Revert "CircleCI switch to singularity orb"

This reverts commit a3da6ad.

Author: nx10

.circleci/main.yml

@@ -12,9 +12,6 @@ parameters:
     type: boolean
     default: false
 
-orbs:
-  singularity: singularity/[email protected]
-
 commands:
   push-to-docker-hub:
     parameters:
@@ -71,6 +68,42 @@ commands:
       - run:
           name: Getting Sample BIDS Data
           command: git clone https://github.com/bids-standard/bids-examples.git
+  get-singularity:
+    parameters:
+      version:
+        description: "Version of Singularity to clone"
+        type: string
+        default: v3.8.7
+    steps:
+      - install-singularity-requirements
+      - restore_cache:
+          keys:
+            - singularity-<< parameters.version >>
+      - run:
+          name: "Cloning Singularity << parameters.version >>"
+          command: |
+            if [[ ! -d singularity-<< parameters.version >> ]]
+            then
+              git clone -b << parameters.version >> https://github.com/apptainer/singularity singularity-<< parameters.version >>
+            fi
+      - save_cache:
+          key: singularity-<< parameters.version >>
+          paths:
+            - singularity-<< parameters.version >>
+      - run:
+         name: "Setting up Singularity"
+         command: |
+           cd singularity-<< parameters.version >>
+           ./mconfig
+           make -C builddir
+           sudo make -C builddir install
+           cd ..
+  install-singularity-requirements:
+    steps:
+      - run:
+          name: "Installing Singularity requirements"
+          command: |
+           sudo apt-get update && sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.1 libarchive-dev libgpgme11-dev libseccomp-dev -y
   run-pytest-docker:
     steps:
       - create-docker-test-container:
@@ -206,9 +239,11 @@ jobs:
       - set-up-variant:
           variant: "<< parameters.variant >>"
       - set-python-version
-      - singularity/build_container_docker_base:
-          from-uri: docker://${DOCKER_TAG}
-          image: cpac-singularity-image${VARIANT}.sif
+      - get-singularity
+      - run:
+          command: singularity pull cpac-singularity-image${VARIANT}.sif docker://${DOCKER_TAG}
+          name: "Pull Singularity image"
+          no_output_timeout: 1h
       - test-singularity-installation
       - run:
           command: "SINGULARITYENV_COVERAGE_FILE=.coverage.singularity${VARIANT} singularity exec -B $PWD:/code cpac-singularity-image${VARIANT}.sif /code/dev/circleci_data/test_in_image.sh"