Merge branch 'dev_master' into oc/metis_wcu_alt1

AstarVienna · Jan 14, 2025 · 6f06ff1 · 6f06ff1
2 parents b4bbbf2 + baf4517
commit 6f06ff1
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Showing 20 changed files with 80 additions and 64 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -22,12 +22,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -39,7 +39,7 @@ jobs:
       - name: Run Pytest
         run: pytest
       - name: Store badge report files
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: badge-report
           path: _REPORTS
@@ -53,12 +53,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -83,9 +83,9 @@ jobs:
     # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows
     if: github.ref == 'dev_master' || github.ref == 'master' || github.base_ref == ''
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           # No matrix is used since this is a time-consuming tosk.
           python-version: 3.11
@@ -124,9 +124,9 @@ jobs:
     # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows
     if: github.ref == 'dev_master' || github.ref == 'master' || github.base_ref == ''
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           # No matrix is used since this is a time-consuming tosk.
           python-version: 3.11

diff --git a/HAWKI/default.yaml b/HAWKI/default.yaml
@@ -3,6 +3,7 @@ object : configuration
 alias : OBS
 name : HAWKI_default_configuration
 description : default parameters needed for a HAWKI simulation
+status: experimental
 date_modified: 2022-02-22
 changes:
   - 2022-02-22 (MV) formatting

diff --git a/LFOA/default.yaml b/LFOA/default.yaml
@@ -3,6 +3,7 @@ object : configuration
 alias : OBS
 name : LFOA_default_configuration
 description : default parameters needed for a LFOA simulation
+status: experimental
 
 packages :
 - LFOA

diff --git a/METIS/default.yaml b/METIS/default.yaml
@@ -5,6 +5,7 @@ object: configuration
 alias: OBS
 name: METIS_default_configuration
 description: default parameters needed for a METIS simulation
+status: development
 date_modified: 2024-09-04
 changes:
   - 2021-12-16 (OC) chopnod defaults to perpendicular
@@ -65,6 +66,7 @@ mode_yamls:
     alias: OBS
     name: img_lm
     description: "METIS LM-band imaging"
+    status: development
     yamls:
       - Armazones.yaml
       - ELT.yaml
@@ -83,6 +85,7 @@ mode_yamls:
     alias: OBS
     name: img_n
     description: "METIS N-band imaging"
+    status: development
     yamls:
       - Armazones.yaml
       - ELT.yaml
@@ -103,6 +106,7 @@ mode_yamls:
     alias: OBS
     name: lss_l
     description: "METIS L-band slit spectroscopy"
+    status: development
     yamls:
       - Armazones.yaml
       - ELT.yaml
@@ -124,6 +128,7 @@ mode_yamls:
     alias: OBS
     name: lss_m
     description: "METIS M-band slit spectroscopy"
+    status: development
     yamls:
       - Armazones.yaml
       - ELT.yaml
@@ -145,6 +150,7 @@ mode_yamls:
     alias: OBS
     name: lss_n
     description: "METIS N-band slit spectroscopy"
+    status: development
     yamls:
       - Armazones.yaml
       - ELT.yaml
@@ -166,6 +172,7 @@ mode_yamls:
     alias: OBS
     name: lms
     description: "METIS LM-band integral-field spectroscopy, nominal mode"
+    status: experimental
     yamls:
       - Armazones.yaml
       - ELT.yaml
@@ -184,6 +191,7 @@ mode_yamls:
     alias: OBS
     name: lms_extended
     description: "METIS LM-band integral-field spectroscopy, extended mode"
+    status: experimental
     yamls:
       - Armazones.yaml
       - ELT.yaml

diff --git a/METIS/docs/example_notebooks/LSS_AGN-01_preparation.ipynb b/METIS/docs/example_notebooks/LSS_AGN-01_preparation.ipynb
@@ -236,7 +236,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "src = sim.Source(cube=\"AGN_sim_prepared.fits\")"
+    "with fits.open(\"AGN_sim_prepared.fits\") as cube_hdul:\n",
+    "    src = sim.Source(cube=cube_hdul)"
    ]
   },
   {
@@ -439,7 +440,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "src50 = sim.Source(cube=\"AGN_sim_rotated_50.fits\")"
+    "with fits.open(\"AGN_sim_rotated_50.fits\") as cube_hdul:\n",
+    "    src50 = sim.Source(cube=cube_hdul)"
    ]
   },
   {

diff --git a/METIS/docs/example_notebooks/LSS_AGN-02_simulation.ipynb b/METIS/docs/example_notebooks/LSS_AGN-02_simulation.ipynb
@@ -15,6 +15,7 @@
    "source": [
     "from matplotlib import pyplot as plt\n",
     "from matplotlib.colors import LogNorm\n",
+    "from astropy.io import fits\n",
     "%matplotlib inline"
    ]
   },
@@ -54,7 +55,7 @@
    "outputs": [],
    "source": [
     "cmd = sim.UserCommands(use_instrument=\"METIS\", set_modes=['lss_n'],\n",
-    "                      properties={\"!OBS.exptime\": 3600,\n",
+    "                      properties={\"!OBS.exptime\": 3600, \"!OBS.dit\": None, \"!OBS.ndit\": None,\n",
     "                                 \"!SIM.spectral.spectral_bin_width\": 3.0e-3})\n",
     "metis = sim.OpticalTrain(cmd)"
    ]
@@ -75,8 +76,10 @@
     "cube_01 = \"AGN_sim_prepared.fits\"\n",
     "cube_02 = \"AGN_sim_rotated_50.fits\"\n",
     "\n",
-    "src_01 = sim.Source(cube=cube_01)\n",
-    "src_02 = sim.Source(cube=cube_02)\n",
+    "with fits.open(cube_01) as cube_hdul:\n",
+    "    src_01 = sim.Source(cube=cube_hdul)\n",
+    "with fits.open(cube_02) as cube_hdul:\n",
+    "    src_02 = sim.Source(cube=cube_hdul)\n",
     "\n",
     "sky = sim.source.source_templates.empty_sky()"
    ]
@@ -133,9 +136,9 @@
    "source": [
     "plt.figure(figsize=(16, 8))\n",
     "plt.subplot(121)\n",
-    "plt.imshow(hdul_01[1].data - hdul_sky[1].data + 1e5, origin='lower', norm=LogNorm(vmin=1e5, vmax=5e8))\n",
+    "plt.imshow(hdul_01[1].data - hdul_sky[1].data + 1e5, origin='lower', norm=\"log\")\n",
     "plt.subplot(122)\n",
-    "plt.imshow(hdul_02[1].data - hdul_sky[1].data + 1e5, origin='lower', norm=LogNorm(vmin=1e5, vmax=5e8))"
+    "plt.imshow(hdul_02[1].data - hdul_sky[1].data + 1e5, origin='lower', norm=\"log\")"
    ]
   },
   {
@@ -173,7 +176,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/METIS/tests/test_readout_exptime.py b/METIS/tests/test_readout_exptime.py
@@ -8,7 +8,7 @@
 PKGS_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "../.."))
 sim.rc.__config__["!SIM.file.local_packages_path"] = PKGS_DIR
 
-PLOTS = True
+PLOTS = False
 
 
 class TestReadoutExptime:

diff --git a/MICADO/default.yaml b/MICADO/default.yaml
@@ -5,6 +5,7 @@ object : configuration
 alias : OBS
 name : MICADO_default_configuration
 description : default parameters needed for a MICADO simulation
+status: development
 date_modified: 2023-07-13
 changes:
   - 2023-07-13 (OC) add modes for FDR slits, deprecate pre-FDR slits
@@ -61,6 +62,7 @@ mode_yamls :
   alias: OBS
   name : IMG_4mas
   description : "wide-field imager  : 4mas/pix"
+  status: development
   yamls :
   - MICADO_IMG_wide.yaml
   properties :
@@ -72,6 +74,7 @@ mode_yamls :
   alias: OBS
   name : IMG_1.5mas
   description : "high resolution imager  : 1.5mas/pix"
+  status: development
   yamls :
   - MICADO_IMG_zoom.yaml
   properties :
@@ -83,13 +86,15 @@ mode_yamls :
   alias: OBS
   name : IMG_HCI
   description : "High contrast imaging"
+  status: experimental
   yamls :
   - MICADO_IMG_HCI.yaml
 
 - object : observation
   alias: OBS
   name : SPEC_15000x20
   description : "spectrograph : slit size 15000x20mas"
+  status: development
   yamls :
   - MICADO_SPEC.yaml
   properties :
@@ -103,6 +108,7 @@ mode_yamls :
   alias: OBS
   name : SPEC_3000x48
   description : "spectrograph : slit size 3000x48mas"
+  status: development
   yamls :
   - MICADO_SPEC.yaml
   properties :
@@ -116,6 +122,7 @@ mode_yamls :
   alias : OBS
   name : SPEC_3000x16
   description : "spectrograph : slit size 3000x16mas"
+  status: development
   yamls :
   - MICADO_SPEC.yaml
   properties :
@@ -129,6 +136,7 @@ mode_yamls :
   alias: OBS
   name : SPEC_15000x50
   description : "spectrograph : slit size 15000x50mas"
+  status: deprecated
   deprecate : "Deprecated instrument mode. For spectroscopy use
   - SPEC_3000x16
   - SPEC_3000x48
@@ -146,6 +154,7 @@ mode_yamls :
   alias: OBS
   name : SPEC_3000x50
   description : "spectrograph : slit size 3000x50mas"
+  status: deprecated
   deprecate : "Deprecated instrument mode. For spectroscopy use
   - SPEC_3000x16
   - SPEC_3000x48
@@ -163,6 +172,7 @@ mode_yamls :
   alias: OBS
   name : SPEC_3000x20
   description : "spectrograph : slit size 3000x20mas"
+  status: deprecated
   deprecate : "Deprecated instrument mode. For spectroscopy use
   - SPEC_3000x16
   - SPEC_3000x48

diff --git a/MICADO_Sci/README.md b/MICADO_Sci/README.md
@@ -0,0 +1,4 @@
+# MICADO Science package
+
+> [!CAUTION]
+> The MICADO_Sci package is **NO LONGER SUPPORTED**!! Use the MICADO package instead. MICADO_Sci will be removed soon!
diff --git a/MICADO_Sci/default.yaml b/MICADO_Sci/default.yaml
@@ -9,6 +9,7 @@ object : configuration
 alias : OBS
 name : MICADO_sci_default_configuration
 description : default parameters needed for a MICADO-Sci simulation
+status : deprecated
 
 packages :
 - Armazones

diff --git a/MICADO_Sci/sci_readme.md b/MICADO_Sci/sci_readme.md
diff --git a/MICADO_Sci/test_micado_sci/test_micado_sci.py b/MICADO_Sci/test_micado_sci/test_micado_sci.py
@@ -9,6 +9,8 @@
 import scopesim as sim
 from scopesim import rc
 
+pytest.skip(allow_module_level=True)
+
 TOP_PATH = pth.abspath(pth.join(pth.dirname(__file__), "../../"))
 rc.__config__["!SIM.file.local_packages_path"] = TOP_PATH
 

diff --git a/MICADO_Sci/test_micado_sci/test_radiometry.py b/MICADO_Sci/test_micado_sci/test_radiometry.py
@@ -37,6 +37,8 @@
 import scopesim as sim
 from scopesim import rc
 
+pytest.skip(allow_module_level=True)
+
 TOP_PATH = pth.abspath(pth.join(pth.dirname(__file__), "../../"))
 rc.__config__["!SIM.file.local_packages_path"] = TOP_PATH
 

diff --git a/MICADO_Sci/test_micado_sci/test_spectral_trace_files.py b/MICADO_Sci/test_micado_sci/test_spectral_trace_files.py
@@ -9,6 +9,8 @@
 from scopesim.tests.mocks.py_objects import header_objects as ho
 from scopesim import rc
 
+pytest.skip(allow_module_level=True)
+
 PLOTS = False
 DATA_DIR = pth.abspath(pth.join(pth.dirname(__file__), "../"))
 rc.__search_path__.insert(0, DATA_DIR)

diff --git a/OSIRIS/default.yaml b/OSIRIS/default.yaml
@@ -4,6 +4,7 @@ object : configuration
 alias : OBS
 name : OSIRIS_default_configuration
 description : default parameters needed for a OSIRIS simulation
+status: experimental
 date_created: 2022-03-02
 date_modified: 2022-03-02
 changes: