Prepare for 0.5.6 release

.github/workflows/tests.yml

@@ -32,6 +32,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          # Install this version of ScopeSim. Otherwise the PyPI version of
+          # ScopeSim will be installed when the github_actions requirements
+          # are installed, because ScopeSim is a dependency of
+          # ScopeSim_Templates.
+          pip install .
           pip install -r requirements.github_actions.txt
       - name: Run Pytest
         run: pytest
+      - name: Run notebooks
+        run: ./runnotebooks.sh

MANIFEST.in

@@ -2,6 +2,7 @@ include README.md
 include LICENCE
 include scopesim/defaults.yaml
 include scopesim/vega.fits
+recursive-include scopesim/data *
 
 prune *OLD_*
 prune *docs_to_be_sorted*

docs/source/5_liners/source_point_source_arrays.ipynb

@@ -21,7 +21,7 @@
     "import astropy.table as table\n",
     "from astropy import units as u\n",
     "\n",
-    "import scopesim as sim\n",
+    "import scopesim\n",
     "\n",
     "# how many stars\n",
     "n = 200\n",
@@ -35,7 +35,7 @@
     "weight = 10**(-0.4*np.linspace(10, 20, n))\n",
     "\n",
     "# Note: The Pyckles and SpeXtra libraries contain many more stellar and galactic spectra\n",
-    "vega = sim.source.source_templates.vega_spectrum(mag=20)"
+    "vega = scopesim.source.source_templates.vega_spectrum(mag=20)"
    ]
   },
   {
@@ -103,7 +103,7 @@
     }
    ],
    "source": [
-    "point_source = sim.Source(spectra=[vega], x=x, y=y, ref=ref, weight=weight)\n",
+    "point_source = scopesim.Source(spectra=[vega], x=x, y=y, ref=ref, weight=weight)\n",
     "\n",
     "point_source.plot()"
    ]

docs/source/examples/1_scopesim_intro.ipynb

@@ -167,7 +167,7 @@
    ],
    "source": [
     "plt.figure(figsize=(10,8))\n",
-    "plt.imshow(hdus[0][1].data, norm=LogNorm(), vmax=3E4, vmin=3E3, cmap=\"hot\")\n",
+    "plt.imshow(hdus[0][1].data, norm=LogNorm(vmax=3E4, vmin=3E3), cmap=\"hot\")\n",
     "plt.colorbar()"
    ]
   },

docs/source/examples/2_multiple_telescopes.ipynb

@@ -212,7 +212,7 @@
     "plt.title(\"1.5m LFOA\")\n",
     "\n",
     "plt.subplot(122)\n",
-    "plt.imshow(hdus_micado[0][1].data, norm=LogNorm(), origin=\"lower\", vmax=1E6, vmin=1e5)\n",
+    "plt.imshow(hdus_micado[0][1].data, norm=LogNorm(vmax=1E6, vmin=1e5), origin=\"lower\")\n",
     "plt.colorbar()\n",
     "plt.title(\"39m ELT\")"
    ]

docs/source/getting_started.ipynb

@@ -65,7 +65,7 @@
     "hdulist = opt.readout()[0]\n",
     "\n",
     "plt.figure(figsize=(10,8))\n",
-    "plt.imshow(hdulist[1].data, norm=LogNorm(), vmin=1)\n",
+    "plt.imshow(hdulist[1].data, norm=LogNorm(vmin=1))\n",
     "plt.colorbar()"
    ]
   },

requirements.github_actions.txt

@@ -5,6 +5,7 @@ scipy
 astropy
 matplotlib
 jupyter
+jupytext
 
 docutils
 requests

runnotebooks.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+# https://github.com/koalaman/shellcheck/wiki/SC2044
+find . -iname "*.ipynb" -print0 | while IFS= read -r -d '' fnnotebook
+do
+  echo "Testing ${fnnotebook}"
+  fnpy="${fnnotebook%.ipynb}.py"
+
+  # Convert .ipynb file to .py.
+  jupytext --to py "${fnnotebook}"
+
+  # Run the python script and quit on first error.
+  python "${fnpy}" || exit 1
+
+  # Delete generated files if --delete is specified.
+  # By default do not delete any files.
+  if [ "x$1" = "x--delete" ]
+  then
+    rm "${fnpy}"
+  fi
+
+done