From 3e05386fe9bd7c82262bd43d649f3f4a322f9a4d Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 08:55:23 +0200
Subject: [PATCH 01/26] Add basic CI and clean up more.

---
 .github/workflows/test.yml         | 42 ++++++++++++++++++++
 examples/touch_display_convert.cpp | 62 ------------------------------
 2 files changed, 42 insertions(+), 62 deletions(-)
 create mode 100644 .github/workflows/test.yml
 delete mode 100644 examples/touch_display_convert.cpp

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..c12a28a
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,42 @@
+name: Run tests
+
+on:
+  push:
+    branches: ['main']
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        packages: [""]
+        submodules: [true]
+        include:
+          - packages: "catch2 libcli11-dev"
+            submodules: false
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: ${{ matrix.submodules }}
+
+    - name: Set up Apache Arrow repositories
+      run: |
+        apt-get update
+        apt-get install -y ca-certificates lsb-release wget
+        wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
+        apt-get install -y ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
+        apt-get update
+
+    - name: Install build dependencies
+      run: |
+        apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build ${{ matrix.packages }}
+        ls -l /var/cache/apt/archives
+        apt-get install -y libarrow-dev libparquet-dev
+        ls -l /var/cache/apt/archives
+
+    - name: Configure
+      run: |
+        cmake -B build -S . -GNinja \
+          -DCMAKE_CXX_COMPILER=$(which mpicxx)
diff --git a/examples/touch_display_convert.cpp b/examples/touch_display_convert.cpp
deleted file mode 100644
index 7049d63..0000000
--- a/examples/touch_display_convert.cpp
+++ /dev/null
@@ -1,62 +0,0 @@
-#include <iostream>
-#include "touch_reader.h"
-#include "parquet_reader.h"
-#include "converter.h"
-#include "progress.h"
-
-using namespace std;
-
-#define TEST_N_ENTRIES 20
-
-int main(int argc, char *argv[])
-{
-    if( argc < 2) {
-        printf("usage: %s <touch_files ...>\n", argv[0]);
-        return 1;
-    }
-
-    //It will swap endians if we use the xxx_endian executable
-    int len = strlen(argv[0]);
-    bool swap_endians = false;
-    if( strcmp( &(argv[0][len-6]), "endian" ) == 0 ) {
-        swap_endians=true;
-        printf("[Info] Swapping endians\n");
-    }
-    
-    TouchReader reader(argv[1], swap_endians);
-
-    printf( "| NRN_SRC | NRN_DST | SECTION/SEGMENT/OFFSET[SRC->DST] | DIST SOMA | BRANCH |\n" );
-    printf( "|---------------------------------------------------------------------------------------------|\n" );
-        for( int i=0; i<TEST_N_ENTRIES; i++) {
-        Touch &t = reader.getNext();
-        printf("| %7u | %7u | [%2u/%2u/%6.2f] -> [%2u/%2u/%6.2f] | %9.2f | %6d |\n",
-                t.pre_synapse_ids[NEURON_ID],
-                t.post_synapse_ids[NEURON_ID],
-                t.pre_synapse_ids[SECTION_ID],
-                t.pre_synapse_ids[SEGMENT_ID],
-                t.pre_offset,
-                t.post_synapse_ids[SECTION_ID],
-                t.post_synapse_ids[SEGMENT_ID],
-                t.post_offset,
-                t.distance_soma, 
-                t.branch
-        );
-
-    }
-
-    string parquetFilename( argv[1] );
-    std::size_t slashPos = parquetFilename.find_last_of("/\\");
-    parquetFilename = parquetFilename.substr(slashPos+1);
-    parquetFilename += ".parquet";
- 
-    TouchWriterParquet writer(parquetFilename);
-
-    Converter<Touch> converter(reader, writer);
-    ProgressMonitor p;
-    converter.setProgressHandler(p.getNewHandler());
-    
-    converter.exportN( TEST_N_ENTRIES );
-    printf("Done exporting\n");
-    
-    return 0;
-}

From a04519e671adc623f0dae45a6dfac0706949ee7f Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 08:56:42 +0200
Subject: [PATCH 02/26] Use sudo

---
 .github/workflows/test.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c12a28a..7e1a724 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -23,17 +23,17 @@ jobs:
 
     - name: Set up Apache Arrow repositories
       run: |
-        apt-get update
-        apt-get install -y ca-certificates lsb-release wget
+        sudo apt-get update
+        sudo apt-get install -y ca-certificates lsb-release wget
         wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
-        apt-get install -y ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
-        apt-get update
+        sudo apt-get install -y ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
+        sudo apt-get update
 
     - name: Install build dependencies
       run: |
-        apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build ${{ matrix.packages }}
+        sudo apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build ${{ matrix.packages }}
         ls -l /var/cache/apt/archives
-        apt-get install -y libarrow-dev libparquet-dev
+        sudo apt-get install -y libarrow-dev libparquet-dev
         ls -l /var/cache/apt/archives
 
     - name: Configure

From bf0f60b3247147e17a975a7e353f61c2aa69c381 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 09:08:49 +0200
Subject: [PATCH 03/26] Tune workflow

---
 .github/workflows/test.yml | 19 ++++++++++++++++---
 Dockerfile                 |  1 +
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7e1a724..d3316df 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -31,10 +31,23 @@ jobs:
 
     - name: Install build dependencies
       run: |
-        sudo apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build ${{ matrix.packages }}
-        ls -l /var/cache/apt/archives
+        sudo apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build nlohmann-json3-dev ${{ matrix.packages }}
         sudo apt-get install -y libarrow-dev libparquet-dev
-        ls -l /var/cache/apt/archives
+
+    - name: Clone HighFive
+      uses: actions/checkout@3
+      if: ${{ ! matrix.submodules }}
+      with:
+        repository: BlueBrain/HighFive
+        path: HighFive
+
+    - name: Install HighFive
+      if: ${{ ! matrix.submodules }}
+      run: |
+        cmake -B highfive_build -S highfive -DCMAKE_INSTALL_PREFIX=highfive_install
+        cmake --build highfive_build
+        cmake --install highfive_build
+        echo "CMAKE_PREFIX_PATH=$PWD/highfive_build" >> "$GITHUB_ENV"
 
     - name: Configure
       run: |
diff --git a/Dockerfile b/Dockerfile
index 47c5d06..05470dc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,6 +11,7 @@ RUN apt-get update \
         librange-v3-dev \
         lsb-release \
         ninja-build \
+        nlohmann-json3-dev \
         wget
 RUN wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb \
  && apt-get install -y ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb \

From ba56e73927e21bf73d1d91f02d950f680e1ccc2a Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 09:11:01 +0200
Subject: [PATCH 04/26] Use right version

---
 .github/workflows/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d3316df..1de9e09 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -17,7 +17,7 @@ jobs:
             submodules: false
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: ${{ matrix.submodules }}
 
@@ -35,7 +35,7 @@ jobs:
         sudo apt-get install -y libarrow-dev libparquet-dev
 
     - name: Clone HighFive
-      uses: actions/checkout@3
+      uses: actions/checkout@v4
       if: ${{ ! matrix.submodules }}
       with:
         repository: BlueBrain/HighFive

From 31d5ae398f9210a09a0935b7013490c02ce52d25 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 09:12:49 +0200
Subject: [PATCH 05/26] Matching paths

---
 .github/workflows/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1de9e09..ff3b9c5 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -39,12 +39,12 @@ jobs:
       if: ${{ ! matrix.submodules }}
       with:
         repository: BlueBrain/HighFive
-        path: HighFive
+        path: highfive_source
 
     - name: Install HighFive
       if: ${{ ! matrix.submodules }}
       run: |
-        cmake -B highfive_build -S highfive -DCMAKE_INSTALL_PREFIX=highfive_install
+        cmake -B highfive_build -S highfive_source -DCMAKE_INSTALL_PREFIX=highfive_install
         cmake --build highfive_build
         cmake --install highfive_build
         echo "CMAKE_PREFIX_PATH=$PWD/highfive_build" >> "$GITHUB_ENV"

From 39ed1a75e81fc4aceba69bc79e82e0323ce5e9a5 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 09:17:37 +0200
Subject: [PATCH 06/26] Less highfive cruft

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ff3b9c5..9805da0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -44,7 +44,7 @@ jobs:
     - name: Install HighFive
       if: ${{ ! matrix.submodules }}
       run: |
-        cmake -B highfive_build -S highfive_source -DCMAKE_INSTALL_PREFIX=highfive_install
+        cmake -B highfive_build -S highfive_source -DCMAKE_INSTALL_PREFIX=highfive_install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF
         cmake --build highfive_build
         cmake --install highfive_build
         echo "CMAKE_PREFIX_PATH=$PWD/highfive_build" >> "$GITHUB_ENV"

From 794e827b0e0017f437a66bde9c567e7c34c93124 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 09:22:19 +0200
Subject: [PATCH 07/26] More path matching

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 9805da0..d9ca28f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -47,7 +47,7 @@ jobs:
         cmake -B highfive_build -S highfive_source -DCMAKE_INSTALL_PREFIX=highfive_install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF
         cmake --build highfive_build
         cmake --install highfive_build
-        echo "CMAKE_PREFIX_PATH=$PWD/highfive_build" >> "$GITHUB_ENV"
+        echo "CMAKE_PREFIX_PATH=$PWD/highfive_install" >> "$GITHUB_ENV"
 
     - name: Configure
       run: |

From 78218ae6e060bd893daa6ccaf91a137560d72644 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 09:30:27 +0200
Subject: [PATCH 08/26] Run tests

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d9ca28f..8f0926e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -53,3 +53,4 @@ jobs:
       run: |
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)
+        cd build && ctest -VV

From 7d43a22ee3562d672826613f730e46b7628cf16d Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 09:37:00 +0200
Subject: [PATCH 09/26] Actually build

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8f0926e..e59fd45 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -53,4 +53,5 @@ jobs:
       run: |
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)
+        cmake --build build
         cd build && ctest -VV

From 50095665883b5ac63520b4b4b08bdcdc56d075e4 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:08:15 +0200
Subject: [PATCH 10/26] =?UTF-8?q?D-=F0=9F=90=9B?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e59fd45..e54a3b9 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -51,6 +51,7 @@ jobs:
 
     - name: Configure
       run: |
+        echo $CMAKE_PREFIX_PATH
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)
         cmake --build build

From 1ebf8f0359be598786f27c7853957ae0fd3e1098 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:10:43 +0200
Subject: [PATCH 11/26] =?UTF-8?q?D-=F0=9F=90=9B?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e54a3b9..647e4f2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -44,6 +44,7 @@ jobs:
     - name: Install HighFive
       if: ${{ ! matrix.submodules }}
       run: |
+        echo $CMAKE_PREFIX_PATH
         cmake -B highfive_build -S highfive_source -DCMAKE_INSTALL_PREFIX=highfive_install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF
         cmake --build highfive_build
         cmake --install highfive_build

From 28f58ec70def000942805f45ecc18da49232166b Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:14:09 +0200
Subject: [PATCH 12/26] =?UTF-8?q?D-=F0=9F=90=9B?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 647e4f2..4b17305 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -44,7 +44,6 @@ jobs:
     - name: Install HighFive
       if: ${{ ! matrix.submodules }}
       run: |
-        echo $CMAKE_PREFIX_PATH
         cmake -B highfive_build -S highfive_source -DCMAKE_INSTALL_PREFIX=highfive_install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF
         cmake --build highfive_build
         cmake --install highfive_build
@@ -52,6 +51,7 @@ jobs:
 
     - name: Configure
       run: |
+        ls -l /usr/include/catch2
         echo $CMAKE_PREFIX_PATH
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)

From 940d2cec54e36ce542ff83893ec3fda9231d7dd4 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:16:36 +0200
Subject: [PATCH 13/26] =?UTF-8?q?D-=F0=9F=90=9B?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4b17305..582b3f1 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -51,7 +51,7 @@ jobs:
 
     - name: Configure
       run: |
-        ls -l /usr/include/catch2
+        ls -l /usr/include/catch2 || true
         echo $CMAKE_PREFIX_PATH
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)

From 67da624fe3eef73f3f0ca46408a4605230ef3fb1 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:29:52 +0200
Subject: [PATCH 14/26] Ubuntu latest on GH is too old

---
 .github/workflows/test.yml | 40 +++++++++++++-------------------------
 Dockerfile                 |  7 +++++++
 2 files changed, 20 insertions(+), 27 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 582b3f1..846d15e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -6,20 +6,13 @@ on:
   pull_request:
 
 jobs:
-  build:
+  build_w_submodules:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        packages: [""]
-        submodules: [true]
-        include:
-          - packages: "catch2 libcli11-dev"
-            submodules: false
 
     steps:
     - uses: actions/checkout@v4
       with:
-        submodules: ${{ matrix.submodules }}
+        submodules: true
 
     - name: Set up Apache Arrow repositories
       run: |
@@ -31,29 +24,22 @@ jobs:
 
     - name: Install build dependencies
       run: |
-        sudo apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build nlohmann-json3-dev ${{ matrix.packages }}
+        sudo apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build nlohmann-json3-dev
         sudo apt-get install -y libarrow-dev libparquet-dev
 
-    - name: Clone HighFive
-      uses: actions/checkout@v4
-      if: ${{ ! matrix.submodules }}
-      with:
-        repository: BlueBrain/HighFive
-        path: highfive_source
-
-    - name: Install HighFive
-      if: ${{ ! matrix.submodules }}
-      run: |
-        cmake -B highfive_build -S highfive_source -DCMAKE_INSTALL_PREFIX=highfive_install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF
-        cmake --build highfive_build
-        cmake --install highfive_build
-        echo "CMAKE_PREFIX_PATH=$PWD/highfive_install" >> "$GITHUB_ENV"
-
     - name: Configure
       run: |
-        ls -l /usr/include/catch2 || true
-        echo $CMAKE_PREFIX_PATH
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)
         cmake --build build
         cd build && ctest -VV
+
+  build_docker_no_submodules:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Build
+        uses: docker/build-push-action@v5
diff --git a/Dockerfile b/Dockerfile
index 05470dc..a9f0c81 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -20,6 +20,13 @@ RUN wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short |
         libarrow-dev \
         libparquet-dev
 
+RUN mkdir /highfive \
+ && git clone https://github.com/BlueBrain/HighFive /highfive/src \
+ && cmake -B /highfive/build -S /highfive/src -DCMAKE_INSTALL_PREFIX=/highfive/install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF \
+ && cmake --build /highfive/build \
+ && cmake --install /highfive/build
+
+ENV CMAKE_PREFIX_PATH=/highfive/install
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 

From 43582f52b11de181036731888ec1f28750643ae3 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:32:26 +0200
Subject: [PATCH 15/26] Include git in dockre

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index a9f0c81..161a6d2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,6 +6,7 @@ RUN apt-get update \
         catch2 \
         cmake \
         g++ \
+        git \
         libcli11-dev \
         libhdf5-openmpi-dev \
         librange-v3-dev \

From 11395fa3a69c95682967496bdfdf07990f615bdc Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:44:42 +0200
Subject: [PATCH 16/26] Add dockre context

---
 .github/workflows/test.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 846d15e..48a622c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -37,9 +37,13 @@ jobs:
   build_docker_no_submodules:
     runs-on: ubuntu-latest
     steps:
+      - name: Checkout
+        uses: actions/checkout@v4
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
       - name: Build
         uses: docker/build-push-action@v5
+        with:
+          context: .:workspace

From d02c1c7817324428568219f5630f653c2ac4c352 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 10:47:21 +0200
Subject: [PATCH 17/26] Is context in local directory?

---
 .github/workflows/test.yml | 2 --
 Dockerfile                 | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 48a622c..43b3cbe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -45,5 +45,3 @@ jobs:
         uses: docker/setup-buildx-action@v3
       - name: Build
         uses: docker/build-push-action@v5
-        with:
-          context: .:workspace
diff --git a/Dockerfile b/Dockerfile
index 161a6d2..e4f51e3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -31,7 +31,7 @@ ENV CMAKE_PREFIX_PATH=/highfive/install
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
-RUN cmake -GNinja -B /build -S /workspace -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \
+RUN cmake -GNinja -B /build -S . -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \
  && cmake --build /build \
  && cmake --install /build \
  && cd /build \

From 045f0dc394991d2a06b6f46111bd8c1b81cc1992 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 11:00:05 +0200
Subject: [PATCH 18/26] Copy sources

---
 Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index e4f51e3..169fbb9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -31,7 +31,9 @@ ENV CMAKE_PREFIX_PATH=/highfive/install
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
-RUN cmake -GNinja -B /build -S . -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \
+COPY . /src
+
+RUN cmake -GNinja -B /build -S /src -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \
  && cmake --build /build \
  && cmake --install /build \
  && cd /build \

From eac66cebd1ac47ae63ea5fbe4de711c749c70891 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 11:03:13 +0200
Subject: [PATCH 19/26] Try to run with only 2 ranks

---
 tests/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 7c4a9f6..88dd8ac 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -7,7 +7,7 @@ find_program(
   DOC "Executable for running MPI programs.")
 
 add_test(NAME parquet2hdf5_mpi
-         COMMAND ${mpi_launcher} -n 4 $<TARGET_FILE:parquet2hdf5>
+         COMMAND ${mpi_launcher} -n 2 $<TARGET_FILE:parquet2hdf5>
                  ${CMAKE_CURRENT_SOURCE_DIR}/parquets edges_n4.h5 All)
 
 add_test(NAME touches_conversion_v1

From 7de0c67612304241ddbdb640a675c22abbc14c06 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 11:09:11 +0200
Subject: [PATCH 20/26] Allow to oversubscribe

---
 .github/workflows/test.yml | 1 +
 Dockerfile                 | 1 +
 tests/CMakeLists.txt       | 2 +-
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 43b3cbe..7e624d2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -29,6 +29,7 @@ jobs:
 
     - name: Configure
       run: |
+        export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)
         cmake --build build
diff --git a/Dockerfile b/Dockerfile
index 169fbb9..a02e699 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,6 +30,7 @@ RUN mkdir /highfive \
 ENV CMAKE_PREFIX_PATH=/highfive/install
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ENV PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
 
 COPY . /src
 
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 88dd8ac..7c4a9f6 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -7,7 +7,7 @@ find_program(
   DOC "Executable for running MPI programs.")
 
 add_test(NAME parquet2hdf5_mpi
-         COMMAND ${mpi_launcher} -n 2 $<TARGET_FILE:parquet2hdf5>
+         COMMAND ${mpi_launcher} -n 4 $<TARGET_FILE:parquet2hdf5>
                  ${CMAKE_CURRENT_SOURCE_DIR}/parquets edges_n4.h5 All)
 
 add_test(NAME touches_conversion_v1

From 852e36ac0d760427f4ac48c5593712aea1037cc5 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 11:18:22 +0200
Subject: [PATCH 21/26] No real parallelism

---
 .github/workflows/test.yml | 1 -
 Dockerfile                 | 1 -
 2 files changed, 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7e624d2..43b3cbe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -29,7 +29,6 @@ jobs:
 
     - name: Configure
       run: |
-        export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)
         cmake --build build
diff --git a/Dockerfile b/Dockerfile
index a02e699..169fbb9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,7 +30,6 @@ RUN mkdir /highfive \
 ENV CMAKE_PREFIX_PATH=/highfive/install
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-ENV PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
 
 COPY . /src
 

From 28006f546af84458581eaa175bd6b2a3eec97b93 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 11:25:37 +0200
Subject: [PATCH 22/26] Actually "unset" parallelism

---
 tests/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 7c4a9f6..ce2cb58 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -7,7 +7,7 @@ find_program(
   DOC "Executable for running MPI programs.")
 
 add_test(NAME parquet2hdf5_mpi
-         COMMAND ${mpi_launcher} -n 4 $<TARGET_FILE:parquet2hdf5>
+         COMMAND ${mpi_launcher} -n 1 $<TARGET_FILE:parquet2hdf5>
                  ${CMAKE_CURRENT_SOURCE_DIR}/parquets edges_n4.h5 All)
 
 add_test(NAME touches_conversion_v1

From 68332ac56222f01b24ae5e8b16f9f16db0ab9618 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 12:04:22 +0200
Subject: [PATCH 23/26] Update .github/workflows/test.yml

Co-authored-by: Luc Grosheintz <luc.grosheintz@gmail.com>
---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 43b3cbe..171d2ad 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -32,7 +32,7 @@ jobs:
         cmake -B build -S . -GNinja \
           -DCMAKE_CXX_COMPILER=$(which mpicxx)
         cmake --build build
-        cd build && ctest -VV
+        ctest --test-dir build --output-on-failure
 
   build_docker_no_submodules:
     runs-on: ubuntu-latest

From 7bfa03bd493eb451beb16e13696ee7beb4a549eb Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 12:09:12 +0200
Subject: [PATCH 24/26] Try VOLUME in Dockrefile

---
 Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 169fbb9..d290bca 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,6 +21,7 @@ RUN wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short |
         libarrow-dev \
         libparquet-dev
 
+VOLUME /highfive
 RUN mkdir /highfive \
  && git clone https://github.com/BlueBrain/HighFive /highfive/src \
  && cmake -B /highfive/build -S /highfive/src -DCMAKE_INSTALL_PREFIX=/highfive/install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF \
@@ -31,6 +32,7 @@ ENV CMAKE_PREFIX_PATH=/highfive/install
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
+VOLUME /src
 COPY . /src
 
 RUN cmake -GNinja -B /build -S /src -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \

From a1e0304c33253874e84a79be20ad8a9b74b44933 Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 12:14:58 +0200
Subject: [PATCH 25/26] VOLUME creates directory

---
 Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d290bca..846fb85 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,8 +22,7 @@ RUN wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short |
         libparquet-dev
 
 VOLUME /highfive
-RUN mkdir /highfive \
- && git clone https://github.com/BlueBrain/HighFive /highfive/src \
+RUN git clone https://github.com/BlueBrain/HighFive /highfive/src \
  && cmake -B /highfive/build -S /highfive/src -DCMAKE_INSTALL_PREFIX=/highfive/install -DHIGHFIVE_UNIT_TESTS=OFF -DHIGHFIVE_EXAMPLES=OFF -DHIGHFIVE_BUILD_DOCS=OFF \
  && cmake --build /highfive/build \
  && cmake --install /highfive/build

From 5f98fd0d5a970246205a2f140bb8ba254daad9eb Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Fri, 10 May 2024 12:18:46 +0200
Subject: [PATCH 26/26] Cleaner

---
 Dockerfile | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 846fb85..ac95d1f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -31,11 +31,10 @@ ENV CMAKE_PREFIX_PATH=/highfive/install
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
-VOLUME /src
-COPY . /src
+VOLUME /workspace
+COPY . /workspace/src
 
-RUN cmake -GNinja -B /build -S /src -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \
- && cmake --build /build \
- && cmake --install /build \
- && cd /build \
- && ctest --output-on-failure
+RUN cmake -GNinja -B /workspace/build -S /workspace/src -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx \
+ && cmake --build /workspace/build \
+ && cmake --install /workspace/build \
+ && ctest --test-dir /workspace/build --output-on-failure