Merge pull request #401 from gabridele/local_bids_docs

Updated docs explaining the installation for internetless use cases

docs/conf.py

@@ -56,6 +56,7 @@
     "sphinx_gallery.load_style",
     "sphinxarg.ext",  # argparse extension
     "sphinxcontrib.bibtex",  # bibtex-based bibliographies
+    "sphinx_design",   # for adding in-line badges etc
 ]
 
 # Mock modules in autodoc:

docs/example.rst

@@ -174,9 +174,6 @@ Since we ran ``cubids add-nifti-info`` with the ``--use-datalad`` flag set,
 BIDS validation
 ---------------
 
-The next step in the ``CuBIDS`` workflow is to run BIDS validation
-to detect potential curation errors using ``cubids validate``.
-
 .. code-block:: console
 
     $ cubids validate BIDS_Dataset_DataLad v0 --sequential
@@ -187,6 +184,16 @@ to detect potential curation errors using ``cubids validate``.
     This can be helpful for identifying heterogeneous elements,
     but can be slowed down by extremely large datasets.
 
+.. warning::
+    For internetless use cases, please see dedicated section of the `Installation page 
+    <https://cubids.readthedocs.io/en/latest/installation.html>`_ on how to download a local version 
+    of the validator.
+
+    After that, you will need to add ``--local-validator`` option to the command string above.
+
+The next step in the ``CuBIDS`` workflow is to run BIDS validation
+to detect potential curation errors using ``cubids validate``.
+
 This command produces the following tsv:
 
 .. csv-table:: v0_validation.tsv

docs/installation.rst

@@ -54,6 +54,26 @@ We can accomplish this using the following command:
 The new schema-based ``bids-validator`` doesn't need to be installed 
 and will be implemented automatically when `cubids validate` is called
 
+.. dropdown:: If there is no Internet connection on compute nodes
+
+    If your HPC doesn't allow internet access on its compute nodes, it won't be able to run the online 
+    version of the BIDS validator. In that scenario, you need to install the BIDS validator on your HPC 
+    and then point to the installed version in your cubids validate calls. 
+    To do that, you should run one of these commands below, after installing deno, that downloads the latest version 
+    of the bids-validator in your virtual environment either by installing a lightscript version 
+    (into ``$HOME/.deno/bin``) or by compiling, respectively:
+
+    ..  code-block:: console
+
+        $ deno install -ERN -g -n bids-validator jsr:@bids/validator
+    
+    or:
+
+    ..  code-block:: console
+
+        $ deno compile -ERN -o bids-validator jsr:@bids/validator
+
+    For more information, you can read: https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html
 
 We also recommend using ``CuBIDS`` with the optional ``DataLad`` version control capabilities.
 We use ``DataLad`` throughout our walkthrough of the CuBIDS Workflow on

pyproject.toml

@@ -51,6 +51,7 @@ doc = [
     "sphinx_markdown_tables",
     "sphinx_rtd_theme",
     "sphinxcontrib-bibtex",
+    "sphinx_design",
 ]
 tests = [
     "codespell",