diff --git a/.github/workflows/integration01-ci.yml b/.github/workflows/integration01-ci.yml
index 0dbac9cc..6a29d586 100644
--- a/.github/workflows/integration01-ci.yml
+++ b/.github/workflows/integration01-ci.yml
@@ -37,12 +37,17 @@ jobs:
activate-environment: pipeline_env
environment-file: pipeline_env.yaml
# important: this patch is only to test if multivi integration works
-# issues are not related to panpipes https://discourse.scverse.org/t/error-when-training-model-on-m3-max-mps/1896/2
+# pip install -e . #'.[multivipatch]'
+# issues are not related to panpipes
+# https://discourse.scverse.org/t/error-when-training-model-on-m3-max-mps/1896/2
# https://discourse.scverse.org/t/macbook-m1-m2-mps-acceleration-with-scvi/2075/4
+
+# now disabling adversarial training for temp fix to ensure running latest multivi
+# https://github.com/scverse/scvi-tools/issues/2581
- name: Install Panpipes
shell: bash -el {0}
run: |
- pip install '.[multivipatch]'
+ pip install -e .
conda list
- name: Conda info
@@ -98,3 +103,7 @@ jobs:
- name: File tree
if: env.debug == 'true'
run: tree teaseq
+
+ - name: check logs
+ if: always()
+ run: cat teaseq/integration/logs/4_multimodal_multivi.log
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a9fc7fec..1ac8d32d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,8 @@
- fixed calls to new imports matplotlib
- fixed scanpy/muon latest
+- changed default adversarial_training = False to ensure multivi runs with scvi-tools 1.1.3 https://github.com/scverse/scvi-tools/issues/2581
+- updated integration01 action to use updated scvi-tools version
### dependencies
diff --git a/docs/release_notes.md b/docs/release_notes.md
index a9fc7fec..1ac8d32d 100644
--- a/docs/release_notes.md
+++ b/docs/release_notes.md
@@ -9,6 +9,8 @@
- fixed calls to new imports matplotlib
- fixed scanpy/muon latest
+- changed default adversarial_training = False to ensure multivi runs with scvi-tools 1.1.3 https://github.com/scverse/scvi-tools/issues/2581
+- updated integration01 action to use updated scvi-tools version
### dependencies
diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md
index ab81905c..76c8e899 100644
--- a/docs/yaml_docs/pipeline_integration_yml.md
+++ b/docs/yaml_docs/pipeline_integration_yml.md
@@ -350,7 +350,7 @@ For more information on `bbknn` check the [bbknn documentation](https://bbknn.re
- n_steps_kl_warmup `String`, Default: None
Leave blank for the default integer
- n_epochs_kl_warmup `Integer`, Default: 50
- - adversarial_mixing `Boolean`, Default: True
+ - adversarial_mixing `Boolean`, Default: False
- training_plan `String`, Default: None
diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml
index 6ab08960..354e5f2c 100644
--- a/panpipes/panpipes/pipeline_integration/pipeline.yml
+++ b/panpipes/panpipes/pipeline_integration/pipeline.yml
@@ -190,7 +190,7 @@ multimodal:
check_val_every_n_epoch :
n_steps_kl_warmup :
n_epochs_kl_warmup : 50
- adversarial_mixing : True
+ adversarial_mixing : False
training_plan :
# Mofa arguments
diff --git a/panpipes/python_scripts/batch_correct_multivi.py b/panpipes/python_scripts/batch_correct_multivi.py
index f0de9590..58df2736 100644
--- a/panpipes/python_scripts/batch_correct_multivi.py
+++ b/panpipes/python_scripts/batch_correct_multivi.py
@@ -244,6 +244,14 @@
mvi.view_anndata_setup()
+L.info("training args")
+print(multivi_training_args)
+
+
+L.info("training plan")
+print(multivi_training_plan)
+
+
L.info("Running multiVI")
mvi.train( **multivi_training_args, **multivi_training_plan)
diff --git a/pyproject.toml b/pyproject.toml
index d6e0004a..2dc39d84 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,11 +71,6 @@ spatial = [
"tangram-sc"
]
-multivipatch = [
- "scvi-tools<=0.20.3",
- "requests"
-]
-
refmap_old = [
"scvi-tools",
"pandas<2.0.0",
diff --git a/tests/integration_1/pipeline.yml b/tests/integration_1/pipeline.yml
index f5806cd7..1092e866 100644
--- a/tests/integration_1/pipeline.yml
+++ b/tests/integration_1/pipeline.yml
@@ -240,7 +240,6 @@ multimodal:
# you can add any other param from the tutorials and they will
# be parsed alongside the others
# leave arguments blank for default
- seed: 1492
lowmem: True
# Set lowmem to True will subset the atac to the top 25k HVF.
# This is to deal with concatenation of atac,rna on large datasets which at the moment is suboptimally required by scvitools.
@@ -260,14 +259,14 @@ multimodal:
fully_paired : False
training_args:
#(default: 500)
- max_epochs : 500
+ max_epochs : 20
#float (default: 0.0001)
lr : 1.0e-05
- #leave blanck for default str | int | bool | None (default: None)
+ #leave blank for default str | int | bool | None (default: None)
use_gpu :
# float (default: 0.9)
train_size : 0.9
- # leave blanck for default, float | None (default: None)
+ # leave blank for default, float | None (default: None)
validation_size :
# int (default: 128)
batch_size : 128
@@ -279,15 +278,15 @@ multimodal:
early_stopping : True
#bool (default: True)
save_best : True
- #leave blanck for default int | None (default: None)
+ #leave blank for default int | None (default: None)
check_val_every_n_epoch :
- #leave blanck for default int | None (default: None)
+ #leave blank for default int | None (default: None)
n_steps_kl_warmup :
# int | None (default: 50)
n_epochs_kl_warmup : 50
#bool (default: True)
adversarial_mixing : False
- #leave blanck for default dict | None (default: None)
+ #leave blank for default dict | None (default: None)
training_plan :
mofa:
# this is a minimal set of parameters that will be expected