Update readthedocs yml (before deprecation of ubuntu 20 image)

.readthedocs.yaml

@@ -12,7 +12,7 @@ submodules:
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: "mambaforge-4.10"
 

dependencies/conda_env.yml

@@ -1,12 +1,12 @@
-name: magritte
+name: magritte_test_plons
 channels:
   - ensor
   - conda-forge
   - anaconda
   - defaults
 # The order of the channels above is critical!!!
 dependencies:
-  - python>=3.9
+  - python<=3.13
   - cmake
   - numpy
   - jupyterlab
@@ -33,8 +33,9 @@ dependencies:
   - pip:
     - breathe
     - sphinx_rtd_theme 
-    ##install both with pip, otherwise it will install the wrong version, not compatible with sphinx
+    - plons
+    ##install both breathe and sphinx_rtd_theme with pip, otherwise it will install the wrong version, not compatible with sphinx
   - sphinx-copybutton
   - nbsphinx
   - pytest
-  - plons #for importing Phantom models
+

docs/src/1_examples/1_post-processing/3_create_Phantom_3D.ipynb

@@ -170,20 +170,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Loading the data\n",
     "setupData = plons.LoadSetup(wdir, \"wind\")\n",
     "dumpData  = plons.LoadFullDump(dump_file, setupData)\n",
     "\n",
-    "position = dumpData[\"position\"]*1e-2      # position vectors       [cm   -> m]\n",
-    "velocity = dumpData[\"velocity\"]*1e3      # velocity vectors        [km/s -> m/s]\n",
+    "pos_x = dumpData[\"x\"]*1e-2      # x position vectors       [cm   -> m]\n",
+    "pos_y = dumpData[\"y\"]*1e-2      # y position vectors       [cm   -> m]\n",
+    "pos_z = dumpData[\"z\"]*1e-2      # z position vectors       [cm   -> m]\n",
+    "position = np.array((pos_x, pos_y, pos_z)).T\n",
+    "vel_x = dumpData[\"vx\"]*1e3     # x velocity vectors       [km/s -> m/s]\n",
+    "vel_y = dumpData[\"vy\"]*1e3     # y velocity vectors       [km/s -> m/s]\n",
+    "vel_z = dumpData[\"vz\"]*1e3     # z velocity vectors       [km/s -> m/s]\n",
+    "velocity = np.array((vel_x, vel_y, vel_z)).T\n",
     "velocity = velocity/constants.c.si.value # velocity vectors        [m/s  -> 1/c]\n",
     "rho      = dumpData[\"rho\"]               # density                 [g/cm^3]\n",
     "u        = dumpData[\"u\"]                 # internal energy density [erg/g]\n",
-    "tmp      = dumpData[\"Tgas\"]              # temperature             [K]\n",
+    "tmp      = dumpData[\"temp\"]              # temperature             [K]\n",
     "tmp[tmp<2.725] = 2.725                   # Cut-off temperatures below 2.725 K\n",
     "\n",
     "# Extract the number of points\n",

docs/src/1_examples/1_post-processing/3_create_Phantom_3D_column.ipynb

@@ -182,20 +182,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Loading the data\n",
     "setupData = plons.LoadSetup(wdir, \"wind\")\n",
     "dumpData  = plons.LoadFullDump(dump_file, setupData)\n",
     "\n",
-    "position = dumpData[\"position\"]*1e-2      # position vectors       [cm   -> m]\n",
-    "velocity = dumpData[\"velocity\"]*1e3      # velocity vectors        [km/s -> m/s]\n",
+    "pos_x = dumpData[\"x\"]*1e-2      # x position vectors       [cm   -> m]\n",
+    "pos_y = dumpData[\"y\"]*1e-2      # y position vectors       [cm   -> m]\n",
+    "pos_z = dumpData[\"z\"]*1e-2      # z position vectors       [cm   -> m]\n",
+    "position = np.array((pos_x, pos_y, pos_z)).T\n",
+    "vel_x = dumpData[\"vx\"]*1e3     # x velocity vectors       [km/s -> m/s]\n",
+    "vel_y = dumpData[\"vy\"]*1e3     # y velocity vectors       [km/s -> m/s]\n",
+    "vel_z = dumpData[\"vz\"]*1e3     # z velocity vectors       [km/s -> m/s]\n",
+    "velocity = np.array((vel_x, vel_y, vel_z)).T\n",
     "velocity = velocity/constants.c.si.value # velocity vectors        [m/s  -> 1/c]\n",
     "rho      = dumpData[\"rho\"]               # density                 [g/cm^3]\n",
     "u        = dumpData[\"u\"]                 # internal energy density [erg/g]\n",
-    "tmp      = dumpData[\"Tgas\"]              # temperature             [K]\n",
+    "tmp      = dumpData[\"temp\"]              # temperature             [K]\n",
     "tmp[tmp<2.725] = 2.725                   # Cut-off temperatures below 2.725 K\n",
     "\n",
     "# Extract the number of points\n",

tests/benchmarks/analytic/continuum_implementation.py

@@ -134,7 +134,7 @@ def evaluate_dust_opacity(frequency, velocity):
 
     #compute optical depth
     chi_shifted = evaluate_dust_opacity(dust_frequencies, np.array(model.geometry.points.velocity)[:,0])
-    tau_ref = np.trapz(chi_shifted, x=np.array(model.geometry.points.position)[:,0], axis=0)
+    tau_ref = np.trapezoid(chi_shifted, x=np.array(model.geometry.points.position)[:,0], axis=0)
     #TODO: fix the calculation of the reference intensity; currently it is wrong for any model with non-zero velocity field due to not taking into account the doppler shifts properly
     #test attempt below
     # def evaluate_source_function(frequency, velocity):

tests/benchmarks/numeric/import_phantom_3D_model.py

@@ -50,12 +50,18 @@ def import_phantom():
     setupData = plons.LoadSetup(datadir, "wind")
     dumpData  = plons.LoadFullDump(dump_file, setupData)
 
-    position = dumpData["position"]*1e-2      # position vectors       [cm   -> m]
-    velocity = dumpData["velocity"]*1e3      # velocity vectors        [km/s -> m/s]
+    pos_x = dumpData["x"]*1e-2      # x position vectors       [cm   -> m]
+    pos_y = dumpData["y"]*1e-2      # y position vectors       [cm   -> m]
+    pos_z = dumpData["z"]*1e-2      # z position vectors       [cm   -> m]
+    position = np.array((pos_x, pos_y, pos_z)).T
+    vel_x = dumpData["vx"]*1e3     # x velocity vectors       [km/s -> m/s]
+    vel_y = dumpData["vy"]*1e3     # y velocity vectors       [km/s -> m/s]
+    vel_z = dumpData["vz"]*1e3     # z velocity vectors       [km/s -> m/s]
+    velocity = np.array((vel_x, vel_y, vel_z)).T
     velocity = velocity/constants.c.si.value # velocity vectors        [m/s  -> 1/c]
     rho      = dumpData["rho"]               # density                 [g/cm^3]
     u        = dumpData["u"]                 # internal energy density [erg/g]
-    tmp      = dumpData["Tgas"]              # temperature             [K]
+    tmp      = dumpData["temp"]              # temperature             [K]
     tmp[tmp<2.725] = 2.725                   # Cut-off temperatures below 2.725 K
 
     # Extract the number of points