From edc853caf29f6c372e70f1f5dd14ca0b49f8a515 Mon Sep 17 00:00:00 2001
From: bio-la <fabiola.curion@gmail.com>
Date: Wed, 28 Feb 2024 10:50:47 +0100
Subject: [PATCH] multiVI, atac test

---
 .github/workflows/integration01-ci.yml | 98 ++++++++++++++++++++++++++
 tests/integration_1/pipeline.yml       |  9 ++-
 2 files changed, 102 insertions(+), 5 deletions(-)
 create mode 100644 .github/workflows/integration01-ci.yml

diff --git a/.github/workflows/integration01-ci.yml b/.github/workflows/integration01-ci.yml
new file mode 100644
index 00000000..5f3f8c57
--- /dev/null
+++ b/.github/workflows/integration01-ci.yml
@@ -0,0 +1,98 @@
+name: Run tutorials (integration)
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+env:
+  debug: 'true'
+
+jobs:
+  integration:
+    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 .
+          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
+
+      # Note: all three files are renamed during the download to trim the "subsample_" prefix
+      - name: Preparing the data
+        run: |
+          mkdir -p teaseq/integration && cd  teaseq/integration
+          curl -L -o teaseq.h5mu https://figshare.com/ndownloader/files/44471927
+
+      # Note: we run the following to test that the commands works
+      # However, the following task will replacing the file anyway
+      - name: Preparing the configuration file
+        shell: bash -el {0}
+        run: |
+          cd teaseq/integration
+          panpipes integration config
+
+      - name: Edit the submission file
+        run: |
+          cd teaseq/integration
+          curl -o pipeline.yml https://github.com/DendrouLab/panpipes/blob/fc_cipy/tests/integration_1/pipeline.yml
+
+      - name: Replace template contents in configuration file
+        run: |
+          cd teaseq/integration
+          sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_env+pipeline_env+g' pipeline.yml
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree teaseq
+
+      - name: Review pipeline tasks
+        shell: bash -el {0}
+        run: |
+          cd teaseq/integration
+          panpipes integration show full --local
+
+      - name: Run pipeline tasks
+        shell: bash -el {0}
+        run: |
+          cd teaseq/integration
+          panpipes integration make full --local
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree teaseq
diff --git a/tests/integration_1/pipeline.yml b/tests/integration_1/pipeline.yml
index 0f5c7407..e84655fb 100644
--- a/tests/integration_1/pipeline.yml
+++ b/tests/integration_1/pipeline.yml
@@ -40,7 +40,7 @@ preprocessed_obj: teaseq.h5mu
 # unimodal: correct each modality independently
 rna:
   # True or false depending on whether you want to run batch correction
-  run: True 
+  run: False 
   # what method(s) to use to run batch correction, you can specify multiple 
   # choices: harmony,bbknn,scanorama,scvi (comma-seprated string, no spaces)
   tools: harmony,scvi,bbknn
@@ -109,7 +109,7 @@ rna:
 #--------------------------
 prot:
   # True or false depending on whether you want to run batch correction
-  run: True 
+  run: False 
   # what method(s) to use to run batch correction, you can specify multiple 
   # choices: harmony,bbknn,combat
   tools: harmony
@@ -177,7 +177,7 @@ atac:
   # BBKNN args # https://bbknn.readthedocs.io/en/latest/
   #-----------------------------
   bbknn:
-    neighbors_within_batch: 
+    neighbors_within_batch: 30
   #----------------------------
   # find neighbour parameters
   #-----------------------------
@@ -204,8 +204,7 @@ multimodal:
   # choices: totalvi, mofa, MultiVI, WNN
   # list e.g. below
   tools: 
-    - WNN
-    - totalvi
+    - MultiVI
 
   # this is the column you want to batch correct on. if you specify a comma separated list, 
   # they will be all used simultaneosly. if you want to test correction for one at a time,