From e840ad363819680a79bce14771e7d6cab104bcc3 Mon Sep 17 00:00:00 2001
From: Isaac Morales Santana <102816007+imorlxs@users.noreply.github.com>
Date: Tue, 16 Jul 2024 00:20:22 +0200
Subject: [PATCH 1/4] Update CI (#377)
---
.github/workflows/centos-system-ci.yml | 3 ++-
.github/workflows/macos-system-ci.yml | 10 ++++++----
.github/workflows/ubuntu-system-ci.yml | 6 ++++--
util/install | 7 ++++---
4 files changed, 16 insertions(+), 10 deletions(-)
diff --git a/.github/workflows/centos-system-ci.yml b/.github/workflows/centos-system-ci.yml
index 3677a714b..a544c2b03 100644
--- a/.github/workflows/centos-system-ci.yml
+++ b/.github/workflows/centos-system-ci.yml
@@ -32,6 +32,7 @@ jobs:
if [ "${{ github.event_name }}" = "schedule" ]; then
echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
fi
+ echo "GHA_REPOSITORY=${{ github.repository }}" >> $GITHUB_ENV
- name: Set OSVERS
run: |
@@ -62,7 +63,7 @@ jobs:
run: |
yum update -y
yum install -y sudo curl
- curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/${GHA_BRANCH_NAME}/util/install | bash
+ curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash
# remove whole BioDynaMo repository to catch errors related to paths pointing into the build dir
mktemp -d
find /tmp -iname biodynamo -type d || true
diff --git a/.github/workflows/macos-system-ci.yml b/.github/workflows/macos-system-ci.yml
index 4ab5e8336..a08a0912c 100644
--- a/.github/workflows/macos-system-ci.yml
+++ b/.github/workflows/macos-system-ci.yml
@@ -33,7 +33,7 @@ jobs:
sudo ln -s /Applications/Xcode_14.2.app /Applications/Xcode.app
sudo xcode-select -s /Applications/Xcode.app/Contents/Developer
if: matrix.os == 'macos-12'
-
+
- name: Make sure Xcode 15.2 is used on macOS 13 as the default /Application/Xcode.app
shell: bash
run: |
@@ -53,12 +53,14 @@ jobs:
if [ "${{ github.event_name }}" = "schedule" ]; then
echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
fi
-
+
+ echo "GHA_REPOSITORY=${{ github.repository}}" >> $GITHUB_ENV
+
- name: Install BioDynaMo
shell: zsh {0}
run: |
brew install curl
- curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/${GHA_BRANCH_NAME}/util/install | bash
+ curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash
# remove whole bidynamo repository to catch errors related to paths pointing into the build dir
mktemp -d
find /tmp -iname biodynamo -type d || true
@@ -102,7 +104,7 @@ jobs:
cmake --build build --parallel --config Release
# Don't do this in the `Build BioDynaMo step`, because notebooks might time out in GHA
- # runners, while waiting for other targets to be compiled. Run notebooks only on
+ # runners, while waiting for other targets to be compiled. Run notebooks only on
# macOS 10.15 until we managed to compile ROOT for 11.6 again.
- name: Run notebooks
shell: zsh {0}
diff --git a/.github/workflows/ubuntu-system-ci.yml b/.github/workflows/ubuntu-system-ci.yml
index 10e946ccc..23134f345 100644
--- a/.github/workflows/ubuntu-system-ci.yml
+++ b/.github/workflows/ubuntu-system-ci.yml
@@ -34,6 +34,8 @@ jobs:
echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
fi
+ echo "GHA_REPOSITORY=${{ github.repository }}" >> $GITHUB_ENV
+
- name: Set OSVERS
run: |
ID=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"')
@@ -55,7 +57,7 @@ jobs:
run: |
sudo apt update
sudo apt install -y curl
- curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/${GHA_BRANCH_NAME}/util/install | bash
+ curl https://raw.githubusercontent.com/${GHA_REPOSITORY}/${GHA_BRANCH_NAME}/util/install | bash
# remove whole bidynamo repository to catch errors related to paths pointing into the build dir
mktemp -d
find /tmp -iname biodynamo -type d || true
@@ -133,7 +135,7 @@ jobs:
-B build
cmake --build build --parallel --config Release --target notebooks -- -j1
if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-22.04'
-
+
- name: Build BioDynaMo
shell: bash
diff --git a/util/install b/util/install
index 73735fa81..960e579be 100755
--- a/util/install
+++ b/util/install
@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# Adapted from https://github.com/pyenv/pyenv-installer/
-# Usage: curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/master/util/install | bash
+# Usage: curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/master/util/install | bash
set -e
@@ -8,7 +8,7 @@ if [ -z ${BDM_INSTALL} ]; then
export BDM_INSTALL=v1.04-patches
fi
echo "BDM_INSTALL is set to: $BDM_INSTALL"
-
+
temp_dir=$(mktemp -d)
BDM_SRC="${temp_dir}/biodynamo"
mkdir "$BDM_SRC"
@@ -34,8 +34,9 @@ FailedCheckout() {
Checkout() {
# In Github Actions we checkout the branch that is running the install script
+ REPO_URL="${GITHUB}/${GHA_REPOSITORY}.git"
if [ ! -z ${GITHUB_ACTIONS+x} ]; then
- git clone --branch ${GHA_BRANCH_NAME} "$1" . || FailedClone "$1"
+ git clone --branch ${GHA_BRANCH_NAME} "$REPO_URL" . || FailedClone "$REPO_URL"
else
git clone "$1" . || FailedClone "$1"
git checkout "$BDM_INSTALL" || FailedCheckout "$BDM_INSTALL"
From 9b2171097ca5dc8a0a80510d0cb3850f912b4e79 Mon Sep 17 00:00:00 2001
From: Isaac Morales Santana <102816007+imorlxs@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:09:58 +0200
Subject: [PATCH 2/4] Remove deprecated -c flag on root cling call (#378)
See also issue #371
---
cmake/FindROOT.cmake | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake/FindROOT.cmake b/cmake/FindROOT.cmake
index 50bc06ee8..5443a8479 100644
--- a/cmake/FindROOT.cmake
+++ b/cmake/FindROOT.cmake
@@ -146,7 +146,7 @@ function(ROOT_GENERATE_DICTIONARY dictionary)
add_custom_command(OUTPUT ${dictionary}.cxx
OUTPUT ${dictionary}_rdict.pcm
COMMAND ${LAUNCHER} ${ROOTCLING_EXECUTABLE} -f ${dictionary}.cxx
- -c ${ARG_OPTIONS} ${includedirs} ${headerfiles} ${linkdefs}
+ ${ARG_OPTIONS} ${includedirs} ${headerfiles} ${linkdefs}
DEPENDS ${headerfiles} ${linkdefs} VERBATIM)
endfunction()
From e3227c1aaf91e88ba455ac608086afd07b19f677 Mon Sep 17 00:00:00 2001
From: Marco Manca <14293317+markomanka@users.noreply.github.com>
Date: Mon, 22 Jul 2024 13:01:36 +0200
Subject: [PATCH 3/4] Update README.md
changed (deprecated) discord invite to valid one, pointing to the room "curious newcomer" as agreed by the consortium steering group
---
README.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.md b/README.md
index f4a23be9a..d0632cace 100644
--- a/README.md
+++ b/README.md
@@ -24,7 +24,7 @@
- 
+
From d8bb6b7ab254ccb5d92be9ce2a2e2fcc66aa93f9 Mon Sep 17 00:00:00 2001
From: Fons Rademakers
Date: Fri, 2 Aug 2024 20:45:55 +0200
Subject: [PATCH 4/4] Update for macOS 14.6.
---
cmake/external/SHA256Digests.cmake | 2 ++
1 file changed, 2 insertions(+)
diff --git a/cmake/external/SHA256Digests.cmake b/cmake/external/SHA256Digests.cmake
index 1438e7089..7d863ea96 100644
--- a/cmake/external/SHA256Digests.cmake
+++ b/cmake/external/SHA256Digests.cmake
@@ -62,6 +62,8 @@ SET(osx-14.4-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e8055
SET(osx-14.4-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
SET(osx-14.5-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e80554f7fa617ccb)
SET(osx-14.5-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
+SET(osx-14.6-i386-ParaView d2e89df30ab0e2729b28539de37753e09c061b4c434b0a68e80554f7fa617ccb)
+SET(osx-14.6-arm64-ParaView 5e89b785ac0c56bbca31e2ae101a8986953e90227fe42a1ef7adcc70a0ff6fc4)
SET(osx-xcode-13.1-i386-ROOT be97dd72022c8d082fbe4394f18b55c4920f20b138cfff1b5fc2b41d397ac203)
SET(osx-xcode-13.1-arm64-ROOT 0a55b91c6df42d152b7943912e134f05c3872a73e73fcc129ee87fd847240ec8)
SET(osx-xcode-14.1-i386-ROOT 001311608512b24535bb9710b8baf006bd00e9b0595fd6bdf900d28b1e22c395)