Merge pull request #360 from mgxd/rf/fit-apply

RF: Move to fit/apply workflow

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.html,dataset_description.json,*.bib
+# te - TE
+# Weill - name
+# reson - Reson. abbreviation in citation
+ignore-words-list = te,weill,reson

.github/workflows/style.yml

@@ -1,4 +1,4 @@
-name: Style check
+name: Style + spelling check
 
 on:
   push:
@@ -11,30 +11,27 @@ defaults:
   run:
     shell: bash
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 permissions:
   contents: read
 
 jobs:
-  build:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+  style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run ruff check .
+      - run: pipx run ruff format --diff .
+
+  codespell:
+    name: Check for spelling errors
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.11']
 
     steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 1  # Only fetch the latest commit
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install black isort
-    - name: black code formatting check
-      run: |
-        black --check nibabies/
-    - name: isort formatting check
-      run: isort nibabies/ --check-only
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.maint/contributors.json

@@ -1,4 +1,9 @@
 [
+  {
+    "affiliation": "Department of Pediatrics, University of Minnesota, MN, USA",
+    "name": "Madison, Thomas",
+    "orcid": "0000-0003-3030-6580"
+  },
   {
     "affiliation": "Montreal Neurological Institute, McGill University",
     "name": "Huberty, Scott",

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
+exclude: ".*/data/.*"
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
--   repo: https://github.com/psf/black
-    rev: 22.3.0
+      - id: trailing-whitespace
+        exclude: '.*\.svg'
+      - id: end-of-file-fixer
+        exclude: '.*\.svg'
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.0
     hooks:
-    -   id: black
-        files: ^nibabies/
--   repo: https://github.com/pycqa/isort
-    rev: 5.10.1
-    hooks:
-    -   id: isort
-        files: ^nibabies/
+      - id: ruff
+      - id: ruff-format

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
   jobs:
     post_checkout:
       - git fetch --unshallow
@@ -15,3 +15,5 @@ python:
       path: .
       extra_requirements:
         - doc
+    - method: pip
+      path: wrapper/

CHANGES.md

@@ -36,9 +36,9 @@ Previous, *NiBabies* expected input from the `--derivatives` flag to be in T1w s
   * DKR: Add M-CRIB-S to Docker container (#283)
   * DKR: Update dependencies, split into multi-stage build
   * ENH: Add option to exclude projecting high variance voxels to surface (#278)
-  * ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (#279)
+  * ENH: Resample morphometrics to fsLR CIFTI-2 files when outputting CIFTIs (#279)
   * ENH: Add MCRIBReconAll as alternative surface reconstruction method (#283)
-  * ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (#286)
+  * ENH: Reorder anatomical processing, run ANTs DenoiseImage on anatomicals (#286)
   * ENH: Extract participant ages from BIDS sources, deprecate `--age-months` (#287)
   * ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (#296)
   * ENH: Allow precomputed derivatives in T1w or T2w space (#305)

Dockerfile

@@ -23,15 +23,15 @@
 # SOFTWARE.
 
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20230605
+ARG BASE_IMAGE=ubuntu:jammy-20240405
 
 # NiBabies wheel
 FROM python:slim AS src
 RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
-COPY . /src/nibabies
-RUN python -m build /src/nibabies
+COPY . /src
+RUN python -m build /src
 
 # Older Python to support legacy MCRIBS
 FROM python:3.6.15-slim as pyenv
@@ -90,19 +90,26 @@ RUN mkdir /opt/workbench && \
 
 # Micromamba
 FROM downloader as micromamba
+
+# Install a C compiler to build extensions when needed.
+# traits<6.4 wheels are not available for Python 3.11+, but build easily.
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
 WORKDIR /
 # Bump the date to current to force update micromamba
-RUN echo "2023.06.29"
-RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+RUN echo "2024.04.25" && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
+COPY requirements.txt /tmp/requirements.txt
+WORKDIR /tmp
 RUN micromamba create -y -f /tmp/env.yml && \
     micromamba clean -y -a
+
 ENV PATH="/opt/conda/envs/nibabies/bin:$PATH"
-RUN /opt/conda/envs/nibabies/bin/npm install -g svgo@^2.8 bids-validator@1.11.0 && \
+RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
     rm -r ~/.npm
-COPY requirements.txt /tmp/requirements.txt
-RUN /opt/conda/envs/nibabies/bin/pip install --no-cache-dir -r /tmp/requirements.txt
 
 # Main container
 FROM ${BASE_IMAGE} as nibabies
@@ -207,7 +214,7 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
 
 # MCRIBS (required legacy python)
-COPY --from=nipreps/mcribs@sha256:6c7a8dedd61d0ead8c7c4a57ab158928c1c1d787d87dae33ab7ee43226fb1e0f /opt/MCRIBS/ /opt/MCRIBS
+COPY --from=nipreps/mcribs@sha256:d5ea7616402cbc0b80f32634832dce540a32bb1d5e1e61dfdd2cc795dba8944a /opt/MCRIBS/ /opt/MCRIBS
 COPY --from=pyenv /usr/local/lib/ /usr/local/lib/
 ENV PATH="/opt/MCRIBS/bin:/opt/MCRIBS/MIRTK/MIRTK-install/bin:/opt/MCRIBS/MIRTK/MIRTK-install/lib/tools:${PATH}" \
     LD_LIBRARY_PATH="/opt/MCRIBS/lib:/opt/MCRIBS/ITK/ITK-install/lib:/opt/MCRIBS/VTK/VTK-install/lib:/opt/MCRIBS/MIRTK/MIRTK-install/lib:/usr/local/lib:${LD_LIBRARY_PATH}" \
@@ -257,7 +264,7 @@ RUN ${CONDA_PYTHON} -m pip install --no-cache-dir --upgrade templateflow && \
     find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
 
 # Install pre-built wheel
-COPY --from=src /src/nibabies/dist/*.whl .
+COPY --from=src /src/dist/*.whl .
 RUN ${CONDA_PYTHON} -m pip install --no-cache-dir $( ls *.whl )[telemetry,test]
 
 # Facilitate Apptainer use

docs/community.md

@@ -1,6 +1,6 @@
 ## NiPreps Community
 
-Check out the [official NiPreps community page](https://www.nipreps.org/community/), where topics such as contributing, code of coduct, and licensing are outlined.
+Check out the [official NiPreps community page](https://www.nipreps.org/community/), where topics such as contributing, code of conduct, and licensing are outlined.
 
 
 ## NiBabies Coding Style