Deploy to DockerHub with GitHub Action (#46)

* Update parser.py * Update config.yml * Run isort. * Update. * Update pyproject.toml * update * fix. * Update get_data.py * Deploy to DockerHub with GitHub Action. * Update parser.py * Apply suggestions from code review Co-authored-by: Chris Markiewicz <[email protected]> * Update action versions. --------- Co-authored-by: Chris Markiewicz <[email protected]>
nipreps · Aug 28, 2024 · 2d6a11d · 2d6a11d
1 parent 60fbfb2
commit 2d6a11d
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Showing 12 changed files with 142 additions and 102 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -5,7 +5,7 @@ orbs:
 .dockersetup: &dockersetup
   docker:
     - image: cimg/python:3.12
-  working_directory: /src/fmripost_aroma
+  working_directory: /src/fmripost-aroma
 
 runinstall: &runinstall
     name: Install fMRIPost-AROMA
@@ -15,8 +15,8 @@ runinstall: &runinstall
         VERSION="$CIRCLE_TAG"
       fi
       git checkout $CIRCLE_BRANCH
-      echo "${VERSION}" > /src/fmripost_aroma/src/fmripost_aroma/VERSION
-      echo "include src/fmripost_aroma/VERSION" >> /src/fmripost_aroma/src/fmripost_aroma/MANIFEST.in
+      echo "${VERSION}" > /src/fmripost-aroma/src/fmripost_aroma/VERSION
+      echo "include src/fmripost_aroma/VERSION" >> /src/fmripost-aroma/src/fmripost_aroma/MANIFEST.in
       pip install .[tests] --progress-bar off
 
       # Precaching fonts, set 'Agg' as default backend for matplotlib
@@ -48,12 +48,12 @@ jobs:
       - run:
           name: Download ds005115_raw test data
           command: |
-            cd /src/fmripost_aroma/.circleci
+            cd /src/fmripost-aroma/.circleci
             python get_data.py $PWD/data ds005115_raw
       - save_cache:
           key: ds005115_raw-01
           paths:
-            - /src/fmripost_aroma/.circleci/data/ds005115_raw
+            - /src/fmripost-aroma/.circleci/data/ds005115_raw
 
   download_ds005115_resampling:
     <<: *dockersetup
@@ -65,12 +65,12 @@ jobs:
       - run:
           name: Download ds005115_resampling test data
           command: |
-            cd /src/fmripost_aroma/.circleci
+            cd /src/fmripost-aroma/.circleci
             python get_data.py $PWD/data ds005115_resampling
       - save_cache:
           key: ds005115_resampling-01
           paths:
-            - /src/fmripost_aroma/.circleci/data/ds005115_resampling
+            - /src/fmripost-aroma/.circleci/data/ds005115_resampling
 
   download_ds005115_deriv_no_mni6:
     <<: *dockersetup
@@ -82,12 +82,12 @@ jobs:
       - run:
           name: Download ds005115_deriv_no_mni6 test data
           command: |
-            cd /src/fmripost_aroma/.circleci
+            cd /src/fmripost-aroma/.circleci
             python get_data.py $PWD/data ds005115_deriv_no_mni6
       - save_cache:
           key: ds005115_deriv_no_mni6-01
           paths:
-            - /src/fmripost_aroma/.circleci/data/ds005115_deriv_no_mni6
+            - /src/fmripost-aroma/.circleci/data/ds005115_deriv_no_mni6
 
   download_ds005115_deriv_mni6:
     <<: *dockersetup
@@ -99,12 +99,12 @@ jobs:
       - run:
           name: Download ds005115_deriv_mni6 test data
           command: |
-            cd /src/fmripost_aroma/.circleci
+            cd /src/fmripost-aroma/.circleci
             python get_data.py $PWD/data ds005115_deriv_mni6
       - save_cache:
           key: ds005115_deriv_mni6-01
           paths:
-            - /src/fmripost_aroma/.circleci/data/ds005115_deriv_mni6
+            - /src/fmripost-aroma/.circleci/data/ds005115_deriv_mni6
 
   ds005115_deriv_only:
     <<: *dockersetup
@@ -117,18 +117,18 @@ jobs:
           name: Test the PYAFQ standalone recon workflow
           no_output_timeout: 1h
           command: |
-            pytest -rP -o log_cli=true -m "pyafq_recon_full" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            pytest -rP -o log_cli=true -m "pyafq_recon_full" --cov-config=/src/fmripost-aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost-aroma/.circleci/data --output_dir=/src/fmripost-aroma/.circleci/out --working_dir=/src/fmripost-aroma/.circleci/work fmripost_aroma
             mkdir /src/coverage
-            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.pyafq_recon_full
+            mv /src/fmripost-aroma/.coverage /src/coverage/.coverage.pyafq_recon_full
             # remove nifti files before uploading artifacts
-            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
-            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
       - persist_to_workspace:
           root: /src/coverage/
           paths:
             - .coverage.pyafq_recon_full
       - store_artifacts:
-          path: /src/fmripost_aroma/.circleci/out/pyafq_recon_full/
+          path: /src/fmripost-aroma/.circleci/out/pyafq_recon_full/
 
   ds005115_deriv_and_raw:
     <<: *dockersetup
@@ -141,18 +141,18 @@ jobs:
           name: Test the PYAFQ workflow with mrtrix tractography
           no_output_timeout: 1h
           command: |
-            pytest -rP -o log_cli=true -m "pyafq_recon_external_trk" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            pytest -rP -o log_cli=true -m "pyafq_recon_external_trk" --cov-config=/src/fmripost-aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost-aroma/.circleci/data --output_dir=/src/fmripost-aroma/.circleci/out --working_dir=/src/fmripost-aroma/.circleci/work fmripost_aroma
             mkdir /src/coverage
-            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.pyafq_recon_external_trk
+            mv /src/fmripost-aroma/.coverage /src/coverage/.coverage.pyafq_recon_external_trk
             # remove nifti files before uploading artifacts
-            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
-            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
       - persist_to_workspace:
           root: /src/coverage/
           paths:
             - .coverage.pyafq_recon_external_trk
       - store_artifacts:
-          path: /src/fmripost_aroma/.circleci/out/pyafq_recon_external_trk/
+          path: /src/fmripost-aroma/.circleci/out/pyafq_recon_external_trk/
 
   ds005115_resampling_and_raw:
     <<: *dockersetup
@@ -165,18 +165,18 @@ jobs:
           name: Test scalar_mapping workflow
           no_output_timeout: 1h
           command: |
-            pytest -rP -o log_cli=true -m "scalar_mapper" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            pytest -rP -o log_cli=true -m "scalar_mapper" --cov-config=/src/fmripost-aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost-aroma/.circleci/data --output_dir=/src/fmripost-aroma/.circleci/out --working_dir=/src/fmripost-aroma/.circleci/work fmripost_aroma
             mkdir /src/coverage
-            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.scalar_mapper
+            mv /src/fmripost-aroma/.coverage /src/coverage/.coverage.scalar_mapper
             # remove nifti files before uploading artifacts
-            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
-            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
       - persist_to_workspace:
           root: /src/coverage/
           paths:
             - .coverage.scalar_mapper
       - store_artifacts:
-          path: /src/fmripost_aroma/.circleci/out/scalar_mapper/
+          path: /src/fmripost-aroma/.circleci/out/scalar_mapper/
 
   pytests:
     <<: *dockersetup
@@ -191,18 +191,18 @@ jobs:
       - run:
           name: Test the DIPY recon workflows
           command: |
-            pytest -rP -o log_cli=true -m "amico_noddi" --cov-config=/src/fmripost_aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost_aroma/.circleci/data --output_dir=/src/fmripost_aroma/.circleci/out --working_dir=/src/fmripost_aroma/.circleci/work fmripost_aroma
+            pytest -rP -o log_cli=true -m "amico_noddi" --cov-config=/src/fmripost-aroma/pyproject.toml --cov-append --cov-report term-missing --cov=fmripost_aroma --data_dir=/src/fmripost-aroma/.circleci/data --output_dir=/src/fmripost-aroma/.circleci/out --working_dir=/src/fmripost-aroma/.circleci/work fmripost_aroma
             mkdir /src/coverage
-            mv /src/fmripost_aroma/.coverage /src/coverage/.coverage.amico_noddi
+            mv /src/fmripost-aroma/.coverage /src/coverage/.coverage.amico_noddi
             # remove nifti files before uploading artifacts
-            find /src/fmripost_aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
-            find /src/fmripost_aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/fmripost-aroma/.circleci/out/ -name "*.fib.gz" -type f -delete
       - persist_to_workspace:
           root: /src/coverage/
           paths:
             - .coverage.amico_noddi
       - store_artifacts:
-          path: /src/fmripost_aroma/.circleci/out/amico_noddi/
+          path: /src/fmripost-aroma/.circleci/out/amico_noddi/
 
   merge_coverage:
     <<: *dockersetup
@@ -234,7 +234,7 @@ jobs:
       TZ: "/usr/share/zoneinfo/America/New_York"
     docker:
       - image: cimg/base:2020.09
-    working_directory: /tmp/src/fmripost_aroma
+    working_directory: /tmp/src/fmripost-aroma
     steps:
       - checkout
       - setup_remote_docker:
@@ -379,12 +379,3 @@ workflows:
               only: main
             tags:
               only: /.*/
-
-      - build_and_deploy:
-          requires:
-            - deployable
-          filters:
-            branches:
-              only: main
-            tags:
-              only: /.*/
diff --git a/.circleci/get_data.py b/.circleci/get_data.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Download test data."""
+
 import sys
 
 from fmripost_aroma.tests.utils import download_test_data

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -0,0 +1,46 @@
+name: Publish Docker image
+
+on:
+  push:
+    branches: [main]
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+      attestations: write
+      id-token: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/[email protected]
+
+      - name: Log in to Docker Hub
+        uses: docker/[email protected]
+        with:
+          username: niprepsbot
+          password: ${{ secrets.DOCKER_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: nipreps/fmripost-aroma
+
+      - name: Build and push Docker image
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: true
+          tags: |
+            nipreps/fmripost-aroma:unstable
+            ${{ github.event_name == 'release' && 'nipreps/fmripost-aroma:latest' || '' }}
+            ${{ github.event_name == 'release' && 'nipreps/fmripost-aroma:${{ github.event.release.tag_name }}' || '' }}
diff --git a/pyproject.toml b/pyproject.toml
@@ -108,13 +108,13 @@ dependencies = [
 [tool.hatch.envs.style.scripts]
 fix = [
   "black src/",
-  "isort src/",
   "ruff check --fix src/",
+  "isort src/",
 ]
 check = [
   "black --check --diff src/",
-  "isort --check --diff src/",
   "ruff check --diff src/",
+  "isort --check --diff src/",
 ]
 
 [[tool.hatch.envs.test.matrix]]
@@ -169,6 +169,10 @@ ignore = [
   "S311",  # We are not using random for cryptographic purposes
   "ISC001",
   "S603",
+  "PT023",
+  "S113",
+  "S202",
+  "S602",
 ]
 
 [tool.ruff.lint.flake8-quotes]
@@ -183,6 +187,12 @@ inline-quotes = "single"
 [tool.ruff.format]
 quote-style = "single"
 
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+src_paths = ["isort", "test"]
+known_local_folder = ["fmripost_aroma"]
+
 [tool.pytest.ini_options]
 addopts = '-m "not integration"'
 markers = [

diff --git a/src/fmripost_aroma/cli/parser.py b/src/fmripost_aroma/cli/parser.py
@@ -152,6 +152,38 @@ def _bids_filter(value, parser):
         ),
     )
 
+    g_aroma = parser.add_argument_group('Options for running ICA-AROMA')
+    g_aroma.add_argument(
+        '--melodic-dimensionality',
+        dest='melodic_dim',
+        action='store',
+        default=0,
+        type=int,
+        help=(
+            'Exact or maximum number of MELODIC components to estimate '
+            '(positive = exact, negative = maximum)'
+        ),
+    )
+    g_aroma.add_argument(
+        '--error-on-warnings',
+        dest='err_on_warn',
+        action='store_true',
+        default=False,
+        help=(
+            'Raise an error if ICA-AROMA does not produce sensible output '
+            '(e.g., if all the components are classified as signal or noise)'
+        ),
+    )
+    g_aroma.add_argument(
+        '--denoising-method',
+        action='store',
+        nargs='+',
+        choices=['aggr', 'nonaggr', 'orthaggr'],
+        default=None,
+        dest='denoise_method',
+        help='Denoising method to apply, if any.',
+    )
+
     g_bids = parser.add_argument_group('Options for filtering BIDS queries')
     g_bids.add_argument(
         '--skip_bids_validation',
@@ -345,38 +377,6 @@ def _bids_filter(value, parser):
         ),
     )
 
-    g_aroma = parser.add_argument_group('Options for running ICA_AROMA')
-    g_aroma.add_argument(
-        '--melodic-dimensionality',
-        dest='melodic_dim',
-        action='store',
-        default=0,
-        type=int,
-        help=(
-            'Exact or maximum number of MELODIC components to estimate '
-            '(positive = exact, negative = maximum)'
-        ),
-    )
-    g_aroma.add_argument(
-        '--error-on-warnings',
-        dest='err_on_warn',
-        action='store_true',
-        default=False,
-        help=(
-            'Raise an error if ICA_AROMA does not produce sensible output '
-            '(e.g., if all the components are classified as signal or noise)'
-        ),
-    )
-    g_aroma.add_argument(
-        '--denoising-method',
-        action='store',
-        nargs='+',
-        choices=['aggr', 'nonaggr', 'orthaggr'],
-        default=None,
-        dest='denoise_method',
-        help='Denoising method to apply, if any.',
-    )
-
     g_carbon = parser.add_argument_group('Options for carbon usage tracking')
     g_carbon.add_argument(
         '--track-carbon',