/keck_deimos_830g_l_PYPIT.json")))
 spectrum = np.array(spectrum_json["spec"])
 
 # Identify the arc lines
 peaks, _ = find_peaks(spectrum, prominence=200, distance=10)
 peaks = refine_peaks(spectrum, peaks, window_width=3)
 
 c = Calibrator(peaks, spectrum=spectrum)
-c.plot_arc(save_fig="png", filename="output/keck-deimos-arc-spectrum")
+c.plot_arc(save_fig="png", filename=os.path.join(base_dir, "output", "keck-deimos-arc-spectrum"))
 c.set_hough_properties(
     num_slopes=10000.0,
     range_tolerance=500.0,
@@ -66,7 +69,7 @@
     log_spectrum=False,
     tolerance=5.0,
     save_fig="png",
-    filename="output/keck-deimos-wavelength-calibration",
+    filename=os.path.join(base_dir, "output", "keck-deimos-wavelength-calibration"),
 )
 
 # Show the parameter space for searching possible solution
@@ -75,4 +78,4 @@
 print("Peaks utilisation rate: {}%".format(peak_utilisation * 100))
 print("Atlas utilisation rate: {}%".format(atlas_utilisation * 100))
 
-c.plot_search_space(save_fig="png", filename="output/keck-deimos-search-space")
+c.plot_search_space(save_fig="png", filename=os.path.join(base_dir, "output", "keck-deimos-search-space"))

examples/example_lt_sprat_xe_manual_atlas.py

@@ -21,7 +21,8 @@
 plt.xlabel("Spectral Direction / Pix")
 plt.ylabel("Spatial Direction / Pix")
 plt.tight_layout()
-plt.savefig("output/lt-sprat-arc-image.png")
+os.makedirs(os.path.join(base_dir, "output"), exist_ok=True)
+plt.savefig(os.path.join(base_dir, "output", "lt-sprat-arc-image.png"))
 
 # Collapse into 1D spectrum between row 110 and 120
 spectrum = np.median(spectrum2D[110:120], axis=0)
@@ -126,7 +127,7 @@
 print("Atlas utilisation rate: {}%".format(atlas_utilisation * 100))
 
 c.use_matplotlib()
-c.plot_arc(save_fig="png", filename="output/lt-sprat-arc-spectrum")
+c.plot_arc(save_fig="png", filename=os.path.join(base_dir, "output", "lt-sprat-arc-spectrum"))
 
 # Plot the solution
 c.plot_fit(
@@ -136,8 +137,8 @@
     log_spectrum=False,
     tolerance=5.0,
     save_fig="png",
-    filename="output/lt-sprat-wavelength-calibration",
+    filename=os.path.join(base_dir, "output", "lt-sprat-wavelength-calibration"),
 )
 
 # Show the parameter space for searching possible solution
-c.plot_search_space(save_fig="png", filename="output/lt-sprat-search-space")
+c.plot_search_space(save_fig="png", filename=os.path.join(base_dir, "output", "lt-sprat-search-space"))

examples/example_ntt_efosc_grism11.py

@@ -1,3 +1,5 @@
+import os
+
 from astropy.io import fits
 import numpy as np
 from scipy.signal import find_peaks
@@ -7,7 +9,8 @@
 from rascal.util import refine_peaks
 
 # Load the 1D Spectrum from Pypeit
-data = fits.open("data_eso36_efosc/EFOSC_spec_HeAr227_0005.fits")[0]
+base_dir = os.path.dirname(__file__)
+data = fits.open(os.path.join(base_dir, "data_eso36_efosc/EFOSC_spec_HeAr227_0005.fits"))[0]
 spectrum = np.median(data.data.T, axis=0)
 
 # Identify the arc lines

examples/example_wht_isis_r300r.py

@@ -22,15 +22,16 @@
 plt.xlabel("Spectral Direction / Pix")
 plt.ylabel("Spatial Direction / Pix")
 plt.tight_layout()
-plt.savefig("output/wht-isis-arc-image.png")
+os.makedirs(os.path.join(base_dir, "output"), exist_ok=True)
+plt.savefig(os.path.join(base_dir, "output", "wht-isis-arc-image.png"))
 
 # Identify the peaks
 peaks, _ = find_peaks(spectrum, height=500, prominence=100, distance=5, threshold=None)
 peaks = util.refine_peaks(spectrum, peaks, window_width=3)
 
 # Initialise the calibrator
 c = Calibrator(peaks, spectrum=spectrum)
-c.plot_arc(log_spectrum=True, save_fig="png", filename="output/wht-isis-arc-spectrum")
+c.plot_arc(log_spectrum=True, save_fig="png", filename=os.path.join(base_dir, "output", "wht-isis-arc-spectrum"))
 c.set_hough_properties(
     num_slopes=10000,
     xbins=500,
@@ -75,11 +76,11 @@
     log_spectrum=False,
     tolerance=5.0,
     save_fig="png",
-    filename="output/wht-isis-wavelength-calibration",
+    filename=os.path.join(base_dir, "output", "wht-isis-wavelength-calibration"),
 )
 
 # Show the parameter space for searching possible solution
-c.plot_search_space(save_fig="png", filename="output/wht-isis-search-space")
+c.plot_search_space(save_fig="png", filename=os.path.join(base_dir, "output", "wht-isis-search-space"))
 
 print("Stdev error: {} A".format(residual.std()))
 print("Peaks utilisation rate: {}%".format(peak_utilisation * 100))

pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
 [project]
 name = "rascal"
 version = "0.4.0"