Merge dev_master in preparation for release

.github/workflows/notebooktests.yml

@@ -56,7 +56,7 @@ jobs:
         uses: actions/setup-python@v6
         with:
           # No matrix is used since this is a time-consuming task.
-          python-version: 3.11
+          python-version: 3.13
 
       - name: Install dependencies
         run: |
@@ -85,6 +85,40 @@ jobs:
             /usr/bin/time -v jupytext --execute --update "${fn}"
           done
 
+  mosaic_notebooks:
+    name: Run MOSAIC Notebooks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          # No matrix is used since this is a time-consuming task.
+          python-version: 3.13
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.github_actions.txt
+
+      - name: Install ScopeSim from repo
+        if: ${{ inputs.from_pypi == false || inputs.from_pypi == 'false' }}
+        run: |
+          echo "Re-installing ScopeSim from source" >> $GITHUB_STEP_SUMMARY
+          pip uninstall -y scopesim scopesim_templates
+          pip install git+https://github.com/AstarVienna/ScopeSim.git@${{ inputs.ScopeSim }}
+          pip install git+https://github.com/AstarVienna/ScopeSim_Templates.git@${{ inputs.ScopeSim_Templates }}
+      - name: Run Notebooks
+        env:
+          PYDEVD_DISABLE_FILE_VALIDATION: 1
+        run: |
+          echo "## MOSAIC Notebooks tested" >> $GITHUB_STEP_SUMMARY
+          for fn in MOSAIC/docs/example_notebooks/*.ipynb
+          do
+            echo "${fn}"
+            echo "- ${fn}" >> $GITHUB_STEP_SUMMARY
+            /usr/bin/time -v jupytext --execute --update "${fn}"
+          done
+
   metis_notebooks:
     name: Run METIS Notebooks
     runs-on: ubuntu-latest
@@ -94,7 +128,7 @@ jobs:
         uses: actions/setup-python@v6
         with:
           # No matrix is used since this is a time-consuming task.
-          python-version: 3.11
+          python-version: 3.13
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/tests.yml

@@ -53,7 +53,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
       - uses: actions/checkout@v5

ELT/FITS_telescope_keywords.yaml

@@ -1,6 +1,21 @@
 - ext_type: PrimaryHDU
   keywords:
     HIERARCH:
+      ESO:
+        TEL:
+          ALT: [24.5, "Dummy value"]
+          AZ: [-1.3, "Dummy value"]
+          GEOELEV: 3046.0
+          GEOLAT: -24.58928          # Google maps, check
+          GEOLON: -70.19166
+          TARG:
+            DEC: ["!OBS.dec", "Dummy value"]
+            RA: ["!OBS.ra", "Dummy value"]
+            EPOCH: 2000.0
+            EPOCHSYSTEM: "J"
+            PARALLAX: [0.0, "Dummy value"]
+            RADVEL: [0.0, "Dummy value"]
+
       WISE:
         TEL:
           NAME: "ELT"

LFOA/tests/test_lfoa.py

@@ -38,7 +38,7 @@ def test_something_comes_out(self):
         if PLOTS:
             plt.subplot(121)
             wave = np.arange(3000, 11000)
-            plt.plot(wave, lfoa.optics_manager.system_tranmission(wave))
+            plt.plot(wave, lfoa.optics_manager.system_transmission(wave))
 
             plt.subplot(122)
             im = hdus[0][1].data

METIS/LIST_Leiden_telescope.tbl

@@ -0,0 +1,20 @@
+# description: Leiden AIT relay optics for sky observations
+# author: Oliver Czoske
+# source: Zemax model
+# date_created: 2025-08-28
+# date_modified: 2025-10-16
+# status: Zemax model
+# outer_unit: mm
+# inner_unit: mm
+# angle_unit: degree
+# temperature_unit: deg_C
+# changes:
+#    - 2025-08-28 (OC) Initialised based on rough guess
+#    - 2025-10-02 (OC) Zemax model, discussed with J.Brink
+#    - 2025-10-16 (OC) assume Al coating, per I.Politopoulos
+#
+name    outer   inner   angle   temperature action     filename
+Ldn_M4  660.    0.      42.5    10.         reflection TER_mirror_aluminium.dat
+Ldn_M3  160.9   0.      0.      10.         reflection TER_mirror_aluminium.dat
+Ldn_M2   89.6   0.      17.     10.         reflection TER_mirror_aluminium.dat
+Ldn_M1   66.0   0.      45.     10.         reflection TER_mirror_aluminium.dat

METIS/Leiden_sky.yaml

@@ -0,0 +1,40 @@
+---
+### METIS AIT Leiden sky and telescope
+
+object: Leiden sky
+alias: OBS
+name: Leiden_sky
+description: Leiden sky and telescope
+data_modified: 2025-08-26
+changes:
+  - 2025-08-26 (OC) file created
+
+properties:
+  location:    Leiden
+  longitude:    4.45842
+  latitude:    52.16897
+  airmass:     1.0
+
+effects:
+  - name:        leiden_sky
+    description: atmospheric emission and transmission
+    class:       AtmoLibraryTERCurve
+    include:     True
+    kwargs:
+      pwv:       "!ATMO.pwv"
+      remote_filename: "!ATMO.spectrum.filename"
+
+  - name:        telescope
+    description: reflection curve
+    class:       SurfaceList
+    include:     True
+    kwargs:
+      filename:  LIST_Leiden_telescope.tbl
+
+---
+alias: ATMO
+properties:
+  temperature: 15   # Celsius!
+  pwv:         1.0  # mm
+  spectrum:
+    filename: Leiden_atmo_ter.fits

METIS/METIS_DET_IFU.yaml

@@ -72,6 +72,14 @@ effects:
     kwargs:
       filename: "!DET.linearity.file_name"
 
+  - name: ipc
+    description: Inter-pixel capacitance
+    class: InterPixelCapacitance
+    kwargs:   # values from Kannawadi+2016 (H4RG!)
+      alpha_edge:   0.02
+      alpha_corner: 0.002
+      alpha_aniso:  0.
+
   - name: readout_noise
     description: Readout noise frames
     class: BasicReadoutNoise

METIS/METIS_DET_IMG_LM.yaml

@@ -90,6 +90,14 @@ effects:
     kwargs:
       filename: "!DET.linearity.file_name"
 
+  - name: ipc
+    description: Inter-pixel capacitance
+    class: InterPixelCapacitance
+    kwargs:   # values from Kannawadi+2016 (H4RG!)
+      alpha_edge:   0.02
+      alpha_corner: 0.002
+      alpha_aniso:  0.
+
   - name: readout_noise
     description: Readout noise frames
     class: BasicReadoutNoise

METIS/METIS_WCU.yaml

@@ -49,5 +49,8 @@ effects:
 alias: TEL
 properties:
   #area: 975.23478998
+  telescope: none (WCU)
+  ter_curve:
+    filename: none
   area: 1354.593    #### TEST, needed to agree with RvB's calculation
   temperature: "!WCU.temperature"  # Overrides !ATMO.temperature

METIS/TER_mirror_aluminium.dat

@@ -0,0 +1,65 @@
+# author : ESO ELT DRM
+# source : https://www.eso.org/sci/facilities/eelt/science/drm/tech_data/data/reflectivity/
+# description : Bare Aluminium
+# date_created  : 2009-11-04
+# date_modified : 2018-11-19
+# status : Design, pre PDR list of MICADO mirrors for wide-field mode
+# type : mirror:reflection
+# wavelength_unit : um
+#
+# changes :
+# - 2019-07-25 (KL) Changed 2-25um value to 0.98 to match ESO predictions
+# - 2020-08-25 (KL) updated waveunit --> wavelength_unit
+#
+wavelength  reflection
+0.309       0.921
+0.335       0.923
+0.372       0.925
+0.404       0.926
+0.432       0.926
+0.464       0.925
+0.499       0.921
+0.529       0.918
+0.564       0.916
+0.588       0.913
+0.610       0.910
+0.633       0.908
+0.647       0.908
+0.660       0.903
+0.675       0.898
+0.690       0.892
+0.709       0.886
+0.731       0.881
+0.755       0.875
+0.774       0.870
+0.794       0.865
+0.815       0.864
+0.845       0.863
+0.861       0.868
+0.876       0.875
+0.891       0.881
+0.900       0.884
+0.910       0.891
+0.923       0.897
+0.936       0.904
+0.945       0.911
+0.967       0.914
+1.008       0.918
+1.056       0.923
+1.115       0.929
+1.169       0.933
+1.210       0.936
+1.257       0.939
+1.309       0.942
+1.376       0.946
+1.459       0.950
+1.532       0.953
+1.604       0.956
+1.681       0.959
+1.749       0.961
+1.818       0.963
+1.885       0.965
+1.944       0.968
+2.000       0.970
+2.500       0.980
+20.00       0.980

METIS/code/LMS_Traces/add_predisperser_ext.py

@@ -0,0 +1,44 @@
+"""Add an extension with coefficients for the predisperser
+
+Taken from Fig.3-15 of E-REP-ATC-MET-1003_3-0
+"""
+from astropy.io import fits
+from astropy.table import Table
+TRACEFILE = "TRACE_LMS.fits"
+
+
+def add_predisperser():
+    # Coefficients in ascending order of powers of wavelength
+    coeff = fits.Column(name="coefficients", format="E",
+                        array=[-6.0585, 9.1657, -2.7017, 0.3825, -0.0205])
+    power = fits.Column(name="power", format="I",
+                        array=[0, 1, 2, 3, 4])
+    hdu = fits.BinTableHDU.from_columns([power, coeff])
+
+    hdu.header["EXTNAME"] = "Predisperser"
+
+    with fits.open(TRACEFILE) as hdul:
+        # Append the new HDU
+        hdul.append(hdu)
+
+        # Update the catalogue
+        cat = hdul["CATALOGUE"]
+        tab = Table(cat.data)
+        tab.add_row(('Predisperser', 5, 0, 0))
+        nhdu = fits.BinTableHDU(tab)
+        nhdu.header["EXTNAME"] = "CATALOGUE"
+        hdul[1] = nhdu
+
+        # Update the primary header
+        hdul[0].header.update(dict(
+            DATE="2025-10-06",
+            SOURCE="E-REP-ATC-MET-1003_3-0, E-REP-ATC-MET-1016_1-0",
+            DATE_MOD="2025-10-06",
+            HISTORY="2025-10-06 (OC) append predisperser angle fit"))
+        hdul.writeto("test_trace.fits", overwrite=True)
+        print("Output written to test_trace.fits. Rename to", TRACEFILE," when checked for correctness.")
+
+
+
+if __name__ == "__main__":
+    add_predisperser()