From d2d28dd2e89ff9cc639f266af0f1092b832047ec Mon Sep 17 00:00:00 2001
From: Xing Wang <xingwang1991@gmail.com>
Date: Tue, 14 Jan 2025 10:41:29 +0100
Subject: [PATCH 1/4] Use try/except to catch error when install QE (#917)

---
 src/aiidalab_qe/setup/codes.py | 46 +++++++++++++++++++++++++++-------
 1 file changed, 37 insertions(+), 9 deletions(-)

diff --git a/src/aiidalab_qe/setup/codes.py b/src/aiidalab_qe/setup/codes.py
index c63a76bb7..984575c6c 100644
--- a/src/aiidalab_qe/setup/codes.py
+++ b/src/aiidalab_qe/setup/codes.py
@@ -1,3 +1,4 @@
+import json
 import subprocess
 from pathlib import Path
 from shutil import which
@@ -44,18 +45,45 @@ def get_qe_env():
 
 
 def qe_installed():
-    import json
+    """Check if Quantum Espresso (QE) is installed in the specified conda environment.
 
-    env_exist = get_qe_env().exists()
-    proc = subprocess.run(
-        ["conda", "list", "-n", f"{get_qe_env().name}", "--json", "--full-name", "qe"],
-        check=True,
-        capture_output=True,
-    )
+    Returns:
+        bool: True if the environment exists and QE is installed; False otherwise.
+    """
+    try:
+        # Verify if the specified conda environment exists
+        env_exist = get_qe_env().exists()
+
+        if not env_exist:
+            return False
+
+        # Run the conda list command to check for the QE package
+        proc = subprocess.run(
+            [
+                "conda",
+                "list",
+                "-n",
+                f"{get_qe_env().name}",
+                "--json",
+                "--full-name",
+                "qe",
+            ],
+            check=True,
+            capture_output=True,
+        )
 
-    info = json.loads(str(proc.stdout.decode()))[0]
+        # Load and interpret the JSON output
+        info = json.loads(proc.stdout.decode())
 
-    return env_exist and "qe" == info["name"]
+        # Check if 'qe' is listed in the environment
+        for package in info:
+            if package.get("name") == "qe":
+                return True
+        return False  # noqa: TRY300
+    except Exception as error:
+        raise RuntimeError(
+            "Failed to check if Quantum Espresso is installed."
+        ) from error
 
 
 def install_qe():

From 969ba0efaaa48562b6ccbd56fe172614602a17aa Mon Sep 17 00:00:00 2001
From: Edan Bainglass <45081142+edan-bainglass@users.noreply.github.com>
Date: Tue, 14 Jan 2025 11:13:45 +0100
Subject: [PATCH 2/4] Add `schema.json` to package data (#1093)

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index f6c5d894e..b18b40480 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -54,6 +54,7 @@ aiidalab_qe.app.parameters = qeapp.yaml
 aiidalab_qe.app.static.styles = *.css
 aiidalab_qe.app.static.templates = *.jinja
 aiidalab_qe.app.structure.examples = *
+aiidalab_qe.app.result.components.summary = schema.json
 aiidalab_qe.plugins.xas = pseudo_toc.yaml
 aiidalab_qe.plugins.xps.structure_examples = *
 aiidalab_qe.plugins.xas.structure_examples = *

From 74ef3cb52a8be5eb57714f5d2b771c5f743cda4d Mon Sep 17 00:00:00 2001
From: Xing Wang <xingwang1991@gmail.com>
Date: Tue, 14 Jan 2025 11:33:57 +0100
Subject: [PATCH 3/4] Handle cpu and memory check gracefully (#1094)

This old HQ script assumes a cgroupv2 environment, but the issue arises because some system doesn't have the required cgroupv2 files (/sys/fs/cgroup/cpu.max and /sys/fs/cgroup/memory.max).

- If cpu.max and memory.max are missing, fall back to cgroupv1
- If neither cpu.max nor cpu.cfs_quota_us exists, use default values.
---
 before-notebook.d/43_start-hq.sh | 55 +++++++++++++++++++++-----------
 1 file changed, 36 insertions(+), 19 deletions(-)

diff --git a/before-notebook.d/43_start-hq.sh b/before-notebook.d/43_start-hq.sh
index c20a462e4..b90a8e952 100644
--- a/before-notebook.d/43_start-hq.sh
+++ b/before-notebook.d/43_start-hq.sh
@@ -10,34 +10,51 @@ set -x
 # But for developers, please update your cgroup version to v2.
 # See: https://kubernetes.io/docs/concepts/architecture/cgroups/#using-cgroupv2
 
-# computer memory from runtime
-MEMORY_LIMIT=$(cat /sys/fs/cgroup/memory.max)
+# Default to cgroupv1 paths
+CPU_QUOTA_PATH="/sys/fs/cgroup/cpu/cpu.cfs_quota_us"
+CPU_PERIOD_PATH="/sys/fs/cgroup/cpu/cpu.cfs_period_us"
+MEMORY_LIMIT_PATH="/sys/fs/cgroup/memory/memory.limit_in_bytes"
 
-if [ "$MEMORY_LIMIT" = "max" ]; then
-  MEMORY_LIMIT=4096
-  echo "No memory limit set, use 4GiB"
-else
-  MEMORY_LIMIT=$(echo "scale=0; $MEMORY_LIMIT / (1024 * 1024)" | bc)
-  echo "Memory Limit: ${MEMORY_LIMIT} MiB"
+# Fallback if cgroupv2 paths exist
+if [ -f /sys/fs/cgroup/cpu.max ]; then
+  CPU_QUOTA_PATH="/sys/fs/cgroup/cpu.max"
+  CPU_PERIOD_PATH="/sys/fs/cgroup/cpu.max"
+fi
+
+if [ -f /sys/fs/cgroup/memory.max ]; then
+  MEMORY_LIMIT_PATH="/sys/fs/cgroup/memory.max"
 fi
 
-# Compute number of cpus allocated to the container
-CPU_LIMIT=$(awk '{print $1}' /sys/fs/cgroup/cpu.max)
-CPU_PERIOD=$(awk '{print $2}' /sys/fs/cgroup/cpu.max)
+# Compute memory limit
+if [ -f "$MEMORY_LIMIT_PATH" ]; then
+  MEMORY_LIMIT=$(cat "$MEMORY_LIMIT_PATH")
+  if [ "$MEMORY_LIMIT" = "max" ] || [ "$MEMORY_LIMIT" -eq -1 ]; then
+    MEMORY_LIMIT=4096
+  else
+    MEMORY_LIMIT=$(echo "scale=0; $MEMORY_LIMIT / (1024 * 1024)" | bc)
+  fi
+else
+  MEMORY_LIMIT=4096
+fi
+echo "Memory Limit: ${MEMORY_LIMIT} MiB"
 
-if [ "$CPU_PERIOD" -ne 0 ]; then
-  CPU_NUMBER=$(echo "scale=2; $CPU_LIMIT / $CPU_PERIOD" | bc)
-  echo "Number of CPUs allocated: $CPU_NUMBER"
+# Compute CPU limit
+if [ -f "$CPU_QUOTA_PATH" ] && [ -f "$CPU_PERIOD_PATH" ]; then
+  CPU_LIMIT=$(cat "$CPU_QUOTA_PATH")
+  CPU_PERIOD=$(cat "$CPU_PERIOD_PATH")
 
-  # for HQ setting round to integer number of CPUs, the left are for system tasks
-  CPU_LIMIT=$(echo "scale=0; $CPU_LIMIT / $CPU_PERIOD" | bc)
+  if [ "$CPU_LIMIT" != "max" ] && [ "$CPU_PERIOD" -ne 0 ]; then
+    CPU_NUMBER=$(echo "scale=2; $CPU_LIMIT / $CPU_PERIOD" | bc)
+    CPU_LIMIT=$(echo "$CPU_NUMBER / 1" | bc)  # Round down to integer
+  else
+    CPU_LIMIT=$(nproc)
+  fi
 else
-  # if no limit (with local OCI without setting cpu limit, use all CPUs)
   CPU_LIMIT=$(nproc)
-  echo "No CPU limit set"
 fi
+echo "Number of CPUs allocated: $CPU_LIMIT"
 
-# Start hq server with a worker
+# Start HQ server and worker
 run-one-constantly hq server start 1>$HOME/.hq-stdout 2>$HOME/.hq-stderr &
 run-one-constantly hq worker start --cpus=${CPU_LIMIT} --resource "mem=sum(${MEMORY_LIMIT})" --no-detect-resources &
 

From ef43cc729131d35a73640b087817a704d48453b3 Mon Sep 17 00:00:00 2001
From: superstar54 <xingwang1991@gmail.com>
Date: Tue, 14 Jan 2025 10:38:34 +0000
Subject: [PATCH 4/4] Bump version v24.10.0a6 -> v24.10.0a7

---
 docs/source/conf.py        | 2 +-
 setup.cfg                  | 4 ++--
 src/aiidalab_qe/version.py | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 04845b682..d4f31b56c 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -13,7 +13,7 @@
 
 # -- Project information -----------------------------------------------------
 
-version = "v24.10.0a6"
+version = "v24.10.0a7"
 release = f"{version}-dev"
 project = "Quantum ESPRESSO App"
 copyright_first_year = "2023"
diff --git a/setup.cfg b/setup.cfg
index b18b40480..75bf27bfb 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = aiidalab_qe
-version = 24.10.0a6
+version = 24.10.0a7
 description = Package for the AiiDAlab QE app
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -77,7 +77,7 @@ categories =
     quantum
 
 [bumpver]
-current_version = "v24.10.0a6"
+current_version = "v24.10.0a7"
 version_pattern = "v0Y.0M.PATCH[PYTAGNUM]"
 commit_message = "Bump version {old_version} -> {new_version}"
 commit = True
diff --git a/src/aiidalab_qe/version.py b/src/aiidalab_qe/version.py
index b73b302d4..d2908f901 100644
--- a/src/aiidalab_qe/version.py
+++ b/src/aiidalab_qe/version.py
@@ -2,4 +2,4 @@
 
 """This module contains project version information for both the app and the workflow."""
 
-__version__ = "v24.10.0a6"
+__version__ = "v24.10.0a7"