Include code-block directive

tutorials/conf.py

@@ -19,7 +19,7 @@
 
 project = 'pyemir-tutorials'
 copyright = '2018-2024, Universidad Complutense de Madrid'
-author = 'Nicolás Cardiel'
+author = 'Nicolás Cardiel, Sergio Pascual'
 
 # The full version, including alpha/beta/rc tags
 release = 'v1.0'
@@ -53,17 +53,18 @@
 #
 #html_theme = 'alabaster'
 html_theme = 'sphinx_rtd_theme'
-#html_logo = 'logo.png'
+html_logo = '_static/logo.png'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
+# This doesn't work. Use html_logo above (NCL, 20241015)
 html_theme_options = {
-    'logo': 'logo.png',
-    'show_related': True,
-    'show_relbar_bottom': True,
-    'show_relbar_top': False
+    #'logo': 'logo.png',
+    #'show_related': True,
+    #'show_relbar_bottom': True,
+    #'show_relbar_top': False
 }
 

tutorials/preliminaries/preliminaries.rst

@@ -20,7 +20,7 @@ Running PyEmir recipes from Numina
 The ``numina`` script is the interface with GTC pipelines. In order to execute
 PyEmir recipes you should use execute something like:
 
-::
+.. code-block:: console
 
    (emir) $ numina run <observation_result_file.yaml> -r <requirements_file.yaml>
 
@@ -48,7 +48,7 @@ Download the following file: `pyemir_initial_tree_v2a.tgz
 If you find any trouble trying to download the previous file, try with the
 following command line:
 
-::
+.. code-block:: console
 
    (emir) $ curl -O https://guaix.fis.ucm.es/data/pyemir/pyemir_initial_tree_v2a.tgz
 
@@ -65,7 +65,7 @@ following command line:
 It is advisable to decompress the previous file in a pristine directory where
 you can comfortably start the reduction of your data:
 
-::
+.. code-block:: console
 
    (emir) $ mkdir newdir
    (emir) $ cd newdir
@@ -138,7 +138,7 @@ Installing ds9
 Probably you already have ds9 installed in your system. If this is not the
 case, you can use conda to do it!
 
-::
+.. code-block:: console
 
    (emir) $ conda install ds9
 

tutorials/tutorial_flat/index.rst

@@ -52,7 +52,7 @@ flatfield in the initial basic reduction of the original images is not
 essential. The user can easily check this by setting ``MasterIntensityFlat`` to
 ``master_flat_ones.fits`` in the ``control.yaml`` file, i.e.:
 
-::
+.. code-block:: yaml
 
     - {id: 4, type: 'MasterIntensityFlat', tags: {}, content: 'master_flat_ones.fits'}
 
@@ -124,7 +124,7 @@ containing the basic PyEmir calibration files (see  :ref:`initial_file_tree`).
 
 Decompress there the previously mentioned tgz file:
 
-::
+.. code-block:: console
 
    (emir) $ tar zxvf pyemir_flatpix2pix_tutorial_v1.tgz
    ...
@@ -135,7 +135,7 @@ This action should have populated the file tree with the
 20 tungsten FITS images (placed wihtin the ``data``
 subdirectory) and some additional auxiliary files:
 
-::
+.. code-block:: console
 
    (emir) $ tree
    .
@@ -175,7 +175,7 @@ subdirectory) and some additional auxiliary files:
 You can easily examine the header of the scientific FITS images using the
 astropy utility ``fitsheader``:
 
-::
+.. code-block:: console
 
    (emir) $ fitsheader data/0002069*.fits -k object -k lampincd -k lampintn -f
                        filename                         OBJECT    LAMPINCD     LAMPINTN    
@@ -213,7 +213,7 @@ and the last 10 images to lamp OFF.
 
 Let's have a look to the CSU configuration:
 
-::
+.. code-block:: console
 
    (emir) $ pyemir-display_slitlet_arrangement data/0002069432-20190519-EMIR-STARE_SPECTRA.fits \
      --longslits --n_clusters 2
@@ -249,7 +249,7 @@ We can also display the first image with lamp ON and the first with lamp OFF:
 
 An estimate of the integer vertical offset (in pixels) can be obtained using:
 
-::
+.. code-block:: console
 
    $ pyemir-overplot_boundary_model data/0002069432-20190519-EMIR-STARE_SPECTRA.fits \
      --rect_wpoly_MOSlibrary data/rect_wpoly_MOSlibrary_grism_H_filter_H.json
@@ -314,7 +314,7 @@ properly for all combinations of grism+filter.
 
 You can now execute the reduction recipe:
 
-::
+.. code-block:: console
 
    (emir) $ numina run flatpix2pix.yaml --link-files -r control.yaml
    ...
@@ -325,7 +325,7 @@ The resulting pixel-to-pixel flatfield can be found in the corresponding
 
 .. numina-ximshow obsid_flat_results/reduced_flatpix2pix.fits --geometry 0,0,650,850
 
-::
+.. code-block:: console
 
    (emir) $ numina-ximshow obsid_flat_results/reduced_flatpix2pix.fits
 

tutorials/tutorial_imaging/preliminary_combination.rst

@@ -53,7 +53,7 @@ containing the basic PyEmir calibration files (see  :ref:`initial_file_tree`).
 
 Decompress there the previously mentioned tgz file:
 
-::
+.. code-block:: console
 
    (emir) $ tar zxvf pyemir_imaging_tutorial_v4.tgz
    ...
@@ -64,7 +64,7 @@ This action should have populated the file tree with the
 14 scientific raw FITS (placed wihtin the ``data``
 subdirectory) and some additional auxiliary files:
 
-::
+.. code-block:: console
 
    (emir) $ tree
    .
@@ -105,7 +105,7 @@ subdirectory) and some additional auxiliary files:
 You can easily examine the header of the scientific FITS images using the
 astropy utility ``fitsheader``:
 
-::
+.. code-block:: console
 
    (emir) $ fitsheader data/0001877* \
      -k nobsblck -k obsblock -k nimgobbl -k imgobbl \
@@ -142,7 +142,7 @@ flatfielding, and image reprojection.
    Remember that the ``numina`` script is the interface with GTC pipelines. 
    In order to execute PyEmir recipes you should type something like:
 
-   ::
+   .. code-block:: console
    
       (emir) $ numina run <observation_result_file.yaml> -r <requirements_file.yaml>
 
@@ -235,7 +235,7 @@ highlighting the first block (first eight lines):
    In particular, the file used in this example can be easily created using a
    few simple commands:
 
-   ::
+   .. code-block:: console
 
       (emir) $ cd data/
       (emir) $ ls 0001877*fits > list_images.txt
@@ -282,7 +282,7 @@ You are ready to execute the reduction recipe indicated in the file
 ``dithered_ini.yaml`` (in this case the reduccion recipe named
 ``STARE_IMAGE``):
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_ini.yaml -r control.yaml
    ...
@@ -291,7 +291,7 @@ You are ready to execute the reduction recipe indicated in the file
 After the execution of the previous command line, two subdirectories for each
 block should have appeared:
 
-::
+.. code-block:: console
 
    (emir) $ ls
    control.yaml              obsid_0001877565_results/ obsid_0001877601_work/
@@ -316,7 +316,7 @@ of a particular block of the observation result file are copied into the
 
 In particular, for the first block:
 
-::
+.. code-block:: console
 
    (emir) $ tree obsid_0001877553_work/
    obsid_0001877553_work/
@@ -331,7 +331,7 @@ links (instead of actual copies of the original raw files) must be placed in
 the* ``work`` *subdirectory.* This behaviour is set using the parameter
 ``--link-files``:
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_ini.yaml --link-files -r control.yaml
    ...
@@ -351,7 +351,7 @@ the* ``work`` *subdirectory.* This behaviour is set using the parameter
 These subdirectories store the result of the execution of the reduction
 recipes. In particular, for the first block:
 
-:: 
+.. code-block:: console
 
    $ tree obsid_0001877553_results/
    obsid_0001877553_results/
@@ -433,7 +433,7 @@ a combined image.
    The file ``dithered_v0.yaml`` can also be automatically generated using
    the same script previously mentioned in step 1:
 
-   ::
+   .. code-block:: console
 
       (emir) $ pyemir-generate_yaml_for_dithered_image \
         data/list_images.txt --step 1 --repeat 1 \
@@ -451,15 +451,15 @@ a combined image.
 
 The combination of the images is finally performed using numina:
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_v0.yaml --link-files -r control.yaml
 
 The previous execution also generates two auxiliary subdirectories ``work`` and
 ``results``. The resulting combined image can be found in
 ``obsid_combined_v0_result/reduced_image.fits``:
 
-::
+.. code-block:: console
 
    (emir) $ tree obsid_combined_v0_results/
    obsid_combined_v0_results/
@@ -471,7 +471,7 @@ The previous execution also generates two auxiliary subdirectories ``work`` and
 You can display the image using ``ds9``, using ``numina-ximshow`` (the display
 tool shipped with numina based on matplotlib), or with any other tool:
 
-::
+.. code-block:: console
 
    (emir) $ numina-ximshow obsid_combined_v0_results/reduced_image.fits
 

tutorials/tutorial_imaging/refined_combination.rst

@@ -67,7 +67,7 @@ line 127 has also been changed in order to avoid overwriting the ``work`` and
 The refined version of the combined image is then obtained by executing numina
 again with this new observation result file:
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_v1.yaml --link-files -r control.yaml
 
@@ -139,7 +139,7 @@ number 148; note also the ``id`` change in line 127):
 
 The contents of the ASCII file with the measured offsets is the following:
 
-::
+.. code-block:: console
 
    (emir) $ cat data/user_offsets.txt
    822 907
@@ -159,7 +159,7 @@ The contents of the ASCII file with the measured offsets is the following:
 
 Execute numina to obtain the new version of the combined image:
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_v2.yaml --link-files -r control.yaml
 
@@ -225,7 +225,7 @@ In this case we have modified the ``id`` (line 127) and set
 
 Execute numina again with this new observation result file:
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_v3.yaml --link-files -r control.yaml
 
@@ -329,13 +329,13 @@ computed from the WCS information in the image headers).
 
 Execute numina to start the reduction including object masking:
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_v4.yaml --link-files -r control.yaml
 
 It is useful to subtract the new result from the one derived previously:
 
-::
+.. code-block:: console
 
    (emir) $ numina-imath obsid_combined_v1_results/reduced_image.fits - \
       obsid_combined_v4_results/reduced_image.fits difference_v4.fits
@@ -523,7 +523,7 @@ we are using a pattern of 10 x 10 regions in each quadrant. The median value in
 each of these 100 subregions is computed (masking pixels affected by objects)
 and a smooth spline surface is fitted to that collection of points.
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_v5.yaml --link-files -r control.yaml
 
@@ -582,7 +582,7 @@ change in the ``id`` in line 127):
 **by default, which means that the correction described next is not performed
 unless splicitly stated.**
 
-::
+.. code-block:: console
 
    (emir) $ numina run dithered_v6.yaml --link-files -r control.yaml
 
@@ -638,7 +638,7 @@ strategy is followed in order to perform this latter reduction step:
 We can easily compare the new result with the one obtained using
 ``dithered_v5.yaml``. For that purpose is useful to subtract the new result from the one derived previously:
 
-::
+.. code-block:: console
 
    (emir) $ numina-imath obsid_combined_v6_results/reduced_image.fits - \
       obsid_combined_v5_results/reduced_image.fits difference_v6.fits