Merge pull request #873 from bids-standard/rel/0.15.2

REL: 0.15.2

.mailmap

@@ -4,6 +4,7 @@ Alexander Ivanov <[email protected]>
 Bertrand Thirion <[email protected]>
 Christopher J. Markiewicz <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
 Chris Holdgraf <[email protected]>
 Chris Holdgraf <[email protected]> <[email protected]>
 Dimitri Papadopoulos Orfanos <[email protected]>

.zenodo.json

@@ -32,6 +32,11 @@
       "name": "Halchenko, Yaroslav O.",
       "orcid": "0000-0003-3456-2493"
     },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Esteban, Oscar",
+      "orcid": "0000-0001-8435-6191"
+    },
     {
       "affiliation": "University of Texas at Austin",
       "name": "McNamara, Quinten"
@@ -52,9 +57,9 @@
       "orcid": "0000-0001-9513-2660"
     },
     {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Esteban, Oscar",
-      "orcid": "0000-0001-8435-6191"
+      "affiliation": "Université catholique de Louvain",
+      "name": "Gau, Remi",
+      "orcid": "0000-0002-1535-9767"
     },
     {
       "name": "Kalenkovich, Evgenii",
@@ -65,9 +70,9 @@
       "name": "Petrov, Dmitry"
     },
     {
-      "affiliation": "Universit\u00e9 catholique de Louvain",
-      "name": "Gau, Remi",
-      "orcid": "0000-0002-1535-9767"
+      "affiliation": "National Institute of Mental Health",
+      "name": "Nielson, Dylan M.",
+      "orcid": "0000-0003-4613-6643"
     },
     {
       "affiliation": "Neuroscience Program, University of Iowa",
@@ -79,6 +84,11 @@
       "name": "Appelhoff, Stefan",
       "orcid": "0000-0001-8002-0877"
     },
+    {
+      "affiliation": "University of Texas at Austin",
+      "orcid": "0000-0002-4892-2659",
+      "name": "James Kent"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Goncalves, Mathias",
@@ -91,14 +101,9 @@
     },
     {
       "affiliation": "Concordia University",
-      "name": "Hayot-Sasson, Val\u00e9rie",
+      "name": "Hayot-Sasson, Valérie",
       "orcid": "0000-0002-4830-4535"
     },
-    {
-      "affiliation": "National Institute of Mental Health",
-      "name": "Nielson, Dylan M.",
-      "orcid": "0000-0003-4613-6643"
-    },
     {
       "name": "Papadopoulos Orfanos, Dimitri"
     },
@@ -164,7 +169,7 @@
       "orcid": "0000-0001-8421-365X"
     },
     {
-      "affiliation": "Universit\u00e9 de Sherbrooke",
+      "affiliation": "Université de Sherbrooke",
       "name": "Legarreta, Jon Haitz",
       "orcid": "0000-0002-9661-1396"
     },
@@ -174,7 +179,7 @@
       "orcid": "0000-0002-3239-6957"
     },
     {
-      "affiliation": "T\u00e9l\u00e9com ParisTech, France",
+      "affiliation": "Télécom ParisTech, France",
       "name": "Jas, Mainak",
       "orcid": "0000-0002-3199-9027"
     },
@@ -184,7 +189,7 @@
       "orcid": "0000-0001-6398-6370"
     },
     {
-      "affiliation": "Polytechnique Montr\u00e9al",
+      "affiliation": "Polytechnique Montréal",
       "name": "Guenther, Nick"
     },
     {
@@ -202,6 +207,11 @@
       "name": "Boulay, Chadwick",
       "orcid": "0000-0003-1747-3931"
     },
+    {
+      "affiliation": "Stanford University",
+      "name": "Mumford, Jeanette",
+      "orcid": "0000-0002-0926-3531"
+    },
     {
       "affiliation": "Berkeley Institute for Data Science; University of California at Berkeley",
       "name": "Holdgraf, Chris",
@@ -212,11 +222,6 @@
       "name": "Staden, Isla",
       "orcid": "0000-0002-0795-1154"
     },
-    {
-      "affiliation": "University of Texas at Austin",
-      "orcid": "0000-0002-4892-2659",
-      "name": "James Kent"
-    },
     {
       "name": "Staph, Jason A.",
       "orcid": "0000-0002-5226-3350"
@@ -260,7 +265,7 @@
       "orcid": "0000-0002-5866-047X"
     },
     {
-      "affiliation": "Sainte-Anne Hospital Center, Universit\u00e9 Paris Descartes",
+      "affiliation": "Sainte-Anne Hospital Center, Université Paris Descartes",
       "name": "Roca, Pauline",
       "orcid": "0000-0003-2089-6636"
     },

CHANGELOG.rst

@@ -1,6 +1,33 @@
 Changelog
 =========
 
+Version 0.15.2 (July 25, 2022)
+------------------------------
+
+Bug-fix release in 0.15.x series.
+
+* FIX: Synchronize kwargs in transformations, e.g., in Assign (#836)
+* FIX: Add HRF derivatives to variable collection when created (#838)
+* FIX: Interpolate derivative pipeline name in error message (#847)
+* FIX: Match only within relative path when indexer is validating (#859)
+* FIX: Rename intercept in DummyContrast (#866)
+* FIX: Add variables to correct Node in load_tsv_variables (#872)
+* FIX: Repair variable IO so scans.tsv is found (#869)
+* FIX: Restore automodel functionality (#853)
+* FIX: Allow ``pybids layout --derivatives`` to be a boolean flag or accept a path (#848)
+* ENH: Add default path patterns to derivatives.json (#605)
+* ENH: Rename statsmodels contrasts if they cannot be uniquely identified downstream (#861)
+* ENH: Make intercept-only first level models throw a NotImplementedError (#854)
+* ENH: Update config to support microscopy, qMRI, PET, ASL (#840)
+* TEST: Add bids-examples submodule and bids_examples pytest fixture (#842)
+* TEST: Add tests for default path patterns (#846)
+* TEST: Update bids-examples and remove expected failing tests (#845)
+* MNT: Update git submodules (#874)
+* MNT: Add workflow top automatically update submodule (#870)
+* MNT: Remove deprecated no dot config (#841)
+* CI: Upgrade several GitHub actions to v3 (#867)
+* CI: Add cron jobs to avoid sneaky failures during low activity periods (#860)
+
 Version 0.15.1 (April 04, 2022)
 -------------------------------
 

tools/prep_zenodo.py

@@ -13,7 +13,7 @@ def decommify(name):
 # XXX We should add a shortlog since the most recent tag and explicitly note
 # that a blacklisted user has contributed again recently, and verify they still
 # do not want to be cited.
-blacklist = {'Cecile Madjar', 'Matthew Wardrop', 'Peter Van Dyken'}
+blacklist = {'Cecile Madjar', 'Matthew Wardrop', 'Peter Van Dyken', 'github-actions[bot]'}
 
 # List of repositories whose commits should be counted as contributions
 codependents = [('https://github.com/grabbles/grabbit.git', '0.2.6')]
@@ -84,4 +84,4 @@ def decommify(name):
     ]
 
 zenodo['creators'] = creators
-zenodo_file.write_text(json.dumps(zenodo, indent=2) + '\n')
+zenodo_file.write_text(json.dumps(zenodo, indent=2, ensure_ascii=False) + '\n')

tools/update_changes.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 # Collects the pull-requests since the latest release and
-# aranges them in the CHANGELOG.rst file.
+# arranges them in the CHANGELOG.rst file.
 #
 # This is a script to be run before releasing a new version.
 #
@@ -13,13 +13,12 @@
 set -u         # Treat unset variables as an error when substituting.
 set -x         # Print command traces before executing command.
 
-CHANGES=CHANGELOG.rst
+ROOT=$( git rev-parse --show-toplevel )
+CHANGES=$ROOT/CHANGELOG.rst
 
 # Elaborate today's release header
 HEADER="Version $1 ($(date '+%B %d, %Y'))"
-LEN=${#HEADER}
-UNDERLINE=$(printf "%0.s-" $(seq 1 $LEN))
-
+UNDERLINE=$( printf "%${#HEADER}s" | tr " " "-" )
 cat <<END > newchanges
 Changelog
 =========
@@ -30,7 +29,20 @@ $UNDERLINE
 END
 
 # Search for PRs since previous release
-git log --grep="Merge pull request" `git describe --tags --abbrev=0`..HEAD --pretty='format:* %b %s' | sed  's+Merge pull request \(\#[^\d]*\)\ from\ .*+(\1)+' >> newchanges
+MERGE_COMMITS=$( git log --grep="Merge pull request\|(#.*)$" `git describe --tags --abbrev=0`..HEAD --pretty='format:%h' )
+for COMMIT in ${MERGE_COMMITS//\n}; do
+    SUB=$( git log -n 1 --pretty="format:%s" $COMMIT )
+    if ( echo $SUB | grep "^Merge pull request" ); then
+        # Merge commit
+        PR=$( echo $SUB | sed -e "s/Merge pull request \#\([0-9]*\).*/\1/" )
+        TITLE=$( git log -n 1 --pretty="format:%b" $COMMIT )
+    else
+        # Squashed merge
+        PR=$( echo $SUB | sed -e "s/.*(\#\([0-9]*\))$/\1/" )
+        TITLE=$( echo $SUB | sed -e "s/\(.*\)(\#[0-9]*)$/\1/" )
+    fi
+    echo "* $TITLE (#$PR)" >> newchanges
+done
 
 # Append old changes
 tail -n+3 $CHANGES >> newchanges