Improve error explanation on potential inadequate combinations of sam…

…ples and factor fields (#323)

* Warn on potential inadequate combinations of samples and factor fields

* Use black line lengths on flake8 linter

* Lint issues and others

* More linting

* Bump build number

.github/workflows/pr.yaml

@@ -172,7 +172,7 @@ jobs:
     - name: Install flake8
       run: pip install flake8 flake8-import-order
     - name: Flake8
-      run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --ignore=I201,W503 --output-file pylint_report.txt --tee
+      run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --max-line-length 88 --ignore=I201,W503 --output-file pylint_report.txt --tee
     - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:

tools/tertiary-analysis/decoupler/decoupler_pseudobulk.py

@@ -320,6 +320,21 @@ def main(args):
         min_counts=args.min_counts,
     )
 
+    print("Created pseudo-bulk AnnData, checking if fields still make sense.")
+    print(
+        "If this fails this check, it might mean that you asked for factors "
+        + "that are not compatible with you sample identifiers (ie. asked for "
+        + "phase in the factors, but each sample contains more than one phase, "
+        + "try joining fields)"
+    )
+    if factor_fields:
+        check_fields(
+            factor_fields,
+            pseudobulk_data,
+            context=" after creation of pseudo-bulk AnnData",
+        )
+    print("Factors requested are adequate for the pseudo-bulked AnnData!")
+
     # Plot pseudobulk samples
     plot_pseudobulk_samples(
         pseudobulk_data,

tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml

@@ -1,4 +1,4 @@
-<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy3" profile="20.05">
+<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy4" profile="20.05">
     <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description>
     <requirements>
         <requirement type="package" version="1.4.0">decoupler</requirement>