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Installation script test #238

Installation script test

Installation script test #238

Workflow file for this run

# Lingfei Wang, 2022, 2023. All rights reserved.
name: Installation script test
on:
schedule:
- cron: '20 7 * * 1'
push:
paths:
- '.github/workflows/ci-install.yml'
- '.github/actions/install-bash/**'
- README.rst
branches:
- master
- dev
workflow_dispatch:
inputs:
ref:
description: 'Commit or branch to run action on'
required: true
default: 'dev'
jobs:
install-script-bash:
runs-on: ubuntu-latest
outputs:
run: ${{ steps.runscript.outputs.run }}
steps:
- name: Show version
id: version
run: |
if [ "a${{ inputs.ref }}" != "a" ]; then
v="${{ inputs.ref }}"
elif [ "a${GITHUB_REF}" != "a" ]; then
v="${GITHUB_REF}"
elif [ "a${{ github.event.repository.default_branch }}" != "a" ]; then
v="${{ github.event.repository.default_branch }}"
else
exit 1
fi
echo "$v"
echo "version=$v" >> $GITHUB_OUTPUT
- uses: actions/checkout@v4
with:
ref: ${{ steps.version.outputs.version }}
- name: Set up Python 3.8
uses: actions/setup-python@v5
with:
python-version: 3.8
- name: Obtain install script
id: runscript
run: |
# Install command in README.rst (indented in Installation section)
# Get first code-block in section Installation
linestart=$(grep -n '^Installation' README.rst | awk -F: '{print $1}' | head -n 1)
lineend=$(tail -n +$(( linestart + 2 )) README.rst | grep -n '^==' | awk -F: '{print $1}' | head -n 1)
linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^Option [0-9]: with .*bash script' | awk -F: '{print $1}' | head -n 1)
echo "Step 1"
tail -n +$linestart README.rst | head -n $lineend
linestart=$(( linestart + linestart2 ))
lineend=$(tail -n +$(( linestart + 2 )) README.rst | head -n $lineend | grep -n '^--' | awk -F: '{print $1}' | head -n 1)
echo "Step 2"
tail -n +$(( linestart + 2 )) README.rst | head -n $lineend
linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1)
echo "Step 3"
tail -n +$linestart README.rst | head -n $lineend
lineend2=$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 )) | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1)
echo "Step 4"
tail -n +$linestart README.rst | head -n $lineend
echo "Step 5"
tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 ))
s1="$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2 | grep '^[[:blank:]]' | sed 's/^[[:space:]]*//g')"
echo "Step 6"
tail -n +$linestart README.rst | head -n $lineend
echo "Step 7"
tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2
echo "Step 8"
echo "$s1"
#If failed here: update this line and the same line in /.github/actions/install-bash/action.yml to match the lines in /README.rst
cmp <(echo "$s1") <(echo "wget https://tinyurl.com/dictys -O - | bash") || exit 1
echo "run=$s1" >> $GITHUB_OUTPUT
install-linux-bash:
runs-on: ubuntu-latest
needs: install-script-bash
steps:
- name: Set up Python 3.8
uses: actions/setup-python@v5
with:
python-version: 3.8
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
echo $CONDA/bin >> $GITHUB_PATH
- name: Test install
run: |
echo '::group::Test install output'
${{ needs.install-script-bash.outputs.run }}
echo '::endgroup::'
install-script-conda:
runs-on: ubuntu-latest
outputs:
run: ${{ steps.runscript.outputs.run }}
steps:
- name: Show version
id: version
run: |
if [ "a${{ inputs.ref }}" != "a" ]; then
v="${{ inputs.ref }}"
elif [ "a${GITHUB_REF}" != "a" ]; then
v="${GITHUB_REF}"
elif [ "a${{ github.event.repository.default_branch }}" != "a" ]; then
v="${{ github.event.repository.default_branch }}"
else
exit 1
fi
echo "$v"
echo "version=$v" >> $GITHUB_OUTPUT
- uses: actions/checkout@v4
with:
ref: ${{ steps.version.outputs.version }}
- name: Set up Python 3.8
uses: actions/setup-python@v5
with:
python-version: 3.8
- name: Obtain install script
id: run0
run: |
# Install command in README.rst (indented in Installation section)
# Get first code-block in section Installation
linestart=$(grep -n '^Installation' README.rst | awk -F: '{print $1}' | head -n 1)
lineend=$(tail -n +$(( linestart + 2 )) README.rst | grep -n '^==' | awk -F: '{print $1}' | head -n 1)
echo "Step 1"
tail -n +$linestart README.rst | head -n $lineend
linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^Option [0-9]: with .*conda$' | awk -F: '{print $1}' | head -n 1)
linestart=$(( linestart + linestart2 ))
echo "Step 2"
tail -n +$(( linestart + 2 )) README.rst | head -n $lineend
lineend=$(tail -n +$(( linestart + 2 )) README.rst | head -n $lineend | grep -n '^--' | awk -F: '{print $1}' | head -n 1)
linestart2=$(tail -n +$linestart README.rst | head -n $lineend | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1)
echo "Step 3"
tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 ))
lineend2=$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$(( linestart2 + 1 )) | grep -n '^.. code-block::' | awk -F: '{print $1}' | head -n 1)
echo "Step 4"
echo "$linestart"
echo "$lineend"
tail -n +$linestart README.rst | head -n $lineend
echo "Step 5"
echo "$linestart2"
echo "$lineend2"
tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2
s1="$(tail -n +$linestart README.rst | head -n $lineend | tail -n +$linestart2 | head -n $lineend2 | grep '^[[:blank:]]' | sed 's/^[[:space:]]*//g')"
#If failed here: update this line and the same line in /.github/actions/install-conda/action.yml to match the lines in /README.rst
cmp <(echo "$s1") <(echo "conda create -y -n dictys -c conda-forge python=3.9 mamba"; echo ". activate dictys"; echo "mamba install -y -c lingfeiwang -c bioconda -c conda-forge -c pytorch dictys pytorch torchvision torchaudio cpuonly") || exit 1
echo "run<<EOF" >> $GITHUB_ENV
echo "$s1" >> $GITHUB_ENV
echo "EOF" >> $GITHUB_ENV
- id: runscript
uses: actions/github-script@v7
with:
script: |
core.setOutput("run", `${{ env.run }}`);
install-linux-conda:
runs-on: ubuntu-latest
needs: install-script-conda
steps:
- name: Set up Python 3.8
uses: actions/setup-python@v5
with:
python-version: 3.8
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
echo $CONDA/bin >> $GITHUB_PATH
- name: Test install
run: |
echo '::group::Test install output'
${{ needs.install-script-conda.outputs.run }}
echo '::endgroup::'
install-linux:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9","3.10",""]
cuda-version: ["11.7",""]
steps:
- name: Show version
id: version
run: |
if [ "a${{ inputs.ref }}" != "a" ]; then
v="${{ inputs.ref }}"
elif [ "a${GITHUB_REF}" != "a" ]; then
v="${GITHUB_REF}"
elif [ "a${{ github.event.repository.default_branch }}" != "a" ]; then
v="${{ github.event.repository.default_branch }}"
else
exit 1
fi
echo "$v"
echo "version=$v" >> $GITHUB_OUTPUT
- uses: actions/checkout@v4
with:
ref: ${{ steps.version.outputs.version }}
- name: Install
uses: ./.github/actions/install-bash
with:
python-version: ${{ matrix.python-version }}
cuda-version: ${{ matrix.cuda-version }}