From de3a0402681eaa85d56eac3f03986ddb352c210d Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 16:57:11 -0400
Subject: [PATCH 01/48] integrated pmd into CI (#646)

---
 .github/workflows/pmd.yml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .github/workflows/pmd.yml

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
new file mode 100644
index 0000000000..961b25c6e0
--- /dev/null
+++ b/.github/workflows/pmd.yml
@@ -0,0 +1,21 @@
+name: PMD Analysis
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  pmd:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-java@v4
+        with:
+            distribution: 'temurin'
+            java-version: '11'
+      - uses: pmd/pmd-github-action@v2
+        id: pmd
+        with:
+            rulesets: 'ruleset.xml'
+            analyzeModifiedFilesOnly: true
+            createGitHubAnnotations: false
+            uploadSarifReport: true
+

From a1fe811848ceacf368455b012c13fa696260acde Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 17:24:47 -0400
Subject: [PATCH 02/48] create rulset file

---
 .github/workflows/ruleset.xml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 .github/workflows/ruleset.xml

diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
new file mode 100644
index 0000000000..7ab6044077
--- /dev/null
+++ b/.github/workflows/ruleset.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ruleset name="Fortran Files in src Directory"
+         xmlns="http://pmd.sourceforge.net/ruleset/2.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://pmd.sourceforge.net/ruleset/2.0.0
+         http://pmd.sourceforge.net/ruleset_2_0_0.xsd">
+    <description>
+        Ruleset to analyze only Fortran files within the src directory.
+    </description>
+
+    <!-- Only run on Fortran files in src/ directory and Python files in toolchain/ directory -->
+    <filepattern><MFC/>src/.*\.(f|fpp|for|f90|f95|f03|f08)$</filepattern>
+    <filepattern><MFC/>toolchain/.*\.(py)$</filepattern>
+
+</ruleset>
\ No newline at end of file

From 8defa9aaacf26040b9d0f770e8f156e1edf9684d Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 17:27:51 -0400
Subject: [PATCH 03/48] corrected directory

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 961b25c6e0..9340ba4c85 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -14,7 +14,7 @@ jobs:
       - uses: pmd/pmd-github-action@v2
         id: pmd
         with:
-            rulesets: 'ruleset.xml'
+            rulesets: '.github/workflows/ruleset.xml'
             analyzeModifiedFilesOnly: true
             createGitHubAnnotations: false
             uploadSarifReport: true

From 1fde2bc26dd5a7050ddf9b4d82510afe588e836a Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 17:31:37 -0400
Subject: [PATCH 04/48] changed ruleset pattern typo

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

diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
index 7ab6044077..46514c4406 100644
--- a/.github/workflows/ruleset.xml
+++ b/.github/workflows/ruleset.xml
@@ -9,7 +9,7 @@
     </description>
 
     <!-- Only run on Fortran files in src/ directory and Python files in toolchain/ directory -->
-    <filepattern><MFC/>src/.*\.(f|fpp|for|f90|f95|f03|f08)$</filepattern>
-    <filepattern><MFC/>toolchain/.*\.(py)$</filepattern>
+    <include-pattern>.*/src/.*\.(f|fpp|for|f90|f95|f03|f08)$</include-pattern>
+    <include-pattern>.*/toolchain/.*\.py$</include-pattern>
 
 </ruleset>
\ No newline at end of file

From 0332cf142b20e861902443faa30ddb4ea30bb3a0 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 17:35:59 -0400
Subject: [PATCH 05/48] added rules to python and fortran

---
 .github/workflows/ruleset.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
index 46514c4406..413db8992d 100644
--- a/.github/workflows/ruleset.xml
+++ b/.github/workflows/ruleset.xml
@@ -12,4 +12,13 @@
     <include-pattern>.*/src/.*\.(f|fpp|for|f90|f95|f03|f08)$</include-pattern>
     <include-pattern>.*/toolchain/.*\.py$</include-pattern>
 
+    <!-- For Python files -->
+    <rule ref="category/python/bestpractices.xml"/>
+    <rule ref="category/python/codestyle.xml"/>
+    <rule ref="category/python/design.xml"/>
+    <rule ref="category/python/errorprone.xml"/>
+
+    <!-- For Fortran files -->
+    <rule ref="category/fortran/bestpractices.xml"/>
+
 </ruleset>
\ No newline at end of file

From 9f46e719aa29643ad53d766e453f43e8ae809acd Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 17:53:34 -0400
Subject: [PATCH 06/48] ruleset for py

---
 .github/workflows/ruleset.xml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
index 413db8992d..8bc7d4d305 100644
--- a/.github/workflows/ruleset.xml
+++ b/.github/workflows/ruleset.xml
@@ -18,7 +18,4 @@
     <rule ref="category/python/design.xml"/>
     <rule ref="category/python/errorprone.xml"/>
 
-    <!-- For Fortran files -->
-    <rule ref="category/fortran/bestpractices.xml"/>
-
 </ruleset>
\ No newline at end of file

From 8c3fb0863c5ea749506961485e8831bac3c4efaf Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 17:55:42 -0400
Subject: [PATCH 07/48] individual rules

---
 .github/workflows/ruleset.xml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
index 8bc7d4d305..0c217b3437 100644
--- a/.github/workflows/ruleset.xml
+++ b/.github/workflows/ruleset.xml
@@ -12,10 +12,11 @@
     <include-pattern>.*/src/.*\.(f|fpp|for|f90|f95|f03|f08)$</include-pattern>
     <include-pattern>.*/toolchain/.*\.py$</include-pattern>
 
-    <!-- For Python files -->
-    <rule ref="category/python/bestpractices.xml"/>
-    <rule ref="category/python/codestyle.xml"/>
-    <rule ref="category/python/design.xml"/>
-    <rule ref="category/python/errorprone.xml"/>
+    <!-- Rules -->
+    <rule ref="EmptyIfStmt"/>
+    <rule ref="EmptyWhileStmt"/>
+    <rule ref="EmptyTryBlock"/>
+    <rule ref="EmptyFinallyBlock"/>
+    <rule ref="EmptySwitchStatements"/>
 
 </ruleset>
\ No newline at end of file

From cd8e2a5b280ea3dc66552b0b7506c6e28ec7c626 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 17:58:40 -0400
Subject: [PATCH 08/48] java rules - errorprone

---
 .github/workflows/ruleset.xml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
index 0c217b3437..6c1e646324 100644
--- a/.github/workflows/ruleset.xml
+++ b/.github/workflows/ruleset.xml
@@ -13,10 +13,6 @@
     <include-pattern>.*/toolchain/.*\.py$</include-pattern>
 
     <!-- Rules -->
-    <rule ref="EmptyIfStmt"/>
-    <rule ref="EmptyWhileStmt"/>
-    <rule ref="EmptyTryBlock"/>
-    <rule ref="EmptyFinallyBlock"/>
-    <rule ref="EmptySwitchStatements"/>
+    <rule ref="category/java/errorprone.xml/"/>
 
 </ruleset>
\ No newline at end of file

From 4db4277a0fabc631c067c719de150369f009bbf0 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 18:00:51 -0400
Subject: [PATCH 09/48] java rules

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

diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
index 6c1e646324..66ca166ad6 100644
--- a/.github/workflows/ruleset.xml
+++ b/.github/workflows/ruleset.xml
@@ -13,6 +13,6 @@
     <include-pattern>.*/toolchain/.*\.py$</include-pattern>
 
     <!-- Rules -->
-    <rule ref="category/java/errorprone.xml/"/>
+    <rule ref="category/java/errorprone.xml"/>
 
 </ruleset>
\ No newline at end of file

From d6d3bc865c69e7e6eae32ff4b09265cb9a10d30f Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 19:49:20 -0400
Subject: [PATCH 10/48] old school integration of PMD into workflow

---
 .github/workflows/pmd.yml     | 63 +++++++++++++++++++++++++++--------
 .github/workflows/ruleset.xml | 18 ----------
 2 files changed, 49 insertions(+), 32 deletions(-)
 delete mode 100644 .github/workflows/ruleset.xml

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 9340ba4c85..5b061705ad 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -3,19 +3,54 @@ name: PMD Analysis
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
-  pmd:
-    runs-on: ubuntu-latest
+  file-changes:
+    name: Detect File Changes
+    runs-on: 'ubuntu-latest'
+    outputs: 
+      checkall: ${{ steps.changes.outputs.checkall }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-java@v4
-        with:
-            distribution: 'temurin'
-            java-version: '11'
-      - uses: pmd/pmd-github-action@v2
-        id: pmd
-        with:
-            rulesets: '.github/workflows/ruleset.xml'
-            analyzeModifiedFilesOnly: true
-            createGitHubAnnotations: false
-            uploadSarifReport: true
+      - name: Clone
+        uses: actions/checkout@v4
+
+      - name: Detect Changes
+        uses: dorny/paths-filter@v3
+        id: changes
+        with: 
+          filters: ".github/file-filter.yml"
+    
+  pmd:
+      name: PMD Analysis
+      if: needs.file-changes.outputs.checkall == 'true'
+      needs: file-changes
+      runs-on: "ubuntu-latest"
+      env:
+          pr_everything: 0
+      steps:
+          - name: Clone - PR
+            uses: actions/checkout@v4
+            with:
+              path: pr
+
+          - name: Clone PMD
+            run: |
+              sudo apt update -y
+              sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
+              git clone https://github.com/pmd/pmd.git pmd
+              (cd pmd && git checkout pmd)
+
+          - name: Build PMD
+            run: |
+              (cd pmd && ./mvnw clean install -DskipTests> ../pmd.txt)
+          
+          - name: Running PMD
+            run: |
+              (cd pmd &&  ./pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
+              (cd pmd &&  ./pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
 
+          - name: Display PMD Reports
+            uses: actions/upload-artifact@v2
+            with:
+                name: pmd-reports
+                path: |
+                    pmd-fort.txt
+                    pmd-py.txt
\ No newline at end of file
diff --git a/.github/workflows/ruleset.xml b/.github/workflows/ruleset.xml
deleted file mode 100644
index 66ca166ad6..0000000000
--- a/.github/workflows/ruleset.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ruleset name="Fortran Files in src Directory"
-         xmlns="http://pmd.sourceforge.net/ruleset/2.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://pmd.sourceforge.net/ruleset/2.0.0
-         http://pmd.sourceforge.net/ruleset_2_0_0.xsd">
-    <description>
-        Ruleset to analyze only Fortran files within the src directory.
-    </description>
-
-    <!-- Only run on Fortran files in src/ directory and Python files in toolchain/ directory -->
-    <include-pattern>.*/src/.*\.(f|fpp|for|f90|f95|f03|f08)$</include-pattern>
-    <include-pattern>.*/toolchain/.*\.py$</include-pattern>
-
-    <!-- Rules -->
-    <rule ref="category/java/errorprone.xml"/>
-
-</ruleset>
\ No newline at end of file

From 54a6fc9c0eb2ddba82ebc654fe45a3d5c6d638a7 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 19:55:28 -0400
Subject: [PATCH 11/48] removed Detect File Changes

---
 .github/workflows/pmd.yml | 19 +------------------
 1 file changed, 1 insertion(+), 18 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 5b061705ad..4d65511cd1 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -2,26 +2,9 @@ name: PMD Analysis
 
 on: [push, pull_request, workflow_dispatch]
 
-jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-    
+jobs:    
   pmd:
       name: PMD Analysis
-      if: needs.file-changes.outputs.checkall == 'true'
-      needs: file-changes
       runs-on: "ubuntu-latest"
       env:
           pr_everything: 0

From 515c32a623c294ad8aedf52c857f61897132915c Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 20:01:14 -0400
Subject: [PATCH 12/48] changed to cat to display reports

---
 .github/workflows/pmd.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 4d65511cd1..f293612b59 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -31,9 +31,8 @@ jobs:
               (cd pmd &&  ./pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
 
           - name: Display PMD Reports
-            uses: actions/upload-artifact@v2
-            with:
-                name: pmd-reports
-                path: |
-                    pmd-fort.txt
-                    pmd-py.txt
\ No newline at end of file
+            run: |
+              echo "PMD Fortran Report:"
+              cat /pmd/pmd-fort.txt
+              echo "PMD Python Report:"
+              cat /pmd/pmd-py.txt
\ No newline at end of file

From 4f4134ae11443db1ce959aab140386eea23d34ae Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 20:36:01 -0400
Subject: [PATCH 13/48] added java compiler as dependency

---
 .github/workflows/pmd.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index f293612b59..96bdb52b27 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -1,4 +1,4 @@
-name: PMD Analysis
+name: PMD
 
 on: [push, pull_request, workflow_dispatch]
 
@@ -17,22 +17,23 @@ jobs:
           - name: Clone PMD
             run: |
               sudo apt update -y
-              sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
+              sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev maven
+              sudo apt install -y default-jdk
               git clone https://github.com/pmd/pmd.git pmd
-              (cd pmd && git checkout pmd)
+              (cd pmd && git checkout master)
 
           - name: Build PMD
             run: |
-              (cd pmd && ./mvnw clean install -DskipTests> ../pmd.txt)
+              (cd pmd && mvn clean install -DskipTests> ../pmd.txt)
           
           - name: Running PMD
             run: |
-              (cd pmd &&  ./pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
-              (cd pmd &&  ./pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
+              (cd pmd &&  pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
+              (cd pmd &&  pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
 
           - name: Display PMD Reports
             run: |
               echo "PMD Fortran Report:"
-              cat /pmd/pmd-fort.txt
+              cat pmd-fort.txt
               echo "PMD Python Report:"
-              cat /pmd/pmd-py.txt
\ No newline at end of file
+              cat pmd-py.txt
\ No newline at end of file

From b3ae8fa604a5ecb58fa43a852f1e8f4673a1e53b Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 20:39:19 -0400
Subject: [PATCH 14/48] removed something

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 96bdb52b27..27c6ee9311 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -20,7 +20,7 @@ jobs:
               sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev maven
               sudo apt install -y default-jdk
               git clone https://github.com/pmd/pmd.git pmd
-              (cd pmd && git checkout master)
+              (cd pmd && git checkout)
 
           - name: Build PMD
             run: |

From 085eaa5e81a38b9b7feed9e3b1043f3ec10c28c0 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Thu, 12 Jun 2025 20:52:33 -0400
Subject: [PATCH 15/48] just checking syntax

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 27c6ee9311..2f6f45ade6 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -28,8 +28,8 @@ jobs:
           
           - name: Running PMD
             run: |
-              (cd pmd &&  pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
-              (cd pmd &&  pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
+              (cd pmd &&  ./pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
+              (cd pmd &&  ./pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
 
           - name: Display PMD Reports
             run: |

From e3626f6967922714fc3493d36c4efda676256d05 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Fri, 13 Jun 2025 16:03:08 -0400
Subject: [PATCH 16/48] set env var pmd=/pmd/bin/pmd

---
 .github/workflows/pmd.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 2f6f45ade6..1bc59b4354 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -25,11 +25,12 @@ jobs:
           - name: Build PMD
             run: |
               (cd pmd && mvn clean install -DskipTests> ../pmd.txt)
+              alias pmd=/pmd/bin/pmd
           
           - name: Running PMD
             run: |
-              (cd pmd &&  ./pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
-              (cd pmd &&  ./pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
+              (cd pmd &&  $pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
+              (cd pmd &&  $pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
 
           - name: Display PMD Reports
             run: |

From f022a85eb2110266f68d1b4c518c1369e2182dfe Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Fri, 13 Jun 2025 16:06:52 -0400
Subject: [PATCH 17/48] quick syntax correction

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 1bc59b4354..2970a32a56 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -29,8 +29,8 @@ jobs:
           
           - name: Running PMD
             run: |
-              (cd pmd &&  $pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
-              (cd pmd &&  $pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
+              (cd pmd && pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
+              (cd pmd && pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
 
           - name: Display PMD Reports
             run: |

From 4fdb0c33bda788751587df4bd227b0c166c4998a Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Fri, 13 Jun 2025 16:22:04 -0400
Subject: [PATCH 18/48] made PMD_COMMAND globally recognized

---
 .github/workflows/pmd.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 2970a32a56..99d24494fa 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -25,12 +25,12 @@ jobs:
           - name: Build PMD
             run: |
               (cd pmd && mvn clean install -DskipTests> ../pmd.txt)
-              alias pmd=/pmd/bin/pmd
-          
+              export PMD_COMMAND="$(pwd)/pmd/bin/pmd"
+
           - name: Running PMD
             run: |
-              (cd pmd && pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt)
-              (cd pmd && pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt)
+              $PMD_COMMAND cpd -l fortran pr/src/*  > ../pmd-fort.txt
+              $PMD_COMMAND cpd -l python pr/toolchain/*  > ../pmd-py.txt
 
           - name: Display PMD Reports
             run: |

From c7c1bdbfdb9b533d268fcafb20721782b72a89dc Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Fri, 13 Jun 2025 16:38:26 -0400
Subject: [PATCH 19/48] corrected package path

---
 .github/workflows/pmd.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 99d24494fa..3b3520c4a5 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -25,12 +25,12 @@ jobs:
           - name: Build PMD
             run: |
               (cd pmd && mvn clean install -DskipTests> ../pmd.txt)
-              export PMD_COMMAND="$(pwd)/pmd/bin/pmd"
+              export PATH=$PATH:$(pwd)/bin/pmd
 
           - name: Running PMD
             run: |
-              $PMD_COMMAND cpd -l fortran pr/src/*  > ../pmd-fort.txt
-              $PMD_COMMAND cpd -l python pr/toolchain/*  > ../pmd-py.txt
+              pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt
+              pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt
 
           - name: Display PMD Reports
             run: |

From 393d69b41580bf8726042f45268105136da875e4 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Fri, 13 Jun 2025 16:52:33 -0400
Subject: [PATCH 20/48] moved alias command under Running PMD

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 3b3520c4a5..386dabfbfc 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -25,10 +25,10 @@ jobs:
           - name: Build PMD
             run: |
               (cd pmd && mvn clean install -DskipTests> ../pmd.txt)
-              export PATH=$PATH:$(pwd)/bin/pmd
 
           - name: Running PMD
             run: |
+              alias pmd="$HOME/pmd/bin/pmd"
               pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt
               pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt
 

From 74486098c780acebdfcb8472f75425ab453c7a2e Mon Sep 17 00:00:00 2001
From: mohdsaid497566 <mohdsaid497566@gmail.com>
Date: Mon, 16 Jun 2025 16:44:07 -0400
Subject: [PATCH 21/48] comments removal

---
 .github/workflows/pmd.yml | 45 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 44 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 386dabfbfc..e7e971ad0f 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -29,7 +29,50 @@ jobs:
           - name: Running PMD
             run: |
               alias pmd="$HOME/pmd/bin/pmd"
-              pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt
+
+              SOURCE_DIR="${1:-pr/src}"
+              total_files=$(find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) | wc -l)
+              processed=0
+
+              find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) -print0 | 
+              while IFS= read -r -d $'\0' file; do
+                  processed=$((processed + 1))
+                  echo -e "[$processed/$total_files] Processing ${file}..."
+                  
+                  # Create a temporary file with same permissions as original
+                  TMP_FILE=$(mktemp)
+                  if [ $? -ne 0 ]; then
+                      echo -e "Failed to create temporary file for $file, skipping"
+                      continue
+                  fi
+                  
+                  # Copy permissions from original file
+                  chmod --reference="$file" "$TMP_FILE"
+                  
+                  # More comprehensive sed command to handle different Fortran comment styles:
+                  # 1. Replace lines that are entirely comments with an empty line:
+                  #    - Lines starting with '!' (free form comments)
+                  #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
+                  # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
+                  # 3. Preserve strings containing '!' characters
+                  sed -E \
+                      -e '/^\s*!/s/.*//' \
+                      -e '/^[cC*dD]/s/.*//' \
+                      -e '/^[ \t]*[cC*dD]/s/.*//' \
+                      -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
+                      "$file" > "$TMP_FILE"
+                  
+                  # Check if file was actually modified before replacing
+                  if cmp -s "$file" "$TMP_FILE"; then
+                      echo -e "No changes needed for $file"
+                      rm "$TMP_FILE"
+                  else
+                      # Overwrite the original file with the processed content
+                      mv "$TMP_FILE" "$file"
+                      echo -e "Successfully processed $file"
+                  fi
+              done
+              pmd cpd -l fortran /*  > ../pmd-fort.txt
               pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt
 
           - name: Display PMD Reports

From 36fb29e32ad900c1b99162124049514775a76e84 Mon Sep 17 00:00:00 2001
From: mohdsaid497566 <mohdsaid497566@gmail.com>
Date: Mon, 16 Jun 2025 16:50:07 -0400
Subject: [PATCH 22/48] comments removal 2

---
 .github/workflows/pmd.yml | 48 ++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index e7e971ad0f..2f295d2914 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -1,36 +1,36 @@
-name: PMD
+name: Source DRYness
 
 on: [push, pull_request, workflow_dispatch]
 
 jobs:    
   pmd:
-      name: PMD Analysis
+      name: PMD
       runs-on: "ubuntu-latest"
       env:
           pr_everything: 0
       steps:
           - name: Clone - PR
             uses: actions/checkout@v4
-            with:
-              path: pr
-
-          - name: Clone PMD
-            run: |
-              sudo apt update -y
-              sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev maven
-              sudo apt install -y default-jdk
-              git clone https://github.com/pmd/pmd.git pmd
-              (cd pmd && git checkout)
 
-          - name: Build PMD
-            run: |
-              (cd pmd && mvn clean install -DskipTests> ../pmd.txt)
+          - name: Set up Java
+            uses: actions/setup-java@v4
+            with:
+              distribution: temurin
+              java-version: '17'
 
-          - name: Running PMD
+          - name: Run CPD for Fortran
+            continue-on-error: true
             run: |
-              alias pmd="$HOME/pmd/bin/pmd"
+              # Get latest PMD version from GitHub API
+              PMD_VERSION=$(curl -s https://api.github.com/repos/pmd/pmd/releases/latest | grep '"tag_name":' | cut -d'"' -f4 | sed 's/pmd_releases\///')
+              echo "Using PMD version: $PMD_VERSION"
 
-              SOURCE_DIR="${1:-pr/src}"
+              curl -sSL -o pmd.zip \
+                "https://github.com/pmd/pmd/releases/download/pmd_releases/${PMD_VERSION}/pmd-dist-${PMD_VERSION}-bin.zip"
+              unzip -q pmd.zip
+              PMD_HOME="pmd-bin-${PMD_VERSION}"
+          
+                            SOURCE_DIR="${1:-pr/src}"
               total_files=$(find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) | wc -l)
               processed=0
 
@@ -72,12 +72,8 @@ jobs:
                       echo -e "Successfully processed $file"
                   fi
               done
-              pmd cpd -l fortran /*  > ../pmd-fort.txt
-              pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt
 
-          - name: Display PMD Reports
-            run: |
-              echo "PMD Fortran Report:"
-              cat pmd-fort.txt
-              echo "PMD Python Report:"
-              cat pmd-py.txt
\ No newline at end of file
+              "${PMD_HOME}/bin/pmd" cpd \
+                --dir src \
+                --language fortran \
+                --minimum-tokens=40
\ No newline at end of file

From 76352ddbebae3d53f58d7e14782e77f519b35ff9 Mon Sep 17 00:00:00 2001
From: mohdsaid497566 <mohdsaid497566@gmail.com>
Date: Mon, 16 Jun 2025 16:52:50 -0400
Subject: [PATCH 23/48] comments removal 3

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 2f295d2914..da7f9e452f 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -30,7 +30,7 @@ jobs:
               unzip -q pmd.zip
               PMD_HOME="pmd-bin-${PMD_VERSION}"
           
-                            SOURCE_DIR="${1:-pr/src}"
+              SOURCE_DIR="${1:-src}"
               total_files=$(find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) | wc -l)
               processed=0
 

From 0aa7abee6b5f85d7748ecddd03e35650058ca783 Mon Sep 17 00:00:00 2001
From: mohdsaid497566 <mohdsaid497566@gmail.com>
Date: Mon, 16 Jun 2025 18:48:56 -0400
Subject: [PATCH 24/48] reduced number of tokens

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index da7f9e452f..fb35db7aa1 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -76,4 +76,4 @@ jobs:
               "${PMD_HOME}/bin/pmd" cpd \
                 --dir src \
                 --language fortran \
-                --minimum-tokens=40
\ No newline at end of file
+                --minimum-tokens=10

From 52aeefce4186d844f0aa0227772da3575b51ac4f Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:17:29 -0400
Subject: [PATCH 25/48] Update pmd.yml

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index ef209bc0d4..842ebb3475 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -76,4 +76,6 @@ jobs:
               "${PMD_HOME}/bin/pmd" cpd \
                 --dir src \
                 --language fortran \
-                --minimum-tokens=10
\ No newline at end of file
+                --minimum-tokens=20 \
+                --no-fail-on-violation \
+                --no-fail-on-error

From 037c2e6449be9f176dee1b3a26605cc3c594782a Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:21:12 -0400
Subject: [PATCH 26/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 842ebb3475..b3cc99f341 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,6 +55,8 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
+                  sed -E ' :a /[[:space:]]*&[[:space:]]*$/ { N; s/[[:space:]]*&[[:space:]]*\n[[:space:]]*/ /; ba } s/^[[:space:]]*!\$acc[[:space:]]*/!$acc / :b s/[[:space:]]+!\$acc[[:space:]]*/ /g tb ' "$file" > "$file"
+                  
                   sed -E \
                       -e '/^\s*!/s/.*//' \
                       -e '/^[cC*dD]/s/.*//' \

From 26f3228b013135df33f5ccc90b24c4f2dab40cf0 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:24:37 -0400
Subject: [PATCH 27/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index b3cc99f341..9994521d43 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,15 +55,15 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
-                  sed -E ' :a /[[:space:]]*&[[:space:]]*$/ { N; s/[[:space:]]*&[[:space:]]*\n[[:space:]]*/ /; ba } s/^[[:space:]]*!\$acc[[:space:]]*/!$acc / :b s/[[:space:]]+!\$acc[[:space:]]*/ /g tb ' "$file" > "$file"
+                  TMP_FILE=$(mktemp)
+                  sed -E ' :a /[[:space:]]*&[[:space:]]*$/ { N; s/[[:space:]]*&[[:space:]]*\n[[:space:]]*/ /; ba } s/^[[:space:]]*!\$acc[[:space:]]*/!$acc / :b s/[[:space:]]+!\$acc[[:space:]]*/ /g tb ' "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"
                   
                   sed -E \
                       -e '/^\s*!/s/.*//' \
                       -e '/^[cC*dD]/s/.*//' \
                       -e '/^[ \t]*[cC*dD]/s/.*//' \
                       -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
-                      "$file" > "$TMP_FILE"
-                  
+                      "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"
                   # Check if file was actually modified before replacing
                   if cmp -s "$file" "$TMP_FILE"; then
                       echo -e "No changes needed for $file"

From 9605a29132d41486c4c91c4e2b0e13706b478756 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:25:53 -0400
Subject: [PATCH 28/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 9994521d43..a8c5a1007b 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -56,8 +56,7 @@ jobs:
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
                   TMP_FILE=$(mktemp)
-                  sed -E ' :a /[[:space:]]*&[[:space:]]*$/ { N; s/[[:space:]]*&[[:space:]]*\n[[:space:]]*/ /; ba } s/^[[:space:]]*!\$acc[[:space:]]*/!$acc / :b s/[[:space:]]+!\$acc[[:space:]]*/ /g tb ' "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"
-                  
+                  sed -E ' :a /[[:space:]]*&[[:space:]]*$/ { N; s/[[:space:]]*&[[:space:]]*\n[[:space:]]*/ /; ba } s/^[[:space:]]*!\$acc[[:space:]]*/!$acc / :b s/[[:space:]]+!\$acc[[:space:]]*/ /g tb ' "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"                  
                   sed -E \
                       -e '/^\s*!/s/.*//' \
                       -e '/^[cC*dD]/s/.*//' \

From 3c01cfa8db4ba8de21af00f5ca73097951e8401e Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:30:02 -0400
Subject: [PATCH 29/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index a8c5a1007b..057e8014fe 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,8 +55,20 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
-                  TMP_FILE=$(mktemp)
-                  sed -E ' :a /[[:space:]]*&[[:space:]]*$/ { N; s/[[:space:]]*&[[:space:]]*\n[[:space:]]*/ /; ba } s/^[[:space:]]*!\$acc[[:space:]]*/!$acc / :b s/[[:space:]]+!\$acc[[:space:]]*/ /g tb ' "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"                  
+                  sed -E '
+                    :a                      # ① label for looping
+                    /&$/ {                  # ② if the *current* line ends with “&”
+                          N                 #    read the *next* line into the pattern space
+                          s/&[[:space:]]*\n[[:space:]]*&/ /   # ③ delete the trailing “&”,
+                                                              #    the following newline, the
+                                                              #    leading “&” on the next line,
+                                                              #    and join them with one space
+                          ba                # ④ repeat until the next line no longer starts
+                                            #    with “&” (handles runs of many “&” lines)
+                    }
+                    s/&//g                  # ⑤ finally strip any stray “&” left in the file
+                  ' "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"
+                  
                   sed -E \
                       -e '/^\s*!/s/.*//' \
                       -e '/^[cC*dD]/s/.*//' \

From d2fff04672c09f129d276a4cf3047c730c4f6c20 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:32:24 -0400
Subject: [PATCH 30/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 057e8014fe..50f995e47a 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -56,25 +56,21 @@ jobs:
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
                   sed -E '
-                    :a                      # ① label for looping
-                    /&$/ {                  # ② if the *current* line ends with “&”
-                          N                 #    read the *next* line into the pattern space
-                          s/&[[:space:]]*\n[[:space:]]*&/ /   # ③ delete the trailing “&”,
-                                                              #    the following newline, the
-                                                              #    leading “&” on the next line,
-                                                              #    and join them with one space
-                          ba                # ④ repeat until the next line no longer starts
-                                            #    with “&” (handles runs of many “&” lines)
+                    :a
+                    /&$/ {
+                          N
+                          s/&[[:space:]]*\n[[:space:]]*&/ /
+                          ba
                     }
-                    s/&//g                  # ⑤ finally strip any stray “&” left in the file
-                  ' "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"
-                  
+                    s/&//g
+                  ' "$file" | \
                   sed -E \
                       -e '/^\s*!/s/.*//' \
                       -e '/^[cC*dD]/s/.*//' \
                       -e '/^[ \t]*[cC*dD]/s/.*//' \
                       -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
-                      "$file" > "$TMP_FILE" && mv "$TMP_FILE" "$file"
+                      > "$TMP_FILE"
+                      
                   # Check if file was actually modified before replacing
                   if cmp -s "$file" "$TMP_FILE"; then
                       echo -e "No changes needed for $file"

From 3bd04f3e553e091b000c7ce586215db93b7f733d Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Tue, 17 Jun 2025 15:40:17 -0400
Subject: [PATCH 31/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 36 +++++++++++++++++++++---------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 50f995e47a..2a160f7d76 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,21 +55,27 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
-                  sed -E '
-                    :a
-                    /&$/ {
-                          N
-                          s/&[[:space:]]*\n[[:space:]]*&/ /
-                          ba
-                    }
-                    s/&//g
-                  ' "$file" | \
-                  sed -E \
-                      -e '/^\s*!/s/.*//' \
-                      -e '/^[cC*dD]/s/.*//' \
-                      -e '/^[ \t]*[cC*dD]/s/.*//' \
-                      -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
-                      > "$TMP_FILE"
+                  sed -E '
+                    # First pass: Remove comments
+                    # Remove lines that are entirely comments
+                    /^\s*!/s/.*//
+                    /^[cC*dD]/s/.*//
+                    /^[ \t]*[cC*dD]/s/.*//
+                    # Remove end-of-line comments, preserving strings
+                    s/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/
+
+                    # Second pass: Handle line continuations
+                    :a
+                    # If a line ends with '&' (possibly with trailing whitespace), read the next line
+                    /&\s*$/ {
+                          N
+                          # Replace '&' at the end of the first line, newline, and potential leading '&' on the second line with a single space
+                          s/&\s*\n\s*&/\ /
+                          ba # Loop back to 'a' to handle multiple continuations
+                    }
+                    # If a line ends with '&' but is the last line or next line doesn't start with '&', remove the trailing '&'
+                    s/&\s*$//
+                  ' "$file" > "$TMP_FILE"
                       
                   # Check if file was actually modified before replacing
                   if cmp -s "$file" "$TMP_FILE"; then

From d4b77fb21a65ca2746204a68af0faa0bb7896cdf Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Tue, 17 Jun 2025 16:13:02 -0400
Subject: [PATCH 32/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 36 +++++++++++++++---------------------
 1 file changed, 15 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 2a160f7d76..50f995e47a 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,27 +55,21 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
-                  sed -E '
-                    # First pass: Remove comments
-                    # Remove lines that are entirely comments
-                    /^\s*!/s/.*//
-                    /^[cC*dD]/s/.*//
-                    /^[ \t]*[cC*dD]/s/.*//
-                    # Remove end-of-line comments, preserving strings
-                    s/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/
-
-                    # Second pass: Handle line continuations
-                    :a
-                    # If a line ends with '&' (possibly with trailing whitespace), read the next line
-                    /&\s*$/ {
-                          N
-                          # Replace '&' at the end of the first line, newline, and potential leading '&' on the second line with a single space
-                          s/&\s*\n\s*&/\ /
-                          ba # Loop back to 'a' to handle multiple continuations
-                    }
-                    # If a line ends with '&' but is the last line or next line doesn't start with '&', remove the trailing '&'
-                    s/&\s*$//
-                  ' "$file" > "$TMP_FILE"
+                  sed -E '
+                    :a
+                    /&$/ {
+                          N
+                          s/&[[:space:]]*\n[[:space:]]*&/ /
+                          ba
+                    }
+                    s/&//g
+                  ' "$file" | \
+                  sed -E \
+                      -e '/^\s*!/s/.*//' \
+                      -e '/^[cC*dD]/s/.*//' \
+                      -e '/^[ \t]*[cC*dD]/s/.*//' \
+                      -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
+                      > "$TMP_FILE"
                       
                   # Check if file was actually modified before replacing
                   if cmp -s "$file" "$TMP_FILE"; then

From 502ab2cf52094c8871b3a183a4da61a9a87502d3 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Tue, 17 Jun 2025 16:29:16 -0400
Subject: [PATCH 33/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 50f995e47a..a157e72344 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,22 +55,26 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
-                  sed -E '
-                    :a
-                    /&$/ {
-                          N
-                          s/&[[:space:]]*\n[[:space:]]*&/ /
-                          ba
-                    }
-                    s/&//g
-                  ' "$file" | \
                   sed -E \
                       -e '/^\s*!/s/.*//' \
                       -e '/^[cC*dD]/s/.*//' \
                       -e '/^[ \t]*[cC*dD]/s/.*//' \
                       -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
-                      > "$TMP_FILE"
-                      
+                      "$file" | \
+                  sed -E '
+                      :a
+                      /\s*(\S+)\s*\n\s*([+*/=()-])/ {
+                          N
+                          s/([+*/=()-])\s*\n\s*([+*/=()-])/\1\2/
+                          s/\s*\n\s*/ /
+                          ba
+                      }
+                      /\s*\n\s*\+/ {
+                          N
+                          s/\s*\n\s*\+/ +/
+                          ba
+                      }
+                  ' > "$TMP_FILE"                      
                   # Check if file was actually modified before replacing
                   if cmp -s "$file" "$TMP_FILE"; then
                       echo -e "No changes needed for $file"

From 31b873c8876d51bde82404afee2d6601ace340de Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Tue, 17 Jun 2025 16:45:30 -0400
Subject: [PATCH 34/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 43 ++++++++++++++++++++++-----------------
 1 file changed, 24 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index a157e72344..90f3503eba 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,26 +55,31 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
-                  sed -E \
-                      -e '/^\s*!/s/.*//' \
-                      -e '/^[cC*dD]/s/.*//' \
-                      -e '/^[ \t]*[cC*dD]/s/.*//' \
-                      -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
-                      "$file" | \
                   sed -E '
-                      :a
-                      /\s*(\S+)\s*\n\s*([+*/=()-])/ {
-                          N
-                          s/([+*/=()-])\s*\n\s*([+*/=()-])/\1\2/
-                          s/\s*\n\s*/ /
-                          ba
-                      }
-                      /\s*\n\s*\+/ {
-                          N
-                          s/\s*\n\s*\+/ +/
-                          ba
-                      }
-                  ' > "$TMP_FILE"                      
+                    # Label for loop to handle multi-line continuations
+                    :a
+                    # If line ends with '&' (continuation character), append next line
+                    /&$/ {
+                        N
+                        # Replace '&' followed by newline, optional spaces, and another '&' with a single space
+                        s/&[[:space:]]*\n[[:space:]]*&/ /
+                        ba # Go back to label 'a' to process more continuations if present
+                    }
+                    # After handling all continuations, remove any remaining '&' characters
+                    s/&//g
+                    # Remove lines that are entirely comments:
+                    # - Lines starting with '!' (free form)
+                    /^\s*!/s/.*//
+                    # - Lines starting with 'c', 'C', '*', 'd', 'D' (fixed form, column 1)
+                    /^[cC*dD]/s/.*//
+                    # - Lines starting with space/tab and then 'c', 'C', '*', 'd', 'D' (fixed form with leading space)
+                    /^[ \t]*[cC*dD]/s/.*//
+                    
+                    # Remove end-of-line comments, preserving '!' inside strings.
+                    # This pattern looks for '!' not preceded by an odd number of quotes.
+                    # It captures everything before the '!' as group 1 and replaces the whole line with group 1.
+                    s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
+                  ' "$file" > "$TMP_FILE"
                   # Check if file was actually modified before replacing
                   if cmp -s "$file" "$TMP_FILE"; then
                       echo -e "No changes needed for $file"

From 8cf02c0789b707effb09f935d39d2c0861903866 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Tue, 17 Jun 2025 16:47:18 -0400
Subject: [PATCH 35/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 90f3503eba..55b6a1b6fc 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -56,28 +56,16 @@ jobs:
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters
                   sed -E '
-                    # Label for loop to handle multi-line continuations
                     :a
-                    # If line ends with '&' (continuation character), append next line
                     /&$/ {
                         N
-                        # Replace '&' followed by newline, optional spaces, and another '&' with a single space
                         s/&[[:space:]]*\n[[:space:]]*&/ /
-                        ba # Go back to label 'a' to process more continuations if present
+                        ba
                     }
-                    # After handling all continuations, remove any remaining '&' characters
                     s/&//g
-                    # Remove lines that are entirely comments:
-                    # - Lines starting with '!' (free form)
                     /^\s*!/s/.*//
-                    # - Lines starting with 'c', 'C', '*', 'd', 'D' (fixed form, column 1)
                     /^[cC*dD]/s/.*//
-                    # - Lines starting with space/tab and then 'c', 'C', '*', 'd', 'D' (fixed form with leading space)
                     /^[ \t]*[cC*dD]/s/.*//
-                    
-                    # Remove end-of-line comments, preserving '!' inside strings.
-                    # This pattern looks for '!' not preceded by an odd number of quotes.
-                    # It captures everything before the '!' as group 1 and replaces the whole line with group 1.
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"
                   # Check if file was actually modified before replacing

From 10082468cc5e27f0deab38e85fb5403e7764fd16 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Tue, 17 Jun 2025 16:53:04 -0400
Subject: [PATCH 36/48] Update pmd.yml

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 55b6a1b6fc..472a69754a 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -54,8 +54,8 @@ jobs:
                   #    - Lines starting with '!' (free form comments)
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
-                  # 3. Preserve strings containing '!' characters
-                  sed -E '
+                  # 3. Preserve strings containing '!' characters                  
+                    sed -E '
                     :a
                     /&$/ {
                         N

From cd8f90823112211c403d62fabfe1d4baa1ef78ed Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Tue, 17 Jun 2025 16:56:52 -0400
Subject: [PATCH 37/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 472a69754a..245c1ffb0a 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -55,20 +55,25 @@ jobs:
                   #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters                  
-                    sed -E '
+                  sed -E '
                     :a
                     /&$/ {
                         N
                         s/&[[:space:]]*\n[[:space:]]*&/ /
                         ba
                     }
+                    /^[[:space:]]{5}[^[:space:]]/ {
+                        N
+                        s/\n([[:space:]]{5}[^[:space:]])/\1/
+                        ba
+                    }
                     s/&//g
                     /^\s*!/s/.*//
                     /^[cC*dD]/s/.*//
                     /^[ \t]*[cC*dD]/s/.*//
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"
-                  # Check if file was actually modified before replacing
+                  
                   if cmp -s "$file" "$TMP_FILE"; then
                       echo -e "No changes needed for $file"
                       rm "$TMP_FILE"

From ae4cbf5db1b2d27425d5e8d786f4516f98417e48 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Tue, 17 Jun 2025 18:00:11 -0400
Subject: [PATCH 38/48] more cleanup

---
 .github/workflows/pmd.yml | 48 +++++++++++++++++++++++++++------------
 1 file changed, 34 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 245c1ffb0a..cd23acf85c 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -56,24 +56,44 @@ jobs:
                   # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
                   # 3. Preserve strings containing '!' characters                  
                   sed -E '
-                    :a
-                    /&$/ {
-                        N
-                        s/&[[:space:]]*\n[[:space:]]*&/ /
-                        ba
+                    # First handle & continuation style (modern Fortran)
+                    :ampersand_loop
+                    /&[[:space:]]*$/ {
+                      N
+                      s/&[[:space:]]*\n[[:space:]]*(&)?/ /g
+                      tampersand_loop
                     }
-                    /^[[:space:]]{5}[^[:space:]]/ {
-                        N
-                        s/\n([[:space:]]{5}[^[:space:]])/\1/
-                        ba
+                    
+                    # Handle fixed-form continuation (column 6 indicator)
+                    :fixed_form_loop
+                    /^[[:space:]]{0,5}[^[:space:]!&]/ {
+                      N
+                      s/\n[[:space:]]{5}[^[:space:]]/ /g
+                      tfixed_form_loop
                     }
+                    
+                    # Remove any remaining continuation markers
                     s/&//g
-                    /^\s*!/s/.*//
-                    /^[cC*dD]/s/.*//
-                    /^[ \t]*[cC*dD]/s/.*//
+                    
+                    # Normalize spacing - replace multiple spaces with single space
+                    s/[[:space:]]{2,}/ /g
+                    
+                    # Remove spaces around mathematical operators
+                    s/[[:space:]]*\*[[:space:]]*/*/g
+                    s/[[:space:]]*\+[[:space:]]*/+/g
+                    s/[[:space:]]*-[[:space:]]*/-/g
+                    s/[[:space:]]*\/[[:space:]]*/\//g
+                    s/[[:space:]]*\*\*[[:space:]]*/\*\*/g
+                    
+                    # Remove full-line comments
+                    /^\s*!/d
+                    /^[cC*dD]/d
+                    /^[ \t]*[cC*dD]/d
+                    
+                    # Remove end-of-line comments, preserving quoted strings
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"
-                  
+                
                   if cmp -s "$file" "$TMP_FILE"; then
                       echo -e "No changes needed for $file"
                       rm "$TMP_FILE"
@@ -87,6 +107,6 @@ jobs:
               "${PMD_HOME}/bin/pmd" cpd \
                 --dir src \
                 --language fortran \
-                --minimum-tokens=20 \
+                --minimum-tokens=50 \
                 --no-fail-on-violation \
                 --no-fail-on-error

From 27c9932169dfb1bf5e8e00f21bf418a080b215e4 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Tue, 17 Jun 2025 18:00:29 -0400
Subject: [PATCH 39/48] tokens=20

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index cd23acf85c..0b1650313a 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -107,6 +107,6 @@ jobs:
               "${PMD_HOME}/bin/pmd" cpd \
                 --dir src \
                 --language fortran \
-                --minimum-tokens=50 \
+                --minimum-tokens=20 \
                 --no-fail-on-violation \
                 --no-fail-on-error

From 3c0682d91a17f79620b6d701f68e73b6f5cf39e6 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Tue, 17 Jun 2025 18:41:42 -0400
Subject: [PATCH 40/48] strip out majority of spaces

---
 .github/workflows/pmd.yml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 0b1650313a..5ef99ad7d3 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -85,6 +85,27 @@ jobs:
                     s/[[:space:]]*\/[[:space:]]*/\//g
                     s/[[:space:]]*\*\*[[:space:]]*/\*\*/g
                     
+                    # Remove spaces in common Fortran constructs (array indexing, function calls)
+                    s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*,/(\1,/g      # First argument
+                    s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*,/,\1,/g       # Middle arguments
+                    s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/,\1)/g      # Last argument
+                    s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/(\1)/g     # Single argument
+                    
+                    # Remove spaces around brackets and parentheses
+                    s/\[[[:space:]]*/</g
+                    s/\[[[:space:]]*/>/g
+                    s/\[[[:space:]]*/</g
+                    s/[[:space:]]*\]/]/g
+                    s/\([[:space:]]*/(/g
+                    s/[[:space:]]*\)/)/g
+
+                    # Remove spaces around comparison operators
+                    s/[[:space:]]*<=[[:space:]]*/</g
+                    s/[[:space:]]*>=[[:space:]]*/>/g
+                    s/[[:space:]]*<[[:space:]]*/</g
+                    s/[[:space:]]*>[[:space:]]*/>/g
+                    s/[[:space:]]*==[[:space:]]*/==/g
+
                     # Remove full-line comments
                     /^\s*!/d
                     /^[cC*dD]/d

From d5f882e6bfc3173c73b883bdf6f195e3ed681057 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Wed, 18 Jun 2025 10:43:56 -0400
Subject: [PATCH 41/48] Update pmd.yml

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 5ef99ad7d3..28e9257de4 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -110,7 +110,9 @@ jobs:
                     /^\s*!/d
                     /^[cC*dD]/d
                     /^[ \t]*[cC*dD]/d
-                    
+                    /^[Cc*]/d
+                     /^[[:blank:]]*!/
+
                     # Remove end-of-line comments, preserving quoted strings
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"

From 0806ba9f6afedd5830f065b0fdaeecd8bb8a9318 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Wed, 18 Jun 2025 10:49:45 -0400
Subject: [PATCH 42/48] Update pmd.yml

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

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 28e9257de4..8129b8c0ea 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -107,12 +107,7 @@ jobs:
                     s/[[:space:]]*==[[:space:]]*/==/g
 
                     # Remove full-line comments
-                    /^\s*!/d
-                    /^[cC*dD]/d
-                    /^[ \t]*[cC*dD]/d
-                    /^[Cc*]/d
-                     /^[[:blank:]]*!/
-
+                    /^[[:space:]]*[!cC*dD]/d
                     # Remove end-of-line comments, preserving quoted strings
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"

From 972ae380cc22d4eabf502d97dedb37df994c11fb Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Wed, 18 Jun 2025 10:59:18 -0400
Subject: [PATCH 43/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 8129b8c0ea..a0ff441bbd 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -106,8 +106,12 @@ jobs:
                     s/[[:space:]]*>[[:space:]]*/>/g
                     s/[[:space:]]*==[[:space:]]*/==/g
 
-                    # Remove full-line comments
-                    /^[[:space:]]*[!cC*dD]/d
+                    # Remove full-line comments
+                    /^\s*!/d
+                    /^[cC*dD]/d
+                    /^[ \t]*[cC*dD]/d
+                    /^[[:space:]]*$/d
+
                     # Remove end-of-line comments, preserving quoted strings
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"

From c20dacd1497a3501cc7a0b411075bb190cf837fa Mon Sep 17 00:00:00 2001
From: mohdsaid497566 <mohdsaid497566@gmail.com>
Date: Thu, 19 Jun 2025 18:44:32 -0400
Subject: [PATCH 44/48] removed insignificant echo's

---
 .github/workflows/pmd.yml | 19 +++++--------------
 1 file changed, 5 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index a0ff441bbd..21fef0ba5f 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -106,24 +106,15 @@ jobs:
                     s/[[:space:]]*>[[:space:]]*/>/g
                     s/[[:space:]]*==[[:space:]]*/==/g
 
-                    # Remove full-line comments
-                    /^\s*!/d
-                    /^[cC*dD]/d
-                    /^[ \t]*[cC*dD]/d
-                    /^[[:space:]]*$/d
+                    # Remove full-line comments
+                    /^\s*!/d
+                    /^[cC*dD]/d
+                    /^[ \t]*[cC*dD]/d
+                    /^[[:space:]]*$/d
 
                     # Remove end-of-line comments, preserving quoted strings
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"
-                
-                  if cmp -s "$file" "$TMP_FILE"; then
-                      echo -e "No changes needed for $file"
-                      rm "$TMP_FILE"
-                  else
-                      # Overwrite the original file with the processed content
-                      mv "$TMP_FILE" "$file"
-                      echo -e "Successfully processed $file"
-                  fi
               done
 
               "${PMD_HOME}/bin/pmd" cpd \

From 48359893de29a9555b0709fac1f5b0e0381d08d9 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Thu, 19 Jun 2025 18:52:11 -0400
Subject: [PATCH 45/48] Update pmd.yml


From ce046e288ac6184506f6fbfe6440551190c6dab1 Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Thu, 19 Jun 2025 18:53:58 -0400
Subject: [PATCH 46/48] Update pmd.yml


From dbd4489cc39a2099cbb4fd5d35188af54d70ac8a Mon Sep 17 00:00:00 2001
From: "Mohammed S. Al-Mahrouqi"
 <145478595+Malmahrouqi3@users.noreply.github.com>
Date: Thu, 19 Jun 2025 18:56:44 -0400
Subject: [PATCH 47/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 21fef0ba5f..59e7e8c304 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -115,6 +115,13 @@ jobs:
                     # Remove end-of-line comments, preserving quoted strings
                     s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
                   ' "$file" > "$TMP_FILE"
+
+                  if cmp -s "$file" "$TMP_FILE"; then
+                      rm "$TMP_FILE"
+                  else
+                      # Overwrite the original file with the processed content
+                      mv "$TMP_FILE" "$file"
+                  fi
               done
 
               "${PMD_HOME}/bin/pmd" cpd \

From 9fc63716a17e083f2cc1a63e8e5fc728c24a28a5 Mon Sep 17 00:00:00 2001
From: Spencer Bryngelson <shb@gatech.edu>
Date: Thu, 19 Jun 2025 19:11:24 -0400
Subject: [PATCH 48/48] Update pmd.yml

---
 .github/workflows/pmd.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
index 59e7e8c304..24361e777c 100644
--- a/.github/workflows/pmd.yml
+++ b/.github/workflows/pmd.yml
@@ -37,7 +37,6 @@ jobs:
               find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) -print0 | 
               while IFS= read -r -d $'\0' file; do
                   processed=$((processed + 1))
-                  echo -e "[$processed/$total_files] Processing ${file}..."
                   
                   # Create a temporary file with same permissions as original
                   TMP_FILE=$(mktemp)