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chore: multiple python version support with latest pyspark and hail #974

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merged 47 commits into from
Jan 28, 2025
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90e6028
chore(pyspark): update to 3.5.X
SzymonSzyszkowski Jan 17, 2025
630c0c9
chore: fix doctest syntax
SzymonSzyszkowski Jan 17, 2025
1dbe1b0
chore: bump temurin version to 11
SzymonSzyszkowski Jan 17, 2025
bcf0b9a
feat: allow multiple python versions
Jan 21, 2025
4d3380a
feat: python matrix for gha
Jan 21, 2025
28b3e2c
chore: pre-commit auto fixes [...]
pre-commit-ci[bot] Jan 21, 2025
9cc2c78
Merge branch 'dev' into pyspark-bump
project-defiant Jan 21, 2025
fbaa8d9
chore: typos
Jan 21, 2025
7f416ed
chore: fix python version in setup dev script
Jan 21, 2025
5a9cd8f
fix: attempt to fix the 3.11 tests
Jan 21, 2025
c46cdab
fix: set the session correctly in variant_index_config
Jan 21, 2025
18c66b1
Revert "chore: fix doctest syntax"
Jan 21, 2025
def0fbb
chore: update dependencies
Jan 21, 2025
4eabc51
Revert "Revert "chore: fix doctest syntax""
Jan 21, 2025
c350211
chore: bump image to 2.2
Jan 21, 2025
8c2fa2b
chore: update lock files
Jan 21, 2025
1719b5c
build: poetry cleanup
Jan 22, 2025
c45ac1c
build: uv checks droped
Jan 22, 2025
1fccce6
chore: fix dockerfile and install test deps
Jan 22, 2025
4c1efbd
build(uv): add all dependencies to run tests
Jan 22, 2025
1e913a8
Merge branch 'dev' into pyspark-bump
project-defiant Jan 22, 2025
08e03e3
chore: fix test issue with rounding error
Jan 22, 2025
f9fc356
chore: fix dependency version lower bounds
Jan 22, 2025
f1ff1f9
chore: add .python-version file to ignored
Jan 22, 2025
98d464d
build: new setup
Jan 23, 2025
aa64db9
build: new setup
Jan 23, 2025
570e33e
build: new setup
Jan 23, 2025
89a9c34
build: new setup
Jan 23, 2025
2db0610
build: new setup
Jan 23, 2025
b392368
revert: bring back initialization actions
Jan 23, 2025
2329a8a
chore: align variable name
Jan 23, 2025
04c2ed2
chore: update pre-commit python version
Jan 23, 2025
979325d
chore: docs update
Jan 23, 2025
3eb7d55
Merge branch 'dev' into pyspark-bump
project-defiant Jan 24, 2025
79022b9
feat: more complex uv installation
SzymonSzyszkowski Jan 27, 2025
9adc76a
feat: notify to source shellrc file when installing uv
SzymonSzyszkowski Jan 27, 2025
7d10b63
fix: checks
SzymonSzyszkowski Jan 27, 2025
a17290d
chore: debug gha
SzymonSzyszkowski Jan 27, 2025
79de16b
chore: debug gha
SzymonSzyszkowski Jan 27, 2025
e7d5cd8
feat: debug gha
SzymonSzyszkowski Jan 27, 2025
f4ab0d0
feat: debug gha
SzymonSzyszkowski Jan 27, 2025
3bc1318
feat: debug gha
SzymonSzyszkowski Jan 27, 2025
a82b86c
feat: force user shell
SzymonSzyszkowski Jan 27, 2025
09b83a8
feat: gha debug
SzymonSzyszkowski Jan 27, 2025
640f493
feat: gha debug
SzymonSzyszkowski Jan 27, 2025
4a2018a
feat: gha debug
SzymonSzyszkowski Jan 27, 2025
e3ea829
feat: gha debug
SzymonSzyszkowski Jan 27, 2025
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chore: fix python version in setup dev script
Szymon Szyszkowski committed Jan 21, 2025

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This commit was created on GitHub.com and signed with GitHub’s verified signature.
commit 7f416eded4bea7c029e4ca65ecbe53c947250d4c
23 changes: 10 additions & 13 deletions utils/install_dependencies.sh
Original file line number Diff line number Diff line change
@@ -1,23 +1,20 @@
readonly PYTHON_VERSION=3.10.8
export SHELL_RC=$(echo "$HOME/.${SHELL##*/}rc")

if ! command -v pyenv &>/dev/null; then
echo "Installing Pyenv, a tool to manage multiple Python versions..."
curl -sSL https://pyenv.run | bash
# Add Pyenv configuration to ~/.bashrc.
echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc
echo 'command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
echo 'eval "$(pyenv init -)"' >> ~/.bashrc
# Add Pyenv configuration to rc file.
echo 'export PYENV_ROOT="$HOME/.pyenv"' >>$SHELL_RC
echo 'command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"' >>$SHELL_RC
echo 'eval "$(pyenv init -)"' >>$SHELL_RC
# And also execute it right now.
. <(tail -n3 ~/.bashrc)
. <(tail -n3 $SHELL_RC)
fi

echo "Activating Pyenv environment with a Python version required for the project..."
if [ -f ".python-version" ]; then
PYTHON_VERSION=$(cat .python-version)
pyenv install --skip-existing $PYTHON_VERSION
pyenv shell $PYTHON_VERSION
else
echo ".python-version file not found."
exit 1
fi
pyenv install --skip-existing $PYTHON_VERSION
pyenv shell $PYTHON_VERSION

if ! command -v poetry &>/dev/null; then
echo "Installing Poetry, a tool to manage Python dependencies..."