add jq cookbook (#1488)

* add jq code blocks

* use tutorial data

* news

Author: atravitz

docs/cookbook/index.rst

@@ -153,6 +153,7 @@ List of Cookbooks
 
     loading_molecules
     dumping_transformation
+    jq_inspection
     choose_protocol
     generate_ligand_network
     rfe_alchemical_planners

docs/cookbook/jq_inspection.rst

@@ -0,0 +1,61 @@
+.. _jq_inspection:
+
+Using ``jq`` to inspect OpenFE JSONs
+==============================================
+Sometimes you may want to get a sense of the contents of JSON files, but the files are too unwieldy to inspect one-by-one in a code editor.
+
+`jq <https://github.com/jqlang/jq>`_ is a helpful command-line tool that we recommend for for quickly inspecting JSON files.
+
+Below is a common use-case to get you started, but you can do much more by checking out the `jq manual <https://jqlang.org/manual/>`_.
+
+To view all the top-level JSON keys, use ``jq "keys" filename.json``, for example with a results JSON from the tutorial:
+
+.. code:: bash
+
+    $ jq "keys" rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json
+    [
+    "estimate",
+    "protocol_result",
+    "uncertainty",
+    "unit_results"
+    ]
+
+.. note::
+
+    You can use ``"keys[]"`` instead of ``"keys"`` for a cleaner output.
+
+Now that we know ``estimate`` is at the top-level of the JSON, we can use the following command to see all the values for the ``estimate`` key:
+
+.. code:: bash
+
+    $ jq ".estimate" rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json
+    {
+    "magnitude": 23.347074789078682,
+    "unit": "kilocalorie / mole",
+    ":is_custom:": true,
+    "pint_unit_registry": "openff_units"
+    }
+
+This can be very helpful for quickly checking results for many files, for example:
+
+.. code:: bash
+
+    $ jq ".estimate.magnitude" rbfe*.json
+    -14.925911852820793
+    -40.72063957254803
+    -27.76541486479537
+    -16.023754604070007
+    -57.38608716292447
+    -15.748326155729705
+    -39.933880531487326
+    -27.780933075807425
+    -16.76023951588401
+    -58.36294851896545
+    -19.038006312251575
+    -20.26856586311034
+    17.338257573349775
+    15.775784163095102
+    23.134622420900932
+    17.071712542470248
+    15.873122071409249
+    23.347074789078682

news/add_jq_docs.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Added a cookbook for using ``jq`` to inspect JSON files.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>