From 3ed9cf268001cb02f99d8b5d67f75c0aed3378a5 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 17:55:29 +0200 Subject: [PATCH 01/10] chore: trim trailing whitespace across codebase --- .github/ISSUE_TEMPLATE/dataset-request.yml | 2 +- docs/Makefile | 2 +- docs/_templates/versions.html | 2 +- docs/api/index.rst | 2 +- examples/yamls/ukb_gmd_mean.yaml | 3 +-- junifer/api/res/afni/run_afni_docker.sh | 2 +- junifer/data/VOIs/meta/CogAR_VOIs.txt | 1 - junifer/data/VOIs/meta/DMNBuckner_VOIs.txt | 1 - junifer/data/VOIs/meta/MultiTask_VOIs.txt | 1 - junifer/data/VOIs/meta/VigAtt_VOIs.txt | 4 ++-- junifer/data/VOIs/meta/WM_VOIs.txt | 8 ++++---- tools/create_aomicpiop1_example_dataset.py | 2 +- 12 files changed, 13 insertions(+), 17 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/dataset-request.yml b/.github/ISSUE_TEMPLATE/dataset-request.yml index 13c144225..e633e7063 100644 --- a/.github/ISSUE_TEMPLATE/dataset-request.yml +++ b/.github/ISSUE_TEMPLATE/dataset-request.yml @@ -10,7 +10,7 @@ body: attributes: value: | Fill in this form if you want that junifer includes a new dataset. - + As a reminder, junifer supports customising the `PatternDataGrabber` and `PatternDataladDatagrabber` which should work in most cases. If it is a widely used dataset, we could alternatevely create a new _DataGrabber_ that simplifies the usage, by already configuring the underlying `PatternDataGrabber` or `PatternDataladDatagrabber` diff --git a/docs/Makefile b/docs/Makefile index 8b7100909..8ad9ee70a 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -22,7 +22,7 @@ clean: local: news make _build_local; STATUS=$$?; make news_cleanup; exit $$STATUS -news: +news: @echo "Generating whats_new.rst" cd ../ && towncrier build --keep diff --git a/docs/_templates/versions.html b/docs/_templates/versions.html index 08b7d02bf..0ebc2ffb5 100644 --- a/docs/_templates/versions.html +++ b/docs/_templates/versions.html @@ -2,7 +2,7 @@

Other Versions -

+

{% if versions.branches %} {{ _('Branches') }} diff --git a/docs/api/index.rst b/docs/api/index.rst index 875204997..9e8ee16c4 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -41,7 +41,7 @@ Configs External -------- -.. toctree:: +.. toctree:: :maxdepth: 2 :caption: Contents: diff --git a/examples/yamls/ukb_gmd_mean.yaml b/examples/yamls/ukb_gmd_mean.yaml index 1a4f5963f..921410a1a 100644 --- a/examples/yamls/ukb_gmd_mean.yaml +++ b/examples/yamls/ukb_gmd_mean.yaml @@ -19,7 +19,6 @@ markers: kind: ParcelAggregation parcellation: Schaefer1000x7 method: std -storage: +storage: kind: SQLiteFeatureStorage uri: /data/project/ukb_motor/junifer_test/test.sqlite - diff --git a/junifer/api/res/afni/run_afni_docker.sh b/junifer/api/res/afni/run_afni_docker.sh index 3519c2f1d..3de59757e 100755 --- a/junifer/api/res/afni/run_afni_docker.sh +++ b/junifer/api/res/afni/run_afni_docker.sh @@ -4,7 +4,7 @@ corrected_args=() docker_args=() mounts=0 for var in "$@" -do +do if [ -d "${var}" ]; then echo "$var is a directory" var=$(realpath "${var}") diff --git a/junifer/data/VOIs/meta/CogAR_VOIs.txt b/junifer/data/VOIs/meta/CogAR_VOIs.txt index 2a0044c69..f5c477b9a 100644 --- a/junifer/data/VOIs/meta/CogAR_VOIs.txt +++ b/junifer/data/VOIs/meta/CogAR_VOIs.txt @@ -6,4 +6,3 @@ -36 -46 46 Parietal_Inf_L 38 -46 44 Parietal_Inf_R -26 0 54 Frontal_Mid_L - diff --git a/junifer/data/VOIs/meta/DMNBuckner_VOIs.txt b/junifer/data/VOIs/meta/DMNBuckner_VOIs.txt index 631879bbd..e03a949bd 100644 --- a/junifer/data/VOIs/meta/DMNBuckner_VOIs.txt +++ b/junifer/data/VOIs/meta/DMNBuckner_VOIs.txt @@ -4,4 +4,3 @@ 46 -62 32 rAG -24 -22 -20 lHF 24 -22 -20 rHF - diff --git a/junifer/data/VOIs/meta/MultiTask_VOIs.txt b/junifer/data/VOIs/meta/MultiTask_VOIs.txt index bc7fa5676..19383f19a 100644 --- a/junifer/data/VOIs/meta/MultiTask_VOIs.txt +++ b/junifer/data/VOIs/meta/MultiTask_VOIs.txt @@ -7,4 +7,3 @@ -34 -52 56 Parietal_Inf_L 32 -52 50 Parietal_Inf_R 32 6 58 Frontal_Mid_R - diff --git a/junifer/data/VOIs/meta/VigAtt_VOIs.txt b/junifer/data/VOIs/meta/VigAtt_VOIs.txt index 5efc95faf..10a244cc3 100644 --- a/junifer/data/VOIs/meta/VigAtt_VOIs.txt +++ b/junifer/data/VOIs/meta/VigAtt_VOIs.txt @@ -1,5 +1,5 @@ --2.0 8.0 50.0 aParacentralL -8.0 32.0 46.0 rmpSFG +-2.0 8.0 50.0 aParacentralL +8.0 32.0 46.0 rmpSFG 0.0 26.0 34.0 dMCC 50.0 8.0 32.0 rIFJ 40.0 22.0 -4.0 raI diff --git a/junifer/data/VOIs/meta/WM_VOIs.txt b/junifer/data/VOIs/meta/WM_VOIs.txt index ae2839eda..426b061f8 100644 --- a/junifer/data/VOIs/meta/WM_VOIs.txt +++ b/junifer/data/VOIs/meta/WM_VOIs.txt @@ -1,5 +1,5 @@ --32.0 22.0 -2.0 aIns_l --48.0 10.0 26.0 IFG_l +-32.0 22.0 -2.0 aIns_l +-48.0 10.0 26.0 IFG_l -46.0 26.0 24.0 lPFCc_l -38.0 50.0 10.0 lPFCr_l 36.0 22.0 -6.0 aIns_r @@ -18,6 +18,6 @@ -12.0 -12.0 12.0 Thal_l -16.0 2.0 14.0 Ncaud_l -16.0 0.0 2.0 GP_l -12.0 -10.0 10.0 Thal_r +12.0 -10.0 10.0 Thal_r -34.0 -66.0 -20.0 Cb_FG_l -32.0 -64.0 -18.0 Cb_FG_r \ No newline at end of file +32.0 -64.0 -18.0 Cb_FG_r diff --git a/tools/create_aomicpiop1_example_dataset.py b/tools/create_aomicpiop1_example_dataset.py index a5ff9a192..d9690867c 100644 --- a/tools/create_aomicpiop1_example_dataset.py +++ b/tools/create_aomicpiop1_example_dataset.py @@ -40,7 +40,7 @@ with TemporaryDirectory() as tmpdir_name: ), ( f"anat/{t_sub}_space-MNI152NLin2009cAsym_" - "desc-brain_mask.nii.gz" + "desc-brain_mask.nii.gz" ), ( f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-" -- 2.52.0 From f29bbfa46fec7d10a449294340bc2ea67e673eaa Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 17:57:10 +0200 Subject: [PATCH 02/10] chore: fix end of file newline across codebase --- .github/workflows/ci-docs.yml | 2 +- .gitignore | 2 +- LICENSE.md | 2 +- codecov.yml | 2 +- docs/_static/css/custom.css | 2 +- docs/_static/js/custom.js | 2 +- docs/api/index.rst | 2 +- docs/changes/newsfragments/.gitignore | 2 +- docs/changes/newsfragments/220.doc | 2 +- docs/changes/newsfragments/222.change | 2 +- docs/changes/newsfragments/222.enh | 2 +- docs/changes/newsfragments/223.bugfix | 2 +- docs/changes/newsfragments/223.enh | 2 +- docs/changes/newsfragments/229.misc | 2 +- docs/links.inc | 2 +- docs/redirect.html | 2 +- examples/README.rst | 2 +- junifer/api/res/afni/3dAFNItoNIFTI | 2 +- junifer/api/res/afni/3dRSFC | 2 +- junifer/api/res/afni/3dReHo | 2 +- junifer/api/res/afni/afni | 2 +- junifer/api/res/afni/run_afni_docker.sh | 2 +- junifer/api/res/run_conda.sh | 2 +- junifer/data/VOIs/meta/CogAC_VOIs.txt | 2 +- junifer/data/VOIs/meta/Dosenbach2010_MNI_VOIs.txt | 2 +- junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt | 2 +- junifer/data/VOIs/meta/ToM_VOIs.txt | 2 +- junifer/data/VOIs/meta/eMDN_VOIs.txt | 2 +- 28 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index ac5b6c0c1..68235bb80 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -47,4 +47,4 @@ jobs: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: true flags: docs - if: success() && matrix.python-version == 3.10 \ No newline at end of file + if: success() && matrix.python-version == 3.10 diff --git a/.gitignore b/.gitignore index 94ac529c9..78053c736 100644 --- a/.gitignore +++ b/.gitignore @@ -134,4 +134,4 @@ cython_debug/ junifer/_version.py scratch/ -junifer_jobs/ \ No newline at end of file +junifer_jobs/ diff --git a/LICENSE.md b/LICENSE.md index 6124431c9..4ef32f083 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -648,4 +648,4 @@ specific requirements. You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU AGPL, see -<>. \ No newline at end of file +<>. diff --git a/codecov.yml b/codecov.yml index 17e51fd9a..9dede3927 100644 --- a/codecov.yml +++ b/codecov.yml @@ -36,4 +36,4 @@ flag_management: threshold: 1% - type: patch target: 95% - threshold: 1% \ No newline at end of file + threshold: 1% diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css index c929f98d0..af8fd1721 100644 --- a/docs/_static/css/custom.css +++ b/docs/_static/css/custom.css @@ -43,4 +43,4 @@ body:not([data-theme="light"]) .mermaid svg .edgeLabel { body:not([data-theme="light"]) .mermaid svg .marker{ stroke: white !important; fill: white !important; -} \ No newline at end of file +} diff --git a/docs/_static/js/custom.js b/docs/_static/js/custom.js index c661f2221..fa8ecefd6 100644 --- a/docs/_static/js/custom.js +++ b/docs/_static/js/custom.js @@ -11,4 +11,4 @@ for (i = 0; i < coll.length; i++) { content.style.display = "block"; } }); -} \ No newline at end of file +} diff --git a/docs/api/index.rst b/docs/api/index.rst index 9e8ee16c4..482837a30 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -45,4 +45,4 @@ External :maxdepth: 2 :caption: Contents: - nilearn.rst \ No newline at end of file + nilearn.rst diff --git a/docs/changes/newsfragments/.gitignore b/docs/changes/newsfragments/.gitignore index b722e9e13..f935021a8 100644 --- a/docs/changes/newsfragments/.gitignore +++ b/docs/changes/newsfragments/.gitignore @@ -1 +1 @@ -!.gitignore \ No newline at end of file +!.gitignore diff --git a/docs/changes/newsfragments/220.doc b/docs/changes/newsfragments/220.doc index 53e822b1b..10d77bb23 100644 --- a/docs/changes/newsfragments/220.doc +++ b/docs/changes/newsfragments/220.doc @@ -1 +1 @@ -Improve general prose, formatting and code blocks in docs and set line length for ``.rst`` files to 80 by `Synchon Mandal`_ \ No newline at end of file +Improve general prose, formatting and code blocks in docs and set line length for ``.rst`` files to 80 by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/222.change b/docs/changes/newsfragments/222.change index 3a64c2eb8..7771cf404 100644 --- a/docs/changes/newsfragments/222.change +++ b/docs/changes/newsfragments/222.change @@ -1 +1 @@ -Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to :class:`.SPMAuditoryTestingDataGrabber` and ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_ \ No newline at end of file +Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to :class:`.SPMAuditoryTestingDataGrabber` and ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/222.enh b/docs/changes/newsfragments/222.enh index fd3f4a8ed..7ba6a197e 100644 --- a/docs/changes/newsfragments/222.enh +++ b/docs/changes/newsfragments/222.enh @@ -1 +1 @@ -Rename instances of "Datagrabber" to "DataGrabber" especially in ``junifer.testing`` to be consistent by `Synchon Mandal`_ \ No newline at end of file +Rename instances of "Datagrabber" to "DataGrabber" especially in ``junifer.testing`` to be consistent by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/223.bugfix b/docs/changes/newsfragments/223.bugfix index a709cb2e0..8fa64e86e 100644 --- a/docs/changes/newsfragments/223.bugfix +++ b/docs/changes/newsfragments/223.bugfix @@ -1 +1 @@ -Enable YAML 1.2 support and allow multiline strings in YAML which would not work earlier by `Synchon Mandal`_ \ No newline at end of file +Enable YAML 1.2 support and allow multiline strings in YAML which would not work earlier by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/223.enh b/docs/changes/newsfragments/223.enh index 54e3befe5..0014eed50 100644 --- a/docs/changes/newsfragments/223.enh +++ b/docs/changes/newsfragments/223.enh @@ -1 +1 @@ -Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon Mandal`_ \ No newline at end of file +Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/229.misc b/docs/changes/newsfragments/229.misc index 6978c04c1..ac42da01f 100644 --- a/docs/changes/newsfragments/229.misc +++ b/docs/changes/newsfragments/229.misc @@ -1 +1 @@ -Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_ \ No newline at end of file +Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_ diff --git a/docs/links.inc b/docs/links.inc index 304214509..c6cc2d280 100644 --- a/docs/links.inc +++ b/docs/links.inc @@ -42,4 +42,4 @@ .. _`HTCondor`: https://research.cs.wisc.edu/htcondor/ .. _`SLURM`: https://slurm.schedmd.com -.. _`GNU Parallel`: https://www.gnu.org/software/parallel/ \ No newline at end of file +.. _`GNU Parallel`: https://www.gnu.org/software/parallel/ diff --git a/docs/redirect.html b/docs/redirect.html index cfd7dc137..3ae364d1f 100644 --- a/docs/redirect.html +++ b/docs/redirect.html @@ -6,4 +6,4 @@ - \ No newline at end of file + diff --git a/examples/README.rst b/examples/README.rst index 2df726e94..a8c8f87df 100644 --- a/examples/README.rst +++ b/examples/README.rst @@ -1,4 +1,4 @@ Examples ======== -The following are a set of examples. \ No newline at end of file +The following are a set of examples. diff --git a/junifer/api/res/afni/3dAFNItoNIFTI b/junifer/api/res/afni/3dAFNItoNIFTI index 37e77f583..a91a7ab93 100755 --- a/junifer/api/res/afni/3dAFNItoNIFTI +++ b/junifer/api/res/afni/3dAFNItoNIFTI @@ -1,3 +1,3 @@ #!/bin/bash -run_afni_docker.sh 3dAFNItoNIFTI "$@" \ No newline at end of file +run_afni_docker.sh 3dAFNItoNIFTI "$@" diff --git a/junifer/api/res/afni/3dRSFC b/junifer/api/res/afni/3dRSFC index f3036ac16..b335c2d8f 100755 --- a/junifer/api/res/afni/3dRSFC +++ b/junifer/api/res/afni/3dRSFC @@ -1,3 +1,3 @@ #!/bin/bash -run_afni_docker.sh 3dRSFC "$@" \ No newline at end of file +run_afni_docker.sh 3dRSFC "$@" diff --git a/junifer/api/res/afni/3dReHo b/junifer/api/res/afni/3dReHo index 62e09b7e2..8b8e61f7e 100755 --- a/junifer/api/res/afni/3dReHo +++ b/junifer/api/res/afni/3dReHo @@ -1,3 +1,3 @@ #!/bin/bash -run_afni_docker.sh 3dReHo "$@" \ No newline at end of file +run_afni_docker.sh 3dReHo "$@" diff --git a/junifer/api/res/afni/afni b/junifer/api/res/afni/afni index 32584bb7b..0d090b96e 100755 --- a/junifer/api/res/afni/afni +++ b/junifer/api/res/afni/afni @@ -1,3 +1,3 @@ #!/bin/bash -run_afni_docker.sh afni "$@" \ No newline at end of file +run_afni_docker.sh afni "$@" diff --git a/junifer/api/res/afni/run_afni_docker.sh b/junifer/api/res/afni/run_afni_docker.sh index 3de59757e..dd1ac88c9 100755 --- a/junifer/api/res/afni/run_afni_docker.sh +++ b/junifer/api/res/afni/run_afni_docker.sh @@ -36,4 +36,4 @@ echo "Corrected args for afni: ${corrected_args[*]}" cwd=$(pwd) cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} afni/afni_make_build ${corrected_args[*]}" echo "Running command: ${cmd}" -${cmd} \ No newline at end of file +${cmd} diff --git a/junifer/api/res/run_conda.sh b/junifer/api/res/run_conda.sh index fe202ad8d..114247feb 100755 --- a/junifer/api/res/run_conda.sh +++ b/junifer/api/res/run_conda.sh @@ -20,4 +20,4 @@ if [ -f "pre_run.sh" ]; then fi echo "Running ${*} in virtual environment" -"$@" \ No newline at end of file +"$@" diff --git a/junifer/data/VOIs/meta/CogAC_VOIs.txt b/junifer/data/VOIs/meta/CogAC_VOIs.txt index 05184cea7..de0a46bdd 100644 --- a/junifer/data/VOIs/meta/CogAC_VOIs.txt +++ b/junifer/data/VOIs/meta/CogAC_VOIs.txt @@ -16,4 +16,4 @@ 48.0 19.0 6.0 rIFG 8.0 29.0 30.0 aMCC -45.0 27.0 30.0 lIFG -11.0 7.0 7.0 rNcaud \ No newline at end of file +11.0 7.0 7.0 rNcaud diff --git a/junifer/data/VOIs/meta/Dosenbach2010_MNI_VOIs.txt b/junifer/data/VOIs/meta/Dosenbach2010_MNI_VOIs.txt index 9c45fcc24..37a70997b 100644 --- a/junifer/data/VOIs/meta/Dosenbach2010_MNI_VOIs.txt +++ b/junifer/data/VOIs/meta/Dosenbach2010_MNI_VOIs.txt @@ -157,4 +157,4 @@ -29 -88 8 post occipital 13 -91 2 post occipital 27 -91 2 post occipital --4 -94 12 post occipital \ No newline at end of file +-4 -94 12 post occipital diff --git a/junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt b/junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt index d8de553e2..b9ba98236 100644 --- a/junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt +++ b/junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt @@ -261,4 +261,4 @@ -32 -1 54 261 -42 -60 -9 262 -17 -59 64 263 -29 -5 54 264 \ No newline at end of file +29 -5 54 264 diff --git a/junifer/data/VOIs/meta/ToM_VOIs.txt b/junifer/data/VOIs/meta/ToM_VOIs.txt index c520734b7..8f0dcccb2 100644 --- a/junifer/data/VOIs/meta/ToM_VOIs.txt +++ b/junifer/data/VOIs/meta/ToM_VOIs.txt @@ -12,4 +12,4 @@ -58.0 -44.0 4.0 lpSTS 54.0 28.0 6.0 rIFG -48.0 30.0 -12.0 lIFG -48.0 -72.0 8.0 rV5 \ No newline at end of file +48.0 -72.0 8.0 rV5 diff --git a/junifer/data/VOIs/meta/eMDN_VOIs.txt b/junifer/data/VOIs/meta/eMDN_VOIs.txt index ece04c248..aa93cda2e 100644 --- a/junifer/data/VOIs/meta/eMDN_VOIs.txt +++ b/junifer/data/VOIs/meta/eMDN_VOIs.txt @@ -14,4 +14,4 @@ 10.0 -12.0 8.0 Thal_r -46.0 -60.0 -10.0 ITG_l 22.0 6.0 4.0 Put_r --10.0 -16.0 6.0 Thal_l \ No newline at end of file +-10.0 -16.0 6.0 Thal_l -- 2.52.0 From 296addacf3eceb6f64ce4030cbb70c3d7b7baf5f Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 17:57:56 +0200 Subject: [PATCH 03/10] docs: fix backticks in rst files --- docs/extending/datagrabber.rst | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/extending/datagrabber.rst b/docs/extending/datagrabber.rst index 22c388a80..4cbf893e2 100644 --- a/docs/extending/datagrabber.rst +++ b/docs/extending/datagrabber.rst @@ -35,9 +35,9 @@ c. the experiment included resting-stage fMRI and a task named *stroop* then the *element* should be composed of 3 items: -* ``subject``: The subject IDs, e.g. `sub001`, `sub002`, ... `sub020` -* ``session``: The session number, e.g. `ses1`, `ses2` -* ``task``: The task performed, e.g. `rest`, `stroop` +* ``subject``: The subject IDs, e.g. ``sub001``, ``sub002``, ... ``sub020`` +* ``session``: The session number, e.g. ``ses1``, ``ses2`` +* ``task``: The task performed, e.g. ``rest``, ``stroop`` If any of these items were not part of the element, then we will have more than one ``T1w`` and / or ``BOLD`` image for each subject, which is not allowed. @@ -49,9 +49,10 @@ for the element (``sub001``, ``ses1``, ``rest``) will be the same as the ``T1w`` image for the element (``sub001``, ``ses1``, ``stroop``). We will now continue this section using as an example, a dataset in BIDS format -in which 9 subjects (`sub-01` to `sub-09`) were scanned each during 3 -sessions (`ses-01`, `ses-02`, `ses-03`) and each session included a `T1w` and -a `BOLD` image (resting-state), except for `ses-03` which was only anatomical. +in which 9 subjects (``sub-01`` to ``sub-09``) were scanned each during 3 +sessions (``ses-01``, ``ses-02``, ``ses-03``) and each session included a +``T1w`` and a ``BOLD`` image (resting-state), except for ``ses-03`` which was +only anatomical. Step 2: Think about the dataset's structure ------------------------------------------- @@ -63,7 +64,7 @@ the Data Grabber needs to be implemented. Junifer provides an abstract class to deal with datasets that can be thought in terms of *patterns*. A *pattern* is a string that contains placeholders that are replaced by the actual values of the element. In our BIDS example, the path -to the T1w image of subject `sub-01` and session `ses-01`, relative to the +to the T1w image of subject ``sub-01`` and session ``ses-01``, relative to the dataset location, is ``sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz``. By replacing ``sub-01`` with ``sub-02``, we can obtain the T1w image of the first session of the second subject. Indeed, the path to the T1w images can be -- 2.52.0 From 1c570a7bee8c511be8b48f04cdffbba38b06a4e8 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 17:58:25 +0200 Subject: [PATCH 04/10] chore: fix multi-line comment acting as duplicate docstring across codebase --- junifer/data/coordinates.py | 12 ++--- junifer/data/masks.py | 14 +++-- junifer/data/parcellations.py | 16 +++--- .../nilearn/junifer_nifti_spheres_masker.py | 52 +++++++++---------- .../test_junifer_nifti_spheres_masker.py | 52 +++++++++---------- 5 files changed, 68 insertions(+), 78 deletions(-) diff --git a/junifer/data/coordinates.py b/junifer/data/coordinates.py index 2c9fccaaf..ff6adc8c7 100644 --- a/junifer/data/coordinates.py +++ b/junifer/data/coordinates.py @@ -20,14 +20,12 @@ _vois_path = Path(__file__).parent / "VOIs" # Path to the metadata of the VOIs _vois_meta_path = _vois_path / "meta" -""" -A dictionary containing all supported coordinates and their respective file or -data. +# A dictionary containing all supported coordinates and their respective file +# or data. -The built-in coordinates are files that are shipped with the package in the -data/VOIs directory. The user can also register their own coordinates, which -will be stored as numpy arrays in the dictionary. -""" +# The built-in coordinates are files that are shipped with the package in the +# data/VOIs directory. The user can also register their own coordinates, which +# will be stored as numpy arrays in the dictionary. _available_coordinates: Dict[ str, Union[Path, Dict[str, Union[ArrayLike, List[str]]]] ] = { diff --git a/junifer/data/masks.py b/junifer/data/masks.py index e86988301..df63fdc12 100644 --- a/junifer/data/masks.py +++ b/junifer/data/masks.py @@ -63,16 +63,14 @@ def _fetch_icbm152_brain_gm_mask( return mask -""" -A dictionary containing all supported masks and their respective file or -data. +# A dictionary containing all supported masks and their respective file or +# data. -The built-in masks are files that are shipped with the package in the -data/masks directory. The user can also register their own masks. +# The built-in masks are files that are shipped with the package in the +# data/masks directory. The user can also register their own masks. -Callable masks should be functions that take at least one parameter: -* `target_img`: the image to which the mask will be applied. -""" +# Callable masks should be functions that take at least one parameter: +# * `target_img`: the image to which the mask will be applied. _available_masks: Dict[str, Dict[str, Any]] = { "GM_prob0.2": {"family": "Vickery-Patil"}, "GM_prob0.2_cortex": {"family": "Vickery-Patil"}, diff --git a/junifer/data/parcellations.py b/junifer/data/parcellations.py index 8562a1823..b246863c7 100644 --- a/junifer/data/parcellations.py +++ b/junifer/data/parcellations.py @@ -26,18 +26,16 @@ if TYPE_CHECKING: from nibabel import Nifti1Image -""" -A dictionary containing all supported parcellations and their respective valid -parameters. +# A dictionary containing all supported parcellations and their respective +# valid parameters. -Each entry is a dictionary that must contain at least the following keys: -* 'family': the parcellation's family name (e.g. 'Schaefer', 'SUIT') +# Each entry is a dictionary that must contain at least the following keys: +# * 'family': the parcellation's family name (e.g. 'Schaefer', 'SUIT') -Optional keys: -* 'valid_resolutions': a list of valid resolutions for the parcellation -(e.g. [1, 2]) +# Optional keys: +# * 'valid_resolutions': a list of valid resolutions for the parcellation +# (e.g. [1, 2]) -""" # TODO: have separate dictionary for built-in _available_parcellations: Dict[str, Dict[Any, Any]] = { "SUITxSUIT": {"family": "SUIT", "space": "SUIT"}, diff --git a/junifer/external/nilearn/junifer_nifti_spheres_masker.py b/junifer/external/nilearn/junifer_nifti_spheres_masker.py index 4654941f1..d09320a19 100644 --- a/junifer/external/nilearn/junifer_nifti_spheres_masker.py +++ b/junifer/external/nilearn/junifer_nifti_spheres_masker.py @@ -29,39 +29,37 @@ if TYPE_CHECKING: from pandas import DataFrame -""" -New BSD License +# New BSD License -Copyright (c) 2007 - 2022 The nilearn developers. -All rights reserved. +# Copyright (c) 2007 - 2022 The nilearn developers. +# All rights reserved. -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: - a. Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - b. Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - c. Neither the name of the nilearn developers nor the names of - its contributors may be used to endorse or promote products - derived from this software without specific prior written - permission. +# a. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. +# b. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# c. Neither the name of the nilearn developers nor the names of +# its contributors may be used to endorse or promote products +# derived from this software without specific prior written +# permission. -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR -ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT -LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY -OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH -DAMAGE. -""" +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR +# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +# DAMAGE. def _apply_mask_and_get_affinity( diff --git a/junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py b/junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py index 44be953c9..a36c8f2ff 100644 --- a/junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py +++ b/junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py @@ -15,39 +15,37 @@ from numpy.testing import assert_array_equal from junifer.external.nilearn import JuniferNiftiSpheresMasker -""" -New BSD License +# New BSD License -Copyright (c) 2007 - 2022 The nilearn developers. -All rights reserved. +# Copyright (c) 2007 - 2022 The nilearn developers. +# All rights reserved. -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: - a. Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - b. Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - c. Neither the name of the nilearn developers nor the names of - its contributors may be used to endorse or promote products - derived from this software without specific prior written - permission. +# a. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. +# b. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# c. Neither the name of the nilearn developers nor the names of +# its contributors may be used to endorse or promote products +# derived from this software without specific prior written +# permission. -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR -ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT -LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY -OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH -DAMAGE. -""" +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR +# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +# DAMAGE. def test_seed_extraction() -> None: -- 2.52.0 From 7fc84c7a065aca995ab1172b4fa6c9d6c0a13f21 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 17:59:27 +0200 Subject: [PATCH 05/10] chore: add pre-commit badge in README --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 636995d2d..4808f0659 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,7 @@ ![Codecov](https://img.shields.io/codecov/c/github/juaml/junifer?style=flat-square) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff) +[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit) ## About -- 2.52.0 From 62762a83e0e75415e397db85b4b9657bc3b09a1b Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 17:59:39 +0200 Subject: [PATCH 06/10] update: add .pre-commit-config.yaml --- .pre-commit-config.yaml | 48 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 000000000..9212d6c9d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,48 @@ +ci: + autofix_prs: false + autoupdate_commit_msg: "chore: bump pre-commit repositories" + +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-ast + - id: check-docstring-first + - id: check-executables-have-shebangs + - id: check-merge-conflict + - id: check-yaml + - id: check-toml + - id: debug-statements + - id: end-of-file-fixer + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + - repo: https://github.com/abravalheri/validate-pyproject + rev: v0.12.2 + hooks: + - id: validate-pyproject + - repo: https://github.com/psf/black + rev: 23.3.0 + hooks: + - id: black + exclude: ^(docs/|examples/|tools/) + args: [--check] + - repo: https://github.com/charliermarsh/ruff-pre-commit + rev: v0.0.267 + hooks: + - id: ruff + exclude: ^(__init__.py) + args: [--format, grouped, --show-fixes] + - repo: https://github.com/codespell-project/codespell + rev: v2.2.4 + hooks: + - id: codespell + exclude: ^(.github/|docs/) + args: [--config, tox.ini] + - repo: https://github.com/pre-commit/pygrep-hooks + rev: v1.10.0 + hooks: + - id: python-no-eval + - id: python-no-log-warn + - id: rst-backticks + - id: rst-directive-colons + - id: rst-inline-touching-normal -- 2.52.0 From ac94b9dbb2a70d96791ec0c4267402bf8d0b797d Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 18:03:26 +0200 Subject: [PATCH 07/10] docs: add info about installing pre-commit hooks --- docs/contribution.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/contribution.rst b/docs/contribution.rst index 29239f690..65e862dd0 100644 --- a/docs/contribution.rst +++ b/docs/contribution.rst @@ -38,6 +38,12 @@ Setting up the local development environment Now you can make your changes locally. +#. Make sure you install git pre-commit hooks like so: + + .. code-block:: bash + + pre-commit install + #. When making changes locally, it is helpful to ``git commit`` your work regularly. On one hand to save your work and on the other hand, the smaller the steps, the easier it is to review your work later. Please use `semantic -- 2.52.0 From 7970875046f960c93282b9ef885f22a8cae1c129 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 18:03:45 +0200 Subject: [PATCH 08/10] chore: add pre-commit to dev install in pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 56fce3c59..214ca524a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ repository = "https://github.com/juaml/junifer" junifer = "junifer.api.cli:cli" [project.optional-dependencies] -dev = ["tox"] +dev = ["tox", "pre-commit"] docs = [ "seaborn>=0.11.2,<0.12", "Sphinx>=5.3.0,<5.4", -- 2.52.0 From 00857ed6467cc5f8573bd45cbdf3c39d754ba502 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 22 May 2023 18:11:55 +0200 Subject: [PATCH 09/10] chore: add changelog 232.misc --- docs/changes/newsfragments/232.misc | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/changes/newsfragments/232.misc diff --git a/docs/changes/newsfragments/232.misc b/docs/changes/newsfragments/232.misc new file mode 100644 index 000000000..55628be7a --- /dev/null +++ b/docs/changes/newsfragments/232.misc @@ -0,0 +1 @@ +Adopt ``pre-commmit`` for adding and managing git pre-commit hooks by `Synchon Mandal`_ -- 2.52.0 From d0316152a2dce93580072ee726c6d6883cb18024 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 5 Jun 2023 14:21:07 +0200 Subject: [PATCH 10/10] docs: add information about bypassing git commit hooks in contribution.rst --- docs/contribution.rst | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/docs/contribution.rst b/docs/contribution.rst index 65e862dd0..7caf569ad 100644 --- a/docs/contribution.rst +++ b/docs/contribution.rst @@ -55,6 +55,14 @@ Setting up the local development environment git add . git commit -m ": " + In case, you want to commit some WIP (work-in-progress) code, please indicate + that in the commit message and use the flag ``--no-verify`` with + ``git commit`` like so: + + .. code-block:: bash + + git commit --no-verify -m "WIP: " + #. When you're done making changes, check that your changes pass our test suite. This is all included with ``tox``. @@ -68,7 +76,6 @@ Setting up the local development environment tox --parallel - #. Push your branch to GitHub. .. code-block:: bash -- 2.52.0