Repository: templateflow/python-client

Issue:
TemplateFlow should re-index the BIDS layout after update
Currently, when `TEMPLATEFLOW_HOME` has been updated in the same python session, the index of the archive remains out-of-date.

Comments:

Patch:
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 115902f..f9399f7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,7 +45,7 @@ jobs:
             source /tmp/venv/bin/activate
             pip install -U pip
             pip install -r /tmp/src/templateflow/requirements.txt
-            pip install "datalad ~= 0.11.8" doi2bib
+            pip install "datalad ~= 0.11.8" "doi2bib < 0.4"
             pip install "setuptools>=42.0" "setuptools_scm[toml] >= 3.4" twine codecov
 
       - run:
diff --git a/setup.cfg b/setup.cfg
index 16b5cc9..1012368 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,7 +49,7 @@ exclude =
 
 [options.extras_require]
 citations =
-    doi2bib
+    doi2bib < 0.4.0
 datalad =
     datalad ~= 0.12.0
 doc =
diff --git a/templateflow/conf/__init__.py b/templateflow/conf/__init__.py
index f4b387b..9d29cf2 100644
--- a/templateflow/conf/__init__.py
+++ b/templateflow/conf/__init__.py
@@ -45,11 +45,19 @@ please set the TEMPLATEFLOW_HOME environment variable.\
 def update(local=False, overwrite=True, silent=False):
     """Update an existing DataLad or S3 home."""
     if TF_USE_DATALAD and _update_datalad():
-        return True
-
-    from ._s3 import update as _update_s3
+        success = True
+    else:
+        from ._s3 import update as _update_s3
+        success = _update_s3(TF_HOME, local=local, overwrite=overwrite, silent=silent)
 
-    return _update_s3(TF_HOME, local=local, overwrite=overwrite, silent=silent)
+    # update Layout only if necessary
+    if success and TF_LAYOUT is not None:
+        init_layout()
+        # ensure the api uses the updated layout
+        import importlib
+        from .. import api
+        importlib.reload(api)
+    return success
 
 
 def setup_home(force=False):
@@ -76,9 +84,12 @@ def _update_datalad():
 
 
 TF_LAYOUT = None
-try:
+
+
+def init_layout():
     from .bids import Layout
 
+    global TF_LAYOUT
     TF_LAYOUT = Layout(
         TF_HOME,
         validate=False,
@@ -92,5 +103,9 @@ try:
             "scripts",
         ],
     )
+
+
+try:
+    init_layout()
 except ImportError:
     pass
diff --git a/templateflow/conf/_s3.py b/templateflow/conf/_s3.py
index 9e20cbe..4051ce8 100644
--- a/templateflow/conf/_s3.py
+++ b/templateflow/conf/_s3.py
@@ -27,7 +27,7 @@ def _get_skeleton_file():
     import requests
 
     try:
-        r = requests.get(TF_SKEL_URL(release="master", ext="md5", allow_redirects=True))
+        r = requests.get(TF_SKEL_URL(release="master", ext="md5"), allow_redirects=True)
     except requests.exceptions.ConnectionError:
         return
 
@@ -35,7 +35,7 @@ def _get_skeleton_file():
         return
 
     if r.content.decode().split()[0] != TF_SKEL_MD5:
-        r = requests.get(TF_SKEL_URL(release="master", ext="zip", allow_redirects=True))
+        r = requests.get(TF_SKEL_URL(release="master", ext="zip"), allow_redirects=True)
         if r.ok:
             from os import close
 


Test patch:
diff --git a/templateflow/tests/test_conf.py b/templateflow/tests/test_conf.py
new file mode 100644
index 0000000..c2d95f2
--- /dev/null
+++ b/templateflow/tests/test_conf.py
@@ -0,0 +1,27 @@
+from pathlib import Path
+import pytest
+from .. import conf, api
+
+
+@pytest.mark.skipif(conf.TF_USE_DATALAD, reason="S3 only")
+def test_update_s3(tmp_path):
+    conf.TF_HOME = tmp_path / 'templateflow'
+    conf.TF_HOME.mkdir(exist_ok=True)
+
+    # replace TF_SKEL_URL with the path of a legacy skeleton
+    _skel_url = conf._s3.TF_SKEL_URL
+    conf._s3.TF_SKEL_URL = (
+        "https://github.com/templateflow/python-client/raw/0.5.0/"
+        "templateflow/conf/templateflow-skel.{ext}".format
+    )
+    # initialize templateflow home, making sure to pull the legacy skeleton
+    conf.update(local=False)
+    # ensure we can grab a file
+    assert Path(api.get('MNI152NLin2009cAsym', resolution=2, desc='brain', suffix='mask')).exists()
+    # and ensure we can't fetch one that doesn't yet exist
+    assert not api.get('Fischer344', hemi='L', desc='brain', suffix='mask')
+
+    # refresh the skeleton using the most recent skeleton
+    conf._s3.TF_SKEL_URL = _skel_url
+    conf.update(local=True, overwrite=True)
+    assert Path(api.get('Fischer344', hemi='L', desc='brain', suffix='mask')).exists()