Add Basic CI to the project #3

AdityaPandeyCN · 2025-08-14T14:41:02Z

This PR adds basic CI to the ramtools repository.

Signed-off-by: AdityaPandeyCN <[email protected]>

vgvassilev · 2025-08-14T15:02:43Z

test/samexample.sam

Why is this file uploaded. Seems huge.

This was in the original repository as an example file so added it for testing I can compress it

Can’t we generate that file. It should be some random genetic sequence…

I reduced the file content to some 100 line as most of them were repetitive. Will this work? The file size is now 10 kb

That should work but we should do it as a separate pr.

Should I revert to the original file or like generate one ?

Removed the example sam file

mcbarton · 2025-08-14T14:59:55Z

.github/workflows/ci.yml

+jobs:
+  build-and-test:
+    name: Build and Test
+    runs-on: ubuntu-22.04


Maybe use the newer Ubuntu runner (ubuntu-24.04)

mcbarton · 2025-08-14T15:00:38Z

.github/workflows/ci.yml

+    runs-on: ubuntu-22.04
+
+    steps:
+    - uses: actions/checkout@v4


checkout@v5 came out recently, so this can be updated to that.

mcbarton · 2025-08-14T15:04:06Z

.github/workflows/ci.yml

+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y cmake build-essential wget gnupg libtbb-dev


Although you can put it, sudo is redundant on Github runners I believe, as the account you get has admin privileges.

cmake build-essential wget gnupg are already on Github runners (see
https://github.com/actions/runner-images/blob/main/images/ubuntu/Ubuntu2404-Readme.md)

I cannot see where you are using libtbb-dev

mcbarton · 2025-08-14T15:04:32Z

.github/workflows/ci.yml

+      run: |
+        ROOT_URL="https://root.cern/download/root_v6.34.00.Linux-ubuntu22.04-x86_64-gcc11.4.tar.gz"
+        wget -O root.tar.gz $ROOT_URL
+        sudo tar -xzf root.tar.gz -C /opt/


redundant sudo

mcbarton · 2025-08-14T15:07:00Z

.github/workflows/ci.yml

+    - name: Configure CMake
+      run: |
+        source /opt/root/bin/thisroot.sh
+        mkdir -p build


Your starting from scratch with each github workflow run, so -p is not needed. build is guaranteed not to exist

mcbarton · 2025-08-14T15:08:11Z

.github/workflows/ci.yml

+
+    - name: Install ROOT
+      run: |
+        ROOT_URL="https://root.cern/download/root_v6.34.00.Linux-ubuntu22.04-x86_64-gcc11.4.tar.gz"


root version 6.36 exists. Are you sure you want 6.34?

You'd need to change the link if you change to Ubuntu 24.04 runner.

mcbarton · 2025-08-14T15:11:41Z

test/samexample.sam

Have you tried compressing this file when added to the repo to reduce its size from 5.26 MB?

You could then have the ci uncompress the file if yes.

I reduced the file size by deleting it contents which were repetitive.

Signed-off-by: AdityaPandeyCN <[email protected]> updating ci.yml Signed-off-by: AdityaPandeyCN <[email protected]> updating versions in ci.yml Signed-off-by: AdityaPandeyCN <[email protected]> changes Signed-off-by: AdityaPandeyCN <[email protected]> changes Signed-off-by: AdityaPandeyCN <[email protected]>

mcbarton · 2025-08-15T14:48:30Z

.github/workflows/ci.yml

+        echo "LD_LIBRARY_PATH=/opt/root/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "CMAKE_PREFIX_PATH=/opt/root:$CMAKE_PREFIX_PATH" >> $GITHUB_ENV


These look like they are redundant since these variables are set by the thisroot.sh script you source

mcbarton · 2025-08-15T14:49:21Z

.github/workflows/ci.yml

+
+    - name: Configure CMake
+      run: |
+        source /opt/root/bin/thisroot.sh


Given /opt/root/bin is now part of the path environment variable (e.g. echo "/opt/root/bin" >> $GITHUB_PATH) then this can just be source thisroot.sh

mcbarton · 2025-08-15T14:49:44Z

.github/workflows/ci.yml

+
+    - name: Build
+      run: |
+        source /opt/root/bin/thisroot.sh


Given /opt/root/bin is now part of the path environment variable (e.g. echo "/opt/root/bin" >> $GITHUB_PATH) then this can just be source thisroot.sh

mcbarton · 2025-08-15T14:50:36Z

.github/workflows/ci.yml

+
+    - name: Run tests
+      run: |
+        source /opt/root/bin/thisroot.sh


Given /opt/root/bin is now part of the path environment variable (e.g. echo "/opt/root/bin" >> $GITHUB_PATH) then this can just be source thisroot.sh

mcbarton · 2025-08-15T14:51:21Z

.github/workflows/ci.yml

+        sudo apt-get update
+        sudo apt-get install -y libvdt-dev libtbb-dev


sudo not needed I believe, since Github runner workflows are on an admin account by default

Run apt-get update Reading package lists... E: Could not open lock file /var/lib/apt/lists/lock - open (13: Permission denied) E: Unable to lock directory /var/lib/apt/lists/ Error: Process completed with exit code 100.
getting permission issues if not using sudo

mcbarton · 2025-08-15T14:55:46Z

.github/workflows/ci.yml

+
+    - name: Install ROOT
+      run: |
+        ROOT_URL="https://root.cern/download/root_v6.34.06.Linux-ubuntu24.04-x86_64-gcc13.3.tar.gz"


I see that you updated to Ubuntu 24.04 , but not to root 6.36 version? There is a root_v6.36.00.Linux-ubuntu24.04-x86_64-gcc13.3.tar.gz file you can download

vgvassilev · 2025-08-17T07:23:28Z

.github/workflows/ci.yml

+  push:
+    branches: [add_ci]
+  pull_request:
+    branches: [develop]


We should probably change the default branch to main...

Signed-off-by: AdityaPandeyCN <[email protected]> cleanup5 Signed-off-by: AdityaPandeyCN <[email protected]>

Signed-off-by: AdityaPandeyCN <[email protected]>

.github/workflows/ci.yml

Signed-off-by: AdityaPandeyCN <[email protected]>

vgvassilev

LGTM!

AdityaPandeyCN added 3 commits August 14, 2025 19:55

added basic CI

36a8fdd

Signed-off-by: AdityaPandeyCN <[email protected]>

modified gitignore

e2199f0

Signed-off-by: AdityaPandeyCN <[email protected]>

code changes

230be96

Signed-off-by: AdityaPandeyCN <[email protected]>

AdityaPandeyCN marked this pull request as draft August 14, 2025 14:41

AdityaPandeyCN marked this pull request as ready for review August 14, 2025 14:44

vgvassilev reviewed Aug 14, 2025

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mcbarton reviewed Aug 14, 2025

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AdityaPandeyCN marked this pull request as draft August 14, 2025 16:05

AdityaPandeyCN force-pushed the add_ci branch from 1b69633 to a4254d6 Compare August 14, 2025 17:07

AdityaPandeyCN marked this pull request as ready for review August 14, 2025 17:08

mcbarton reviewed Aug 15, 2025

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vgvassilev reviewed Aug 17, 2025

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updating file path

ae0ff1c

Signed-off-by: AdityaPandeyCN <[email protected]> cleanup5 Signed-off-by: AdityaPandeyCN <[email protected]>

AdityaPandeyCN force-pushed the add_ci branch from 1ad9a06 to ae0ff1c Compare August 19, 2025 10:12

file path correction

d3dfb49

Signed-off-by: AdityaPandeyCN <[email protected]>

vgvassilev reviewed Aug 19, 2025

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.github/workflows/ci.yml Outdated Show resolved Hide resolved

vgvassilev and others added 2 commits August 19, 2025 16:52

Update .github/workflows/ci.yml

b38ac09

removed sam file

98c491d

Signed-off-by: AdityaPandeyCN <[email protected]>

vgvassilev approved these changes Aug 23, 2025

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vgvassilev merged commit 0df2c87 into compiler-research:develop Aug 23, 2025

		echo "LD_LIBRARY_PATH=/opt/root/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
		echo "CMAKE_PREFIX_PATH=/opt/root:$CMAKE_PREFIX_PATH" >> $GITHUB_ENV

		sudo apt-get update
		sudo apt-get install -y libvdt-dev libtbb-dev

Add Basic CI to the project #3

Add Basic CI to the project #3

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AdityaPandeyCN commented Aug 14, 2025

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AdityaPandeyCN Aug 19, 2025 •

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mcbarton Aug 14, 2025 •

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