From 8e2314233ad487ed0d8a0053c72c64637cf7c95b Mon Sep 17 00:00:00 2001 From: SarahOuologuem Date: Mon, 11 Mar 2024 13:02:59 +0000 Subject: [PATCH 1/4] add visium ingest ci --- .../workflows/spatial_ingestion_visium-ci.yml | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100644 .github/workflows/spatial_ingestion_visium-ci.yml diff --git a/.github/workflows/spatial_ingestion_visium-ci.yml b/.github/workflows/spatial_ingestion_visium-ci.yml new file mode 100644 index 00000000..57241428 --- /dev/null +++ b/.github/workflows/spatial_ingestion_visium-ci.yml @@ -0,0 +1,112 @@ +name: Run tutorials (spatial ingest visium) + +on: + push: + branches: + - main + pull_request: + branches: + - main + +env: + debug: 'true' + +jobs: + spatial_ingest_visium: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + os: ["ubuntu-latest"] # , "macos-latest", "windows-latest" + python-version: ["3.10"] + + steps: + - uses: actions/checkout@v4 + + - name: File tree + if: env.debug == 'true' + run: tree + + - uses: conda-incubator/setup-miniconda@v3 + with: + miniforge-version: latest + auto-activate-base: true + auto-update-conda: true + channels: conda-forge + channel-priority: strict + activate-environment: pipeline_env + environment-file: pipeline_env.yaml + + - name: Install Panpipes + shell: bash -el {0} + run: | + pip install -e . + pip install .[spatial] + conda list + + - name: Conda info + if: env.debug == 'true' + shell: bash -el {0} + run: conda info + + - name: Conda list + if: env.debug == 'true' + shell: pwsh + run: conda list + + + - name: Preparing the data + run: | + mkdir spatial spatial/ingestion spatial/ingestion/data + cd spatial/ingestion/data + mkdir V1_Human_Heart V1_Human_Lymph_Node + cd V1_Human_Heart + curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_filtered_feature_bc_matrix.h5 + curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_spatial.tar.gz + tar -xf V1_Human_Heart_spatial.tar.gz + cd ../V1_Human_Lymph_Node + curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5 + curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_spatial.tar.gz + tar -xf V1_Human_Lymph_Node_spatial.tar.gz + + # Note: we run the following to test that the commands works + - name: Preparing the configuration file + shell: bash -el {0} + run: | + cd spatial/ingestion + panpipes qc_spatial config + + - name: Preparing the submission file + run: | + cd spatial/ingestion + curl -o sample_file_qc_spatial.txt https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/ingesting_visium_data/sample_file_qc_spatial.txt + + - name: Preparing the yaml file + run: | + cd spatial/ingestion + curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/ingesting_visium_data/pipeline.yml + + - name: Replace template contents in configuration file + run: | + cd spatial/ingestion + sed -i 's+condaenv:+conda_env: pipeline_env+g' pipeline.yml + + - name: File tree + if: env.debug == 'true' + run: tree spatial/ingestion + + - name: Review pipeline tasks + shell: bash -el {0} + run: | + cd spatial/ingestion + panpipes qc_spatial show full --local + + - name: Run pipeline tasks + shell: bash -el {0} + run: | + cd spatial/ingestion + panpipes qc_spatial make full --local + + - name: File tree + if: env.debug == 'true' + run: tree spatial/ingestion From 6c0e8d60dc11606c63525909be7475be521cf40b Mon Sep 17 00:00:00 2001 From: SarahOuologuem Date: Mon, 11 Mar 2024 13:44:37 +0000 Subject: [PATCH 2/4] remove install cmd --- .github/workflows/spatial_ingestion_visium-ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/spatial_ingestion_visium-ci.yml b/.github/workflows/spatial_ingestion_visium-ci.yml index 57241428..c8113205 100644 --- a/.github/workflows/spatial_ingestion_visium-ci.yml +++ b/.github/workflows/spatial_ingestion_visium-ci.yml @@ -40,7 +40,6 @@ jobs: - name: Install Panpipes shell: bash -el {0} run: | - pip install -e . pip install .[spatial] conda list From 95c5c48e094358c88957aa0d242a259212356c14 Mon Sep 17 00:00:00 2001 From: SarahOuologuem Date: Mon, 11 Mar 2024 14:06:59 +0000 Subject: [PATCH 3/4] downgrade jax version --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8eb2c04a..695f1448 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,8 +20,8 @@ classifiers = [ requires-python = ">= 3.10" dependencies = [ - "jax", - "jaxlib", + "jax==0.4.23", + "jaxlib==0.4.23", "apsw", "bbknn", "cgatcore", From 5687231bf242101d2b9f46de26980361db45cd36 Mon Sep 17 00:00:00 2001 From: SarahOuologuem Date: Mon, 11 Mar 2024 14:31:24 +0000 Subject: [PATCH 4/4] downgrade jax for spatial --- pyproject.toml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 695f1448..6aa05566 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,8 +20,8 @@ classifiers = [ requires-python = ">= 3.10" dependencies = [ - "jax==0.4.23", - "jaxlib==0.4.23", + "jax", + "jaxlib", "apsw", "bbknn", "cgatcore", @@ -59,6 +59,8 @@ notebook = [ "jupyterlab" ] spatial = [ + "jax==0.4.23", + "jaxlib==0.4.23", "squidpy", "cell2location", "tangram-sc"