Improvements for the update_reference section [docs] (#1008)

* Initial commit

* Minor changes

* Last changes

docs/development/git_workflow.rst

@@ -476,6 +476,8 @@ If you forgot to make a backup branch::
    git reset --hard cool-feature@{2}
 
 
+.. _reviewing-and-helping-with-pr:
+
 Reviewing and helping others with Pull Requests
 -----------------------------------------------
 

docs/development/update_refdata.rst

@@ -2,71 +2,83 @@
 Procedure to update the reference data
 **************************************
 
-We assume that you have added the necessary changes to TARDIS and have a
-PR open.
+We assume that you have added the necessary changes to TARDIS and have an open pull request.
 
-#. Fork the tardis ref-data repository like described in :ref:`development-workflow`.
+#. Fork the ``tardis-refdata`` repository like described in :ref:`development-workflow`.
 
-#. Clone tardis-refdata. Then make a new branch named the same as your new tardis feature branch. Make sure to set the upstream of the repository to `https://github.com/tardis-sn/tardis-refdata.git`
-    * You can check that you have the right upstream set using:
-    .. code-block:: None
-
-        git checkout upstream/pr/11
+#. Clone ``tardis-refdata`` to your computer. Then make a new branch named the same as your new TARDIS feature branch. Make sure to have correctly set up the ``upstream`` remote as explained in :ref:`reviewing-and-helping-with-pr`. 
 
-#. Make sure to have sure to have git-lfs installed. If not already done, the process can be seen here: :ref:`git_lfs_instructions`
+#. Activate your ``tardis`` conda environment.
 
-#. Open tardis-refdata directory. Fetch from upstream and then use git-lfs to pull ref-data files from github using:
     .. code-block:: None
+    
+        conda activate tardis
+
+#. Navigate to your ``tardis-refdata`` directory and type:
 
+    .. code-block:: None
+    
+        git lfs install
         git lfs fetch upstream
         git lfs pull
 
-#. Open into tardis directory. Generate new reference data (in the correct branch) offline using:
+#. Go to your ``tardis`` directory. Make sure you are working on the correct branch and generate new reference data using:
 
     .. code-block:: None
 
-        python setup.py test --args="--tardis-refdata=<path to refdata repo/with the right branch> --generate-reference"
+        python setup.py test --args="--tardis-refdata=<path to refdata repo on the right branch> --generate-reference"
 
-#. Rerun the tests to make sure it does not fail using:
+#. Re-run the tests to make sure it does not fail using:
 
     .. code-block:: None
 
-        python setup.py test --args="--tardis-refdata=<path to refdata repo/with the right branch>"
+        python setup.py test --args="--tardis-refdata=<path to refdata repo on the right branch>"
 
-#. Open and run the refdata comparer notebook provided in TARDIS-refdata to check if there are any unexpected changes in the updated reference data and the previous reference data.
+#. Go back to your ``tardis-refdata`` folder, and run a Jupyter Notebook session inside the ``notebook`` folder. 
 
-#. Switch to tardis-refdata. Commit the changed ref-data and open a PR on tardis-refdata
+#. Open the ``ref_data_compare.ipynb`` file notebook and look for the cell with the following code:
 
-#. Switch back to the TARDIS directory. Open `.travis.yml`
+    .. code-block:: None
 
-#. Change the following lines
+        comparer = ReferenceComparer(ref2_hash='upstream/pr/24')
+        
+   Replace '24' for the number of the last merged pull request showed `here <https://github.com/tardis-sn/tardis-refdata/pulls?utf8=%E2%9C%93&q=is%3Apr+is%3Aclosed>`_.
+
+#. Run all cells and check if there are any unexpected changes in the updated reference data respect the previous one.
+
+#. Commit the changes made to the reference data and open a PR on ``tardis-refdata``.
+
+#. Switch back to the ``tardis`` directory. Open the ``.travis.yml`` file and change the following lines:
 
     .. code-block:: None
 
-        - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin pull/<your TARDIS-refdata PR number; not the TARDIS PR number>/head:<some descriptive name>; fi
+        - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin pull/<your tardis-refdata PR number; not the TARDIS PR number>/head:<some descriptive name>; fi
         - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout <some descriptive name>; fi```
 
-#. Commit the `.travis.yml` to your Pull request
-#. Make sure that your TARDIS PR now passes on TRAVIS.
-#. Then merge the PR on tardis-refdata.
-#. Then change `.travis.yml` to
+#. Commit the ``.travis.yml`` to your pull request.
+
+#. Make sure that your TARDIS pull request now passes all tests on Travis-CI.
+
+#. Ask for review for your PR on ``tardis-refdata`` and wait for merge.
+
+#. Then change the ``.travis.yml`` in ``tardis`` directory to:
 
     .. code-block:: None
 
         - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi
         - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout origin/master; fi```
-#. Then make sure that your TARDIS PR passes again.
-#. Then merge your PR to TARDIS master
-#. Congratulations - you updated TARDIS to be better. Have a beer and steak (or Tofu if you are vegetarian/vegan)
+
+#. Ensure TARDIS pull request passes Travis-CI again and ping someone to merge your PR to the TARDIS master branch.
+
+
+Congratulations! You have updated TARDIS to be better. Have a beer and steak (or Tofu if you are vegetarian/vegan)
+
 
 Troubleshooting
 ###############
 
 * Unable to generate reference data
-    * If generating fails due to an inability to open chianti_He.h5, make sure that you have installed git-lfs and have pulled the files from github (See steps 3 and 4).
-
-* Error in running `comparer = ReferenceComparer(ref2_hash='upstream/pr/11')` on the comparer notebook: `No such file or directory: '.../unit_test_data.h5'`
-    * If notebook file is unable to find the file /unit_test_data.h5, make sure you have correctly set your upstream. To check this, use:
-
+    * If generating fails due to an inability to open ``chianti_He.h5``, make sure that you have activated your `tardis` conda environment, and ``git-lfs`` is installed. Fetch and pull the files from GitHub as explained in step 4.
 
-    * If this fails, make sure that your upstream is set correctly to `https://github.com/tardis-sn/tardis-refdata.git` (See step 2).
+* Error when running ``comparer = ReferenceComparer(ref2_hash='upstream/pr/XX')`` on the comparer notebook: ``No such file or directory: '.../unit_test_data.h5'``
+    * If notebook file is unable to find the file ``unit_test_data.h5``, make sure you have correctly set your upstream as explained in :ref:`reviewing-and-helping-with-pr`.