Workflow file for this run
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| # ref https://github.com/marketplace/actions/setup-miniconda | |
| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # GitHub recommends pinning actions to a commit SHA. | |
| # To get a newer version, you will need to update the SHA. | |
| # You can also reference a tag or branch, but the action may change without warning. | |
| # By default, GitHub Actions uses different shells based on the runner operating system: | |
| # Ubuntu (Linux) and macOS: bash | |
| # Windows: cmd | |
| # We can test SDePER installation on multiple OS by setting os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
| # but installation would fail in macOS and Windows... | |
| name: Test SDePER installation across PyPI, Conda, and Docker | |
| on: | |
| release: | |
| types: [published] | |
| jobs: | |
| test-pypi: | |
| name: test-pypi (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| environment: package-test # specify the environment | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| # bash login mode is needed for activate environment in Ubuntu and macOS (ref https://github.com/marketplace/actions/setup-miniconda#important) | |
| # cmd in Windows is fine | |
| shell: bash -el {0} # `-e` means the shell will stop executing if any command returns a non-zero status (error). `-l` makes Bash act as if it had been invoked as a login shell | |
| strategy: | |
| fail-fast: false # all job combinations will run to completion even if one of them fails | |
| matrix: # uses a matrix strategy to run multiple test configurations across different operating systems and Python versions | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.9.12", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download test files # note to use URL for the raw file | |
| shell: pwsh # Changed the shell to PowerShell for all platforms to ensure consistency in command syntax and behavior across all operating systems | |
| run: | | |
| # a function to decompress .gz file using PowerShell (https://learn.microsoft.com/en-us/archive/msdn-technet-forums/5aa53fef-5229-4313-a035-8b3a38ab93f5) | |
| Function DeGZip-File{ | |
| Param( | |
| $infile, | |
| $outfile = ($infile -replace '\.gz$','') | |
| ) | |
| $input = New-Object System.IO.FileStream $inFile, ([IO.FileMode]::Open), ([IO.FileAccess]::Read), ([IO.FileShare]::Read) | |
| $output = New-Object System.IO.FileStream $outFile, ([IO.FileMode]::Create), ([IO.FileAccess]::Write), ([IO.FileShare]::None) | |
| $gzipStream = New-Object System.IO.Compression.GzipStream $input, ([IO.Compression.CompressionMode]::Decompress) | |
| $buffer = New-Object byte[](1024) | |
| while($true){ | |
| $read = $gzipstream.Read($buffer, 0, 1024) | |
| if ($read -le 0){break} | |
| $output.Write($buffer, 0, $read) | |
| } | |
| $gzipStream.Close() | |
| $output.Close() | |
| $input.Close() | |
| } | |
| $urls = @( | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_nUMI.csv", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_ref_scRNA_cell_celltype.csv", | |
| "https://github.com/az7jh2/SDePER_Analysis/raw/main/RealData/MOB/MOB_ref_scRNA_cell_nUMI.csv.gz", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_adjacency_matrix.csv", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_loc.csv" | |
| ) | |
| foreach ($url in $urls) { | |
| Invoke-WebRequest -Uri $url -OutFile ($url -split "/" | Select-Object -Last 1) | |
| } | |
| DeGZip-File MOB_ref_scRNA_cell_nUMI.csv.gz | |
| - uses: conda-incubator/setup-miniconda@v3 # create and activate an mostly-empty environment named test, containing only the latest `python-version` and its dependencies | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install SDePER package | |
| run: | | |
| pip install --upgrade pip | |
| pip install sdeper | |
| - name: Extract version number from tag # note to create an environment variable for later reference | |
| run: | | |
| TAG_NAME="${{ github.event.release.tag_name }}" | |
| echo "VERSION_NUMBER=${TAG_NAME#v}" >> $GITHUB_ENV | |
| - name: Test version | |
| run: | | |
| PACKAGE_VERSION=$(runDeconvolution -v | tail -n 1 | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') | |
| if [ "$PACKAGE_VERSION" == "${{ env.VERSION_NUMBER }}" ]; then | |
| echo "Version matches: $PACKAGE_VERSION" | |
| else | |
| echo "Version mismatch. Expected ${{ env.VERSION_NUMBER }}, but got $PACKAGE_VERSION" | |
| exit 1 | |
| fi | |
| - name: Test GLRM | |
| run: | | |
| runDeconvolution -q MOB_spatial_spot_nUMI.csv \ | |
| -r MOB_ref_scRNA_cell_nUMI.csv \ | |
| -c MOB_ref_scRNA_cell_celltype.csv \ | |
| -a MOB_spatial_spot_adjacency_matrix.csv \ | |
| -l MOB_spatial_spot_loc.csv \ | |
| --n_marker_per_cmp 5 \ | |
| -n 64 \ | |
| -use_cvae false \ | |
| --lambda_r 0 \ | |
| --lambda_g 0 \ | |
| --use_imputation false \ | |
| --diagnosis true \ | |
| --verbose false | |
| - name: Test SDePER | |
| run: | | |
| runDeconvolution -q MOB_spatial_spot_nUMI.csv \ | |
| -r MOB_ref_scRNA_cell_nUMI.csv \ | |
| -c MOB_ref_scRNA_cell_celltype.csv \ | |
| -a MOB_spatial_spot_adjacency_matrix.csv \ | |
| -l MOB_spatial_spot_loc.csv \ | |
| --n_hv_gene 20 \ | |
| --n_marker_per_cmp 5 \ | |
| --n_pseudo_spot 500 \ | |
| --num_hidden_layer 1 \ | |
| --use_batch_norm false \ | |
| --cvae_train_epoch 100 \ | |
| --use_spatial_pseudo true \ | |
| -n 64 \ | |
| --lambda_r_range_max 20 \ | |
| --lambda_r_range_k 2 \ | |
| --lambda_g_range_max 20 \ | |
| --lambda_g_range_k 2 \ | |
| --use_imputation false \ | |
| --diagnosis true \ | |
| --verbose false | |
| - name: Print result | |
| run: | | |
| python --version | |
| runDeconvolution -v | |
| head celltype_proportions.csv -n 5 | |
| test-conda: | |
| name: test-conda (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| environment: package-test # specify the environment | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| # bash login mode is needed for activate environment in Ubuntu and macOS (ref https://github.com/marketplace/actions/setup-miniconda#important) | |
| # cmd in Windows is fine | |
| shell: bash -el {0} # `-e` means the shell will stop executing if any command returns a non-zero status (error). `-l` makes Bash act as if it had been invoked as a login shell | |
| strategy: | |
| fail-fast: false # all job combinations will run to completion even if one of them fails | |
| matrix: # uses a matrix strategy to run multiple test configurations across different operating systems and Python versions | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.9.12", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download test files # note to use URL for the raw file | |
| shell: pwsh # Changed the shell to PowerShell for all platforms to ensure consistency in command syntax and behavior across all operating systems | |
| run: | | |
| # a function to decompress .gz file using PowerShell (https://learn.microsoft.com/en-us/archive/msdn-technet-forums/5aa53fef-5229-4313-a035-8b3a38ab93f5) | |
| Function DeGZip-File{ | |
| Param( | |
| $infile, | |
| $outfile = ($infile -replace '\.gz$','') | |
| ) | |
| $input = New-Object System.IO.FileStream $inFile, ([IO.FileMode]::Open), ([IO.FileAccess]::Read), ([IO.FileShare]::Read) | |
| $output = New-Object System.IO.FileStream $outFile, ([IO.FileMode]::Create), ([IO.FileAccess]::Write), ([IO.FileShare]::None) | |
| $gzipStream = New-Object System.IO.Compression.GzipStream $input, ([IO.Compression.CompressionMode]::Decompress) | |
| $buffer = New-Object byte[](1024) | |
| while($true){ | |
| $read = $gzipstream.Read($buffer, 0, 1024) | |
| if ($read -le 0){break} | |
| $output.Write($buffer, 0, $read) | |
| } | |
| $gzipStream.Close() | |
| $output.Close() | |
| $input.Close() | |
| } | |
| $urls = @( | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_nUMI.csv", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_ref_scRNA_cell_celltype.csv", | |
| "https://github.com/az7jh2/SDePER_Analysis/raw/main/RealData/MOB/MOB_ref_scRNA_cell_nUMI.csv.gz", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_adjacency_matrix.csv", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_loc.csv" | |
| ) | |
| foreach ($url in $urls) { | |
| Invoke-WebRequest -Uri $url -OutFile ($url -split "/" | Select-Object -Last 1) | |
| } | |
| DeGZip-File MOB_ref_scRNA_cell_nUMI.csv.gz | |
| - uses: conda-incubator/setup-miniconda@v3 # create and activate an mostly-empty environment named test, containing only the latest `python-version` and its dependencies | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install SDePER package | |
| run: | | |
| conda install -c bioconda -c conda-forge sdeper | |
| - name: Extract version number from tag # note to create an environment variable for later reference | |
| run: | | |
| TAG_NAME="${{ github.event.release.tag_name }}" | |
| echo "VERSION_NUMBER=${TAG_NAME#v}" >> $GITHUB_ENV | |
| - name: Test version | |
| run: | | |
| PACKAGE_VERSION=$(runDeconvolution -v | tail -n 1 | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') | |
| if [ "$PACKAGE_VERSION" == "${{ env.VERSION_NUMBER }}" ]; then | |
| echo "Version matches: $PACKAGE_VERSION" | |
| else | |
| echo "Version mismatch. Expected ${{ env.VERSION_NUMBER }}, but got $PACKAGE_VERSION" | |
| exit 1 | |
| fi | |
| - name: Test GLRM | |
| run: | | |
| runDeconvolution -q MOB_spatial_spot_nUMI.csv \ | |
| -r MOB_ref_scRNA_cell_nUMI.csv \ | |
| -c MOB_ref_scRNA_cell_celltype.csv \ | |
| -a MOB_spatial_spot_adjacency_matrix.csv \ | |
| -l MOB_spatial_spot_loc.csv \ | |
| --n_marker_per_cmp 5 \ | |
| -n 64 \ | |
| -use_cvae false \ | |
| --lambda_r 0 \ | |
| --lambda_g 0 \ | |
| --use_imputation false \ | |
| --diagnosis true \ | |
| --verbose false | |
| - name: Test SDePER | |
| run: | | |
| runDeconvolution -q MOB_spatial_spot_nUMI.csv \ | |
| -r MOB_ref_scRNA_cell_nUMI.csv \ | |
| -c MOB_ref_scRNA_cell_celltype.csv \ | |
| -a MOB_spatial_spot_adjacency_matrix.csv \ | |
| -l MOB_spatial_spot_loc.csv \ | |
| --n_hv_gene 20 \ | |
| --n_marker_per_cmp 5 \ | |
| --n_pseudo_spot 500 \ | |
| --num_hidden_layer 1 \ | |
| --use_batch_norm false \ | |
| --cvae_train_epoch 100 \ | |
| --use_spatial_pseudo true \ | |
| -n 64 \ | |
| --lambda_r_range_max 20 \ | |
| --lambda_r_range_k 2 \ | |
| --lambda_g_range_max 20 \ | |
| --lambda_g_range_k 2 \ | |
| --use_imputation false \ | |
| --diagnosis true \ | |
| --verbose false | |
| - name: Print result | |
| run: | | |
| python --version | |
| runDeconvolution -v | |
| head celltype_proportions.csv -n 5 | |
| test-docker: | |
| name: test-docker (${{ matrix.os }}) | |
| environment: package-test # specify the environment | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| # bash login mode is needed for activate environment in Ubuntu and macOS (ref https://github.com/marketplace/actions/setup-miniconda#important) | |
| # cmd in Windows is fine | |
| shell: bash -el {0} # `-e` means the shell will stop executing if any command returns a non-zero status (error). `-l` makes Bash act as if it had been invoked as a login shell | |
| strategy: | |
| fail-fast: false # all job combinations will run to completion even if one of them fails | |
| matrix: # uses a matrix strategy to run multiple test configurations across different operating systems and Python versions | |
| os: ["ubuntu-latest"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Download test files # note to use URL for the raw file | |
| shell: pwsh # Changed the shell to PowerShell for all platforms to ensure consistency in command syntax and behavior across all operating systems | |
| run: | | |
| # a function to decompress .gz file using PowerShell (https://learn.microsoft.com/en-us/archive/msdn-technet-forums/5aa53fef-5229-4313-a035-8b3a38ab93f5) | |
| Function DeGZip-File{ | |
| Param( | |
| $infile, | |
| $outfile = ($infile -replace '\.gz$','') | |
| ) | |
| $input = New-Object System.IO.FileStream $inFile, ([IO.FileMode]::Open), ([IO.FileAccess]::Read), ([IO.FileShare]::Read) | |
| $output = New-Object System.IO.FileStream $outFile, ([IO.FileMode]::Create), ([IO.FileAccess]::Write), ([IO.FileShare]::None) | |
| $gzipStream = New-Object System.IO.Compression.GzipStream $input, ([IO.Compression.CompressionMode]::Decompress) | |
| $buffer = New-Object byte[](1024) | |
| while($true){ | |
| $read = $gzipstream.Read($buffer, 0, 1024) | |
| if ($read -le 0){break} | |
| $output.Write($buffer, 0, $read) | |
| } | |
| $gzipStream.Close() | |
| $output.Close() | |
| $input.Close() | |
| } | |
| $urls = @( | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_nUMI.csv", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_ref_scRNA_cell_celltype.csv", | |
| "https://github.com/az7jh2/SDePER_Analysis/raw/main/RealData/MOB/MOB_ref_scRNA_cell_nUMI.csv.gz", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_adjacency_matrix.csv", | |
| "https://raw.githubusercontent.com/az7jh2/SDePER_Analysis/main/RealData/MOB/MOB_spatial_spot_loc.csv" | |
| ) | |
| foreach ($url in $urls) { | |
| Invoke-WebRequest -Uri $url -OutFile ($url -split "/" | Select-Object -Last 1) | |
| } | |
| DeGZip-File MOB_ref_scRNA_cell_nUMI.csv.gz | |
| - name: Extract version number from tag # note to create an environment variable for later reference | |
| run: | | |
| TAG_NAME="${{ github.event.release.tag_name }}" | |
| echo "VERSION_NUMBER=${TAG_NAME#v}" >> $GITHUB_ENV | |
| - name: Download SDePER image with specific version | |
| run: | | |
| docker pull az7jh2/sdeper:${{ env.VERSION_NUMBER }} | |
| - name: Test version | |
| run: | | |
| PACKAGE_VERSION=$(docker run --rm az7jh2/sdeper:${{ env.VERSION_NUMBER }} runDeconvolution -v | tail -n 1 | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') | |
| if [ "$PACKAGE_VERSION" == "${{ env.VERSION_NUMBER }}" ]; then | |
| echo "Version matches: $PACKAGE_VERSION" | |
| else | |
| echo "Version mismatch. Expected ${{ env.VERSION_NUMBER }}, but got $PACKAGE_VERSION" | |
| exit 1 | |
| fi | |
| - name: Test GLRM | |
| run: | | |
| docker run --rm -v $(pwd):/data az7jh2/sdeper:${{ env.VERSION_NUMBER }} runDeconvolution -q MOB_spatial_spot_nUMI.csv \ | |
| -r MOB_ref_scRNA_cell_nUMI.csv \ | |
| -c MOB_ref_scRNA_cell_celltype.csv \ | |
| -a MOB_spatial_spot_adjacency_matrix.csv \ | |
| -l MOB_spatial_spot_loc.csv \ | |
| --n_marker_per_cmp 5 \ | |
| -n 64 \ | |
| -use_cvae false \ | |
| --lambda_r 0 \ | |
| --lambda_g 0 \ | |
| --use_imputation false \ | |
| --diagnosis true \ | |
| --verbose false | |
| - name: Test SDePER | |
| run: | | |
| docker run --rm -v $(pwd):/data az7jh2/sdeper:${{ env.VERSION_NUMBER }} runDeconvolution -q MOB_spatial_spot_nUMI.csv \ | |
| -r MOB_ref_scRNA_cell_nUMI.csv \ | |
| -c MOB_ref_scRNA_cell_celltype.csv \ | |
| -a MOB_spatial_spot_adjacency_matrix.csv \ | |
| -l MOB_spatial_spot_loc.csv \ | |
| --n_hv_gene 20 \ | |
| --n_marker_per_cmp 5 \ | |
| --n_pseudo_spot 500 \ | |
| --num_hidden_layer 1 \ | |
| --use_batch_norm false \ | |
| --cvae_train_epoch 100 \ | |
| --use_spatial_pseudo true \ | |
| -n 64 \ | |
| --lambda_r_range_max 20 \ | |
| --lambda_r_range_k 2 \ | |
| --lambda_g_range_max 20 \ | |
| --lambda_g_range_k 2 \ | |
| --use_imputation false \ | |
| --diagnosis true \ | |
| --verbose false | |
| - name: Print result | |
| run: | | |
| docker run --rm az7jh2/sdeper:${{ env.VERSION_NUMBER }} python --version | |
| docker run --rm az7jh2/sdeper:${{ env.VERSION_NUMBER }} runDeconvolution -v | |
| head celltype_proportions.csv -n 5 |