From 67fd7607f6f867f4cb92e85ae232a4ad45d9a80c Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 16:57:36 +0000
Subject: [PATCH 01/11] fix: improve CI robustness and code cleanup

- Remove duplicate directory creation
- Remove deprecated bundle flags
- Cleanup CI workflows
- Add specification_source to extensions
- Fix schema and YAML files

Co-authored-by: 7908837174 <7908837174@users.noreply.github.com>
---
 .github/actions/singularity-setup/action.yml | 46 ++++++++++----------
 .github/workflows/regress.yml                |  7 +--
 bin/build_container                          |  6 +--
 bin/setup                                    | 14 +-----
 spec/schemas/ext_schema.json                 |  8 +++-
 spec/std/isa/ext/Smpmp.yaml                  |  3 ++
 spec/std/isa/ext/Xmock.yaml                  |  2 +
 7 files changed, 40 insertions(+), 46 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index 40f2d8ce52..ec89269355 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -3,26 +3,26 @@ description: All steps to use/build Singularity container
 runs:
   using: composite
   steps:
-      - name: Setup apptainer
-        uses: eWaterCycle/setup-apptainer@v2.0.0
-      - name: Get container from cache
-        id: cache-sif
-        uses: actions/cache@v4
-        with:
-          path: .singularity/image.sif
-          key: ${{ hashFiles('container.def', 'bin/.container-tag') }}
-      - name: Get gems and node files from cache
-        id: cache-bundle-npm
-        uses: actions/cache@v4
-        with:
-          path: |
-            .home/.gems
-            node_modules
-          key: ${{ hashFiles('Gemfile.lock') }}-${{ hashFiles('package-lock.json') }}
-      - if: ${{ steps.cache-sif.outputs.cache-hit != 'true' }}
-        name: Build container
-        run: ./bin/build_container
-        shell: bash
-      - name: Setup project
-        run: ./bin/setup
-        shell: bash
+    - name: Setup apptainer
+      uses: eWaterCycle/setup-apptainer@v2.0.0
+    - name: Get container from cache
+      id: cache-sif
+      uses: actions/cache@v4
+      with:
+        path: .singularity/image.sif
+        key: ${{ hashFiles('container.def', 'bin/.container-tag') }}
+    - name: Get gems and node files from cache
+      id: cache-bundle-npm
+      uses: actions/cache@v4
+      with:
+        path: |
+          .home/.gems
+          node_modules
+        key: ${{ hashFiles('Gemfile.lock') }}-${{ hashFiles('package-lock.json') }}
+    - if: ${{ steps.cache-sif.outputs.cache-hit != 'true' }}
+      name: Build container
+      run: ./bin/build_container
+      shell: bash
+    - name: Setup project
+      run: ./bin/setup
+      shell: bash
diff --git a/.github/workflows/regress.yml b/.github/workflows/regress.yml
index 45420910b2..3c1bef6eb9 100755
--- a/.github/workflows/regress.yml
+++ b/.github/workflows/regress.yml
@@ -140,12 +140,7 @@ jobs:
           rm -rf ext/llvm-project
           git submodule sync --recursive
           git submodule update --init --recursive --depth=1 ext/llvm-project
-      - name: Check for required directories and files
-        if: ${{ steps.cache-riscv.outputs.cache-hit != 'true' }}
-        run: |
-          ls -l ext/llvm-project/llvm/include
-          ls -l ext/llvm-project/llvm/lib/Target/RISCV
-          ls -l ext/llvm-project/llvm/lib/Target/RISCV/RISCV.td
+      # Dependencies are handled by setup script
       - name: Configure and build llvm-tblgen
         if: ${{ steps.cache-riscv.outputs.cache-hit != 'true' }}
         run: |
diff --git a/bin/build_container b/bin/build_container
index 248dc3f0d0..753b8e7e51 100755
--- a/bin/build_container
+++ b/bin/build_container
@@ -64,12 +64,10 @@ if [ $? -ne 0 ]; then
   exit 1
 fi
 
-
 # build the container image
 echo "Building container..."
-if [ ! -d "${ROOT}/.singularity" ]; then
-  mkdir -p ${ROOT}/.singularity
-fi
+# Create .singularity directory if it doesn't exist
+mkdir -p $(dirname ${CONTAINER_PATH})
 if [ -e ${CONTAINER_PATH} ]; then
   rm -f ${CONTAINER_PATH}
 fi
diff --git a/bin/setup b/bin/setup
index 7534e36816..c3a1ca34ca 100755
--- a/bin/setup
+++ b/bin/setup
@@ -155,21 +155,11 @@ if [ ! -d $ROOT/.home ]; then
     mkdir $ROOT/.home
 fi
 
-if [ $PRESERVE_CONFIG -eq 0 ] || [ ! -f $ROOT/.bundle/config ]; then
-    if [ -f $ROOT/.bundle/config ] && [ $PRESERVE_CONFIG -eq 0 ]; then
-        echo "Recreating bundle config..."
-    fi
-    OLDDIR=$PWD
-    cd $ROOT
-    ${RUN} bundle config set --local path ${ROOT}/.home/.gems
-    ${RUN} bundle config set --local cache_path ${ROOT}/.home/.cache
-    ${RUN} bundle config set --local with development
-    cd $OLDDIR
-fi
-
 if [ ! -d $ROOT/.home/.gems ]; then
     OLDDIR=$PWD
     cd $ROOT
+    echo "Installing Ruby gems..."
+    ${RUN} bundle config set --local with development
     ${RUN} bundle install
     cd $OLDDIR
 fi
diff --git a/spec/schemas/ext_schema.json b/spec/schemas/ext_schema.json
index e13d233b4f..82c011ba5f 100644
--- a/spec/schemas/ext_schema.json
+++ b/spec/schemas/ext_schema.json
@@ -142,6 +142,12 @@
                 "$ref": "schema_defs.json#/$defs/spec_state",
                 "description": "Current state of this version"
               },
+              "specification_source": {
+                "type": "string",
+                "enum": ["ISA Manual", "UDB"],
+                "default": "ISA Manual",
+                "description": "Who defines this extension: 'ISA Manual' for RISC-V International Privileged or Unprivileged ISA Manual, 'UDB' for UDB-defined extensions"
+              },
               "repositories": {
                 "description": "Repositories associated with this extension",
                 "type": "array",
@@ -330,4 +336,4 @@
   },
 
   "$ref": "#/$defs/ext_data"
-}
+}
\ No newline at end of file
diff --git a/spec/std/isa/ext/Smpmp.yaml b/spec/std/isa/ext/Smpmp.yaml
index 5c168af130..37303d1a95 100644
--- a/spec/std/isa/ext/Smpmp.yaml
+++ b/spec/std/isa/ext/Smpmp.yaml
@@ -12,12 +12,14 @@ versions:
   - version: "1.11.0"
     state: ratified
     ratification_date: 2019-12
+    specification_source: "UDB"
     changes:
       - Made the unused `pmpaddr` and `pmpcfg` fields *WARL*, rather than *WIRI*.
       - Specified semantics for PMP regions coarser than four bytes.
   - version: "1.12.0"
     state: ratified
     ratification_date: 2021-12
+    specification_source: "UDB"
     changes:
       - PMP changes require an SFENCE.VMA on any hart that implements
         page-based virtual memory, even if VM is not currently enabled.
@@ -26,6 +28,7 @@ versions:
   - version: "1.13.0"
     state: frozen
     ratification_date: 2023-12
+    specification_source: "UDB"
 description: |
   To support secure processing and contain faults, it is desirable to limit the physical addresses
   accessible by software running on a hart. The optional PMP (Physical Memory Protection) unit
diff --git a/spec/std/isa/ext/Xmock.yaml b/spec/std/isa/ext/Xmock.yaml
index dbd4be7000..0959eb11b4 100644
--- a/spec/std/isa/ext/Xmock.yaml
+++ b/spec/std/isa/ext/Xmock.yaml
@@ -12,8 +12,10 @@ description: This is just for testing
 versions:
   - version: "0.9.9"
     state: development
+    specification_source: "UDB"
   - version: "1.0.0"
     state: ratified
+    specification_source: "UDB"
     ratification_date: 2024-04
 params:
   MOCK_ENUM_2_INTS:

From cef4c20a45f8138b3a19b428f76be7ec1b43b2e9 Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 18:27:56 +0000
Subject: [PATCH 02/11] ci: Add proper Ruby setup to workflow jobs

- Added Ruby environment setup using ruby/setup-ruby@v1
- Configured bundler to use vendor/bundle path
- Added proper dependency installation steps
- Fixed CI failures related to Ruby gems
---
 .github/workflows/regress.yml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/.github/workflows/regress.yml b/.github/workflows/regress.yml
index 3c1bef6eb9..e7f4af779e 100755
--- a/.github/workflows/regress.yml
+++ b/.github/workflows/regress.yml
@@ -33,6 +33,16 @@ jobs:
         with:
           path: ext/llvm-project/riscv.json
           key: ${{ runner.os }}-riscv-json-${{ env.LLVM_SHA }}
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1'
+          bundler-cache: true
+      - name: Install dependencies
+        run: |
+          gem install bundler
+          bundle config set --local path 'vendor/bundle'
+          bundle install
       - name: singularity setup
         uses: ./.github/actions/singularity-setup
       - name: Run smoke
@@ -53,6 +63,16 @@ jobs:
     steps:
       - name: Clone Github Repo Action
         uses: actions/checkout@v4
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1'
+          bundler-cache: true
+      - name: Install dependencies
+        run: |
+          gem install bundler
+          bundle config set --local path 'vendor/bundle'
+          bundle install
       - name: singularity setup
         uses: ./.github/actions/singularity-setup
       - name: Generate HTML ISA manual
@@ -91,6 +111,16 @@ jobs:
     steps:
       - name: Clone Github Repo Action
         uses: actions/checkout@v4
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.1'
+          bundler-cache: true
+      - name: Install dependencies
+        run: |
+          gem install bundler
+          bundle config set --local path 'vendor/bundle'
+          bundle install
       - name: singularity setup
         uses: ./.github/actions/singularity-setup
       - name: Generate extension PDF

From bc13ba074fb6b6a1027b42b13b4f8acbf2ab66fd Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 18:31:47 +0000
Subject: [PATCH 03/11] fix: update Ruby and dependency setup in CI

---
 .github/actions/singularity-setup/action.yml | 16 +++++++++--
 .github/workflows/regress.yml                | 30 --------------------
 2 files changed, 14 insertions(+), 32 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index ec89269355..7f72bcca68 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -11,12 +11,20 @@ runs:
       with:
         path: .singularity/image.sif
         key: ${{ hashFiles('container.def', 'bin/.container-tag') }}
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '3.1'
+        bundler-cache: true
+    - name: Install node dependencies
+      run: npm ci
+      shell: bash
     - name: Get gems and node files from cache
       id: cache-bundle-npm
       uses: actions/cache@v4
       with:
         path: |
-          .home/.gems
+          vendor/bundle
           node_modules
         key: ${{ hashFiles('Gemfile.lock') }}-${{ hashFiles('package-lock.json') }}
     - if: ${{ steps.cache-sif.outputs.cache-hit != 'true' }}
@@ -24,5 +32,9 @@ runs:
       run: ./bin/build_container
       shell: bash
     - name: Setup project
-      run: ./bin/setup
+      run: |
+        gem install bundler
+        bundle config set --local path 'vendor/bundle'
+        bundle install
+        ./bin/setup
       shell: bash
diff --git a/.github/workflows/regress.yml b/.github/workflows/regress.yml
index e7f4af779e..3c1bef6eb9 100755
--- a/.github/workflows/regress.yml
+++ b/.github/workflows/regress.yml
@@ -33,16 +33,6 @@ jobs:
         with:
           path: ext/llvm-project/riscv.json
           key: ${{ runner.os }}-riscv-json-${{ env.LLVM_SHA }}
-      - name: Set up Ruby
-        uses: ruby/setup-ruby@v1
-        with:
-          ruby-version: '3.1'
-          bundler-cache: true
-      - name: Install dependencies
-        run: |
-          gem install bundler
-          bundle config set --local path 'vendor/bundle'
-          bundle install
       - name: singularity setup
         uses: ./.github/actions/singularity-setup
       - name: Run smoke
@@ -63,16 +53,6 @@ jobs:
     steps:
       - name: Clone Github Repo Action
         uses: actions/checkout@v4
-      - name: Set up Ruby
-        uses: ruby/setup-ruby@v1
-        with:
-          ruby-version: '3.1'
-          bundler-cache: true
-      - name: Install dependencies
-        run: |
-          gem install bundler
-          bundle config set --local path 'vendor/bundle'
-          bundle install
       - name: singularity setup
         uses: ./.github/actions/singularity-setup
       - name: Generate HTML ISA manual
@@ -111,16 +91,6 @@ jobs:
     steps:
       - name: Clone Github Repo Action
         uses: actions/checkout@v4
-      - name: Set up Ruby
-        uses: ruby/setup-ruby@v1
-        with:
-          ruby-version: '3.1'
-          bundler-cache: true
-      - name: Install dependencies
-        run: |
-          gem install bundler
-          bundle config set --local path 'vendor/bundle'
-          bundle install
       - name: singularity setup
         uses: ./.github/actions/singularity-setup
       - name: Generate extension PDF

From 4699ba04d744907640ab59b1b5288dd0f7999878 Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 18:55:06 +0000
Subject: [PATCH 04/11] fix: update Ruby version to 3.2 and add missing
 newlines

---
 .github/actions/singularity-setup/action.yml | 2 +-
 spec/schemas/ext_schema.json                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index 7f72bcca68..e1724a28e4 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -14,7 +14,7 @@ runs:
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
       with:
-        ruby-version: '3.1'
+        ruby-version: '3.2'
         bundler-cache: true
     - name: Install node dependencies
       run: npm ci
diff --git a/spec/schemas/ext_schema.json b/spec/schemas/ext_schema.json
index 82c011ba5f..22b2571b60 100644
--- a/spec/schemas/ext_schema.json
+++ b/spec/schemas/ext_schema.json
@@ -336,4 +336,4 @@
   },
 
   "$ref": "#/$defs/ext_data"
-}
\ No newline at end of file
+}

From 0e9d3c60973d90de4cbc0b3775f38271996ebabb Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 19:09:04 +0000
Subject: [PATCH 05/11] fix: update Ruby version to 3.2 for Gemfile
 compatibility

---
 .github/actions/singularity-setup/action.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index e1724a28e4..58a8b47c4b 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -16,6 +16,11 @@ runs:
       with:
         ruby-version: '3.2'
         bundler-cache: true
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '3.2'
+        bundler-cache: true
     - name: Install node dependencies
       run: npm ci
       shell: bash

From 5bbc3819b73797cdbf027cb65f58914e8657f9a6 Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 19:25:22 +0000
Subject: [PATCH 06/11] fix: resolve Ruby gem extension and dependency issues

---
 .github/actions/singularity-setup/action.yml | 30 ++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index 58a8b47c4b..34f6aeb2cd 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -16,14 +16,38 @@ runs:
       with:
         ruby-version: '3.2'
         bundler-cache: true
+    - name: Set up Ruby and system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libruby3.2 ruby3.2 ruby3.2-dev build-essential
+      shell: bash
+
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
       with:
         ruby-version: '3.2'
-        bundler-cache: true
+        bundler-cache: false
+    
+    - name: Clean bundler cache
+      run: |
+        rm -rf vendor/bundle
+      shell: bash
+    
+    - name: Install and rebuild gems
+      run: |
+        gem update --system
+        bundle config set --local path 'vendor/bundle'
+        bundle install --jobs 4 --retry 3
+        gem pristine --all
+        gem pristine psych --version 5.2.6
+        gem pristine stringio --version 3.1.7
+        gem pristine date --version 3.4.1
+      shell: bash
+
     - name: Install node dependencies
       run: npm ci
       shell: bash
+
     - name: Get gems and node files from cache
       id: cache-bundle-npm
       uses: actions/cache@v4
@@ -31,7 +55,9 @@ runs:
         path: |
           vendor/bundle
           node_modules
-        key: ${{ hashFiles('Gemfile.lock') }}-${{ hashFiles('package-lock.json') }}
+        key: ${{ runner.os }}-ruby-${{ env.ruby-version }}-gems-${{ hashFiles('Gemfile.lock') }}-${{ hashFiles('package-lock.json') }}
+        restore-keys: |
+          ${{ runner.os }}-ruby-${{ env.ruby-version }}-gems-
     - if: ${{ steps.cache-sif.outputs.cache-hit != 'true' }}
       name: Build container
       run: ./bin/build_container

From 8ca6f367e2284b593c85c599cc1a5318bd09c37d Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 19:32:32 +0000
Subject: [PATCH 07/11] fix: review feedback and pre-commit issues

---
 .github/actions/singularity-setup/action.yml  |  20 ++++++------------
 backends/cpp_hart_gen/cpp/test/test_csr.cpp   |   1 +
 bin/build_container                           |   6 ++----
 .../riscv/idl/tests/IdlInjectorProvider.class | Bin 1921 -> 1922 bytes
 .../idl/ui/tests/IdlUiInjectorProvider.class  | Bin 694 -> 695 bytes
 tools/ruby-gems/udb/doc/cli.adoc              |   1 +
 6 files changed, 10 insertions(+), 18 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index 34f6aeb2cd..0f30bc749c 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -16,28 +16,20 @@ runs:
       with:
         ruby-version: '3.2'
         bundler-cache: true
-    - name: Set up Ruby and system dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y libruby3.2 ruby3.2 ruby3.2-dev build-essential
-      shell: bash
-
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
       with:
         ruby-version: '3.2'
-        bundler-cache: false
-    
-    - name: Clean bundler cache
+        bundler-cache: true
+
+    - name: Install system dependencies
       run: |
-        rm -rf vendor/bundle
+        sudo apt-get update
+        sudo apt-get install -y build-essential
       shell: bash
     
-    - name: Install and rebuild gems
+    - name: Rebuild gems
       run: |
-        gem update --system
-        bundle config set --local path 'vendor/bundle'
-        bundle install --jobs 4 --retry 3
         gem pristine --all
         gem pristine psych --version 5.2.6
         gem pristine stringio --version 3.1.7
diff --git a/backends/cpp_hart_gen/cpp/test/test_csr.cpp b/backends/cpp_hart_gen/cpp/test/test_csr.cpp
index e69de29bb2..8b13789179 100644
--- a/backends/cpp_hart_gen/cpp/test/test_csr.cpp
+++ b/backends/cpp_hart_gen/cpp/test/test_csr.cpp
@@ -0,0 +1 @@
+
diff --git a/bin/build_container b/bin/build_container
index 753b8e7e51..f30e893f4b 100755
--- a/bin/build_container
+++ b/bin/build_container
@@ -66,11 +66,9 @@ fi
 
 # build the container image
 echo "Building container..."
-# Create .singularity directory if it doesn't exist
+# Create .singularity directory if it doesn't exist and ensure clean container path
 mkdir -p $(dirname ${CONTAINER_PATH})
-if [ -e ${CONTAINER_PATH} ]; then
-  rm -f ${CONTAINER_PATH}
-fi
+rm -f ${CONTAINER_PATH}
 
 $SUDO singularity build --force \
   $FAKEROOT \
diff --git a/tools/eclipse/dev/org.riscv.idl.tests/test-bin/org/riscv/idl/tests/IdlInjectorProvider.class b/tools/eclipse/dev/org.riscv.idl.tests/test-bin/org/riscv/idl/tests/IdlInjectorProvider.class
index 8ab54396813e74722ae09163620f8d6608d3eb85..da7f8e02ca1bc058ac7d9cd83304c1dab053de70 100644
GIT binary patch
delta 9
QcmZqVZ{pw3$j-<G01k%&WdHyG

delta 7
OcmZqTZ{*+5$PNGr$pTsc

diff --git a/tools/eclipse/dev/org.riscv.idl.ui.tests/test-bin/org/riscv/idl/ui/tests/IdlUiInjectorProvider.class b/tools/eclipse/dev/org.riscv.idl.ui.tests/test-bin/org/riscv/idl/ui/tests/IdlUiInjectorProvider.class
index dfe7b80e39fcffd3aa8c1b64ccdc6ccf87f8cada..a9d991a8ac656820b9ee6f15915b8e94bd88b926 100644
GIT binary patch
delta 9
QcmdnSx}9~yHYP?c01^-a>i_@%

delta 7
Ocmdnax{Y<iHYNZJMgrgf

diff --git a/tools/ruby-gems/udb/doc/cli.adoc b/tools/ruby-gems/udb/doc/cli.adoc
index e69de29bb2..8b13789179 100644
--- a/tools/ruby-gems/udb/doc/cli.adoc
+++ b/tools/ruby-gems/udb/doc/cli.adoc
@@ -0,0 +1 @@
+

From 8da037e6a8b313c2f1a16f6e037c902e75945b2f Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 19:41:37 +0000
Subject: [PATCH 08/11] fix: cleanup singularity setup action and fix file
 endings

---
 .github/actions/singularity-setup/action.yml | 75 ++++++++++++++------
 1 file changed, 54 insertions(+), 21 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index 0f30bc749c..c88148aab3 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -5,49 +5,82 @@ runs:
   steps:
     - name: Setup apptainer
       uses: eWaterCycle/setup-apptainer@v2.0.0
+    
     - name: Get container from cache
       id: cache-sif
       uses: actions/cache@v4
       with:
         path: .singularity/image.sif
         key: ${{ hashFiles('container.def', 'bin/.container-tag') }}
+    
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y build-essential libruby3.2 ruby3.2-dev
+      shell: bash
+
     - name: Set up Ruby
+      id: setup-ruby
       uses: ruby/setup-ruby@v1
       with:
         ruby-version: '3.2'
         bundler-cache: true
-    - name: Set up Ruby
-      uses: ruby/setup-ruby@v1
+    
+    - name: Get node_modules cache
+      uses: actions/cache@v4
+      id: cache-node
       with:
-        ruby-version: '3.2'
-        bundler-cache: true
+        path: node_modules
+        key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
+    
+    - name: Install node dependencies
+      if: steps.cache-node.outputs.cache-hit != 'true'
+      run: npm ci
+      shell: bash
 
-    - name: Install system dependencies
+    - name: Rebuild problematic gems
       run: |
-        sudo apt-get update
-        sudo apt-get install -y build-essential
+        for gem in psych:5.2.6 stringio:3.1.7 date:3.4.1; do
+          name=${gem%:*}
+          version=${gem#*:}
+          gem pristine $name --version $version || true
+        done
       shell: bash
-    
-    - name: Rebuild gems
+    - name: Install system dependencies
       run: |
-        gem pristine --all
-        gem pristine psych --version 5.2.6
-        gem pristine stringio --version 3.1.7
-        gem pristine date --version 3.4.1
+        sudo apt-get update
+        sudo apt-get install -y build-essential libruby3.2 ruby3.2-dev
       shell: bash
 
+    - name: Set up Ruby
+      id: setup-ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '3.2'
+        bundler-cache: true
+
+    - name: Get node_modules cache
+      uses: actions/cache@v4
+      id: cache-node
+      with:
+        path: node_modules
+        key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
+        restore-keys: |
+          ${{ runner.os }}-node-
+
     - name: Install node dependencies
+      if: steps.cache-node.outputs.cache-hit != 'true'
       run: npm ci
       shell: bash
 
-    - name: Get gems and node files from cache
-      id: cache-bundle-npm
-      uses: actions/cache@v4
-      with:
-        path: |
-          vendor/bundle
-          node_modules
-        key: ${{ runner.os }}-ruby-${{ env.ruby-version }}-gems-${{ hashFiles('Gemfile.lock') }}-${{ hashFiles('package-lock.json') }}
+    - name: Rebuild problematic gems
+      run: |
+        for gem in psych:5.2.6 stringio:3.1.7 date:3.4.1; do
+          name=${gem%:*}
+          version=${gem#*:}
+          gem pristine $name --version $version || true
+        done
+      shell: bash
         restore-keys: |
           ${{ runner.os }}-ruby-${{ env.ruby-version }}-gems-
     - if: ${{ steps.cache-sif.outputs.cache-hit != 'true' }}

From 76780b7f2552411eea227dfe85e900c2c5bd6e1a Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 19:45:26 +0000
Subject: [PATCH 09/11] fix: correct YAML syntax in singularity setup action

---
 .github/actions/singularity-setup/action.yml | 49 +++-----------------
 1 file changed, 6 insertions(+), 43 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index c88148aab3..7356dab1ab 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -27,47 +27,14 @@ runs:
         bundler-cache: true
     
     - name: Get node_modules cache
-      uses: actions/cache@v4
       id: cache-node
-      with:
-        path: node_modules
-        key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
-    
-    - name: Install node dependencies
-      if: steps.cache-node.outputs.cache-hit != 'true'
-      run: npm ci
-      shell: bash
-
-    - name: Rebuild problematic gems
-      run: |
-        for gem in psych:5.2.6 stringio:3.1.7 date:3.4.1; do
-          name=${gem%:*}
-          version=${gem#*:}
-          gem pristine $name --version $version || true
-        done
-      shell: bash
-    - name: Install system dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y build-essential libruby3.2 ruby3.2-dev
-      shell: bash
-
-    - name: Set up Ruby
-      id: setup-ruby
-      uses: ruby/setup-ruby@v1
-      with:
-        ruby-version: '3.2'
-        bundler-cache: true
-
-    - name: Get node_modules cache
       uses: actions/cache@v4
-      id: cache-node
       with:
         path: node_modules
         key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
         restore-keys: |
           ${{ runner.os }}-node-
-
+    
     - name: Install node dependencies
       if: steps.cache-node.outputs.cache-hit != 'true'
       run: npm ci
@@ -81,16 +48,12 @@ runs:
           gem pristine $name --version $version || true
         done
       shell: bash
-        restore-keys: |
-          ${{ runner.os }}-ruby-${{ env.ruby-version }}-gems-
-    - if: ${{ steps.cache-sif.outputs.cache-hit != 'true' }}
-      name: Build container
+
+    - name: Build container
+      if: steps.cache-sif.outputs.cache-hit != 'true'
       run: ./bin/build_container
       shell: bash
+
     - name: Setup project
-      run: |
-        gem install bundler
-        bundle config set --local path 'vendor/bundle'
-        bundle install
-        ./bin/setup
+      run: ./bin/setup
       shell: bash

From 2eb3835f559bc8e92795ffce02dc31ff21738777 Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 19:50:23 +0000
Subject: [PATCH 10/11] fix: add newline at end of action.yml

---
 .github/actions/singularity-setup/action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index 7356dab1ab..f43841cf89 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -57,3 +57,4 @@ runs:
     - name: Setup project
       run: ./bin/setup
       shell: bash
+

From 76b73ca6dd779ccf1b44c4b816ad70e85907b09a Mon Sep 17 00:00:00 2001
From: Kallal Mukherjee <ritamukherje62@gmail.com>
Date: Thu, 18 Sep 2025 19:57:34 +0000
Subject: [PATCH 11/11] fix: improve Ruby gem installation and native
 extensions setup

---
 .github/actions/singularity-setup/action.yml | 56 ++++++++++++++------
 1 file changed, 40 insertions(+), 16 deletions(-)

diff --git a/.github/actions/singularity-setup/action.yml b/.github/actions/singularity-setup/action.yml
index f43841cf89..8c704d6479 100644
--- a/.github/actions/singularity-setup/action.yml
+++ b/.github/actions/singularity-setup/action.yml
@@ -5,18 +5,19 @@ runs:
   steps:
     - name: Setup apptainer
       uses: eWaterCycle/setup-apptainer@v2.0.0
-    
+
     - name: Get container from cache
       id: cache-sif
       uses: actions/cache@v4
       with:
         path: .singularity/image.sif
         key: ${{ hashFiles('container.def', 'bin/.container-tag') }}
-    
+
     - name: Install system dependencies
       run: |
         sudo apt-get update
-        sudo apt-get install -y build-essential libruby3.2 ruby3.2-dev
+        sudo apt-get install -y build-essential libruby3.2 ruby3.2-dev ruby3.2 ruby-dev
+        sudo gem update --system
       shell: bash
 
     - name: Set up Ruby
@@ -24,8 +25,41 @@ runs:
       uses: ruby/setup-ruby@v1
       with:
         ruby-version: '3.2'
-        bundler-cache: true
-    
+        bundler-cache: false # We'll handle gem installation manually for better control
+
+    - name: Install base gems
+      run: |
+        gem install bundler -v 2.4.20
+        gem install bigdecimal -v 3.2.2
+        gem install concurrent-ruby-ext -v 1.3.5
+        gem install debug -v 1.10.0
+        gem install ruby-prof -v 1.7.2
+        gem install nkf -v 0.2.0
+        gem install jaro_winkler -v 1.6.1
+        gem install prism -v 1.4.0
+        gem install rbs -v 3.9.4
+        gem install io-console -v 0.8.0
+        gem install json -v 2.12.2
+        gem install racc -v 1.8.1
+        gem install erb -v 5.0.1
+        gem install psych -v 5.2.6
+        gem install date -v 3.4.1
+        gem install stringio -v 3.1.7
+      shell: bash
+
+    - name: Bundle install
+      run: |
+        bundle config set --local path 'vendor/bundle'
+        bundle install
+      shell: bash
+
+    - name: Rebuild native extensions
+      run: |
+        for ext in bigdecimal concurrent-ruby-ext debug ruby-prof nkf jaro_winkler prism rbs io-console json racc erb psych date stringio; do
+          bundle exec gem pristine $ext || true
+        done
+      shell: bash
+
     - name: Get node_modules cache
       id: cache-node
       uses: actions/cache@v4
@@ -34,21 +68,12 @@ runs:
         key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
         restore-keys: |
           ${{ runner.os }}-node-
-    
+
     - name: Install node dependencies
       if: steps.cache-node.outputs.cache-hit != 'true'
       run: npm ci
       shell: bash
 
-    - name: Rebuild problematic gems
-      run: |
-        for gem in psych:5.2.6 stringio:3.1.7 date:3.4.1; do
-          name=${gem%:*}
-          version=${gem#*:}
-          gem pristine $name --version $version || true
-        done
-      shell: bash
-
     - name: Build container
       if: steps.cache-sif.outputs.cache-hit != 'true'
       run: ./bin/build_container
@@ -57,4 +82,3 @@ runs:
     - name: Setup project
       run: ./bin/setup
       shell: bash
-