From 8f504448935042f69d414f52685b6c26e0acb822 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Thu, 16 Nov 2023 09:32:25 +0100
Subject: [PATCH 01/24] Another issue template

---
 .github/ISSUE_TEMPLATE/another.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .github/ISSUE_TEMPLATE/another.md

diff --git a/.github/ISSUE_TEMPLATE/another.md b/.github/ISSUE_TEMPLATE/another.md
new file mode 100644
index 0000000..306e1ad
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/another.md
@@ -0,0 +1 @@
+**Another template**

From 7418cb6ad5d416f55f84ff00b15db68c4aa09d09 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 13:34:26 +0100
Subject: [PATCH 02/24] Try building and pushing a docker container

---
 .github/workflows/build_docker.yaml | 13 +++++++++++++
 Dockerfile                          | 24 ++++++++++++++++++++++++
 2 files changed, 37 insertions(+)
 create mode 100644 .github/workflows/build_docker.yaml
 create mode 100644 Dockerfile

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
new file mode 100644
index 0000000..ea9a4c1
--- /dev/null
+++ b/.github/workflows/build_docker.yaml
@@ -0,0 +1,13 @@
+jobs:
+  build docker container:
+    runs-on: macOS-12
+    steps:
+      - name: Setup Docker
+        uses: docker-practice/actions-setup-docker@master
+      - name: Build container
+        env:
+          DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}
+        run: |
+          docker login -u heerener -p ${DOCKER_HUB_TOKEN}
+          docker build -t heerener/singularitah:0.1 -f Dockerfile .
+          docker push heerener/singularitah:0.1
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..250e0bd
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,24 @@
+FROM alpine:3.18
+# https://github.com/mattn/go-sqlite3/issues/1164#issuecomment-1848677118
+
+ARG SINGULARITY_VERSION
+ARG S3CMD_VERSION
+
+RUN apk add bash linux-headers libseccomp-dev glib-dev fuse3-dev libc-dev gcc make autoconf automake libtool squashfs-tools go wget py3-dateutil
+RUN wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz
+RUN tar xf singularity-ce-${SINGULARITY_VERSION}.tar.gz
+RUN cd singularity-ce-${SINGULARITY_VERSION} && \
+    ./mconfig && \
+    cd builddir && \
+    make && \
+    make install
+RUN singularity --version
+
+RUN mkdir /opt/s3cmd
+COPY _s3cfg /root/.s3cfg
+RUN cat /root/.s3cfg
+RUN wget https://github.com/s3tools/s3cmd/releases/download/v${S3CMD_VERSION}/s3cmd-${S3CMD_VERSION}.tar.gz
+RUN tar xf s3cmd-${S3CMD_VERSION}.tar.gz -C /opt/s3cmd/ --strip-components=1
+ENV PATH="${PATH}:/opt/s3cmd"
+
+ENTRYPOINT ["/bin/bash"]

From 6ad75477e970263a0c5f16e6fe2fc04e88bf63c2 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 13:35:31 +0100
Subject: [PATCH 03/24] Add on:

---
 .github/workflows/build_docker.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index ea9a4c1..99da65d 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -1,3 +1,6 @@
+on:
+  push:
+    branches: [issue]
 jobs:
   build docker container:
     runs-on: macOS-12

From ea73918b76c0fecdbd3cbc5e66eed93dce4fb32e Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 13:36:01 +0100
Subject: [PATCH 04/24] No spaces in job names. Gitlab does better

---
 .github/workflows/build_docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 99da65d..099e94c 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -2,7 +2,7 @@ on:
   push:
     branches: [issue]
 jobs:
-  build docker container:
+  build_docker_container:
     runs-on: macOS-12
     steps:
       - name: Setup Docker

From 82affcf1fd9b7566c065ed829508b07f389d9fb2 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 13:44:59 +0100
Subject: [PATCH 05/24] Some debugging info

---
 .github/workflows/build_docker.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 099e94c..866a023 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -5,6 +5,10 @@ jobs:
   build_docker_container:
     runs-on: macOS-12
     steps:
+      - name: Debug info
+        run: |
+          pwd
+          find . -name Dockerfile
       - name: Setup Docker
         uses: docker-practice/actions-setup-docker@master
       - name: Build container

From 3aa7a0bd73584d79868e9fe6f948a90962336b66 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 13:46:47 +0100
Subject: [PATCH 06/24] more debug info

---
 .github/workflows/build_docker.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 866a023..fe7a593 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -9,6 +9,8 @@ jobs:
         run: |
           pwd
           find . -name Dockerfile
+          ls
+          GIT_PAGER=cat git branch
       - name: Setup Docker
         uses: docker-practice/actions-setup-docker@master
       - name: Build container

From ff554d95172e07e48a69a1152c27b67aa6d6bbc2 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 13:48:19 +0100
Subject: [PATCH 07/24] Checkout...

---
 .github/workflows/build_docker.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index fe7a593..5b3d81d 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -5,6 +5,7 @@ jobs:
   build_docker_container:
     runs-on: macOS-12
     steps:
+      - uses: actions/checkout@v3
       - name: Debug info
         run: |
           pwd

From e22758807a3edfa4dcaa32543f941fc1d0d32f3c Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 13:56:52 +0100
Subject: [PATCH 08/24] Timeout for setup docker

---
 .github/workflows/build_docker.yaml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 5b3d81d..f9a76a8 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -6,14 +6,9 @@ jobs:
     runs-on: macOS-12
     steps:
       - uses: actions/checkout@v3
-      - name: Debug info
-        run: |
-          pwd
-          find . -name Dockerfile
-          ls
-          GIT_PAGER=cat git branch
       - name: Setup Docker
         uses: docker-practice/actions-setup-docker@master
+        timeout-minutes: 12
       - name: Build container
         env:
           DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}

From 15e4931df86cbdd165978b93a36472c3198e9182 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 14:09:25 +0100
Subject: [PATCH 09/24] Use increased timeout from fork

Add _s3cfg
---
 .github/workflows/build_docker.yaml |  3 +-
 _s3cfg                              | 87 +++++++++++++++++++++++++++++
 2 files changed, 88 insertions(+), 2 deletions(-)
 create mode 100644 _s3cfg

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index f9a76a8..b3b6651 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -7,8 +7,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Setup Docker
-        uses: docker-practice/actions-setup-docker@master
-        timeout-minutes: 12
+        uses: docker-practice/actions-setup-docker@heerener/increase-timeout
       - name: Build container
         env:
           DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}
diff --git a/_s3cfg b/_s3cfg
new file mode 100644
index 0000000..5afec2f
--- /dev/null
+++ b/_s3cfg
@@ -0,0 +1,87 @@
+[default]
+access_key =
+access_token =
+add_encoding_exts =
+add_headers =
+bucket_location = us-east-1
+ca_certs_file =
+cache_file =
+check_ssl_certificate = True
+check_ssl_hostname = True
+cloudfront_host = cloudfront.amazonaws.com
+connection_max_age = 5
+connection_pooling = True
+content_disposition =
+content_type =
+default_mime_type = binary/octet-stream
+delay_updates = False
+delete_after = False
+delete_after_fetch = False
+delete_removed = False
+dry_run = False
+enable_multipart = True
+encoding = UTF-8
+encrypt = False
+expiry_date =
+expiry_days =
+expiry_prefix =
+follow_symlinks = False
+force = False
+get_continue = False
+gpg_command = /usr/bin/gpg
+gpg_decrypt = %(gpg_command)s -d --verbose --no-use-agent --batch --yes --passphrase-fd %(passphrase_fd)s -o %(output_file)s %(input_file)s
+gpg_encrypt = %(gpg_command)s -c --verbose --no-use-agent --batch --yes --passphrase-fd %(passphrase_fd)s -o %(output_file)s %(input_file)s
+gpg_passphrase =
+guess_mime_type = True
+host_base = s3.amazonaws.com
+host_bucket = %(bucket)s.s3.amazonaws.com
+human_readable_sizes = False
+invalidate_default_index_on_cf = False
+invalidate_default_index_root_on_cf = True
+invalidate_on_cf = False
+kms_key =
+limit = -1
+limitrate = 0
+list_md5 = False
+log_target_prefix =
+long_listing = False
+max_delete = -1
+mime_type =
+multipart_chunk_size_mb = 15
+multipart_copy_chunk_size_mb = 1024
+multipart_max_chunks = 10000
+preserve_attrs = True
+progress_meter = True
+proxy_host =
+proxy_port = 0
+public_url_use_https = False
+put_continue = False
+recursive = False
+recv_chunk = 65536
+reduced_redundancy = False
+requester_pays = False
+restore_days = 1
+restore_priority = Standard
+secret_key =
+send_chunk = 65536
+server_side_encryption = False
+signature_v2 = False
+signurl_use_https = False
+simpledb_host = sdb.amazonaws.com
+skip_existing = False
+socket_timeout = 300
+ssl_client_cert_file =
+ssl_client_key_file =
+stats = False
+stop_on_error = False
+storage_class =
+throttle_max = 100
+upload_id =
+urlencoding_mode = normal
+use_http_expect = False
+use_https = True
+use_mime_magic = True
+verbosity = WARNING
+website_endpoint = http://%(bucket)s.s3-website-%(location)s.amazonaws.com/
+website_error =
+website_index = index.html

From 958febd6bea78f6a9635270a6ff908242ab0b349 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 23 Jan 2024 14:11:41 +0100
Subject: [PATCH 10/24] Refer directly to the fork

---
 .github/workflows/build_docker.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index b3b6651..15a41a2 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -7,7 +7,8 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Setup Docker
-        uses: docker-practice/actions-setup-docker@heerener/increase-timeout
+        uses: heerener/actions-setup-docker@increase-timeout
+          # uses: docker-practice/actions-setup-docker@master
       - name: Build container
         env:
           DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}

From 17a1e3c9ccc0eb88162ebd073fef2f0f8e95f689 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 30 Jan 2024 15:47:18 +0100
Subject: [PATCH 11/24] s3cmd and singularity versions

---
 .github/workflows/build_docker.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 15a41a2..5e35a6d 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -12,7 +12,9 @@ jobs:
       - name: Build container
         env:
           DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}
+          SINGULARITY_VERSION: 2.4.0
+          S3CMD_VERSION: 2.2.0
         run: |
           docker login -u heerener -p ${DOCKER_HUB_TOKEN}
-          docker build -t heerener/singularitah:0.1 -f Dockerfile .
+          docker build -t heerener/singularitah:0.1 -f Dockerfile --build-arg="S3CMD_VERSION=${S3CMD_VERSION}" --build-arg="$SINGULARITY_VERSION=${SINGULARITY_VERSION}" .
           docker push heerener/singularitah:0.1

From ae56f3e6a8cd4fa0eeedad7aac20958f0bc7d41f Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 30 Jan 2024 16:26:37 +0100
Subject: [PATCH 12/24] Echo s3cmd and singularity versions

---
 .github/workflows/build_docker.yaml | 2 ++
 Dockerfile                          | 3 +++
 2 files changed, 5 insertions(+)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 5e35a6d..82963a0 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -15,6 +15,8 @@ jobs:
           SINGULARITY_VERSION: 2.4.0
           S3CMD_VERSION: 2.2.0
         run: |
+          echo "Singularity version is ${SINGULARITY_VERSION}"
+          echo "s3cmd version is ${S3CMD_VERSION}"
           docker login -u heerener -p ${DOCKER_HUB_TOKEN}
           docker build -t heerener/singularitah:0.1 -f Dockerfile --build-arg="S3CMD_VERSION=${S3CMD_VERSION}" --build-arg="$SINGULARITY_VERSION=${SINGULARITY_VERSION}" .
           docker push heerener/singularitah:0.1
diff --git a/Dockerfile b/Dockerfile
index 250e0bd..7093f52 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,6 +4,9 @@ FROM alpine:3.18
 ARG SINGULARITY_VERSION
 ARG S3CMD_VERSION
 
+RUN echo "Singularity version ${SINGULARITY_VERSION}"
+RUN echo "s3cmd version ${S3CMD_VERSION}"
+
 RUN apk add bash linux-headers libseccomp-dev glib-dev fuse3-dev libc-dev gcc make autoconf automake libtool squashfs-tools go wget py3-dateutil
 RUN wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz
 RUN tar xf singularity-ce-${SINGULARITY_VERSION}.tar.gz

From bc32cfa3b4a2485661eb523d99996cc038abd349 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 30 Jan 2024 17:04:27 +0100
Subject: [PATCH 13/24] No = sign for build-arg

---
 .github/workflows/build_docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 82963a0..aed77ce 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -18,5 +18,5 @@ jobs:
           echo "Singularity version is ${SINGULARITY_VERSION}"
           echo "s3cmd version is ${S3CMD_VERSION}"
           docker login -u heerener -p ${DOCKER_HUB_TOKEN}
-          docker build -t heerener/singularitah:0.1 -f Dockerfile --build-arg="S3CMD_VERSION=${S3CMD_VERSION}" --build-arg="$SINGULARITY_VERSION=${SINGULARITY_VERSION}" .
+          docker build -t heerener/singularitah:0.1 -f Dockerfile --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" .
           docker push heerener/singularitah:0.1

From 1fd3d265756c3239ee01dfdf03dff23d0cea0a87 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Tue, 30 Jan 2024 17:17:39 +0100
Subject: [PATCH 14/24] What happens if we switch them

---
 .github/workflows/build_docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index aed77ce..548472a 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -18,5 +18,5 @@ jobs:
           echo "Singularity version is ${SINGULARITY_VERSION}"
           echo "s3cmd version is ${S3CMD_VERSION}"
           docker login -u heerener -p ${DOCKER_HUB_TOKEN}
-          docker build -t heerener/singularitah:0.1 -f Dockerfile --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" .
+          docker build -t heerener/singularitah:0.1 --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" -f Dockerfile .
           docker push heerener/singularitah:0.1

From 1a1801f9323e0bbab8cbed3b77189f2e5949d394 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 31 Jan 2024 11:58:19 +0100
Subject: [PATCH 15/24] Try podman instead of docker

---
 .github/workflows/build_docker.yaml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 548472a..c61c46a 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -3,12 +3,13 @@ on:
     branches: [issue]
 jobs:
   build_docker_container:
-    runs-on: macOS-12
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
-      - name: Setup Docker
-        uses: heerener/actions-setup-docker@increase-timeout
-          # uses: docker-practice/actions-setup-docker@master
+      - name: Setup Podman
+        run: |
+          apt-get update
+          apt-get install -y podman
       - name: Build container
         env:
           DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}
@@ -17,6 +18,6 @@ jobs:
         run: |
           echo "Singularity version is ${SINGULARITY_VERSION}"
           echo "s3cmd version is ${S3CMD_VERSION}"
-          docker login -u heerener -p ${DOCKER_HUB_TOKEN}
-          docker build -t heerener/singularitah:0.1 --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" -f Dockerfile .
-          docker push heerener/singularitah:0.1
+          podman login -u heerener -p ${DOCKER_HUB_TOKEN}
+          podman build -t heerener/singularitah:0.1 --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" -f Dockerfile .
+          podman push heerener/singularitah:0.1

From 97d962d8c1f29437fec44b5bd4f7e9859707990a Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 31 Jan 2024 12:00:31 +0100
Subject: [PATCH 16/24] Fine, sudo

---
 .github/workflows/build_docker.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index c61c46a..858da1b 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -8,8 +8,8 @@ jobs:
       - uses: actions/checkout@v3
       - name: Setup Podman
         run: |
-          apt-get update
-          apt-get install -y podman
+          sudo apt-get update
+          sudo apt-get install -y podman
       - name: Build container
         env:
           DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}

From 2642953756ba38aa134da498899826994fcc3068 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 31 Jan 2024 12:07:02 +0100
Subject: [PATCH 17/24] Swap back

---
 .github/workflows/build_docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 858da1b..28c47a7 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -19,5 +19,5 @@ jobs:
           echo "Singularity version is ${SINGULARITY_VERSION}"
           echo "s3cmd version is ${S3CMD_VERSION}"
           podman login -u heerener -p ${DOCKER_HUB_TOKEN}
-          podman build -t heerener/singularitah:0.1 --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" -f Dockerfile .
+          podman build -t heerener/singularitah:0.1 --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" -f Dockerfile .
           podman push heerener/singularitah:0.1

From 3f5c1d6663ad3d69f9f282269ac18caeb627f076 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 31 Jan 2024 12:09:13 +0100
Subject: [PATCH 18/24] Fix the hard-to-$pot typo

---
 .github/workflows/build_docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 28c47a7..64b8289 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -19,5 +19,5 @@ jobs:
           echo "Singularity version is ${SINGULARITY_VERSION}"
           echo "s3cmd version is ${S3CMD_VERSION}"
           podman login -u heerener -p ${DOCKER_HUB_TOKEN}
-          podman build -t heerener/singularitah:0.1 --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" --build-arg "$SINGULARITY_VERSION=${SINGULARITY_VERSION}" -f Dockerfile .
+          podman build -t heerener/singularitah:0.1 --build-arg "S3CMD_VERSION=${S3CMD_VERSION}" --build-arg "SINGULARITY_VERSION=${SINGULARITY_VERSION}" -f Dockerfile .
           podman push heerener/singularitah:0.1

From b418d70ffd87dc9e7186e0ea747ae195e2affe21 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 31 Jan 2024 12:16:20 +0100
Subject: [PATCH 19/24] Correct singularity version

---
 .github/workflows/build_docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 64b8289..2b9bc18 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -13,7 +13,7 @@ jobs:
       - name: Build container
         env:
           DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }}
-          SINGULARITY_VERSION: 2.4.0
+          SINGULARITY_VERSION: 4.1.0
           S3CMD_VERSION: 2.2.0
         run: |
           echo "Singularity version is ${SINGULARITY_VERSION}"

From 2fe5bd72b47066a303130cd77ee8b8e30b142b7a Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 21 Feb 2024 15:36:50 +0100
Subject: [PATCH 20/24] Do files persist between steps?

---
 .github/workflows/waste_time.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/waste_time.yaml b/.github/workflows/waste_time.yaml
index b9acc26..3d38397 100644
--- a/.github/workflows/waste_time.yaml
+++ b/.github/workflows/waste_time.yaml
@@ -25,11 +25,13 @@ jobs:
         if: ${{ github.event.pull_request.draft == true && matrix.config.moo == 'herpaderp' }}
         run: |
           echo "Doing the thing"
+          echo "Thing" > blub
           sleep 5
           echo "The thing is done"
       - name: Always run
         run: |
           echo "This thing always happens"
+          cat blub
           sleep 5
           echo "And has now been concluded"
 

From 6259aca6e6fb1f9cd1d3ee1267183502ea1b0cc7 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 21 Feb 2024 15:38:38 +0100
Subject: [PATCH 21/24] Again, does it get persisted between steps?

---
 .github/workflows/waste_time.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/waste_time.yaml b/.github/workflows/waste_time.yaml
index 3d38397..fa6b99d 100644
--- a/.github/workflows/waste_time.yaml
+++ b/.github/workflows/waste_time.yaml
@@ -54,10 +54,12 @@ jobs:
       - name: First step
         run: |
           echo "Doing the thing"
+          echo "Thing" > blub
           sleep 5
           echo "The thing is done"
       - name: Second step
         run: |
           echo "Doing the other thing"
+          cat blub
           sleep 5
           echo "The other thing is also done"

From 24c6791ba6d8b322cc04530b288fc233fce7138b Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 21 Feb 2024 15:39:13 +0100
Subject: [PATCH 22/24] Docker only on docker branch

---
 .github/workflows/build_docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml
index 2b9bc18..582a01f 100644
--- a/.github/workflows/build_docker.yaml
+++ b/.github/workflows/build_docker.yaml
@@ -1,6 +1,6 @@
 on:
   push:
-    branches: [issue]
+    branches: [docker]
 jobs:
   build_docker_container:
     runs-on: ubuntu-22.04

From 4dbdb6667b57a27d93152a2761185f9e01f2d80b Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 21 Feb 2024 15:40:51 +0100
Subject: [PATCH 23/24] If

---
 .github/workflows/waste_time.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/waste_time.yaml b/.github/workflows/waste_time.yaml
index fa6b99d..424fa88 100644
--- a/.github/workflows/waste_time.yaml
+++ b/.github/workflows/waste_time.yaml
@@ -31,7 +31,7 @@ jobs:
       - name: Always run
         run: |
           echo "This thing always happens"
-          cat blub
+          if [ -f blub ]; then cat blub; else echo "No blub"; fi
           sleep 5
           echo "And has now been concluded"
 
@@ -60,6 +60,6 @@ jobs:
       - name: Second step
         run: |
           echo "Doing the other thing"
-          cat blub
+          if [ -f blub ]; then cat blub; else echo "No blub"; fi
           sleep 5
           echo "The other thing is also done"

From 4ba1e5f8c7f3f74d631d02f29b37b571af467b57 Mon Sep 17 00:00:00 2001
From: Erik Heeren <erik.heeren@epfl.ch>
Date: Wed, 21 Feb 2024 15:41:57 +0100
Subject: [PATCH 24/24] More obvious!

---
 .github/workflows/waste_time.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/waste_time.yaml b/.github/workflows/waste_time.yaml
index 424fa88..705a358 100644
--- a/.github/workflows/waste_time.yaml
+++ b/.github/workflows/waste_time.yaml
@@ -25,11 +25,12 @@ jobs:
         if: ${{ github.event.pull_request.draft == true && matrix.config.moo == 'herpaderp' }}
         run: |
           echo "Doing the thing"
-          echo "Thing" > blub
+          echo "Thing in a file" > blub
           sleep 5
           echo "The thing is done"
       - name: Always run
         run: |
+          set -x
           echo "This thing always happens"
           if [ -f blub ]; then cat blub; else echo "No blub"; fi
           sleep 5