From 8f7e5c050ee99d277b4ed0c596962ee79fc769a8 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 27 Oct 2021 12:20:31 -0500
Subject: [PATCH] ci: Revert back to one job branch

---
 .github/workflows/pytest-workflow.yml | 118 ++------------------------
 1 file changed, 6 insertions(+), 112 deletions(-)

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index 0b509527..7cbb2689 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -6,11 +6,8 @@ on:
     branches: [master]
 
 jobs:
-  ###########
-  # Modules #
-  ###########
-  module_changes:
-    name: Check for changes in the modules
+  changes:
+    name: Check for changes
     runs-on: ubuntu-latest
     outputs:
       # Expose matched filters as job 'modules' output variable
@@ -23,120 +20,17 @@ jobs:
         with:
           filters: "tests/config/pytest_modules.yml"
 
-  module_test:
+  test:
     runs-on: ubuntu-20.04
 
     name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
-    needs: module_changes
-    if: needs.module_changes.outputs.modules != '[]'
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
         nxf_version: ["21.04.0"]
-        tags: ${{ fromJson(needs.module_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: ${{ fromJson(needs.subworkflow_changes.outputs.subworkflows) }}
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
         profile: ["docker", "singularity", "conda"]
     env:
       NXF_ANSI_LOG: false