uncomment rendering, etc (#36)

* uncomment rendering, etc * do the broken ones first * add --pre for astroquery req * pip install reqs in all notebooks * remove ids * rm id * use issue 874 hack to fix SpectralCubeReprojectExample * use issue 874 hack to fix SpectralCubeReprojectMaskExample * add astroquery version checks * install --pre astroquery in build.yml * expand installation a bit * fix flagrant typo * fix another flagrant typo
radio-astro-tools · Jun 1, 2024 · 432341e · 432341e
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -29,18 +29,19 @@ jobs:
           echo "datapath=['${GITHUB_WORKSPACE}/.casa/']; measurespath=datapath[0]; measures_auto_update=True; data_auto_update=True" > $GITHUB_WORKSPACE/config.py
           export CASASITECONFIG=$GITHUB_WORKSPACE/config.py
           pip install -r requirements.txt
+          pip install -U --pre astroquery # required to be separate; requirements.txt does not respect --pre
 
       - name: Export notebooks
         run: |
+            CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+            CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectMaskExample_v4p1.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert spectral_fitting/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert casa_to_spectralcube_guide/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert masking_and_moments/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert parallel_spectral_fitting/*.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert DameCube.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert PVDiagramPlotting.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert DiskPVExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
-            # JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
-            # JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectMaskExample_v4p1.ipynb.ipynb --execute --to html --ExecutePreprocessor.kerne]l_name=python
 
       - name: Prepare public folder
         id: folder

diff --git a/.github/workflows/build_and_deploy_site.yml b/.github/workflows/build_and_deploy_site.yml
@@ -28,6 +28,7 @@ jobs:
           echo "datapath=['${GITHUB_WORKSPACE}/.casa/']; measurespath=datapath[0]; measures_auto_update=True; data_auto_update=True" > $GITHUB_WORKSPACE/config.py
           export CASASITECONFIG=$GITHUB_WORKSPACE/config.py
           pip install -r requirements.txt
+          pip install -U --pre astroquery # required to be separate; requirements.txt does not respect --pre
 
       - name: Export notebooks
         run: |
@@ -38,8 +39,8 @@ jobs:
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert DameCube.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert PVDiagramPlotting.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
             CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert DiskPVExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
-            # JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
-            # JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectMaskExample_v4p1.ipynb.ipynb --execute --to html --ExecutePreprocessor.kerne]l_name=python
+            CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectExample.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
+            CASASITECONFIG=$GITHUB_WORKSPACE/config.py JUPYTER_CONFIG_DIR=./.jupyter jupyter nbconvert SpectralCubeReprojectMaskExample_v4p1.ipynb --execute --to html --ExecutePreprocessor.kernel_name=python
 
       - name: Prepare public folder
         id: folder

diff --git a/DameCube.ipynb b/DameCube.ipynb
@@ -14,6 +14,16 @@
     "The key result is in [Dame & Thaddeus (2008)](https://ui.adsabs.harvard.edu/abs/2008ApJ...683L.143D/abstract)."
    ]
   },
+  {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+      "%pip install -r https://github.com/radio-astro-tools/tutorials/raw/master/requirements.txt\n",
+      "%pip install --pre -U astroquery"
+      ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/DiskPVExample.ipynb b/DiskPVExample.ipynb
@@ -33,6 +33,16 @@
     "!pip install --upgrade spectral-cube git+https://github.com/radio-astro-tools/pvextractor.git@61e118aaf28e2d746deeccf06af8fdd7f405b815 radio-beam regions reproject"
    ]
   },
+  {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+      "%pip install -r https://github.com/radio-astro-tools/tutorials/raw/master/requirements.txt\n",
+      "%pip install --pre -U astroquery"
+      ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/PVDiagramPlotting.ipynb b/PVDiagramPlotting.ipynb
@@ -32,6 +32,16 @@
     "We import tools from several packages up front:"
    ]
   },
+  {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+      "%pip install -r https://github.com/radio-astro-tools/tutorials/raw/master/requirements.txt\n",
+      "%pip install --pre -U astroquery"
+      ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/SpectralCubeReprojectExample.ipynb b/SpectralCubeReprojectExample.ipynb
@@ -50,6 +50,17 @@
     "(you might not have to do this step, since you may already have data)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2180fbc2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+   "%pip install -r https://github.com/radio-astro-tools/tutorials/raw/master/requirements.txt\n",
+   "%pip install --pre -U astroquery"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -153,14 +164,26 @@
     "We use the `find_lines` tool to query [splatalogue](https://splatalogue.online/) with [astroquery](https://astroquery.readthedocs.io/en/latest/splatalogue/splatalogue.html) over the spectral range covered by the cube.  It returns a table of matching lines.  Note that some line names will be repeated because Splatalogue includes several different databases and most chemical species are present in all of these."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b00a5e87-0437-4b3b-83c7-3da7046ba8df",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# DEBUG\n",
+    "import astroquery\n",
+    "print(astroquery.__version__)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "proud-flood",
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube1.find_lines(chemical_name=' H2CS ').show_in_notebook()"
+    "cube1.find_lines(chemical_name=' H2CS ')"
    ]
   },
   {
@@ -170,7 +193,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube2.find_lines(chemical_name='SiO').show_in_notebook()"
+    "cube2.find_lines(chemical_name='SiO')"
    ]
   },
   {
@@ -516,7 +539,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube2vel_reproj = cube2vel_spatialspectralsmooth.reproject(cube1vel.header)\n",
+    "# these next two lines are a hack to prevent the WCS from trying to convert to frequency\n",
+    "tgt_header = cube1vel.header\n",
+    "tgt_header['RESTFRQ'] = cube2vel_spatialspectralsmooth.header['RESTFRQ']\n",
+    "\n",
+    "cube2vel_reproj = cube2vel_spatialspectralsmooth.reproject(tgt_header)\n",
     "cube2vel_reproj"
    ]
   },
@@ -607,7 +634,7 @@
     "        cube2daskvel_spectralresample = cube2daskvel_smooth.spectral_interpolate(cube1vel.spectral_axis,\n",
     "                                                                             suppress_smooth_warning=True)\n",
     "        cube2daskvel_spatialspectralsmooth = cube2daskvel_spectralresample.convolve_to(common_beam)\n",
-    "        cube2daskvel_reproj = cube2daskvel_spatialspectralsmooth.reproject(cube1vel.header)\n",
+    "        cube2daskvel_reproj = cube2daskvel_spatialspectralsmooth.reproject(tgt_header)\n",
     "cube2daskvel_reproj"
    ]
   },
@@ -636,7 +663,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/SpectralCubeReprojectMaskExample_v3.ipynb b/SpectralCubeReprojectMaskExample_v3.ipynb
@@ -37,6 +37,16 @@
     "(you might not have to do this step, since you may already have data)"
    ]
   },
+  {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+      "%pip install -r https://github.com/radio-astro-tools/tutorials/raw/master/requirements.txt\n",
+      "%pip install --pre -U astroquery"
+      ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/SpectralCubeReprojectMaskExample_v4p1.ipynb b/SpectralCubeReprojectMaskExample_v4p1.ipynb
@@ -42,6 +42,17 @@
     "## Step 0: Some imports and version checks"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "303c0625",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+   "%pip install -r https://github.com/radio-astro-tools/tutorials/raw/master/requirements.txt\n",
+   "%pip install --pre -U astroquery"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -148,14 +159,26 @@
     "cube2"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ffa01793-a147-4c15-8d2c-421c141cf624",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# DEBUG\n",
+    "import astroquery\n",
+    "print(astroquery.__version__)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "765e0051",
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube1.find_lines(chemical_name=' H2CS ').show_in_notebook()"
+    "cube1.find_lines(chemical_name=' H2CS ')"
    ]
   },
   {
@@ -165,7 +188,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube2.find_lines(chemical_name='SiO').show_in_notebook()"
+    "cube2.find_lines(chemical_name='SiO')"
    ]
   },
   {
@@ -489,7 +512,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube2vel_reproj = cube2vel_spatialspectralsmooth.reproject(cube1vel_cutout.header)\n",
+    "# these next two lines are a hack to prevent the WCS from trying to convert to frequency\n",
+    "tgt_header = cube1vel_cutout.header\n",
+    "tgt_header['RESTFRQ'] = cube2vel_spatialspectralsmooth.header['RESTFRQ']\n",
+    "\n",
+    "cube2vel_reproj = cube2vel_spatialspectralsmooth.reproject(tgt_header)\n",
     "cube2vel_reproj "
    ]
   },
@@ -1149,7 +1176,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/SpectralCube_Examples.ipynb b/SpectralCube_Examples.ipynb
@@ -11,6 +11,16 @@
     "This is a quick demo of how you can work with Spectral Cube objects"
    ]
   },
+  {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+      "%pip install -r https://github.com/radio-astro-tools/tutorials/raw/master/requirements.txt\n",
+      "%pip install --pre -U astroquery"
+      ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,