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aff9c89
Refactor/distributed-tests (#493)
bgunnar5 Nov 13, 2024
7530784
Drop Python 3.7 and Add Python 3.12 & 3.13 (#495)
bgunnar5 Feb 19, 2025
fa01af5
Requirements fixes (#501)
bgunnar5 Apr 23, 2025
0a590e1
docs/api_docs (#496)
bgunnar5 Apr 25, 2025
44cdca3
Update README.md to remove lgtm banner (#488)
lucpeterson Apr 25, 2025
bb356d2
Refactor/simplified-ci (#504)
bgunnar5 May 1, 2025
52def66
fix an issue with docs build on python 3.9 (#503)
bgunnar5 May 1, 2025
715f163
fix .wci.yml links (#505)
woutdenolf May 5, 2025
14f6c90
Refactor/config (#498)
bgunnar5 May 15, 2025
11df3f6
Refactor/server-config (#506)
bgunnar5 May 29, 2025
a8fbcd1
bugfix/local-config (#507)
bgunnar5 May 29, 2025
4a72c3b
Update copyright (#510)
bgunnar5 Jun 11, 2025
b253677
Potential fix for code scanning alert no. 23: Workflow does not conta…
bgunnar5 Jun 11, 2025
dce771a
codeql-fixes (#513)
bgunnar5 Jun 13, 2025
5dd846d
refactor/main-module (#515)
bgunnar5 Jun 30, 2025
20626d2
docs/feature-demo-example (#519)
bgunnar5 Jul 7, 2025
492382a
feature/tests-spec-folder (#521)
bgunnar5 Jul 15, 2025
79510de
run fix-style
bgunnar5 Sep 3, 2025
b3a7586
super rough draft at refactor
bgunnar5 Sep 29, 2025
a603272
implement CeleryExecutor abstract methods for task queueing
MarcusHsieh Oct 13, 2025
f39e06f
implement sample expansion for CeleryExecutor
MarcusHsieh Oct 13, 2025
01d2129
add MERLIN_GLOB_PATH substitution to sample expansion
MarcusHsieh Oct 13, 2025
919f5b1
enforce task dependencies and sample workspace isolation
MarcusHsieh Oct 13, 2025
8709768
implement batching and pure chain/group pattern for CeleryExecutor
MarcusHsieh Oct 27, 2025
d4a40c7
implement non-blocking execution for merlin run
MarcusHsieh Oct 28, 2025
33067b5
implement sample expansion for LocalExecutor
MarcusHsieh Nov 24, 2025
c679cce
add unit tests for SampleExpander
MarcusHsieh Nov 24, 2025
6111d7c
make fix-style
MarcusHsieh Nov 25, 2025
e3cc40f
add unit tests for LocalExecutor sample expansion
MarcusHsieh Dec 8, 2025
dee372a
add unit tests for CeleryExecutor batching and workflow patterns
MarcusHsieh Dec 8, 2025
94a1bc1
add unit tests for non-blocking workflow execution
MarcusHsieh Dec 8, 2025
1cae2a4
add unit tests for MerlinStepRecord task_server auto-detection
MarcusHsieh Dec 9, 2025
6526193
fix unused imports and unused variables errors (flake8 linting). Redi…
MarcusHsieh Jan 6, 2026
7504bf8
fix whitespace
MarcusHsieh Jan 6, 2026
d318b65
refactor CeleryExecutor.execute_plan to reduce complexity
MarcusHsieh Jan 7, 2026
70bc920
revert study.py to use merlin.study.dag
MarcusHsieh Jan 18, 2026
6594253
fix WorkflowManager DAG, dry run handling, add restart support
MarcusHsieh Jan 18, 2026
bc74b50
add return
MarcusHsieh Jan 18, 2026
c6437f6
fix unit test mocks for WorkflowManager DAG creation
MarcusHsieh Jan 18, 2026
944fb98
black formatting
MarcusHsieh Jan 20, 2026
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45 changes: 45 additions & 0 deletions .github/actions/setup-python/action.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
name: Setup Python Environment
description: Setup Python, reinstall pip, and install dependencies
inputs:
python-version:
required: true

runs:
using: "composite"
steps:
- name: Cache pip dependencies
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ inputs.python-version }}

- name: Reinstall pip
shell: bash
run: |
PY_VER=$(python -c "import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')")
PY_MAJOR=$(echo $PY_VER | cut -d. -f1)
PY_MINOR=$(echo $PY_VER | cut -d. -f2)

if [ "$PY_MAJOR" -eq 3 ] && [ "$PY_MINOR" -le 8 ]; then
URL="https://bootstrap.pypa.io/pip/${PY_VER}/get-pip.py"
else
URL="https://bootstrap.pypa.io/get-pip.py"
fi

curl -sS "$URL" -o /tmp/get-pip.py
python /tmp/get-pip.py --force-reinstall

pip --version
pip3 --version

- name: Install dependencies
shell: bash
run: |
python3 -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip3 install -r requirements/dev.txt
45 changes: 45 additions & 0 deletions .github/actions/setup-singularity/action.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
name: Install Singularity
description: Install Go and Singularity
inputs:
go-version:
required: true
singularity-version:
required: true
os:
default: linux
arch:
default: amd64

runs:
using: "composite"
steps:
- name: Install system dependencies
shell: bash
run: |
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
pkg-config

- name: Download and install Go
shell: bash
run: |
wget https://go.dev/dl/go${{ inputs.go-version }}.${{ inputs.os }}-${{ inputs.arch }}.tar.gz
sudo tar -C /usr/local -xzf go${{ inputs.go-version }}.${{ inputs.os }}-${{ inputs.arch }}.tar.gz
rm go${{ inputs.go-version }}.${{ inputs.os }}-${{ inputs.arch }}.tar.gz
echo "/usr/local/go/bin" >> $GITHUB_PATH

- name: Download and install Singularity
shell: bash
run: |
wget https://github.com/sylabs/singularity/releases/download/v${{ inputs.singularity-version }}/singularity-ce-${{ inputs.singularity-version }}.tar.gz
tar -xzf singularity-ce-${{ inputs.singularity-version }}.tar.gz
cd singularity-ce-${{ inputs.singularity-version }}
./mconfig
make -C ./builddir
sudo make -C ./builddir install

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