Merge remote-tracking branch 'upstream/maint/1.4.x' into maint/1.5.x

Author: effigies

.circleci/config.yml

@@ -18,7 +18,7 @@ jobs:
             - build-v1-{{ .Branch }}-{{ .Revision }}
             - build-v1--{{ .Revision }}
             - build-v1-{{ .Branch }}-
-            - build-v1-master-
+            - build-v1-maint/1.4.x-
             - build-v1-
           paths:
             - /tmp/docker
@@ -97,9 +97,9 @@ jobs:
     steps:
       - restore_cache:
           keys:
-            - env-v1-{{ .Branch }}-
-            - env-v1-master-
-            - env-v1-
+            - env-v2-{{ .Branch }}-
+            - env-v2-maint/1.4.x-
+            - env-v2-
       - run:
           name: Setup git-annex, DataLad & TemplateFlow
           command: |
@@ -109,15 +109,15 @@ jobs:
             git config --global user.email '[email protected]'
             python -m pip install --no-cache-dir -U templateflow
       - save_cache:
-          key: env-v1-{{ .Branch }}-{{ .BuildNum }}
+          key: env-v2-{{ .Branch }}-{{ .BuildNum }}
           paths:
             - /opt/conda
 
       - restore_cache:
           keys:
             - data-v3-{{ .Branch }}-{{ epoch }}
             - data-v3-{{ .Branch }}-
-            - data-v3-master-
+            - data-v3-maint/1.4.x-
             - data-v3-
       - run:
           name: Get test data from ds000003
@@ -185,7 +185,7 @@ jobs:
             - build-v1-{{ .Branch }}-{{ .Revision }}
             - build-v1--{{ .Revision }}
             - build-v1-{{ .Branch }}-
-            - build-v1-master-
+            - build-v1-maint/1.4.x-
             - build-v1-
       - run:
           name: Docker authentication
@@ -215,7 +215,7 @@ jobs:
           keys:
             - data-v3-{{ .Branch }}-{{ epoch }}
             - data-v3-{{ .Branch }}-
-            - data-v3-master-
+            - data-v3-maint/1.4.x-
             - data-v3-
 
       - run:
@@ -337,7 +337,7 @@ jobs:
             - build-v1-{{ .Branch }}-{{ .Revision }}
             - build-v1--{{ .Revision }}
             - build-v1-{{ .Branch }}-
-            - build-v1-master-
+            - build-v1-maint/1.4.x-
             - build-v1-
           paths:
             - /tmp/docker

.github/workflows/pythonpackage.yml

@@ -9,22 +9,46 @@ on:
     tags: [ '*' ]
   pull_request:
     branches: [ master, 'maint/*' ]
+  schedule:
+    - cron: '0 0 * * *'
+
+concurrency:
+  group: python-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
+  check_if_skip:
+    runs-on: ubuntu-latest
+    outputs:
+      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
+    steps:
+      - name: Get repo
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+      - name: Print head git commit message
+        id: get_commit_message
+        run: |
+          if [[ -z "$COMMIT_MSG" ]]; then
+            COMMIT_MSG=$(git show -s --format=%s)
+          fi
+          echo $COMMIT_MSG
+          echo "::set-output name=commit_message::$COMMIT_MSG"
+        env:
+          COMMIT_MSG: ${{ github.event.head_commit.message }}
+
   build:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+    needs: check_if_skip
+    if: "!contains(needs.check_if_skip.outputs.commit_message, '[skip ci]')"
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10"]
     steps:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+    - name: Set up Python 3
+      uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: 3
     - name: Display Python version
       run: python -c "import sys; print(sys.version)"
     - name: Check python version and install build
@@ -42,24 +66,40 @@ jobs:
 
   get_data:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - name: Create test data directory
       run: mkdir -p $HOME/.cache/stanford-crn
     - name: Load test data cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: stanford-crn
       with:
         path: ~/.cache/stanford-crn/
         key: data-v0-${{ github.ref_name }}-${{ github.sha }}
         restore-keys: |
           data-v0-${{ github.ref_name }}-
           data-v0-
+    - name: Setup conda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-activate-base: true
+        activate-environment: ""
+    - name: Verify environment
+      run: |
+        conda info
+        which python
     - name: Install datalad
       run: |
-        sudo apt-get update -y
-        sudo apt-get install -y git-annex --no-install-recommends
-        python -m pip install datalad==0.14.7 datalad-osf
+        python -m pip install datalad-installer
+        datalad-installer --sudo ok git-annex
+        python -m pip install datalad datalad-osf
         datalad wtf
+    - name: Pacify git
+      run: |
+        git config --global user.email "[email protected]"
+        git config --global user.name "Niworkflows Action"
     - name: Fetch test data
       run: |
         DS=$HOME/.cache/stanford-crn
@@ -83,6 +123,7 @@ jobs:
             install: wheel
           - python-version: 3.9
             install: editable
+
     env:
       INSTALL_TYPE: ${{ matrix.install }}
 
@@ -91,17 +132,17 @@ jobs:
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Load test data cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: stanford-crn
       with:
         path: ~/.cache/stanford-crn/
         key: data-v0-${{ github.ref_name }}-${{ github.sha }}
     - name: Load TemplateFlow cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: templateflow
       with:
         path: ~/.cache/templateflow
@@ -142,20 +183,85 @@ jobs:
         test "${INSTALLED_VERSION}" = "${THISVERSION}"
     - name: Install test dependencies
       run: python -m pip install "niworkflows[tests]"
+    - name: Set TEST_DATA_HOME
+      run: echo "TEST_DATA_HOME=$HOME/.cache/stanford-crn" >> $GITHUB_ENV
     - name: Run tests
       uses: GabrielBB/xvfb-action@v1
       with:
         run: pytest -sv --no-xvfb --doctest-modules --cov niworkflows niworkflows
     - uses: codecov/codecov-action@v2
       name: Submit to CodeCov
 
+  test-pre:
+    needs: [get_data, check_if_skip]
+    if: ${{ !contains(needs.check_if_skip.outputs.commit_message, '[skip pre]') }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9, "3.10"]
+        install: [repo]
+        pip-flags: ['--pre']
+
+    env:
+      INSTALL_TYPE: ${{ matrix.install }}
+      PIP_FLAGS: ${{ matrix.pip-flags }}
+
+    steps:
+    - name: Debug commit message
+      run: echo "${{ needs.check_if_skip.outputs.commit_message }}"
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Load test data cache
+      uses: actions/cache@v3
+      id: stanford-crn
+      with:
+        path: ~/.cache/stanford-crn/
+        key: data-v0-${{ github.ref_name }}-${{ github.sha }}
+    - name: Load TemplateFlow cache
+      uses: actions/cache@v3
+      id: templateflow
+      with:
+        path: ~/.cache/templateflow
+        key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
+        restore-keys: |
+          templateflow-v0-${{ github.ref_name }}-
+          templateflow-v0-
+    - name: Install package
+      run: python -m pip install $PIP_FLAGS .
+    - name: Check version
+      run: |
+        # Interpolate version
+        if [[ "$GITHUB_REF" == refs/tags/* ]]; then
+          TAG=${GITHUB_REF##*/}
+        fi
+        THISVERSION=$( python get_version.py )
+        THISVERSION=${TAG:-$THISVERSION}
+        INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
+        echo "VERSION: \"${THISVERSION}\""
+        echo "INSTALLED: \"${INSTALLED_VERSION}\""
+        test "${INSTALLED_VERSION}" = "${THISVERSION}"
+    - name: Install test dependencies
+      run: python -m pip install $PIP_FLAGS "niworkflows[tests]"
+    - name: Set TEST_DATA_HOME
+      run: echo "TEST_DATA_HOME=$HOME/.cache/stanford-crn" >> $GITHUB_ENV
+    - name: Run tests
+      run: pytest -sv --doctest-modules -n auto --cov niworkflows niworkflows
+    - uses: codecov/codecov-action@v3
+      name: Submit to CodeCov
+
   flake8:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+    needs: check_if_skip
+    if: "!contains(needs.check_if_skip.outputs.commit_message, '[skip ci]')"
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python 3.7
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.7
     - run: pip install flake8

CHANGES.rst

@@ -54,6 +54,26 @@ This release upgrades the Dockerfile to use FSL6, and includes some new interfac
   * FIX: Scipy docs path (#681)
   * TEST: Drop excessively long interface equivalence tests (#674)
 
+1.4.10 (September 14, 2022)
+===========================
+Bug-fix release in the 1.4.x series
+
+Backports and minor maintenance.
+
+* FIX: TSV2JSON should convert empty TSV files to empty JSON files (#747)
+* FIX: Stop relying on deprecated indexing behavior (#730)
+* MNT: Update docs and GitHub actions config from master in LTS branch (#748)
+
+1.4.9 (April 21, 2022)
+======================
+Bug-fix release in the 1.4.x series.
+
+This release includes improvements to the reliability of the BOLD masking workflow,
+as well as an fMRIPrep bug-fix when reusing multi-echo anatomicals.
+
+  * FIX: Account for potential lists of lists in multi-echo cases (#719)
+  * FIX: Improve reliability of BOLD masking workflow (#712)
+
 1.4.8 (April 08, 2022)
 ======================
 Bug-fix release in the 1.4.x series.
@@ -230,6 +250,16 @@ A list of prominent changes can be found below. (With thanks to Lea Waller for t
     * ``NormalizeMotionParams`` now under ``confounds``.
     * ``FMRISummary``, ``CompCorVariancePlot``, ``ConfoundsCorrelationPlot`` from ``plotting``
 
+1.3.8 (September 14, 2022)
+==========================
+Bug-fix release in the 1.3.x series
+
+Backports and minor maintenance.
+
+* FIX: TSV2JSON should convert empty TSV files to empty JSON files (#747)
+* FIX: Stop relying on deprecated indexing behavior (#730)
+* MNT: Update docs and GitHub actions config from master in LTS branch (#748)
+
 1.3.7 (March 31, 2022)
 ======================
 Bug-fix release in the 1.3.x series

docs/conf.py

@@ -14,7 +14,29 @@
 #
 import os
 import sys
+from unittest import mock
+import tempfile
+
 from packaging.version import Version
+import templateflow
+
+# Prevent etelemetry from loading at all
+# Could set NO_ET environment variable, but why?
+MOCKS = [
+    "etelemetry",
+    "matplotlib",
+    "matplotlib.pyplot",
+    "matplotlib.cm",
+    "matplotlib.colors",
+    "matplotlib.colorbar",
+]
+sys.modules.update({mod: mock.Mock() for mod in MOCKS})
+
+# Keep templateflow API intact except for fetching files.
+# Return an existent but empty temporary file
+tffiledesc, tffilename = tempfile.mkstemp()
+os.close(tffiledesc)
+templateflow.api.get = mock.MagicMock(return_value=tffilename)
 
 from niworkflows import __version__, __copyright__, __packagename__
 
@@ -47,7 +69,6 @@
 ]
 
 autodoc_mock_imports = [
-    "matplotlib",
     "nilearn",
     "nitime",
     "numpy",
@@ -57,6 +78,7 @@
     "svgutils",
     "templateflow",
     "transforms3d",
+    "yaml",
 ]
 
 # Accept custom section names to be parsed for numpy-style docstrings
@@ -234,13 +256,13 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     "bids": ("https://bids-standard.github.io/pybids/", None),
-    "matplotlib": ("https://matplotlib.org/", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
     "nibabel": ("https://nipy.org/nibabel/", None),
     "nipype": ("https://nipype.readthedocs.io/en/latest/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/dev", None),
     "python": ("https://docs.python.org/3/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy-1.8.0/html-scipyorg/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "smriprep": ("https://www.nipreps.org/smriprep/", None),
     "surfplot": ("https://surfplot.readthedocs.io/en/latest/", None),
     "templateflow": ("https://www.templateflow.org/python-client", None),