Merge branch 'conda_nii' of github.com:HALFpipe/HALFpipe into conda_nii

install-requirements.sh

@@ -59,7 +59,6 @@ run_cmd() {
 }
 
 conda_packages=()
-pip_packages=()
 
 while read -r requirement; do
     if [ -z "${requirement}" ]; then
@@ -81,33 +80,18 @@ while read -r requirement; do
         echo "Also checking name variations" "${requirement_variations[@]:1}"
     fi
 
-    package_manager="none"
     for requirement_variation in "${requirement_variations[@]}"; do
         if run_cmd "mamba install --dry-run  --use-local \"${requirement_variation}\""; then
             printf 'Using mamba for package "%s"\n' "${requirement_variation}"
             conda_packages+=("${requirement_variation}")
-            package_manager="mamba"
             break
         fi
     done
 
-    if [ "${package_manager}" = "none" ]; then
-        printf 'Using pip for package "%s"\n' "${requirement}"
-        pip_packages+=("\"${requirement}\"")
-        package_manager="pip"
-    fi
-
     printf '%s\n' --------------------
 
 done < <(grep --no-filename -v '#' "${requirements_files[@]}")
 
 if ! run_cmd mamba install --yes --use-local "${conda_packages[@]}"; then
     exit 1
 fi
-# We assume that all python dependencies have already been resolved by `pip-compile`,
-# so there will be no conflicts when we ask `pip` to install them.
-if [ ${#pip_packages[@]} -gt 1 ]; then
-    if ! run_cmd pip install --no-deps "${pip_packages[@]}"; then
-        exit 1
-    fi
-fi

requirements.in

@@ -3,10 +3,10 @@ setuptools_scm>=6.2
 wheel
 
 # Neuroimaging packages
-# fmriprep @ git+https://github.com/HippocampusGirl/fmriprep@20.2.7+halfpipe.2
-# smriprep @ git+https://github.com/HippocampusGirl/smriprep@0.7.2+halfpipe.2
+fmriprep ==20.2.7+halfpipe.2
+smriprep ==0.7.2+halfpipe.2
 niworkflows >= 1.3.10
-# sdcflows @ git+https://github.com/HippocampusGirl/sdcflows@1.3.4+halfpipe.1
+sdcflows==1.3.5
 nipype >= 1.8.1
 nibabel >= 4.0.0
 templateflow >= 0.7.1