From d5673803fd80ca1482d77f8bf67663303d8f6d0b Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 16:36:47 +0100
Subject: [PATCH 01/17] add devcontainer

---
 .devcontainer/devcontainer.json | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 .devcontainer/devcontainer.json

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000000..6793795fa5
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,6 @@
+{
+    "build": {
+        // Path is relataive to the devcontainer.json file.
+        "dockerfile": "../Dockerfile"
+    }
+}
\ No newline at end of file

From e4d012faa2f582bd0cceec131ca06517d998004c Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 16:49:49 +0100
Subject: [PATCH 02/17] add further setup

---
 .devcontainer/devcontainer.json | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 6793795fa5..3659646274 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -2,5 +2,9 @@
     "build": {
         // Path is relataive to the devcontainer.json file.
         "dockerfile": "../Dockerfile"
-    }
+    },
+    "postCreateCommand": [
+        "pip install ./aiida-core[test,pre-commit]",
+        "/opt/configure-aiida.sh"
+    ]
 }
\ No newline at end of file

From 0604d216e2a20a05489de0185916e2c17d1b3335 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 16:08:25 +0000
Subject: [PATCH 03/17] wait for postCreateCommand

---
 .devcontainer/devcontainer.json | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 3659646274..1fe1917d15 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -4,7 +4,8 @@
         "dockerfile": "../Dockerfile"
     },
     "postCreateCommand": [
-        "pip install ./aiida-core[test,pre-commit]",
+        "pip install ./aiida-core[tests,pre-commit]",
         "/opt/configure-aiida.sh"
-    ]
+    ],
+    "waitFor": "postCreateCommand"
 }
\ No newline at end of file

From 293c6628f34bd97c651a22622cb16675f8186cb2 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 16:56:59 +0000
Subject: [PATCH 04/17] proper use of postCreate/postStart

---
 .devcontainer/devcontainer.json | 22 +++++++++++++---------
 .devcontainer/post_create.sh    |  3 +++
 2 files changed, 16 insertions(+), 9 deletions(-)
 create mode 100644 .devcontainer/post_create.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 1fe1917d15..ab2e805288 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,11 +1,15 @@
 {
-    "build": {
-        // Path is relataive to the devcontainer.json file.
-        "dockerfile": "../Dockerfile"
-    },
-    "postCreateCommand": [
-        "pip install ./aiida-core[tests,pre-commit]",
-        "/opt/configure-aiida.sh"
-    ],
-    "waitFor": "postCreateCommand"
+    "image": "aiidateam/aiida-core:main",
+    // "build": {
+    //     // Path is relative to the devcontainer.json file.
+    //     // "dockerfile": "../Dockerfile"
+    // },
+    "postCreateCommand": "bash ./.devcontainer/post_create.sh",
+    "postStartCommand": "/sbin/my_init",
+    "waitFor": "postCreateCommand",
+	"customizations": {
+        "vscode": {
+            "extensions": ["ms-python.python", "eamodio.gitlens"]
+        }
+    }
 }
\ No newline at end of file
diff --git a/.devcontainer/post_create.sh b/.devcontainer/post_create.sh
new file mode 100644
index 0000000000..6e31c71d9a
--- /dev/null
+++ b/.devcontainer/post_create.sh
@@ -0,0 +1,3 @@
+ #!/bin/bash
+ # Add test dependencies (not installed in image)
+ pip install .[tests,pre-commit]
\ No newline at end of file

From 69a08411389089729745595531bd8b3275ce00ff Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 19:18:15 +0000
Subject: [PATCH 05/17] move to docker-compose

---
 .devcontainer/devcontainer.json   |  7 +++--
 .devcontainer/docker-compose.yaml | 49 +++++++++++++++++++++++++++++++
 .docker/opt/configure-aiida.sh    |  3 +-
 3 files changed, 55 insertions(+), 4 deletions(-)
 create mode 100644 .devcontainer/docker-compose.yaml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index ab2e805288..0e9456aef9 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,12 +1,13 @@
 {
-    "image": "aiidateam/aiida-core:main",
+    "dockerComposeFile": "docker-compose.yaml",
+    "service": "aiida",
     // "build": {
     //     // Path is relative to the devcontainer.json file.
     //     // "dockerfile": "../Dockerfile"
     // },
     "postCreateCommand": "bash ./.devcontainer/post_create.sh",
-    "postStartCommand": "/sbin/my_init",
-    "waitFor": "postCreateCommand",
+    "postStartCommand": "/opt/configure-aiida.sh",
+    "waitFor": "postStartCommand",
 	"customizations": {
         "vscode": {
             "extensions": ["ms-python.python", "eamodio.gitlens"]
diff --git a/.devcontainer/docker-compose.yaml b/.devcontainer/docker-compose.yaml
new file mode 100644
index 0000000000..e6e02f1a9c
--- /dev/null
+++ b/.devcontainer/docker-compose.yaml
@@ -0,0 +1,49 @@
+version: '3.4'
+
+services:
+
+  rabbitmq:
+    image: rabbitmq:3.8.3-management
+    container_name: aiida-rabbitmq
+    environment:
+        RABBITMQ_DEFAULT_USER: guest
+        RABBITMQ_DEFAULT_PASS: guest
+    ports:
+      - '5672:5672'
+      - '15672:15672':w
+
+    healthcheck:
+      test: rabbitmq-diagnostics -q ping
+      interval: 30s
+      timeout: 30s
+      retries: 5
+    networks:
+      - aiida-rmq
+
+  postgresql:
+    image: postgres:12
+    container_name: aiida-postgres
+    ports:
+      - '5432:5432'
+    networks:
+      - aiida-rmq
+    # volumes:
+    #   - db-volume:/var/lib/postgresql/data
+
+  aiida:
+    image: "aiidateam/aiida-core:main"
+    container_name: aiida-core
+    env:
+      DB_HOST: postgresql
+      BROKER_HOST: rabbitmq
+    # volumes:
+    #   - db-volume:/var/lib/assets
+    depends_on:
+      - rabbitmq
+      - postgresql
+
+# volumes:
+#   db-volume:
+
+networks:
+  aiida-rmq:
\ No newline at end of file
diff --git a/.docker/opt/configure-aiida.sh b/.docker/opt/configure-aiida.sh
index 371fe3ec0a..822578b4ad 100755
--- a/.docker/opt/configure-aiida.sh
+++ b/.docker/opt/configure-aiida.sh
@@ -29,7 +29,8 @@ if [[ ${NEED_SETUP_PROFILE} == true ]]; then
         --first-name "${USER_FIRST_NAME}"      \
         --last-name "${USER_LAST_NAME}"        \
         --institution "${USER_INSTITUTION}"    \
-        --db-backend "${AIIDADB_BACKEND}"
+        --db-host "${DB_HOST:localhost}"    \
+        --broker-host "${BROKER_HOST:localhost}"
 
     # Setup and configure local computer.
     computer_name=localhost

From cc2ef1768b9ceaf52e47c2c1bf79e95ee42a77d5 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 19:21:51 +0000
Subject: [PATCH 06/17] rename docker-compose

---
 .devcontainer/devcontainer.json                           | 2 +-
 .devcontainer/{docker-compose.yaml => docker-compose.yml} | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename .devcontainer/{docker-compose.yaml => docker-compose.yml} (100%)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 0e9456aef9..5791e2152b 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 {
-    "dockerComposeFile": "docker-compose.yaml",
+    "dockerComposeFile": "docker-compose.yml",
     "service": "aiida",
     // "build": {
     //     // Path is relative to the devcontainer.json file.
diff --git a/.devcontainer/docker-compose.yaml b/.devcontainer/docker-compose.yml
similarity index 100%
rename from .devcontainer/docker-compose.yaml
rename to .devcontainer/docker-compose.yml

From 18892e869ad29f78e1d3454a89d0f466c0cffcf3 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 19:26:45 +0000
Subject: [PATCH 07/17] fixes to docker-compose

---
 .devcontainer/docker-compose.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index e6e02f1a9c..2ec78c52e2 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -10,7 +10,7 @@ services:
         RABBITMQ_DEFAULT_PASS: guest
     ports:
       - '5672:5672'
-      - '15672:15672':w
+      - '15672:15672'
 
     healthcheck:
       test: rabbitmq-diagnostics -q ping
@@ -33,7 +33,7 @@ services:
   aiida:
     image: "aiidateam/aiida-core:main"
     container_name: aiida-core
-    env:
+    environment:
       DB_HOST: postgresql
       BROKER_HOST: rabbitmq
     # volumes:

From d16eb8323aec2a3ed8a88c6d7c8e090ac64a8c4c Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 19:39:33 +0000
Subject: [PATCH 08/17] fixes to docker-compose

---
 .devcontainer/devcontainer.json  |  7 +------
 .devcontainer/docker-compose.yml |  3 +++
 .devcontainer/post_create.sh     | 10 +++++++++-
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 5791e2152b..e09b14d01d 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,13 +1,8 @@
 {
     "dockerComposeFile": "docker-compose.yml",
     "service": "aiida",
-    // "build": {
-    //     // Path is relative to the devcontainer.json file.
-    //     // "dockerfile": "../Dockerfile"
-    // },
     "postCreateCommand": "bash ./.devcontainer/post_create.sh",
-    "postStartCommand": "/opt/configure-aiida.sh",
-    "waitFor": "postStartCommand",
+    "waitFor": "postCreateCommand",
 	"customizations": {
         "vscode": {
             "extensions": ["ms-python.python", "eamodio.gitlens"]
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index 2ec78c52e2..9842b1726c 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -33,11 +33,14 @@ services:
   aiida:
     image: "aiidateam/aiida-core:main"
     container_name: aiida-core
+    user: aiida
     environment:
       DB_HOST: postgresql
       BROKER_HOST: rabbitmq
     # volumes:
     #   - db-volume:/var/lib/assets
+    networks:
+      - aiida-rmq
     depends_on:
       - rabbitmq
       - postgresql
diff --git a/.devcontainer/post_create.sh b/.devcontainer/post_create.sh
index 6e31c71d9a..4d34fe54f7 100644
--- a/.devcontainer/post_create.sh
+++ b/.devcontainer/post_create.sh
@@ -1,3 +1,11 @@
  #!/bin/bash
+ set -e
+
  # Add test dependencies (not installed in image)
- pip install .[tests,pre-commit]
\ No newline at end of file
+ pip install .[tests,pre-commit]
+
+# add aiida user
+/etc/my_init.d/10_create-system-user.sh
+
+# configure aiida
+/opt/configure-aiida.sh
\ No newline at end of file

From 7176fb4780f339c46be25c55633d024f3fac6e2c Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 19:45:40 +0000
Subject: [PATCH 09/17] back to Dockerfile

---
 .devcontainer/Dockerfile         | 7 +++++++
 .devcontainer/docker-compose.yml | 5 ++++-
 .devcontainer/post_create.sh     | 6 ------
 3 files changed, 11 insertions(+), 7 deletions(-)
 create mode 100644 .devcontainer/Dockerfile

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 0000000000..d4996f63e2
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,7 @@
+from aiidateam/aiida-core:main
+
+# Add test dependencies (not installed in image)
+RUN pip install .[tests,pre-commit]
+
+# add aiida user
+RUN /etc/my_init.d/10_create-system-user.sh
\ No newline at end of file
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index 9842b1726c..c184e0fa95 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -31,7 +31,10 @@ services:
     #   - db-volume:/var/lib/postgresql/data
 
   aiida:
-    image: "aiidateam/aiida-core:main"
+    #image: "aiidateam/aiida-core:main"
+    image: "aiida-core"
+    build:
+      dockerfile: Dockerfile
     container_name: aiida-core
     user: aiida
     environment:
diff --git a/.devcontainer/post_create.sh b/.devcontainer/post_create.sh
index 4d34fe54f7..c4939f0b84 100644
--- a/.devcontainer/post_create.sh
+++ b/.devcontainer/post_create.sh
@@ -1,11 +1,5 @@
  #!/bin/bash
  set -e
 
- # Add test dependencies (not installed in image)
- pip install .[tests,pre-commit]
-
-# add aiida user
-/etc/my_init.d/10_create-system-user.sh
-
 # configure aiida
 /opt/configure-aiida.sh
\ No newline at end of file

From d57112640dc3c8dc77ee7ec85d390a4e125b055c Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 19:55:10 +0000
Subject: [PATCH 10/17] fixes

---
 .devcontainer/Dockerfile         | 2 +-
 .devcontainer/docker-compose.yml | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index d4996f63e2..4ae100476c 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,4 +1,4 @@
-from aiidateam/aiida-core:main
+FROM aiidateam/aiida-core:main
 
 # Add test dependencies (not installed in image)
 RUN pip install .[tests,pre-commit]
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index c184e0fa95..cf6c9d756a 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -20,7 +20,7 @@ services:
     networks:
       - aiida-rmq
 
-  postgresql:
+  postgres:
     image: postgres:12
     container_name: aiida-postgres
     ports:
@@ -34,6 +34,7 @@ services:
     #image: "aiidateam/aiida-core:main"
     image: "aiida-core"
     build:
+      context: .
       dockerfile: Dockerfile
     container_name: aiida-core
     user: aiida
@@ -46,7 +47,7 @@ services:
       - aiida-rmq
     depends_on:
       - rabbitmq
-      - postgresql
+      - postgres
 
 # volumes:
 #   db-volume:

From 482ead4412dedbee31c4cbd8524eea5142fc5775 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 20:19:08 +0000
Subject: [PATCH 11/17] fix Dockerfile

---
 .devcontainer/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 4ae100476c..f20bf3a325 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,7 +1,8 @@
+# Additions for dev container
 FROM aiidateam/aiida-core:main
 
 # Add test dependencies (not installed in image)
-RUN pip install .[tests,pre-commit]
+RUN pip install ./aiida-core[tests,rest,docs,pre-commit]
 
 # add aiida user
 RUN /etc/my_init.d/10_create-system-user.sh
\ No newline at end of file

From 20a9d11a635d765fa4ac9dea640428be1bbd6d69 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 21:35:24 +0100
Subject: [PATCH 12/17] fix docker-compose

---
 .devcontainer/devcontainer.json  | 2 ++
 .devcontainer/docker-compose.yml | 8 ++++++++
 2 files changed, 10 insertions(+)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index e09b14d01d..93a8f0efd0 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,4 +1,6 @@
 {
+    "workspaceFolder": "/home/aiida/aiida-core",
+    "workspaceMount": "/home/aiida/aiida-core",
     "dockerComposeFile": "docker-compose.yml",
     "service": "aiida",
     "postCreateCommand": "bash ./.devcontainer/post_create.sh",
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index cf6c9d756a..53db3c0032 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -27,6 +27,9 @@ services:
       - '5432:5432'
     networks:
       - aiida-rmq
+    environment:
+      POSTGRES_HOST_AUTH_METHOD: trust
+      POSTGRES_PASSWORD: password
     # volumes:
     #   - db-volume:/var/lib/postgresql/data
 
@@ -41,6 +44,11 @@ services:
     environment:
       DB_HOST: postgresql
       BROKER_HOST: rabbitmq
+
+    #entrypoint: /opt/configure-aiida.sh
+    # entrypoint: "" 
+    # tty: true
+    entrypoint: tail -f /dev/null
     # volumes:
     #   - db-volume:/var/lib/assets
     networks:

From 1179b2b7d1e4ab6477f43e3d1ee9070d50cf11bf Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 21:42:06 +0000
Subject: [PATCH 13/17] working docker-compose setup

---
 .devcontainer/Dockerfile         |  6 ++-
 .devcontainer/configure-aiida.sh | 81 ++++++++++++++++++++++++++++++++
 .devcontainer/devcontainer.json  |  5 +-
 .devcontainer/docker-compose.yml | 23 ++++-----
 .devcontainer/post_create.sh     |  1 -
 5 files changed, 97 insertions(+), 19 deletions(-)
 create mode 100755 .devcontainer/configure-aiida.sh

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index f20bf3a325..246861fbb4 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -5,4 +5,8 @@ FROM aiidateam/aiida-core:main
 RUN pip install ./aiida-core[tests,rest,docs,pre-commit]
 
 # add aiida user
-RUN /etc/my_init.d/10_create-system-user.sh
\ No newline at end of file
+RUN /etc/my_init.d/10_create-system-user.sh
+
+# copy updated aiida configuration script
+# this line can be deleted after the new script has been merged
+COPY configure-aiida.sh /opt/configure-aiida.sh
\ No newline at end of file
diff --git a/.devcontainer/configure-aiida.sh b/.devcontainer/configure-aiida.sh
new file mode 100755
index 0000000000..822578b4ad
--- /dev/null
+++ b/.devcontainer/configure-aiida.sh
@@ -0,0 +1,81 @@
+#!/bin/bash
+
+# This script is executed whenever the docker container is (re)started.
+
+# Debugging.
+set -x
+
+# Environment.
+export SHELL=/bin/bash
+
+# Setup AiiDA autocompletion.
+grep _VERDI_COMPLETE /home/${SYSTEM_USER}/.bashrc &> /dev/null || echo 'eval "$(_VERDI_COMPLETE=source verdi)"' >> /home/${SYSTEM_USER}/.bashrc
+
+# Check if user requested to set up AiiDA profile (and if it exists already)
+if [[ ${SETUP_DEFAULT_PROFILE} == true ]] && ! verdi profile show ${PROFILE_NAME} &> /dev/null; then
+    NEED_SETUP_PROFILE=true;
+else
+    NEED_SETUP_PROFILE=false;
+fi
+
+# Setup AiiDA profile if needed.
+if [[ ${NEED_SETUP_PROFILE} == true ]]; then
+
+    # Create AiiDA profile.
+    verdi quicksetup                           \
+        --non-interactive                      \
+        --profile "${PROFILE_NAME}"            \
+        --email "${USER_EMAIL}"                \
+        --first-name "${USER_FIRST_NAME}"      \
+        --last-name "${USER_LAST_NAME}"        \
+        --institution "${USER_INSTITUTION}"    \
+        --db-host "${DB_HOST:localhost}"    \
+        --broker-host "${BROKER_HOST:localhost}"
+
+    # Setup and configure local computer.
+    computer_name=localhost
+
+    # Determine the number of physical cores as a default for the number of
+    # available MPI ranks on the localhost. We do not count "logical" cores,
+    # since MPI parallelization over hyper-threaded cores is typically
+    # associated with a significant performance penalty. We use the
+    # `psutil.cpu_count(logical=False)` function as opposed to simply
+    # `os.cpu_count()` since the latter would include hyperthreaded (logical
+    # cores).
+    NUM_PHYSICAL_CORES=$(python -c 'import psutil; print(int(psutil.cpu_count(logical=False)))' 2>/dev/null)
+    LOCALHOST_MPI_PROCS_PER_MACHINE=${LOCALHOST_MPI_PROCS_PER_MACHINE:-${NUM_PHYSICAL_CORES}}
+
+    if [ -z $LOCALHOST_MPI_PROCS_PER_MACHINE ]; then
+      echo "Unable to automatically determine the number of logical CPUs on this "
+      echo "machine. Please set the LOCALHOST_MPI_PROCS_PER_MACHINE variable to "
+      echo "explicitly set the number of available MPI ranks."
+      exit 1
+    fi
+
+    verdi computer show ${computer_name} || verdi computer setup   \
+        --non-interactive                                          \
+        --label "${computer_name}"                                 \
+        --description "this computer"                              \
+        --hostname "${computer_name}"                              \
+        --transport core.local                                          \
+        --scheduler core.direct                                    \
+        --work-dir /home/aiida/aiida_run/                          \
+        --mpirun-command "mpirun -np {tot_num_mpiprocs}"           \
+        --mpiprocs-per-machine ${LOCALHOST_MPI_PROCS_PER_MACHINE} && \
+    verdi computer configure core.local "${computer_name}"              \
+        --non-interactive                                          \
+        --safe-interval 0.0
+fi
+
+
+# Show the default profile
+verdi profile show || echo "The default profile is not set."
+
+# Make sure that the daemon is not running, otherwise the migration will abort.
+verdi daemon stop
+
+# Migration will run for the default profile.
+verdi storage migrate --force || echo "Database migration failed."
+
+# Daemon will start only if the database exists and is migrated to the latest version.
+verdi daemon start || echo "AiiDA daemon is not running."
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 93a8f0efd0..dd893de3b7 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,13 +1,12 @@
 {
-    "workspaceFolder": "/home/aiida/aiida-core",
-    "workspaceMount": "/home/aiida/aiida-core",
     "dockerComposeFile": "docker-compose.yml",
     "service": "aiida",
+    "workspaceFolder": "/home/aiida/aiida-core",
     "postCreateCommand": "bash ./.devcontainer/post_create.sh",
     "waitFor": "postCreateCommand",
 	"customizations": {
         "vscode": {
-            "extensions": ["ms-python.python", "eamodio.gitlens"]
+            "extensions": ["ms-python.python","ms-python.vscode-pylance", "eamodio.gitlens"]
         }
     }
 }
\ No newline at end of file
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index 53db3c0032..52d1a44142 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -4,7 +4,6 @@ services:
 
   rabbitmq:
     image: rabbitmq:3.8.3-management
-    container_name: aiida-rabbitmq
     environment:
         RABBITMQ_DEFAULT_USER: guest
         RABBITMQ_DEFAULT_PASS: guest
@@ -18,41 +17,37 @@ services:
       timeout: 30s
       retries: 5
     networks:
-      - aiida-rmq
+      - aiida
 
   postgres:
     image: postgres:12
-    container_name: aiida-postgres
     ports:
       - '5432:5432'
     networks:
-      - aiida-rmq
+      - aiida
     environment:
       POSTGRES_HOST_AUTH_METHOD: trust
-      POSTGRES_PASSWORD: password
     # volumes:
     #   - db-volume:/var/lib/postgresql/data
 
   aiida:
     #image: "aiidateam/aiida-core:main"
-    image: "aiida-core"
+    image: "aiida-core-dev"
     build:
       context: .
       dockerfile: Dockerfile
-    container_name: aiida-core
     user: aiida
     environment:
-      DB_HOST: postgresql
+      DB_HOST: postgres
       BROKER_HOST: rabbitmq
 
-    #entrypoint: /opt/configure-aiida.sh
-    # entrypoint: "" 
-    # tty: true
+    # no need for /sbin/my_init
     entrypoint: tail -f /dev/null
-    # volumes:
+    volumes:
+      - ..:/home/aiida/aiida-core:cached
     #   - db-volume:/var/lib/assets
     networks:
-      - aiida-rmq
+      - aiida
     depends_on:
       - rabbitmq
       - postgres
@@ -61,4 +56,4 @@ services:
 #   db-volume:
 
 networks:
-  aiida-rmq:
\ No newline at end of file
+  aiida:
\ No newline at end of file
diff --git a/.devcontainer/post_create.sh b/.devcontainer/post_create.sh
index c4939f0b84..c12c4010cc 100644
--- a/.devcontainer/post_create.sh
+++ b/.devcontainer/post_create.sh
@@ -1,5 +1,4 @@
  #!/bin/bash
- set -e
 
 # configure aiida
 /opt/configure-aiida.sh
\ No newline at end of file

From 9acd368b50c25fe13129c048b015fa7517e86515 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 5 Mar 2023 21:49:25 +0000
Subject: [PATCH 14/17] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .devcontainer/Dockerfile         | 2 +-
 .devcontainer/devcontainer.json  | 2 +-
 .devcontainer/docker-compose.yml | 2 +-
 .devcontainer/post_create.sh     | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 246861fbb4..804e567955 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -9,4 +9,4 @@ RUN /etc/my_init.d/10_create-system-user.sh
 
 # copy updated aiida configuration script
 # this line can be deleted after the new script has been merged
-COPY configure-aiida.sh /opt/configure-aiida.sh
\ No newline at end of file
+COPY configure-aiida.sh /opt/configure-aiida.sh
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index dd893de3b7..26eb9cd470 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -9,4 +9,4 @@
             "extensions": ["ms-python.python","ms-python.vscode-pylance", "eamodio.gitlens"]
         }
     }
-}
\ No newline at end of file
+}
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index 52d1a44142..78f7213e49 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -56,4 +56,4 @@ services:
 #   db-volume:
 
 networks:
-  aiida:
\ No newline at end of file
+  aiida:
diff --git a/.devcontainer/post_create.sh b/.devcontainer/post_create.sh
index c12c4010cc..71f8330853 100644
--- a/.devcontainer/post_create.sh
+++ b/.devcontainer/post_create.sh
@@ -1,4 +1,4 @@
  #!/bin/bash
 
 # configure aiida
-/opt/configure-aiida.sh
\ No newline at end of file
+/opt/configure-aiida.sh

From c948905bf225d63cc56684427b8c8ef775ae9661 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 5 Mar 2023 21:57:06 +0000
Subject: [PATCH 15/17] add `locate`

---
 .devcontainer/Dockerfile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 804e567955..15fb9aeac3 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -3,6 +3,10 @@ FROM aiidateam/aiida-core:main
 
 # Add test dependencies (not installed in image)
 RUN pip install ./aiida-core[tests,rest,docs,pre-commit]
+# the `locate` command is needed by many tests
+RUN apt-get update \
+    && apt-get install -y mlocate \
+    && rm -rf /var/lib/apt/lists/*
 
 # add aiida user
 RUN /etc/my_init.d/10_create-system-user.sh

From 10d7b83194329557033db40158bd71a1518790c9 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Wed, 8 Mar 2023 14:22:13 +0000
Subject: [PATCH 16/17] remove duplication of configure-aiida.sh

---
 .devcontainer/Dockerfile         |  2 +-
 .devcontainer/configure-aiida.sh | 81 --------------------------------
 .devcontainer/devcontainer.json  |  2 +-
 .devcontainer/docker-compose.yml |  5 +-
 4 files changed, 5 insertions(+), 85 deletions(-)
 delete mode 100755 .devcontainer/configure-aiida.sh

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 15fb9aeac3..bde97605f6 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -13,4 +13,4 @@ RUN /etc/my_init.d/10_create-system-user.sh
 
 # copy updated aiida configuration script
 # this line can be deleted after the new script has been merged
-COPY configure-aiida.sh /opt/configure-aiida.sh
+COPY ../.docker/opt/configure-aiida.sh /opt/configure-aiida.sh
diff --git a/.devcontainer/configure-aiida.sh b/.devcontainer/configure-aiida.sh
deleted file mode 100755
index 822578b4ad..0000000000
--- a/.devcontainer/configure-aiida.sh
+++ /dev/null
@@ -1,81 +0,0 @@
-#!/bin/bash
-
-# This script is executed whenever the docker container is (re)started.
-
-# Debugging.
-set -x
-
-# Environment.
-export SHELL=/bin/bash
-
-# Setup AiiDA autocompletion.
-grep _VERDI_COMPLETE /home/${SYSTEM_USER}/.bashrc &> /dev/null || echo 'eval "$(_VERDI_COMPLETE=source verdi)"' >> /home/${SYSTEM_USER}/.bashrc
-
-# Check if user requested to set up AiiDA profile (and if it exists already)
-if [[ ${SETUP_DEFAULT_PROFILE} == true ]] && ! verdi profile show ${PROFILE_NAME} &> /dev/null; then
-    NEED_SETUP_PROFILE=true;
-else
-    NEED_SETUP_PROFILE=false;
-fi
-
-# Setup AiiDA profile if needed.
-if [[ ${NEED_SETUP_PROFILE} == true ]]; then
-
-    # Create AiiDA profile.
-    verdi quicksetup                           \
-        --non-interactive                      \
-        --profile "${PROFILE_NAME}"            \
-        --email "${USER_EMAIL}"                \
-        --first-name "${USER_FIRST_NAME}"      \
-        --last-name "${USER_LAST_NAME}"        \
-        --institution "${USER_INSTITUTION}"    \
-        --db-host "${DB_HOST:localhost}"    \
-        --broker-host "${BROKER_HOST:localhost}"
-
-    # Setup and configure local computer.
-    computer_name=localhost
-
-    # Determine the number of physical cores as a default for the number of
-    # available MPI ranks on the localhost. We do not count "logical" cores,
-    # since MPI parallelization over hyper-threaded cores is typically
-    # associated with a significant performance penalty. We use the
-    # `psutil.cpu_count(logical=False)` function as opposed to simply
-    # `os.cpu_count()` since the latter would include hyperthreaded (logical
-    # cores).
-    NUM_PHYSICAL_CORES=$(python -c 'import psutil; print(int(psutil.cpu_count(logical=False)))' 2>/dev/null)
-    LOCALHOST_MPI_PROCS_PER_MACHINE=${LOCALHOST_MPI_PROCS_PER_MACHINE:-${NUM_PHYSICAL_CORES}}
-
-    if [ -z $LOCALHOST_MPI_PROCS_PER_MACHINE ]; then
-      echo "Unable to automatically determine the number of logical CPUs on this "
-      echo "machine. Please set the LOCALHOST_MPI_PROCS_PER_MACHINE variable to "
-      echo "explicitly set the number of available MPI ranks."
-      exit 1
-    fi
-
-    verdi computer show ${computer_name} || verdi computer setup   \
-        --non-interactive                                          \
-        --label "${computer_name}"                                 \
-        --description "this computer"                              \
-        --hostname "${computer_name}"                              \
-        --transport core.local                                          \
-        --scheduler core.direct                                    \
-        --work-dir /home/aiida/aiida_run/                          \
-        --mpirun-command "mpirun -np {tot_num_mpiprocs}"           \
-        --mpiprocs-per-machine ${LOCALHOST_MPI_PROCS_PER_MACHINE} && \
-    verdi computer configure core.local "${computer_name}"              \
-        --non-interactive                                          \
-        --safe-interval 0.0
-fi
-
-
-# Show the default profile
-verdi profile show || echo "The default profile is not set."
-
-# Make sure that the daemon is not running, otherwise the migration will abort.
-verdi daemon stop
-
-# Migration will run for the default profile.
-verdi storage migrate --force || echo "Database migration failed."
-
-# Daemon will start only if the database exists and is migrated to the latest version.
-verdi daemon start || echo "AiiDA daemon is not running."
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 26eb9cd470..5bbcf39152 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -6,7 +6,7 @@
     "waitFor": "postCreateCommand",
 	"customizations": {
         "vscode": {
-            "extensions": ["ms-python.python","ms-python.vscode-pylance", "eamodio.gitlens"]
+            "extensions": ["ms-python.python", "eamodio.gitlens"]
         }
     }
 }
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index 78f7213e49..5d966bcecf 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -34,8 +34,9 @@ services:
     #image: "aiidateam/aiida-core:main"
     image: "aiida-core-dev"
     build:
-      context: .
-      dockerfile: Dockerfile
+      # need to add the parent directory to context to copy over new configure-aiida.sh
+      context: ..
+      dockerfile: .devcontainer/Dockerfile
     user: aiida
     environment:
       DB_HOST: postgres

From 3903362d308260825254cef65376db7d37cec9d2 Mon Sep 17 00:00:00 2001
From: Leopold Talirz <leopold.talirz@gmail.com>
Date: Sun, 12 Mar 2023 01:27:01 +0100
Subject: [PATCH 17/17] Update docker-compose.yml

remove comments
---
 .devcontainer/docker-compose.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
index 5d966bcecf..380a0a4760 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/docker-compose.yml
@@ -27,8 +27,6 @@ services:
       - aiida
     environment:
       POSTGRES_HOST_AUTH_METHOD: trust
-    # volumes:
-    #   - db-volume:/var/lib/postgresql/data
 
   aiida:
     #image: "aiidateam/aiida-core:main"
@@ -46,15 +44,11 @@ services:
     entrypoint: tail -f /dev/null
     volumes:
       - ..:/home/aiida/aiida-core:cached
-    #   - db-volume:/var/lib/assets
     networks:
       - aiida
     depends_on:
       - rabbitmq
       - postgres
 
-# volumes:
-#   db-volume:
-
 networks:
   aiida: