[BF]: updated conda installation and instructions so that pip package…

…s are conda dependencies

.github/workflows/conda-installation.yml

@@ -22,8 +22,10 @@ jobs:
       - name: Install dependencies
         shell:  bash -el {0}
         run: |
+          conda config --set pip_interop_enabled True
           python -m pip install .
-          conda install -c conda-forge heudiconv git-annex=*=alldep* datalad
+          conda update --all
+          conda install -c conda-forge heudiconv bids-validator dcm2niix git-annex=*=alldep* datalad 
 
       # Create virtual env under each python version
       # (optional and a bit redundant because we are already on a specific python)

README.md

@@ -21,8 +21,13 @@ Optionally, rename the `.env.example` to `.env` and set the variables (`shanoir_
 > This installation method is required if shanoir2bids.py is used 
 
 In an active conda virtual environment type 
-```
+```bash
+#use pip packages as dependencies
+conda config --set pip_interop_enabled True
 pip install . 
+#replace pip packages with conda packages when equivalent
+conda update --all
+# install missing conda packages (far simpler than using pip)
 conda install -c conda-forge heudiconv git-annex=*=alldep* datalad
 ```
 ## Usage