MNT: Shift more config into env.yml

Author: effigies

Dockerfile

@@ -103,16 +103,15 @@ RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bi
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
+COPY requirements.txt /tmp/requirements.txt
+WORKDIR /tmp
 RUN micromamba create -y -f /tmp/env.yml && \
     micromamba clean -y -a
 
 ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH"
 RUN /opt/conda/envs/fmriprep/bin/npm install -g svgo@^2.8 [email protected] && \
     rm -r ~/.npm
 
-COPY requirements.txt /tmp/requirements.txt
-RUN /opt/conda/envs/fmriprep/bin/pip install --no-cache-dir -r /tmp/requirements.txt
-
 #
 # Main stage
 #

env.yml

@@ -35,3 +35,8 @@ dependencies:
   - fsl-mcflirt=2111.0
   - fsl-miscmaths=2203.2
   - fsl-topup=2203.1
+  - pip
+  - pip:
+    - -r requirements.txt
+variables:
+  FSLOUTPUTTYPE: NIFTI_GZ