From d0df4b03e35676d5a303027d813c94013c7e0286 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Tue, 12 Oct 2021 07:14:20 +0000
Subject: [PATCH] ci: Duplicate tests for subworkflows (#815)

Causing an issue with only running the subworkflow tests and now the
modules. Just for now, we can come back to this.
---
 .github/workflows/pytest-workflow.yml | 125 +++++++++++++++++++++++---
 1 file changed, 113 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index 6f395409..5ece35b8 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -6,14 +6,12 @@ on:
     branches: [master]
 
 jobs:
-  changes:
-    name: Check for changes
+  ###########
+  # Modules #
+  ###########
+  module_changes:
+    name: Check for changes in the modules
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        filter:
-          ["tests/config/pytest_modules.yml", "tests/config/pytest_subworkflows.yml"]
     outputs:
       # Expose matched filters as job 'modules' output variable
       modules: ${{ steps.filter.outputs.changes }}
@@ -23,19 +21,122 @@ jobs:
       - uses: dorny/paths-filter@v2
         id: filter
         with:
-          filters: ${{ matrix.filter }}
+          filters: "tests/config/pytest_modules.yml"
 
-  test:
+  module_test:
     runs-on: ubuntu-20.04
 
     name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
-    needs: changes
-    if: needs.changes.outputs.modules != '[]'
+    needs: module_changes
+    if: needs.module_changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
         nxf_version: ["21.04.0"]
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        tags: ["${{ fromJson(needs.modules_changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Setup miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}-${{ matrix.nxf_version }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+
+  ################
+  # Subworkflows #
+  ################
+  subworkflow_changes:
+    name: Check for changes in the subworkflows
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'subworkflows' output variable
+      subworkflows: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_subworkflows.yml"
+
+  subworkflow_test:
+    runs-on: ubuntu-20.04
+
+    name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
+    needs: subworkflow_changes
+    if: needs.subworkflow_changes.outputs.subworkflows != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        nxf_version: ["21.04.0"]
+        tags: ["${{ fromJson(needs.subworkflow_changes.outputs.subworkflows) }}"]
         profile: ["docker", "singularity", "conda"]
     env:
       NXF_ANSI_LOG: false