From 8cb732d961c94a7077e3ac2335b80828613f8643 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Wed, 12 Jul 2023 16:10:26 +1000
Subject: [PATCH] combined build and generate into single step

---
 .github/workflows/package-pydra.yml | 60 +++++++----------------------
 pydra/pydra-auto-gen.py             |  2 +-
 2 files changed, 15 insertions(+), 47 deletions(-)

diff --git a/.github/workflows/package-pydra.yml b/.github/workflows/package-pydra.yml
index f433f2740f..758ddac512 100644
--- a/.github/workflows/package-pydra.yml
+++ b/.github/workflows/package-pydra.yml
@@ -17,7 +17,7 @@ on:
 
 jobs:
 
-  build:
+  generate-pydra:
 
     runs-on: ubuntu-latest
 
@@ -29,60 +29,28 @@ jobs:
       CXX_COMPILER_LAUNCHER: sccache
 
     steps:
-    - uses: actions/checkout@v1
-
-    - name: install dependencies
-      run: |
-         sudo apt-get update
-         sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev 
-
-    - name: Run sccache-cache
-      uses: mozilla-actions/sccache-action@v0.0.3
-        
-    - name: configure
-      run: ./configure -assert || { cat configure.log; false; }
-
-    - name: build
-      run: ./build -nowarnings -persistent -nopaginate || { cat build.log; false; }
-    - name: Upload bin directory
-      uses: actions/upload-artifact@v2
-      with:
-        name: Bin
-        path: bin
-    - name: Upload shared lib
-      uses: actions/upload-artifact@v2
-      with:
-        name: Shared
-        path: lib/libmrtrix.so
-
+      - uses: actions/checkout@v1
 
-  generate-pydra:
-    needs: [build]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Download bin directory
-        uses: actions/download-artifact@v2
-        with:
-          name: Bin
-          path: bin
-      - name: Set execute perms on bin
-        run: chmod +x ./bin/*
-      - name: Download shared lib
-        uses: actions/download-artifact@v2
-        with:
-          name: Shared
-          path: lib/libmrtrix.so
+      - name: Install MRtrix dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev 
+      - name: Run sccache-cache
+        uses: mozilla-actions/sccache-action@v0.0.3
+      - name: Configure MRtrix
+        run: ./configure -assert || { cat configure.log; false; }
+      - name: Build MRtrix
+        run: ./build -nowarnings -persistent -nopaginate || { cat build.log; false; }
       - name: Set PATH Variable
         run: echo "PATH=$PATH:$(pwd)/bin" >> $GITHUB_ENV
       - name: Set LD_LIBRARY_PATH Variable
         run: echo "LD_LIBRARY_PATH=$(pwd)/lib" >> $GITHUB_ENV        
       - name: Set up Python
         uses: actions/setup-python@v2
-      - name: Install build dependencies
+      - name: Install Python build dependencies
         run: |
           python -m pip install --upgrade pip
-      - name: Install requirements
+      - name: Install pydra-auto-gen requirements
         run: |
           pip install -r pydra/requirements.txt
       - name: Generate task specifications
diff --git a/pydra/pydra-auto-gen.py b/pydra/pydra-auto-gen.py
index ea2f9cfca7..16c27dfbd5 100644
--- a/pydra/pydra-auto-gen.py
+++ b/pydra/pydra-auto-gen.py
@@ -96,6 +96,6 @@ def auto_gen_mrtrix3_pydra(cmd_dir: Path, output_dir: Path, log_errors: bool):
         [
             str(script_dir.parent / "bin"),
             str(script_dir / "src" / "pydra" / "tasks" / "mrtrix3" / "latest"),
-            "--log-errors",
+            "--raise-errors",
         ]
     )