From 9eaae82cc253e2f95a82c1d372e019fe7f9d4b18 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 20 Sep 2022 15:38:12 -0400 Subject: [PATCH 1/5] DOC: Update changelog --- doc/changelog/1.X.X-changelog.rst | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst index 776014e6c0..587b26a03c 100644 --- a/doc/changelog/1.X.X-changelog.rst +++ b/doc/changelog/1.X.X-changelog.rst @@ -1,3 +1,17 @@ +1.8.5 (September 20, 2022) +========================== + +Bug-fix release in the 1.8.x series. + + * FIX: Use interpolation/method in numpy.percentile as available (https://github.com/nipy/nipype/pull/3506) + * FIX: Deployed Matlab applications must not call addpath() (https://github.com/nipy/nipype/pull/3509) + * FIX: Provide more runtime information when node execution fails (https://github.com/nipy/nipype/pull/3505) + * FIX: Fixed bug for work dirs longer than 255 characters, fixes #2061 (https://github.com/nipy/nipype/pull/3495) + * FIX: Update ApplyVDM to handle 4D inputs (https://github.com/nipy/nipype/pull/3500) + * ENH: Explicitly specify write_text encoding format (https://github.com/nipy/nipype/pull/3508) + * DOC: Fix typos found by copdespell (https://github.com/nipy/nipype/pull/3510) + + 1.8.4 (September 01, 2022) ========================== From ddffcb6035b8893ad1a0d87245a9f4af217e3761 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 20 Sep 2022 15:42:44 -0400 Subject: [PATCH 2/5] Update mailmap --- .mailmap | 1 + 1 file changed, 1 insertion(+) diff --git a/.mailmap b/.mailmap index ca8fe1b171..1f6bdee6fc 100644 --- a/.mailmap +++ b/.mailmap @@ -58,6 +58,7 @@ David Ellis David Mordom David Welch Dimitri Papadopoulos Orfanos +Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Dmytro Belevtsoff Dorian Vogel Dylan M. Nielson From 62a1616283fbbd7995c0e4908c649dcab9b457c4 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 20 Sep 2022 15:44:12 -0400 Subject: [PATCH 3/5] Update zenodo --- .zenodo.json | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 0703ffa351..fd9e5e9658 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -94,16 +94,16 @@ "name": "Salo, Taylor", "orcid": "0000-0001-9813-3167" }, - { - "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University", - "name": "Dewey, Blake E", - "orcid": "0000-0003-4554-5058" - }, { "affiliation": "University of Iowa", "name": "Johnson, Hans", "orcid": "0000-0001-9513-2660" }, + { + "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University", + "name": "Dewey, Blake E", + "orcid": "0000-0003-4554-5058" + }, { "affiliation": "Molecular Imaging Research Center, CEA, France", "name": "Bougacha, Salma" @@ -300,6 +300,11 @@ "name": "Acland, Benjamin", "orcid": "0000-0001-6392-6634" }, + { + "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany", + "name": "Bernardoni, Fabio", + "orcid": "0000-0002-5112-405X" + }, { "name": "Forbes, Jessica" }, @@ -313,11 +318,6 @@ "name": "Gillman, Ashley", "orcid": "0000-0001-9130-1092" }, - { - "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany", - "name": "Bernardoni, Fabio", - "orcid": "0000-0002-5112-405X" - }, { "affiliation": "Sagol School of Neuroscience, Tel Aviv University", "name": "Ben-Zvi, Gal", @@ -414,6 +414,11 @@ { "name": "Haselgrove, Christian" }, + { + "affiliation": "CEA", + "name": "Papadopoulos Orfanos, Dimitri", + "orcid": "0000-0002-1242-8990" + }, { "affiliation": "Department of Psychology, Stanford University; Parietal, INRIA", "name": "Durnez, Joke", @@ -479,11 +484,6 @@ { "name": "Correa, Carlos" }, - { - "affiliation": "CEA", - "name": "Papadopoulos Orfanos, Dimitri", - "orcid": "0000-0002-1242-8990" - }, { "affiliation": "Leibniz Institute for Neurobiology", "name": "Stadler, Jörg", From b0f07d04def788b1bf9fb78f679128d40f8e3051 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 20 Sep 2022 15:49:42 -0400 Subject: [PATCH 4/5] MNT: 1.8.5 --- nipype/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index eb60e4c22b..483fc0d8e6 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -5,7 +5,7 @@ # nipype version information # Remove .dev0 for release -__version__ = "1.8.5.dev0" +__version__ = "1.8.5" def get_nipype_gitversion(): From 44d9e43458d5906f87f88ed6e4ff37df3e9a82c7 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 21 Sep 2022 08:37:46 -0400 Subject: [PATCH 5/5] CI: Fix tutorial GHA --- .github/workflows/tutorials.yml | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/.github/workflows/tutorials.yml b/.github/workflows/tutorials.yml index 0d04e0548f..d6d81c04ac 100644 --- a/.github/workflows/tutorials.yml +++ b/.github/workflows/tutorials.yml @@ -9,49 +9,55 @@ jobs: tutorial: runs-on: ubuntu-latest env: - BRANCH_NAME: ${{ github.head_ref || github.ref_name }} + BRANCH_NAME: ${{ github.ref_name }} steps: - name: Start time id: start run: echo "::set-output name=start_time::$(date +'%Y-%m-%dT%H:%M:%S%z')" - name: Trigger Nipype tutorial Github Action run: | + set -x curl -X POST \ -H "Authorization: Bearer ${{ secrets.TUTORIAL_ACCESS_TOKEN }}" \ -H "Accept: application/vnd.github+json" \ https://api.github.com/repos/miykael/nipype_tutorial/actions/workflows/testing.yml/dispatches \ - -d '{"nipype_branch": "'${BRANCH_NAME:4}'"}' + -d '{"ref": "master", "inputs": {"nipype_branch": "'${BRANCH_NAME}'"}}' + sleep 10 - name: Check Action was successfully dispatched id: dispatched run: | - RUN_ID=$(curl -X POST \ - -H "Accept: application/vnd.github+json" \ - "https://api.github.com/repos/miykael/nipype_tutorial/actions/runs?created=%3E${{%20steps.start.outputs.start_time%20}}&per_page=1" \ + set -x + START=${{ steps.start.outputs.start_time }} + RUN_ID=$(curl -H "Accept: application/vnd.github+json" \ + 'https://api.github.com/repos/miykael/nipype_tutorial/actions/runs?created=%3E'${START}'&per_page=1' \ | jq -r '.workflow_runs[0].id') # fail if not extracted [[ -n $RUN_ID ]] || exit 1 - echo "::set-output name=run_id::$RUN_ID"" + echo "::set-output name=run_id::$RUN_ID" - name: Check if action completed - timeout-minutes: 60 + timeout-minutes: 120 run: | + set -x + RUN_ID=${{ steps.dispatched.outputs.run_id }} while : do TIMESTAMP=$(date +'%Y-%m-%dT%H:%M:%S%z') # check status every 5 minutes STATUS=$(curl -H "Accept: application/vnd.github+json" \ - "https://api.github.com/repos/miykael/nipype_tutorial/actions/runs/$%7B%7B%20steps.dispatched.outputs.run_id%20%7D%7D" \ + https://api.github.com/repos/miykael/nipype_tutorial/actions/runs/${RUN_ID} \ | jq -r '.conclusion') case $STATUS in success) - echo "[$TIMESTAMP] Tutorial run ${{ steps.dispatched.outputs.run_id }} completed successfully." + echo "[$TIMESTAMP] Tutorial run $RUN_ID completed successfully." exit 0 - ;; + ;; failure) - echo "[$TIMESTAMP] Tutorial run ${{ steps.dispatched.outputs.run_id }} failed." + echo "[$TIMESTAMP] Tutorial run $RUN_ID failed." exit 1 - ;; + ;; *) echo "[$TIMESTAMP] Conclusion ($STATUS) is not yet complete" sleep 300 + esac done