ci: GitHub actions workflow

.github/workflows/build_linux.yml

@@ -29,25 +29,13 @@ jobs:
         sudo apt-get install -y cmake wget ninja-build libblas-dev liblapack-dev liblapacke-dev libboost-all-dev libopenmpi-dev libeigen3-dev libhdf5-dev
         sudo apt-get clean all
 
-    - name: Install Catch v3
-      run: |
-        cd /tmp
-        wget -O Catch2.tar.gz https://github.com/catchorg/Catch2/archive/refs/tags/v3.6.0.tar.gz
-        tar xzf Catch2.tar.gz
-        rm Catch2.tar.gz
-        cd Catch2*
-        cmake -S . -B build  -DBUILD_TESTING=OFF
-        cmake --build build
-        sudo cmake --install build
-
     - name: Install HighFive
       run: |
-        cd /tmp
         wget -O HighFive.tar.gz https://github.com/BlueBrain/HighFive/archive/v2.9.0.tar.gz
         tar xzf HighFive.tar.gz
         rm HighFive.tar.gz
         cd HighFive*
-        cmake -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_USE_BOOST=OFF -DHIGHFIVE_UNIT_TESTS=OFF -S . -B build
+        cmake -S . -B build
         cmake --build build
         sudo cmake --install build
 
@@ -59,10 +47,6 @@ jobs:
       run: |-
         cmake --build build.${{ matrix.build.type }}
 
-    - name: Install
-      run: |-
-        sudo cmake --install build.${{ matrix.build.type }}
-
     - name: Run tests
       run: |-
-        smurff --bist
+        ./build.${{ matrix.build.type }}/bin/tests

.github/workflows/wheels.yml

@@ -1,4 +1,4 @@
-name: Build Wheels
+name: Build
 
 on:
   pull_request:

ci/buildwheel/.gitignore

@@ -0,0 +1,2 @@
+hdf5*/
+openblas*/

ci/buildwheel/install_deps.sh

@@ -8,7 +8,7 @@ cd "$SCRIPT_DIR"
 echo "MACOSX_DEPLOYMENT_TARGET: [$MACOSX_DEPLOYMENT_TARGET]"
 echo "PWD: [$PWD]"
 
-brew install  --formulae eigen ../highfive.rb catch2
+brew install  --formulae eigen ../highfive.rb
 brew uninstall --ignore-dependencies hdf5
 
 ./install_hdf5.sh

ci/buildwheel/install_hdf5.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+
+import logging
+from subprocess import check_call
+import os
+import shutil
+from pathlib import Path
+import h5py
+
+logging.basicConfig(level=logging.INFO)
+
+hdf5_basedir = Path(__file__).parent.absolute()
+# hdf5_install_dir = hdf5_basedir / "hdf5"
+hdf5_install_dir = Path("/usr/local/hdf5")
+
+if hdf5_install_dir.exists():
+    logging.warn(f"install dir already exists: {hdf5_install_dir} -- skipping")
+    exit(0)
+
+major, minor, release = h5py.h5.get_libversion()
+full = f"{major}.{minor}.{release}"
+logging.info(f"found h5py version: {full}")
+
+h5py_package_dir = Path(h5py.__file__).parent
+h5py_lib_dir = h5py_package_dir / '.dylibs'
+logging.info(f"found h5py lib_dir: {h5py_lib_dir}")
+
+hdf5_src_dir = hdf5_basedir / f"hdf5-{full}"
+
+logging.info(f"building in : {hdf5_src_dir}")
+logging.info(f"installing in : {hdf5_install_dir}")
+
+url = f"https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{major}.{minor}/hdf5-{full}/src/hdf5-{full}.tar.gz"
+logging.info(f"download: {url}")
+check_call(f"wget -q {url} -O - | tar -xzf -", shell=True, cwd=hdf5_basedir)
+
+logging.info(f"build and install")
+check_call(f"""
+                ./configure --prefix={hdf5_install_dir} &&
+                make -j &&
+                sudo mkdir -m 777 {hdf5_install_dir} &&
+                make install""",
+            shell=True,
+            cwd=hdf5_src_dir)
+
+hdf5_lib_dir = hdf5_install_dir / "lib"
+hdf5_lib_dir_backup = hdf5_install_dir / "lib.orig"
+
+logging.info(f"replace dylibs in {hdf5_lib_dir} from {h5py_lib_dir}")
+for f in h5py_lib_dir.glob('*.dylib'):
+    logging.info(f"  {f} -> {h5py_lib_dir}/")
+    shutil.copy(f, hdf5_lib_dir)
+
+
+
+
+

ci/converted/audit/audit_summary.md

@@ -0,0 +1,120 @@
+# Audit summary
+
+Summary for [Azure DevOps instance](https://dev.azure.com/ExaScience/smurff/_build)
+
+- GitHub Actions Importer version: **1.3.22039 (9432caa2d13df57db8619b9b253cdf994da6625c)**
+- Performed at: **6/3/24 at 12:31**
+
+## Pipelines
+
+Total: **1**
+
+- Successful: **0 (0%)**
+- Partially successful: **1 (100%)**
+- Unsupported: **0 (0%)**
+- Failed: **0 (0%)**
+
+### Job types
+
+Supported: **1 (100%)**
+
+- YAML: **1**
+
+### Build steps
+
+Total: **28**
+
+Known: **27 (96%)**
+
+- script: **10**
+- bash: **9**
+- PublishBuildArtifacts@1: **5**
+- UsePythonVersion@0: **2**
+- powershell: **1**
+
+Unknown: **1 (3%)**
+
+- CMake@1: **1**
+
+Actions: **35**
+
+- run: **20**
+- actions/[email protected]: **6**
+- actions/[email protected]: **5**
+- actions/[email protected]: **2**
+- ./.github/actions/ci_conda_steps: **2**
+
+### Triggers
+
+Total: **2**
+
+Known: **2 (100%)**
+
+- pullRequest: **1**
+- continuousIntegration: **1**
+
+Actions: **2**
+
+- pull_request: **1**
+- push: **1**
+
+### Environment
+
+Total: **2**
+
+Known: **2 (100%)**
+
+- system_debug: **1**
+- CPU_COUNT: **1**
+
+Actions: **2**
+
+- system_debug: **1**
+- CPU_COUNT: **1**
+
+### Other
+
+Total: **20**
+
+Known: **20 (100%)**
+
+- matrix: **6**
+- CIBW_TEST_REQUIRES: **2**
+- CIBW_TEST_COMMAND: **2**
+- CIBW_ENVIRONMENT: **2**
+- CIBW_BUILD_VERBOSITY: **2**
+- CIBW_BUILD: **2**
+- CIBW_MANYLINUX_X86_64_IMAGE: **1**
+- macOS_sdk_url: **1**
+- macOS_sdk_filename: **1**
+- maxParallel: **1**
+
+Actions: **20**
+
+- matrix: **6**
+- CIBW_TEST_REQUIRES: **2**
+- CIBW_TEST_COMMAND: **2**
+- CIBW_ENVIRONMENT: **2**
+- CIBW_BUILD_VERBOSITY: **2**
+- CIBW_BUILD: **2**
+- CIBW_MANYLINUX_X86_64_IMAGE: **1**
+- macOS_sdk_url: **1**
+- macOS_sdk_filename: **1**
+- max_parallel: **1**
+
+### Manual tasks
+
+Total: **2**
+
+Self hosted runners: **2**
+
+- `macOS-latest`: **2**
+
+### Partially successful
+
+#### smurff/ExaScience.smurff
+
+- [pipelines/smurff/ExaScience.smurff/.github/workflows/exascience.smurff.yml](pipelines/smurff/ExaScience.smurff/.github/workflows/exascience.smurff.yml)
+- [pipelines/smurff/ExaScience.smurff/.github/actions/ci_conda_steps/action.yml](pipelines/smurff/ExaScience.smurff/.github/actions/ci_conda_steps/action.yml)
+- [pipelines/smurff/ExaScience.smurff/config.json](pipelines/smurff/ExaScience.smurff/config.json)
+- [pipelines/smurff/ExaScience.smurff/source.yml](pipelines/smurff/ExaScience.smurff/source.yml)

ci/converted/audit/config.yml

@@ -0,0 +1,27 @@
+---
+composite_actions:
+# Usage examples
+# 1. Local composite action in actions folder (Default)
+# Results in `uses: ./.github/actions/my_template`
+# - name: my_template
+#   ref: main
+# 2. Local composite action in another directory
+# Results in `uses: ./path/to/action`
+# - name: my_template
+#   ref: main
+#   path: path/to/action
+# 3. Remote repository with composite action at the root of the repository
+# Results in `uses: org/repo@ref`
+# - name: my_template
+#   target_url: REDACTED
+#   ref: main
+# 4. Remote repository with composite action in another directory
+# Results in `uses: org/repo/path/to/action@ref`
+# - name: my_template
+#   target_url: REDACTED
+#   ref: main
+#   path: path/to/action
+- name: ci_conda_steps
+  ref: main
+- name: ci_conda_steps
+  ref: main

ci/converted/audit/log/valet-20240603-122921.log

@@ -0,0 +1,46 @@
+# Logfile created on 2024-06-03 12:29:21 +0000 by logger.rb/v1.6.0
+I, [2024-06-03T12:29:21.403827 #1]  INFO -- : Using GitHub Features: Defaults
+I, [2024-06-03T12:29:21.403934 #1]  INFO -- : Auditing 'REDACTED_build'
+I, [2024-06-03T12:29:21.407066 #1]  INFO -- request: GET REDACTED_apis/distributedtask/tasks?api-version=5.0-preview
+I, [2024-06-03T12:29:21.752834 #1]  INFO -- response: Status 401
+I, [2024-06-03T12:29:21.786549 #1]  INFO -- request: GET REDACTED
+I, [2024-06-03T12:29:22.048730 #1]  INFO -- response: Status 200
+I, [2024-06-03T12:29:22.066317 #1]  INFO -- : Sending telemetry with transaction id '835c0ed2-d9c2-4c6b-ac88-8f93020fd4bb'
+E, [2024-06-03T12:29:22.388744 #1] ERROR -- : There was an error extracting pipelines from Azure DevOps
+Message: Unable to authenticate
+Please verify your access token is valid and contains the following scopes:
+Build (Read), Agent Pools (Read), Code (Read), Release (Read), Service Connections (Read), Task Groups (Read), Variable Groups (Read)
+(GET 401) Unauthorized: REDACTED_apis/distributedtask/tasks?api-version=5.0-preview
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/services/azure_devops/parse_response.rb:14:in `parse!'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/adapters/azure_devops/client.rb:139:in `block in fetch_all'
+<internal:kernel>:187:in `loop'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/adapters/azure_devops/client.rb:132:in `fetch_all'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/adapters/azure_devops/client.rb:80:in `fetch_known_tasks'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/transformers/azure_devops/utilities/task.rb:18:in `known_tasks'
+/usr/local/bundle/gems/sorbet-runtime-0.5.11108/lib/types/private/methods/call_validation.rb:256:in `bind_call'
+/usr/local/bundle/gems/sorbet-runtime-0.5.11108/lib/types/private/methods/call_validation.rb:256:in `validate_call'
+/usr/local/bundle/gems/sorbet-runtime-0.5.11108/lib/types/private/methods/_methods.rb:275:in `block in _on_method_added'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/services/azure_devops/extract_all_pipelines.rb:28:in `block in call'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/services/azure_devops/extract_all_pipelines.rb:25:in `each'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/services/azure_devops/extract_all_pipelines.rb:25:in `flat_map'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/services/azure_devops/extract_all_pipelines.rb:25:in `call'
+/usr/local/bundle/gems/sorbet-runtime-0.5.11108/lib/types/private/methods/call_validation.rb:256:in `bind_call'
+/usr/local/bundle/gems/sorbet-runtime-0.5.11108/lib/types/private/methods/call_validation.rb:256:in `validate_call'
+/usr/local/bundle/gems/sorbet-runtime-0.5.11108/lib/types/private/methods/_methods.rb:275:in `block in _on_method_added'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/adapters/provider_resolver.rb:66:in `call'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/commands/audit.rb:16:in `block in call'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/logger.rb:96:in `with_progress_bar'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/commands/audit.rb:15:in `call'
+/usr/local/bundle/gems/actions_importer-1.3.22039/lib/valet/subcommands/audit.rb:50:in `azure_devops'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor/command.rb:27:in `run'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor/invocation.rb:127:in `invoke_command'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor.rb:392:in `dispatch'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor/invocation.rb:116:in `invoke'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor.rb:243:in `block in subcommand'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor/command.rb:27:in `run'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor/invocation.rb:127:in `invoke_command'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor.rb:392:in `dispatch'
+/usr/local/bundle/gems/thor-1.2.2/lib/thor/base.rb:485:in `start'
+/usr/local/bundle/gems/actions_importer-1.3.22039/exe/actions-importer:19:in `<top (required)>'
+/usr/local/bundle/bin/actions-importer:25:in `load'
+/usr/local/bundle/bin/actions-importer:25:in `<main>'