refactor(nextflow): lower from a resolved view of the graph

.github/workflows/build_wheel.yml

@@ -31,10 +31,12 @@ jobs:
       - name: Install sophios 🔧
         run: |
           pip install .[test]
+      # The tests marked package and the Nextflow tests that do not run
+      # Nextflow: no other pull-request lane runs them.
       - name: Test with pytest
         run: |
-          python -m pytest -k test_cwl_docker_extract
-          python -m pytest -m "not skip_pypi_ci and not nextflow" -k "not test_cwl_docker_extract" -vv
+          python -m pytest -m "package and not nextflow and not skip_pypi_ci" -vv
+          python -m pytest tests/core/nextflow -m "not nextflow and not nextflow_corpus and not skip_pypi_ci" -vv
 
       - name: Build sophios
         run: |

.github/workflows/lint_and_test.yml

@@ -255,14 +255,13 @@ jobs:
         if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
         run: cd sophios/ && pytest tests/core/test_entry_points.py tests/core/test_ci_coverage.py
 
-      # The packaging lane runs `pytest -m "not skip_pypi_ci"`, so a test with
-      # that marker runs only where a step names its file. This is that place,
-      # filtered to exactly the complement so nothing here is run twice: these
-      # files' unmarked tests are already covered by the packaging lane's
-      # default collection. tests/core/test_ci_coverage.py fails if a
-      # skip_pypi_ci test exists that no lane collects, which is how these came
-      # to light — 26 of them had never executed anywhere; only the files its
-      # LOCAL_ONLY names, which no lane can run, are run by hand instead.
+      # The release lane runs `pytest -m "not skip_pypi_ci"` and the package job
+      # leaves that marker out too, so a test with it runs only where a step
+      # names its file. This is that place, filtered to exactly the complement
+      # so nothing here is run twice. tests/core/test_ci_coverage.py fails if a
+      # test exists that no pull-request or weekly lane collects, which is how
+      # these came to light; only the files its LOCAL_ONLY names, which no lane
+      # can run, are run by hand instead.
       - name: PyTest Environment-Dependent
         if: ${{ !cancelled() && steps.setup.outcome == 'success' }}
         timeout-minutes: 20

.github/workflows/python_matrix_weekly.yml

@@ -1,7 +1,10 @@
 name: Python Matrix Weekly
 
-# The Nextflow tests on every Python Sophios supports, on Ubuntu: the plain
-# ones the package job runs on 3.11, and the ones that run Nextflow.
+# The whole suite on every Python Sophios supports, on Ubuntu, set up as Lint And
+# Test sets up its Linux leg. The corpora need the sibling repositories, which
+# the other lanes check out: cwl_corpus is Run Workflows' and Lint And Test's,
+# nextflow_corpus is Run Workflows', and skip_pypi_ci is what a hosted runner
+# cannot run.
 
 on:
   schedule:
@@ -11,8 +14,12 @@ on:
 permissions:
   contents: read
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
-  nextflow:
+  suite:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -21,8 +28,14 @@ jobs:
     steps:
       - uses: actions/checkout@v5
 
-      - uses: actions/setup-python@v6
+      - name: Setup miniforge
+        uses: conda-incubator/setup-miniconda@v4.0.1
         with:
+          miniforge-variant: Miniforge3
+          miniforge-version: 24.7.1-2
+          environment-file: install/system_deps.yml
+          activate-environment: wic
+          channels: conda-forge
           python-version: ${{ matrix.python }}
 
       - uses: actions/setup-java@v5
@@ -31,7 +44,7 @@ jobs:
           java-version: '17'
 
       - name: Install Sophios
-        run: pip install ".[test]"
+        run: pip install -e ".[all_except_runner_src]"
 
       - name: Install pinned Nextflow
         env:
@@ -42,10 +55,10 @@ jobs:
           echo "${RUNNER_TEMP}" >> "${GITHUB_PATH}"
           NXF_ANSI_LOG=false "${RUNNER_TEMP}/nextflow" -version | grep 'version 26.10.5'
 
-      - name: PyTest Nextflow
-        timeout-minutes: 20
+      - name: PyTest the suite without its corpora
+        timeout-minutes: 60
         env:
           NXF_ANSI_LOG: "false"
           NXF_OFFLINE: "true"
           NXF_VER: "26.10.5"
-        run: pytest tests/core/nextflow -m "not nextflow_corpus"
+        run: pytest tests -m "not cwl_corpus and not nextflow_corpus and not skip_pypi_ci"

.github/workflows/run_workflows.yml

@@ -227,9 +227,8 @@ jobs:
       run: cd sophios/ && pytest tests/core/test_python_api_workflow.py -k "not test_compile_python_workflows"
 
     # Workflow.from_wic and write_wic over every .wic root the config reaches.
-    # Only here does the config reach the mm-workflows and image-workflows
-    # roots: the packaging lane, which also selects this file, checks out
-    # neither, so a round trip that breaks on those roots alone was green.
+    # No other lane runs this round trip over the mm-workflows and
+    # image-workflows roots, so a break on those roots alone would be green.
     - name: PyTest Python API from .wic (corpus round trip)
       if: ${{ !cancelled() && steps.setup.outcome == 'success' && steps.corpus.outcome == 'success' }}
       run: cd sophios/ && pytest tests/core/test_python_api_from_wic.py