From a2fcab5f375469a75de51bdc4abc740a56ab441e Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Tue, 22 Sep 2026 17:17:35 +0100
Subject: [PATCH 01/70] first attempt at improve-quality-job comparison job

---
 .github/workflows/process.yml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index bbe664f884..7e1d9c19eb 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -155,6 +155,31 @@ jobs:
 
           hatch run lint:fmt_extra "${files[@]}"
 
+        env: # need number of errors being flagged in these files
+          num_pr_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
+
+      - name: Get information about the current run
+        uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
+        id: workflow-run-info
+      - name: Checkout main for linting comparison
+        if: steps.workflow-run-info.outputs.pullRequestNumber != ''
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          ref: ${{ workflow-run-info.outputs.targetBranch }}
+      - name: Linting comparison with main
+        env:
+          num_main_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
+          compared_errors: num_pr_errors - num_main_errors
+      - name: Warning comment
+        if: compared_errors > 0
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
+        with:
+          issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
+          body: |
+            ⚠️ improve_quality_job warning!
+            Files changed by this PR have introduced $compared_errors more linting errors when compared to main.
+            Please fix these
+
 
   tracking:
     # update tracker to include the MFILEs created by the run-tracking-inputs job

From f062f8b33a18079326781900fe4a15a72aa0ef83 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Tue, 22 Sep 2026 17:20:38 +0100
Subject: [PATCH 02/70] add env. to access vars

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 7e1d9c19eb..f3849fd31a 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -169,9 +169,9 @@ jobs:
       - name: Linting comparison with main
         env:
           num_main_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
-          compared_errors: num_pr_errors - num_main_errors
+          compared_errors: env.num_pr_errors - env.num_main_errors
       - name: Warning comment
-        if: compared_errors > 0
+        if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}

From 74e7f775769f7696e370d11603adf6ede918fa01 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Wed, 23 Sep 2026 10:29:15 +0100
Subject: [PATCH 03/70] test

---
 .github/workflows/process.yml | 46 +++++++++++++++++------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index f3849fd31a..291a8bd1e6 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -155,30 +155,30 @@ jobs:
 
           hatch run lint:fmt_extra "${files[@]}"
 
-        env: # need number of errors being flagged in these files
-          num_pr_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
+      #   env: # need number of errors being flagged in these files
+      #     num_pr_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
 
-      - name: Get information about the current run
-        uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
-        id: workflow-run-info
-      - name: Checkout main for linting comparison
-        if: steps.workflow-run-info.outputs.pullRequestNumber != ''
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-        with:
-          ref: ${{ workflow-run-info.outputs.targetBranch }}
-      - name: Linting comparison with main
-        env:
-          num_main_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
-          compared_errors: env.num_pr_errors - env.num_main_errors
-      - name: Warning comment
-        if: env.compared_errors > 0
-        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
-        with:
-          issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
-          body: |
-            ⚠️ improve_quality_job warning!
-            Files changed by this PR have introduced $compared_errors more linting errors when compared to main.
-            Please fix these
+      # - name: Get information about the current run
+      #   uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
+      #   id: workflow-run-info
+      # - name: Checkout main for linting comparison
+      #   if: steps.workflow-run-info.outputs.pullRequestNumber != ''
+      #   uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      #   with:
+      #     ref: ${{ workflow-run-info.outputs.targetBranch }}
+      # - name: Linting comparison with main
+      #   env:
+      #     num_main_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
+      #     compared_errors: env.num_pr_errors - env.num_main_errors
+      # - name: Warning comment
+      #   if: env.compared_errors > 0
+      #   uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
+      #   with:
+      #     issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
+      #     body: |
+      #       ⚠️ improve_quality_job warning!
+      #       Files changed by this PR have introduced $compared_errors more linting errors when compared to main.
+      #       Please fix these
 
 
   tracking:

From 6480172251f654aeedc32c42c0b3df291ea6986c Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 14:40:17 +0100
Subject: [PATCH 04/70] trying to get running

---
 .github/workflows/process.yml | 46 +++++++++++++++++------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 291a8bd1e6..4d92b99110 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -155,30 +155,30 @@ jobs:
 
           hatch run lint:fmt_extra "${files[@]}"
 
-      #   env: # need number of errors being flagged in these files
-      #     num_pr_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
+        env: # need number of errors being flagged in these files
+          num_pr_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
 
-      # - name: Get information about the current run
-      #   uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
-      #   id: workflow-run-info
-      # - name: Checkout main for linting comparison
-      #   if: steps.workflow-run-info.outputs.pullRequestNumber != ''
-      #   uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-      #   with:
-      #     ref: ${{ workflow-run-info.outputs.targetBranch }}
-      # - name: Linting comparison with main
-      #   env:
-      #     num_main_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
-      #     compared_errors: env.num_pr_errors - env.num_main_errors
-      # - name: Warning comment
-      #   if: env.compared_errors > 0
-      #   uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
-      #   with:
-      #     issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
-      #     body: |
-      #       ⚠️ improve_quality_job warning!
-      #       Files changed by this PR have introduced $compared_errors more linting errors when compared to main.
-      #       Please fix these
+      - name: Get information about the current run
+        uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
+        id: workflow-run-info
+      - name: Checkout main for linting comparison
+        if: steps.workflow-run-info.outputs.pullRequestNumber != ''
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          ref: ${{ workflow-run-info.outputs.targetBranch }}
+      - name: Linting comparison with main
+        env:
+          num_main_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
+          compared_errors: ${{env.num_pr_errors - env.num_main_errors}}
+      - name: Warning comment
+        if: env.compared_errors > 0
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
+        with:
+          issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
+          body: |
+            ⚠️ improve_quality_job warning!
+            Files changed by this PR have introduced $compared_errors more linting errors when compared to main.
+            Please fix these
 
 
   tracking:

From 71de18598a3b318276e0f27087cdbc50ca85b14e Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 15:32:31 +0100
Subject: [PATCH 05/70] fixes - subtract 1, and subtract correctly for compared
 errors

---
 .github/workflows/process.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 4d92b99110..91c9684d1a 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -156,7 +156,8 @@ jobs:
           hatch run lint:fmt_extra "${files[@]}"
 
         env: # need number of errors being flagged in these files
-          num_pr_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
+          # subtract 1 as final summary line is not an error
+          num_pr_errors: $(($(hatch run lint:fmt_extra "${files[@]}" | wc -l) - 1))
 
       - name: Get information about the current run
         uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
@@ -168,8 +169,8 @@ jobs:
           ref: ${{ workflow-run-info.outputs.targetBranch }}
       - name: Linting comparison with main
         env:
-          num_main_errors: $(hatch run lint:fmt_extra "${files[@]}" | wc -l)
-          compared_errors: ${{env.num_pr_errors - env.num_main_errors}}
+          num_main_errors: $(($(hatch run lint:fmt_extra "${files[@]}" | wc -l) - 1))
+          compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Warning comment
         if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0

From 21b28689e9fafed2ed0823699cf339d47527807c Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 15:34:41 +0100
Subject: [PATCH 06/70] use steps.workflow-run-info

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 91c9684d1a..9e712d7268 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -166,7 +166,7 @@ jobs:
         if: steps.workflow-run-info.outputs.pullRequestNumber != ''
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
-          ref: ${{ workflow-run-info.outputs.targetBranch }}
+          ref: ${{ steps.workflow-run-info.outputs.targetBranch }}
       - name: Linting comparison with main
         env:
           num_main_errors: $(($(hatch run lint:fmt_extra "${files[@]}" | wc -l) - 1))

From d2c00797b7b7d45545857ffd6a9fcc8cae2e42c3 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 15:39:50 +0100
Subject: [PATCH 07/70] get number from final line of output

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 9e712d7268..f3cf95dcbe 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -157,7 +157,7 @@ jobs:
 
         env: # need number of errors being flagged in these files
           # subtract 1 as final summary line is not an error
-          num_pr_errors: $(($(hatch run lint:fmt_extra "${files[@]}" | wc -l) - 1))
+          num_pr_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
 
       - name: Get information about the current run
         uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
@@ -169,7 +169,7 @@ jobs:
           ref: ${{ steps.workflow-run-info.outputs.targetBranch }}
       - name: Linting comparison with main
         env:
-          num_main_errors: $(($(hatch run lint:fmt_extra "${files[@]}" | wc -l) - 1))
+          num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Warning comment
         if: env.compared_errors > 0

From 430943cb6e4693813f7292bf425b0cfe23033834 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 15:46:05 +0100
Subject: [PATCH 08/70] new line

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index f3cf95dcbe..b55e7023d4 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -155,7 +155,8 @@ jobs:
 
           hatch run lint:fmt_extra "${files[@]}"
 
-        env: # need number of errors being flagged in these files
+        env:
+          # need number of errors being flagged in these files
           # subtract 1 as final summary line is not an error
           num_pr_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
 

From 74ee33134deaa9db50ca268f8c5bb246afed5a57 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 15:53:35 +0100
Subject: [PATCH 09/70] try to fix error

---
 .github/workflows/process.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index b55e7023d4..4942467ba3 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -169,6 +169,7 @@ jobs:
         with:
           ref: ${{ steps.workflow-run-info.outputs.targetBranch }}
       - name: Linting comparison with main
+        if: steps.workflow-run-info.outputs.pullRequestNumber != ''
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))

From 3018b9676df1478751a5f04844ec471de08bf878 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 15:54:51 +0100
Subject: [PATCH 10/70] try to fix

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 4942467ba3..58a04acf06 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -163,7 +163,8 @@ jobs:
       - name: Get information about the current run
         uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
         id: workflow-run-info
-      - name: Checkout main for linting comparison
+      - name: Checkout
+        # check out main
         if: steps.workflow-run-info.outputs.pullRequestNumber != ''
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:

From 0f323c3101a447d8ecd3eaeba7980129810dc52d Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 15:59:58 +0100
Subject: [PATCH 11/70] testing

---
 .github/workflows/process.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 58a04acf06..227d3aaf87 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -163,14 +163,12 @@ jobs:
       - name: Get information about the current run
         uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
         id: workflow-run-info
-      - name: Checkout
+      - name: Checkout and lint on main
         # check out main
         if: steps.workflow-run-info.outputs.pullRequestNumber != ''
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           ref: ${{ steps.workflow-run-info.outputs.targetBranch }}
-      - name: Linting comparison with main
-        if: steps.workflow-run-info.outputs.pullRequestNumber != ''
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))

From e96b3489dc9f28b31753693a18cfbcc29084e2fd Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:03:44 +0100
Subject: [PATCH 12/70] test the new job!

---
 process/main.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/process/main.py b/process/main.py
index ad22d34ad5..0446333949 100644
--- a/process/main.py
+++ b/process/main.py
@@ -30,6 +30,8 @@
 Box file F/RS/CIRE5523/PWF (up to 15/01/96)
 Box file F/MI/PJK/PROCESS and F/PL/PJK/PROCESS (15/01/96 to 24/01/12)
 Box file T&amp;M/PKNIGHT/PROCESS (from 24/01/12)
+
+TEST
 """
 
 import logging

From ae4c740e6557fdd994a4632a400e722027aa3769 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:22:15 +0100
Subject: [PATCH 13/70] run job when improve-quality has failed

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 227d3aaf87..457c828bea 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -161,11 +161,12 @@ jobs:
           num_pr_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
 
       - name: Get information about the current run
+        if: failure()
         uses: Fusion-Power-Plant-Framework/fppf-actions/get-workflow-origin@f94a8de5f658cf65c79e1f143a7a31fb94a05793
         id: workflow-run-info
       - name: Checkout and lint on main
         # check out main
-        if: steps.workflow-run-info.outputs.pullRequestNumber != ''
+        if: failure() && steps.workflow-run-info.outputs.pullRequestNumber != ''
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           ref: ${{ steps.workflow-run-info.outputs.targetBranch }}
@@ -173,7 +174,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Warning comment
-        if: env.compared_errors > 0
+        if: failure() && env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}

From 67bc785c6ba4f5049bc4f82219e9f24bcefc6714 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:29:02 +0100
Subject: [PATCH 14/70] test adding more improve-quality errors

---
 process/main.py | 119 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 118 insertions(+), 1 deletion(-)

diff --git a/process/main.py b/process/main.py
index 0446333949..23d846b44c 100644
--- a/process/main.py
+++ b/process/main.py
@@ -31,7 +31,6 @@
 Box file F/MI/PJK/PROCESS and F/PL/PJK/PROCESS (15/01/96 to 24/01/12)
 Box file T&amp;M/PKNIGHT/PROCESS (from 24/01/12)
 
-TEST
 """
 
 import logging
@@ -610,6 +609,124 @@ def validate_input(self, replace_obsolete: bool = False):
         else:
             print("The IN.DAT file does not contain any obsolete variables.")
 
+    def test_another_lint_error(self, replace_obsolete: bool = False):
+        """Checks the input IN.DAT file for any obsolete variables in the OBS_VARS dict
+        contained within obsolete_variables.py.
+        If obsolete variables are found, and if `replace_obsolete` is set to True,
+        they are either removed or replaced by their updated names as specified
+        in the OBS_VARS dictionary.
+
+        Raises
+        ------
+        ValueError
+            If obsolete variables are present in the input file.
+        """
+        obsolete_variables = ov.OBS_VARS
+        obsolete_vars_help_message = ov.OBS_VARS_HELP
+
+        filename = self.input_file
+        variables_in_in_dat = []
+        modified_lines = []
+        changes_made = []  # To store details of the changes
+
+        with open(filename) as file:
+            for line in file:
+                # Skip comment lines or lines without an assignment
+                if line.startswith("*") or "=" not in line:
+                    modified_lines.append(line)
+                    continue
+
+                # Extract the variable name before the separator
+                raw_variable_name = line.split("=", 1)[0].strip()
+                # handle cases where the variable name might have parentheses
+                variable_name = (
+                    raw_variable_name.split("(", 1)[0]
+                    if "(" in raw_variable_name
+                    else raw_variable_name
+                )
+
+                # Check if the variable is obsolete and needs replacing
+                if variable_name in obsolete_variables:
+                    replacement = obsolete_variables.get(variable_name)
+                    if replace_obsolete:
+                        # Prepare replacement or removal
+                        if replacement is None:
+                            # If no replacement is defined, comment out the line
+                            modified_lines.append(f"* Obsolete: {line}")
+                            changes_made.append(
+                                f"Commented out obsolete variable: {variable_name}"
+                            )
+                        else:
+                            if isinstance(replacement, list):
+                                # Raise an error if replacement is a list
+                                replacement_str = ", ".join(replacement)
+                                raise ValueError(
+                                    f"The variable '{variable_name}' is obsolete and "
+                                    "should be replaced by the following variables: "
+                                    f"{replacement_str}. "
+                                    "Please set their values accordingly."
+                                )
+                            # Replace obsolete variable
+                            modified_line = line.replace(variable_name, replacement, 1)
+                            modified_lines.append(
+                                f"* Replaced '{variable_name}' with "
+                                f"'{replacement}'\n{modified_line}"
+                            )
+                            changes_made.append(
+                                f"Replaced '{variable_name}' with '{replacement}'"
+                            )
+                            variables_in_in_dat.append(variable_name)
+                    else:
+                        # If replacement is False, add the line as-is
+                        modified_lines.append(line)
+                        variables_in_in_dat.append(variable_name)
+                else:
+                    modified_lines.append(line)
+
+        obs_vars_in_in_dat = [
+            var for var in variables_in_in_dat if var in obsolete_variables
+        ]
+
+        if obs_vars_in_in_dat:
+            if replace_obsolete:
+                # If replace_obsolete is True, write the modified content to the file
+                with open(filename, "w") as file:
+                    file.writelines(modified_lines)
+                print(
+                    "The IN.DAT file has been updated to replace or "
+                    "comment out obsolete variables."
+                )
+                print("Summary of changes made:")
+                for change in changes_made:
+                    print(f" - {change}")
+            else:
+                # Only print the report if replace_obsolete is False
+                message = (
+                    "The IN.DAT file contains obsolete variables "
+                    "from the OBS_VARS dictionary. "
+                    "The obsolete variables in your IN.DAT file are: "
+                    f"{obs_vars_in_in_dat}. "
+                    "Either remove these or replace them with "
+                    "their updated variable names. "
+                )
+                for obs_var in obs_vars_in_in_dat:
+                    replacement = obsolete_variables.get(obs_var)
+                    if replacement is None:
+                        message += (
+                            f"\n\n{obs_var} is an obsolete variable "
+                            "and needs to be removed."
+                        )
+                    else:
+                        message += (
+                            f"\n\n{obs_var} is an obsolete variable "
+                            f"and needs to be replaced by {replacement}."
+                        )
+                    message += f" {obsolete_vars_help_message.get(obs_var, '')}"
+                raise ValueError(message)
+
+        else:
+            print("The IN.DAT file does not contain any obsolete variables.")
+
     def validate_user_model(self):
         """Checks that a user-created model has been injected correctly
 

From 15bf17e4296e64a1aec3682c221712013573503d Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:31:22 +0100
Subject: [PATCH 15/70] try to fix again

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 457c828bea..a836372cea 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -174,7 +174,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Warning comment
-        if: failure() && env.compared_errors > 0
+        if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}

From 2ffa59b19a17abb4ca3b84d4a84a7cc66af5c4f2 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:40:20 +0100
Subject: [PATCH 16/70] debugging

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index a836372cea..a89b089686 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -155,6 +155,7 @@ jobs:
 
           hatch run lint:fmt_extra "${files[@]}"
 
+          echo $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
         env:
           # need number of errors being flagged in these files
           # subtract 1 as final summary line is not an error
@@ -173,6 +174,9 @@ jobs:
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
+        run: |
+          echo $env.num_main_errors >> "${GITHUB_ENV}"
+          echo $env.compared_errors >> "${GITHUB_ENV}"
       - name: Warning comment
         if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0

From e9c1772c367a5e19fdb78909755842c6076e4f33 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:41:15 +0100
Subject: [PATCH 17/70] try again

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index a89b089686..5ad97fe226 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,8 +175,8 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
         run: |
-          echo $env.num_main_errors >> "${GITHUB_ENV}"
-          echo $env.compared_errors >> "${GITHUB_ENV}"
+          echo $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') >> "${GITHUB_ENV}"
+          echo $((env.num_pr_errors - env.num_main_errors)) >> "${GITHUB_ENV}"
       - name: Warning comment
         if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0

From 1fe3ba3ab7917ce2b712561cea9fc81195d64a9f Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:56:45 +0100
Subject: [PATCH 18/70] try

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 5ad97fe226..ce01970c11 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,8 +175,8 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
         run: |
-          echo $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') >> "${GITHUB_ENV}"
-          echo $((env.num_pr_errors - env.num_main_errors)) >> "${GITHUB_ENV}"
+          echo ${{env.num_main_errors}} >> "${GITHUB_ENV}"
+          echo ${{env.compared_errors}} >> "${GITHUB_ENV}"
       - name: Warning comment
         if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0

From 33c16f7345b470661e3a1727e941e1940ee70e22 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 16:57:57 +0100
Subject: [PATCH 19/70] hmm

---
 .github/workflows/process.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index ce01970c11..207d04955e 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -174,9 +174,6 @@ jobs:
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
-        run: |
-          echo ${{env.num_main_errors}} >> "${GITHUB_ENV}"
-          echo ${{env.compared_errors}} >> "${GITHUB_ENV}"
       - name: Warning comment
         if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0

From 340863bf210b8e9b313872093f0cc9ba2bdb27aa Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 17:01:11 +0100
Subject: [PATCH 20/70] hmmmm

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 207d04955e..36ec6d9e97 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -155,7 +155,6 @@ jobs:
 
           hatch run lint:fmt_extra "${files[@]}"
 
-          echo $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
         env:
           # need number of errors being flagged in these files
           # subtract 1 as final summary line is not an error
@@ -175,7 +174,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Warning comment
-        if: env.compared_errors > 0
+        # if: env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}

From 794015855fc09583ad90fbafe13f832be2ab21ab Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 17:02:57 +0100
Subject: [PATCH 21/70] test agaaaaain

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 36ec6d9e97..54ea2e85f1 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -174,7 +174,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Warning comment
-        # if: env.compared_errors > 0
+        if: failure() # && env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}

From 59f3eea3376f5f872f4974289d601c2b19a63b9f Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:15:35 +0100
Subject: [PATCH 22/70] add find warning report job

---
 .github/workflows/process.yml | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 54ea2e85f1..21a2257311 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -173,15 +173,25 @@ jobs:
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
+      - name: Find warning report comment
+        if: failure () && env.compared_errors > 0 && steps.workflow-run-info.outputs.pullRequestNumber != ''
+        uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
+        id: find-warning-report-comment
+        with:
+          issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
+          comment-author: "github-actions[bot]"
+          body-includes: ⚠️ improve_quality_job warning!
+          direction: last
       - name: Warning comment
-        if: failure() # && env.compared_errors > 0
+        if: failure() && env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
+          comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            ⚠️ improve_quality_job warning!
             Files changed by this PR have introduced $compared_errors more linting errors when compared to main.
             Please fix these
+          edit-mode: replace
 
 
   tracking:

From f51225d5d8fc334e0e31a9582f967056b6849c9a Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:19:09 +0100
Subject: [PATCH 23/70] testing

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 21a2257311..79d431ddff 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -174,7 +174,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Find warning report comment
-        if: failure () && env.compared_errors > 0 && steps.workflow-run-info.outputs.pullRequestNumber != ''
+        if: failure () && steps.workflow-run-info.outputs.pullRequestNumber != '' # && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -183,7 +183,7 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() && env.compared_errors > 0
+        if: failure() # && env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}

From 522dd52563f7953437949b2c3fa1606b22cf9ff4 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:29:49 +0100
Subject: [PATCH 24/70] try permissions write?

---
 .github/workflows/process.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 79d431ddff..dfc5e3b5ce 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -117,6 +117,7 @@ jobs:
         uses: Fusion-Power-Plant-Framework/fppf-actions/hatch-lint@c6af22fc8d00be67cca53a61177301462f499fb2
 
   improve_quality_check:
+    permissions: write
     runs-on: ubuntu-latest
     if: github.event_name == 'pull_request'
     needs: [pre-commit-quality-check]

From bef4cbd7ec6c6f26b721d0f4eb6a4bc9bf75ff61 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:31:03 +0100
Subject: [PATCH 25/70] try permissions write

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index dfc5e3b5ce..2c5f5a6e33 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -117,7 +117,8 @@ jobs:
         uses: Fusion-Power-Plant-Framework/fppf-actions/hatch-lint@c6af22fc8d00be67cca53a61177301462f499fb2
 
   improve_quality_check:
-    permissions: write
+    permissions:
+      pull-requests: write
     runs-on: ubuntu-latest
     if: github.event_name == 'pull_request'
     needs: [pre-commit-quality-check]

From addc56e97203cb213762f95bee69601bf322cb5a Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:34:53 +0100
Subject: [PATCH 26/70] try to fix message

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 2c5f5a6e33..f3ec821e8f 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -191,7 +191,7 @@ jobs:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            Files changed by this PR have introduced $compared_errors more linting errors when compared to main.
+            Files changed by this PR have introduced "$compared_errors" more linting errors when compared to main.
             Please fix these
           edit-mode: replace
 

From 6c80943470e1337e05e03954c8560cf86c612fe5 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:43:40 +0100
Subject: [PATCH 27/70] try again

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index f3ec821e8f..2485685633 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -191,7 +191,7 @@ jobs:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            Files changed by this PR have introduced "$compared_errors" more linting errors when compared to main.
+            Files changed by this PR have introduced ${{compared_errors}} more linting errors when compared to main.
             Please fix these
           edit-mode: replace
 

From fba21cad09de86416dd868ed41283c3c0ef41f7a Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:46:04 +0100
Subject: [PATCH 28/70] fix

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 2485685633..c84464dde0 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -176,7 +176,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Find warning report comment
-        if: failure () && steps.workflow-run-info.outputs.pullRequestNumber != '' # && env.compared_errors > 0
+        if: failure () && steps.workflow-run-info.outputs.pullRequestNumber != '' && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -185,13 +185,13 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() # && env.compared_errors > 0
+        if: failure() && env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            Files changed by this PR have introduced ${{compared_errors}} more linting errors when compared to main.
+            Files changed by this PR have introduced ${{env.compared_errors}} more linting errors when compared to main.
             Please fix these
           edit-mode: replace
 

From 0f317c8931fef294b2df81be016295ba1e8095c3 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:48:23 +0100
Subject: [PATCH 29/70] change if condition to test

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index c84464dde0..e3af6f9ce0 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -176,7 +176,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Find warning report comment
-        if: failure () && steps.workflow-run-info.outputs.pullRequestNumber != '' && env.compared_errors > 0
+        if: failure () # && steps.workflow-run-info.outputs.pullRequestNumber != '' && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -185,7 +185,7 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() && env.compared_errors > 0
+        if: failure() # && env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}

From 93a4385ba4303466dd6e3f9f5ced4822e6782bdc Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Thu, 24 Sep 2026 18:52:02 +0100
Subject: [PATCH 30/70] $

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index e3af6f9ce0..acb0a9afbd 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -191,7 +191,7 @@ jobs:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            Files changed by this PR have introduced ${{env.compared_errors}} more linting errors when compared to main.
+            Files changed by this PR have introduced $env.compared_errors more linting errors when compared to main.
             Please fix these
           edit-mode: replace
 

From 664a0c9e1b98e1615d3cdcba2b8a74f5309306fd Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:08:25 +0100
Subject: [PATCH 31/70] try to print number of errors in comment

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index acb0a9afbd..bc197ea7d1 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -159,7 +159,6 @@ jobs:
 
         env:
           # need number of errors being flagged in these files
-          # subtract 1 as final summary line is not an error
           num_pr_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
 
       - name: Get information about the current run
@@ -191,7 +190,7 @@ jobs:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            Files changed by this PR have introduced $env.compared_errors more linting errors when compared to main.
+            Files changed by this PR have introduced ${{ env.compared_errors }} more linting errors when compared to main.
             Please fix these
           edit-mode: replace
 

From 492cf6e96489399b5f6c858f29ea083744fdeffc Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:08:55 +0100
Subject: [PATCH 32/70] space

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index bc197ea7d1..5f26618d1f 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,7 +175,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Find warning report comment
-        if: failure () # && steps.workflow-run-info.outputs.pullRequestNumber != '' && env.compared_errors > 0
+        if: failure() # && steps.workflow-run-info.outputs.pullRequestNumber != '' && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:

From efbdf51218965707de962fee377aea5f6abf939e Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:14:43 +0100
Subject: [PATCH 33/70] try to only make comment if more errors now

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 5f26618d1f..9a013f519d 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,7 +175,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
       - name: Find warning report comment
-        if: failure() # && steps.workflow-run-info.outputs.pullRequestNumber != '' && env.compared_errors > 0
+        if: failure() && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -184,7 +184,7 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() # && env.compared_errors > 0
+        if: failure() && env.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}

From d504a3d288e19abea03e4361a2aa41551eccd2f2 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:18:23 +0100
Subject: [PATCH 34/70] shorten ci for pr testing

---
 .github/workflows/process.yml | 358 +++++++++++++++++-----------------
 1 file changed, 179 insertions(+), 179 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 9a013f519d..0ac90971b3 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -17,93 +17,93 @@ env:
   python-version: '3.10'
 
 jobs:
-  unit-test:
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macos-latest]
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
-      - name: Setup python and hatch
-        uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
-      - name: Run unit tests with coverage report
-        run: |
-          hatch run test:tests-cov tests/unit
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-        with:
-          fail_ci_if_error: ${{ github.ref_name == 'main' }}
+  # unit-test:
+  #   strategy:
+  #     matrix:
+  #       os: [ubuntu-latest, macos-latest]
+  #   runs-on: ${{ matrix.os }}
+  #   steps:
+  #     - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
+  #     - name: Setup python and hatch
+  #       uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
+  #     - name: Run unit tests with coverage report
+  #       run: |
+  #         hatch run test:tests-cov tests/unit
+  #     - name: Upload coverage to Codecov
+  #       uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7
+  #       env:
+  #         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  #       with:
+  #         fail_ci_if_error: ${{ github.ref_name == 'main' }}
 
-  integration-test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
-      - name: Setup python and hatch
-        uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
-        with:
-          python-version: ${{ env.python-version }}
-      - name: Run integration tests
-        run: hatch run test.py${{ env.python-version }}:tests-integration
+  # integration-test:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
+  #     - name: Setup python and hatch
+  #       uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
+  #       with:
+  #         python-version: ${{ env.python-version }}
+  #     - name: Run integration tests
+  #       run: hatch run test.py${{ env.python-version }}:tests-integration
 
-  example-test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
-      - name: Setup python and hatch
-        uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
-        with:
-          python-version: ${{ env.python-version }}
-      - name: Run example tests
-        run: hatch run test.py${{ env.python-version }}:tests-examples
+  # example-test:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
+  #     - name: Setup python and hatch
+  #       uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
+  #       with:
+  #         python-version: ${{ env.python-version }}
+  #     - name: Run example tests
+  #       run: hatch run test.py${{ env.python-version }}:tests-examples
 
-  regression-test:
-    runs-on: ubuntu-latest
-    needs: [tracking]
-    # depend on make and tracking job but don't skip if tracking was skipped
-    # run PROCESS on the regression test input files and compare results to the tracked files
-    if: always()
-    continue-on-error: true
-    strategy:
-      matrix:
-        tolerance: [0.2, 5]
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
-        with:
-          fetch-depth: 0
-      - name: Setup python and hatch
-        uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
-        with:
-          python-version: ${{ env.python-version }}
-      - name: Run regression tests
-        run: hatch run test.py${{ env.python-version }}:tests-regression --reg-tolerance=${{ matrix.tolerance }}
+  # regression-test:
+  #   runs-on: ubuntu-latest
+  #   needs: [tracking]
+  #   # depend on make and tracking job but don't skip if tracking was skipped
+  #   # run PROCESS on the regression test input files and compare results to the tracked files
+  #   if: always()
+  #   continue-on-error: true
+  #   strategy:
+  #     matrix:
+  #       tolerance: [0.2, 5]
+  #   steps:
+  #     - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
+  #       with:
+  #         fetch-depth: 0
+  #     - name: Setup python and hatch
+  #       uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
+  #       with:
+  #         python-version: ${{ env.python-version }}
+  #     - name: Run regression tests
+  #       run: hatch run test.py${{ env.python-version }}:tests-regression --reg-tolerance=${{ matrix.tolerance }}
 
-  run-tracking-inputs:
-    runs-on: ubuntu-latest
-    # run PROCESS on the regression test input files and archive output MFILEs
-    # only runs upon merge to main
-    if: github.ref == 'refs/heads/main'
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
-      - name: Setup python and hatch
-        uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
-        with:
-          python-version: ${{ env.python-version }}
-      - name: Run regression input files
-        run: hatch run track:create-tracking-inputs
-      - name: Move other files
-        run: mv tests/regression/input_files/*.json tracking/
-      - name: Archive tracked MFILEs
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
-        with:
-          name: tracked-mfiles
-          path: tracking/*_MFILE.DAT
-      - name: Archive tracked SIG_TF.json
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
-        with:
-          name: sig-tfs
-          path: tracking/*.json
+  # run-tracking-inputs:
+  #   runs-on: ubuntu-latest
+  #   # run PROCESS on the regression test input files and archive output MFILEs
+  #   # only runs upon merge to main
+  #   if: github.ref == 'refs/heads/main'
+  #   steps:
+  #     - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
+  #     - name: Setup python and hatch
+  #       uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
+  #       with:
+  #         python-version: ${{ env.python-version }}
+  #     - name: Run regression input files
+  #       run: hatch run track:create-tracking-inputs
+  #     - name: Move other files
+  #       run: mv tests/regression/input_files/*.json tracking/
+  #     - name: Archive tracked MFILEs
+  #       uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
+  #       with:
+  #         name: tracked-mfiles
+  #         path: tracking/*_MFILE.DAT
+  #     - name: Archive tracked SIG_TF.json
+  #       uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
+  #       with:
+  #         name: sig-tfs
+  #         path: tracking/*.json
 
   pre-commit-quality-check:
     runs-on: ubuntu-latest
@@ -195,100 +195,100 @@ jobs:
           edit-mode: replace
 
 
-  tracking:
-    # update tracker to include the MFILEs created by the run-tracking-inputs job
-    concurrency:
-      group: tracking-jobs
-      cancel-in-progress: false
-    runs-on: ubuntu-latest
-    # depends on run-tracking-inputs; only runs upon merge to main
-    needs: run-tracking-inputs
-    if: github.ref == 'refs/heads/main'
-    env:
-      COMMIT_MESSAGE: ${{ github.event.head_commit.message }}
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
-      - name: Setup python and hatch
-        uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
-        with:
-          python-version: ${{ env.python-version }}
-      - name: Setup SSH identity
-        uses: webfactory/ssh-agent@e83874834305fe9a4a2997156cb26c5de65a8555
-        with:
-          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
-      - name: Download tracking data
-        run: git clone git@github.com:timothy-nunn/process-tracking-data.git process-tracking-data
-      - name: Download MFILEs
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
-        with:
-          name: tracked-mfiles
-          path: tracking/
-      - name: Create new tracking entries
-        shell: bash
-        run: |
-          MSG=$(printf "%q " $COMMIT_MESSAGE)
-          git config --global --add safe.directory '*'
-          hatch run track:run-tracker "${MSG}" ${{ github.sha }}
-      - name: Create the tracking dashboard
-        run: hatch run python tracking/tracking_data.py plot process-tracking-data --out tracking.html
-      - name: Archive tracking dashboard
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
-        with:
-          name: tracking-html
-          path: tracking.html
-      - name: Setup Git identity
-        run: |
-          git config --global user.email "${{ github.triggering_actor }}@github.runner"
-          git config --global user.name "${{ github.job }}"
-      - name: Commit and push tracking data
-        run: |
-          cd process-tracking-data
-          git add .
-          git commit -m "${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}"
-          git push
+  # tracking:
+  #   # update tracker to include the MFILEs created by the run-tracking-inputs job
+  #   concurrency:
+  #     group: tracking-jobs
+  #     cancel-in-progress: false
+  #   runs-on: ubuntu-latest
+  #   # depends on run-tracking-inputs; only runs upon merge to main
+  #   needs: run-tracking-inputs
+  #   if: github.ref == 'refs/heads/main'
+  #   env:
+  #     COMMIT_MESSAGE: ${{ github.event.head_commit.message }}
+  #   steps:
+  #     - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
+  #     - name: Setup python and hatch
+  #       uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
+  #       with:
+  #         python-version: ${{ env.python-version }}
+  #     - name: Setup SSH identity
+  #       uses: webfactory/ssh-agent@e83874834305fe9a4a2997156cb26c5de65a8555
+  #       with:
+  #         ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+  #     - name: Download tracking data
+  #       run: git clone git@github.com:timothy-nunn/process-tracking-data.git process-tracking-data
+  #     - name: Download MFILEs
+  #       uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
+  #       with:
+  #         name: tracked-mfiles
+  #         path: tracking/
+  #     - name: Create new tracking entries
+  #       shell: bash
+  #       run: |
+  #         MSG=$(printf "%q " $COMMIT_MESSAGE)
+  #         git config --global --add safe.directory '*'
+  #         hatch run track:run-tracker "${MSG}" ${{ github.sha }}
+  #     - name: Create the tracking dashboard
+  #       run: hatch run python tracking/tracking_data.py plot process-tracking-data --out tracking.html
+  #     - name: Archive tracking dashboard
+  #       uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
+  #       with:
+  #         name: tracking-html
+  #         path: tracking.html
+  #     - name: Setup Git identity
+  #       run: |
+  #         git config --global user.email "${{ github.triggering_actor }}@github.runner"
+  #         git config --global user.name "${{ github.job }}"
+  #     - name: Commit and push tracking data
+  #       run: |
+  #         cd process-tracking-data
+  #         git add .
+  #         git commit -m "${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}"
+  #         git push
 
-  docs:
-    concurrency:
-      group: docs-jobs
-      cancel-in-progress: false
-    runs-on: ubuntu-latest
-    # depends on tracking; only runs upon merge to main
-    needs: tracking
-    if: github.ref == 'refs/heads/main'
-    steps:
-      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
-        with:
-          fetch-depth: 0
-      - name: Setup python and hatch
-        uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
-        with:
-          python-version: ${{ env.python-version }}
-      - run: git config --global --add safe.directory '*'
-      - name: Download STF_TF.json files
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
-        with:
-          name: sig-tfs
-          path: tracking/
-      - name: Download MFILEs
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
-        with:
-          name: tracked-mfiles
-          path: tracking/
-      - run: mv tracking/large_tokamak_nof.SIG_TF.json tracking/large_tokamak_nof_SIG_TF.json
-      - name: Create an example plot summary
-        run: hatch run process plot summary -f tracking/large_tokamak_nof_MFILE.DAT
-      - name: Move plot summary file to docs images
-        run: mv tracking/large_tokamak_nof_MFILE.DATSUMMARY.pdf documentation/source/images/plot_summary.pdf
-      - run: hatch run docs:build
-      - name: Download tracking html
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
-        with:
-          name: tracking-html
-      - run: mv tracking.html site || cp site/404.html site/tracking.html
-      - name: Upload documentation page
-        uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9
-        with:
-          path: site/
-      - name: Deploy GitHub pages
-        id: deployment
-        uses: actions/deploy-pages@368f82528645a54fb793d4d04e342629a3f51346
+  # docs:
+  #   concurrency:
+  #     group: docs-jobs
+  #     cancel-in-progress: false
+  #   runs-on: ubuntu-latest
+  #   # depends on tracking; only runs upon merge to main
+  #   needs: tracking
+  #   if: github.ref == 'refs/heads/main'
+  #   steps:
+  #     - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1
+  #       with:
+  #         fetch-depth: 0
+  #     - name: Setup python and hatch
+  #       uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@c6af22fc8d00be67cca53a61177301462f499fb2
+  #       with:
+  #         python-version: ${{ env.python-version }}
+  #     - run: git config --global --add safe.directory '*'
+  #     - name: Download STF_TF.json files
+  #       uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
+  #       with:
+  #         name: sig-tfs
+  #         path: tracking/
+  #     - name: Download MFILEs
+  #       uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
+  #       with:
+  #         name: tracked-mfiles
+  #         path: tracking/
+  #     - run: mv tracking/large_tokamak_nof.SIG_TF.json tracking/large_tokamak_nof_SIG_TF.json
+  #     - name: Create an example plot summary
+  #       run: hatch run process plot summary -f tracking/large_tokamak_nof_MFILE.DAT
+  #     - name: Move plot summary file to docs images
+  #       run: mv tracking/large_tokamak_nof_MFILE.DATSUMMARY.pdf documentation/source/images/plot_summary.pdf
+  #     - run: hatch run docs:build
+  #     - name: Download tracking html
+  #       uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c
+  #       with:
+  #         name: tracking-html
+  #     - run: mv tracking.html site || cp site/404.html site/tracking.html
+  #     - name: Upload documentation page
+  #       uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9
+  #       with:
+  #         path: site/
+  #     - name: Deploy GitHub pages
+  #       id: deployment
+  #       uses: actions/deploy-pages@368f82528645a54fb793d4d04e342629a3f51346

From d90e9a6d3398ef2019b734952265347969bb3796 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:22:31 +0100
Subject: [PATCH 35/70] print compared errors

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 0ac90971b3..26eb7c9611 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -174,6 +174,8 @@ jobs:
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
+        run: |
+          echo "$env.compared_errors"
       - name: Find warning report comment
         if: failure() && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0

From 546bf600a87e436663f41d78389ee650c6d1db37 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:26:13 +0100
Subject: [PATCH 36/70] try again print

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 26eb7c9611..0e8f2f932f 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,7 +175,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
         run: |
-          echo "$env.compared_errors"
+          echo "$env.compared_errors" >> $GITHUB_OUTPUT
       - name: Find warning report comment
         if: failure() && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0

From 4c3d9935777137aa26f59af4cedda3f6d8d58f5d Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:28:56 +0100
Subject: [PATCH 37/70] try with curly brackets

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 0e8f2f932f..edb0591e7a 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,7 +175,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
         run: |
-          echo "$env.compared_errors" >> $GITHUB_OUTPUT
+          echo "${env.compared_errors}" >> $GITHUB_OUTPUT
       - name: Find warning report comment
         if: failure() && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0

From ca7e65cd9482542e6a546bb19b072744ae8a98d6 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:31:33 +0100
Subject: [PATCH 38/70] trial

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index edb0591e7a..773abb3526 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -171,6 +171,8 @@ jobs:
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           ref: ${{ steps.workflow-run-info.outputs.targetBranch }}
+      - name: Numbers of errors
+        if: failure()
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))

From 7107f2a52ef248779b001c22672cd04491fbd3dd Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:34:03 +0100
Subject: [PATCH 39/70] extra brackets ?

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 773abb3526..909ff5fcf5 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -177,7 +177,7 @@ jobs:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
           compared_errors: $((env.num_pr_errors - env.num_main_errors))
         run: |
-          echo "${env.compared_errors}" >> $GITHUB_OUTPUT
+          echo "${{env.compared_errors}}" >> $GITHUB_OUTPUT
       - name: Find warning report comment
         if: failure() && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0

From 3432fa1745e4b1f536399c1550d8c880a38491c9 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:38:00 +0100
Subject: [PATCH 40/70] add space

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 909ff5fcf5..04bbe432c8 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,7 +175,7 @@ jobs:
         if: failure()
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
-          compared_errors: $((env.num_pr_errors - env.num_main_errors))
+          compared_errors: $(( env.num_pr_errors - env.num_main_errors ))
         run: |
           echo "${{env.compared_errors}}" >> $GITHUB_OUTPUT
       - name: Find warning report comment

From f17c270576d8ce3b3bee658ba8e5cf81ec160a7c Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:45:26 +0100
Subject: [PATCH 41/70] try outputting both

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 04bbe432c8..fc1cad3c36 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,9 +175,10 @@ jobs:
         if: failure()
         env:
           num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
-          compared_errors: $(( env.num_pr_errors - env.num_main_errors ))
+          # compared_errors: $(( env.num_pr_errors - env.num_main_errors ))
         run: |
-          echo "${{env.compared_errors}}" >> $GITHUB_OUTPUT
+          echo "${{env.num_pr_errors}}" >> $GITHUB_OUTPUT
+          echo "${{env.num_main_errors}}" >> $GITHUB_OUTPUT
       - name: Find warning report comment
         if: failure() && env.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0

From 86ae867a9b750fb033e653f68dfb4e3d8f420d0d Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:52:29 +0100
Subject: [PATCH 42/70] give steps id instead of env

---
 .github/workflows/process.yml | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index fc1cad3c36..ec2fe34cd1 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -157,9 +157,9 @@ jobs:
 
           hatch run lint:fmt_extra "${files[@]}"
 
-        env:
           # need number of errors being flagged in these files
           num_pr_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
+        id: improvement_lint
 
       - name: Get information about the current run
         if: failure()
@@ -173,14 +173,12 @@ jobs:
           ref: ${{ steps.workflow-run-info.outputs.targetBranch }}
       - name: Numbers of errors
         if: failure()
-        env:
-          num_main_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
-          # compared_errors: $(( env.num_pr_errors - env.num_main_errors ))
         run: |
-          echo "${{env.num_pr_errors}}" >> $GITHUB_OUTPUT
-          echo "${{env.num_main_errors}}" >> $GITHUB_OUTPUT
+          compared_errors: $(( steps.improvement_lint.outputs.num_pr_errors - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
+        id: num_errors
+
       - name: Find warning report comment
-        if: failure() && env.compared_errors > 0
+        if: failure() && steps.num_errors.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -189,7 +187,7 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() && env.compared_errors > 0
+        if: failure() && && steps.num_errors.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}

From f2b1fab4af54e9ded7b520f151d8efd4d0c7967c Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:52:57 +0100
Subject: [PATCH 43/70] whoops

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index ec2fe34cd1..95ef5c79cf 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -187,7 +187,7 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() && && steps.num_errors.compared_errors > 0
+        if: failure() && steps.num_errors.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}

From 45c21488c2fa9d43fd32ab90efde3566a1c018be Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:56:59 +0100
Subject: [PATCH 44/70] try equals and more brackets

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 95ef5c79cf..44c87e7263 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -174,7 +174,7 @@ jobs:
       - name: Numbers of errors
         if: failure()
         run: |
-          compared_errors: $(( steps.improvement_lint.outputs.num_pr_errors - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
+          compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
         id: num_errors
 
       - name: Find warning report comment

From 5004c6bc2e6215cbb9b8f7da539096a2c997c522 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 15:59:35 +0100
Subject: [PATCH 45/70] print compared errors

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 44c87e7263..69f7ff3f25 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,6 +175,8 @@ jobs:
         if: failure()
         run: |
           compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
+
+          echo "$compared_errors" >> GITHUB_OUTPUT
         id: num_errors
 
       - name: Find warning report comment

From 99fb01d0ca274e018e4424e60a28ee05089ed51a Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 16:04:51 +0100
Subject: [PATCH 46/70] test

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 69f7ff3f25..9b8f7af9b0 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -176,7 +176,7 @@ jobs:
         run: |
           compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
 
-          echo "$compared_errors" >> GITHUB_OUTPUT
+          echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
         id: num_errors
 
       - name: Find warning report comment

From b6b33e472ba5782c06cbd0b9a1a33ab80a9ae7f9 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 16:07:36 +0100
Subject: [PATCH 47/70] print pr errors

---
 .github/workflows/process.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 9b8f7af9b0..f8e3463bc9 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -177,6 +177,7 @@ jobs:
           compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
 
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
+          echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors
 
       - name: Find warning report comment

From 6a2ff6c3d351656130ba9569ae074dc5e0ea0f6b Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 16:16:19 +0100
Subject: [PATCH 48/70] print separately

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index f8e3463bc9..ee592125d6 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -175,7 +175,7 @@ jobs:
         if: failure()
         run: |
           compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
-
+          echo $"(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))"
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From f18152884bf7970c9fc2f34b8157e68cb4fbffc6 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 16:54:47 +0100
Subject: [PATCH 49/70] use =

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index ee592125d6..a3d35e0c68 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -158,7 +158,7 @@ jobs:
           hatch run lint:fmt_extra "${files[@]}"
 
           # need number of errors being flagged in these files
-          num_pr_errors: $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
+          num_pr_errors=$((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
         id: improvement_lint
 
       - name: Get information about the current run

From ef7c45d18c4905bd64b2ced2d9458b020196dd46 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:01:19 +0100
Subject: [PATCH 50/70] default to 0

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index a3d35e0c68..f6b0bcbad8 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -159,6 +159,9 @@ jobs:
 
           # need number of errors being flagged in these files
           num_pr_errors=$((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
+          # default to 0 if no errors found
+          num_pr_errors=${num_pr_errors:-0}
+
         id: improvement_lint
 
       - name: Get information about the current run

From 29a6a658e55384d478516adc5aeab7c904490d58 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:03:46 +0100
Subject: [PATCH 51/70] remove outputs

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index f6b0bcbad8..46fb1283e9 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -177,7 +177,7 @@ jobs:
       - name: Numbers of errors
         if: failure()
         run: |
-          compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
+          compared_errors=$(( ${{ steps.improvement_lint.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
           echo $"(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))"
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT

From 18d173b2c258d9adf8f458707ede361fc6e72c28 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:08:47 +0100
Subject: [PATCH 52/70] move "

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 46fb1283e9..7600d068c6 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -178,7 +178,7 @@ jobs:
         if: failure()
         run: |
           compared_errors=$(( ${{ steps.improvement_lint.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
-          echo $"(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))"
+          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))"
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From 6c02f28af05e39efca09319047ea712787af825e Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:14:43 +0100
Subject: [PATCH 53/70] add .outputs

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 7600d068c6..aad437fae2 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -177,14 +177,14 @@ jobs:
       - name: Numbers of errors
         if: failure()
         run: |
-          compared_errors=$(( ${{ steps.improvement_lint.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
+          compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
           echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))"
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors
 
       - name: Find warning report comment
-        if: failure() && steps.num_errors.compared_errors > 0
+        if: failure() && steps.num_errors.outputs.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -193,7 +193,7 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() && steps.num_errors.compared_errors > 0
+        if: failure() && steps.num_errors.outputs.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}

From 1e215ac559f2a2409cbcda80186721b999d24cf4 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:19:03 +0100
Subject: [PATCH 54/70] bracket

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index aad437fae2..a15f0f48fd 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -177,7 +177,7 @@ jobs:
       - name: Numbers of errors
         if: failure()
         run: |
-          compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))
+          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')))
           echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))"
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT

From 8787b1357fb94c761cd848aef4af2dbb3341ccad Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:21:04 +0100
Subject: [PATCH 55/70] print pr errors

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index a15f0f48fd..9279cfbd56 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -162,6 +162,8 @@ jobs:
           # default to 0 if no errors found
           num_pr_errors=${num_pr_errors:-0}
 
+          echo "num pr errors = $num_pr_errors"
+
         id: improvement_lint
 
       - name: Get information about the current run

From c422e74930acd0f47338a45621c97cf522ec7530 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:21:58 +0100
Subject: [PATCH 56/70] only apply to changed files !!!

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 9279cfbd56..fdce462758 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -158,7 +158,7 @@ jobs:
           hatch run lint:fmt_extra "${files[@]}"
 
           # need number of errors being flagged in these files
-          num_pr_errors=$((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')
+          num_pr_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
           # default to 0 if no errors found
           num_pr_errors=${num_pr_errors:-0}
 
@@ -179,8 +179,8 @@ jobs:
       - name: Numbers of errors
         if: failure()
         run: |
-          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9')))
-          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra | tail -1) | tr -dc '0-9') ))"
+          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')))
+          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9') ))"
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From 80c7780ed594ae986d4485a22032c993d7593ce9 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:23:25 +0100
Subject: [PATCH 57/70] print pr errors

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index fdce462758..9c695accf3 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -162,7 +162,8 @@ jobs:
           # default to 0 if no errors found
           num_pr_errors=${num_pr_errors:-0}
 
-          echo "num pr errors = $num_pr_errors"
+          echo "num pr errors"
+          echo "${num_pr_errors}
 
         id: improvement_lint
 

From 8f32331b20c1a64b5423047ee1b6644c9c98333e Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:28:04 +0100
Subject: [PATCH 58/70] try new condtion

---
 .github/workflows/process.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 9c695accf3..ee26eb2016 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -180,14 +180,13 @@ jobs:
       - name: Numbers of errors
         if: failure()
         run: |
-          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')))
-          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9') ))"
-          echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
-          echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
+          num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
+
         id: num_errors
 
       - name: Find warning report comment
-        if: failure() && steps.num_errors.outputs.compared_errors > 0
+        # if more errors in this PR than on main in the changed files
+        if: failure() && ${{ ${{steps.improvement_lint.outputs.num_pr_errors}} > ${{steps.num_errors.outputs.num_main_errors}} }}
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:

From 9fac3f71fb569e1f9720c8a1b08a3081500e9c3c Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:28:45 +0100
Subject: [PATCH 59/70] again

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index ee26eb2016..373a6d2683 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -186,7 +186,7 @@ jobs:
 
       - name: Find warning report comment
         # if more errors in this PR than on main in the changed files
-        if: failure() && ${{ ${{steps.improvement_lint.outputs.num_pr_errors}} > ${{steps.num_errors.outputs.num_main_errors}} }}
+        if: failure() && ${{ steps.improvement_lint.outputs.num_pr_errors > steps.num_errors.outputs.num_main_errors }}
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:

From 0a536e9186569e5046019aa3b223fe9f5ad3741c Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:31:01 +0100
Subject: [PATCH 60/70] hmm

---
 .github/workflows/process.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 373a6d2683..61aec56302 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -181,12 +181,14 @@ jobs:
         if: failure()
         run: |
           num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
-
+          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - ))
+          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9') ))"
+          echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
+          echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors
 
       - name: Find warning report comment
-        # if more errors in this PR than on main in the changed files
-        if: failure() && ${{ steps.improvement_lint.outputs.num_pr_errors > steps.num_errors.outputs.num_main_errors }}
+        if: failure() && steps.num_errors.outputs.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -201,7 +203,7 @@ jobs:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            Files changed by this PR have introduced ${{ env.compared_errors }} more linting errors when compared to main.
+            Files changed by this PR have introduced ${{ steps.num_errors.outputs.compared_errors }} more linting errors when compared to main.
             Please fix these
           edit-mode: replace
 

From 893deb8f11ae2fd07565bf1ec9f4f4867177f15a Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:32:44 +0100
Subject: [PATCH 61/70] try to get the comment

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 61aec56302..3812f571d1 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -188,7 +188,7 @@ jobs:
         id: num_errors
 
       - name: Find warning report comment
-        if: failure() && steps.num_errors.outputs.compared_errors > 0
+        if: failure() # && steps.num_errors.outputs.compared_errors > 0
         uses: peter-evans/find-comment@b30e6a3c0ed37e7c023ccd3f1db5c6c0b0c23aad # v4.0.0
         id: find-warning-report-comment
         with:
@@ -197,7 +197,7 @@ jobs:
           body-includes: ⚠️ improve_quality_job warning!
           direction: last
       - name: Warning comment
-        if: failure() && steps.num_errors.outputs.compared_errors > 0
+        if: failure() # && steps.num_errors.outputs.compared_errors > 0
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}

From a509def961cc4e8f70c707df91fd437a4eb0d0bc Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:35:54 +0100
Subject: [PATCH 62/70] fix

---
 .github/workflows/process.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 3812f571d1..cd8de861fa 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -181,8 +181,10 @@ jobs:
         if: failure()
         run: |
           num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
-          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - ))
-          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9') ))"
+          num_main_errors=${num_main_errors:-0}
+
+          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - ${{steps.num_errors.outputs.num_main_errors}}))
+          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9') ))" >> GITHUB_OUTPUT
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From 3b2003dd95217a7dd80957408a62d452d3257c42 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:40:14 +0100
Subject: [PATCH 63/70] try again

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index cd8de861fa..1d17804d26 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -183,8 +183,7 @@ jobs:
           num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
           num_main_errors=${num_main_errors:-0}
 
-          compared_errors=$((${{steps.improvement_lint.outputs.num_pr_errors}} - ${{steps.num_errors.outputs.num_main_errors}}))
-          echo "$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - $((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9') ))" >> GITHUB_OUTPUT
+          compared_errors=$((steps.improvement_lint.outputs.num_pr_errors - steps.num_errors.outputs.num_main_errors))
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From d67c5d2216b5cf60157217b3c493322e6d6f09ab Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:42:56 +0100
Subject: [PATCH 64/70] bracket again

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 1d17804d26..ea897ac894 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -183,7 +183,7 @@ jobs:
           num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
           num_main_errors=${num_main_errors:-0}
 
-          compared_errors=$((steps.improvement_lint.outputs.num_pr_errors - steps.num_errors.outputs.num_main_errors))
+          compared_errors=$(( $((steps.improvement_lint.outputs.num_pr_errors)) - $((steps.num_errors.outputs.num_main_errors)) ))
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From 0042f0ec90f709286647d6fa5df371affe7134ab Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:45:14 +0100
Subject: [PATCH 65/70] remove spaces

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index ea897ac894..616200845a 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -183,7 +183,7 @@ jobs:
           num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
           num_main_errors=${num_main_errors:-0}
 
-          compared_errors=$(( $((steps.improvement_lint.outputs.num_pr_errors)) - $((steps.num_errors.outputs.num_main_errors)) ))
+          compared_errors=$(($((steps.improvement_lint.outputs.num_pr_errors))-$((steps.num_errors.outputs.num_main_errors))))
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From eeb4832d846f26f566d738408d3ac05491d8b05d Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:47:55 +0100
Subject: [PATCH 66/70] testing

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 616200845a..7fe9164e7c 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -183,7 +183,8 @@ jobs:
           num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
           num_main_errors=${num_main_errors:-0}
 
-          compared_errors=$(($((steps.improvement_lint.outputs.num_pr_errors))-$((steps.num_errors.outputs.num_main_errors))))
+          ((compared_errors=steps.improvement_lint.outputs.num_pr_errors-steps.num_errors.outputs.num_main_errors))
+          # compared_errors=$(($((steps.improvement_lint.outputs.num_pr_errors))-$((steps.num_errors.outputs.num_main_errors))))
           echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From cc89766a495b771d8dc93a665aa5a217a3740780 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:50:40 +0100
Subject: [PATCH 67/70] try

---
 .github/workflows/process.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 7fe9164e7c..825d5db1d5 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -183,10 +183,11 @@ jobs:
           num_main_errors=$((hatch run lint:fmt_extra "${files[@]}" | tail -1) | tr -dc '0-9')
           num_main_errors=${num_main_errors:-0}
 
-          ((compared_errors=steps.improvement_lint.outputs.num_pr_errors-steps.num_errors.outputs.num_main_errors))
+          echo $num_main_errors
+          #
           # compared_errors=$(($((steps.improvement_lint.outputs.num_pr_errors))-$((steps.num_errors.outputs.num_main_errors))))
-          echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
-          echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
+          # echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
+          # echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors
 
       - name: Find warning report comment

From e597c28c2bacf1651489012232ffaf46ef298f8c Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:54:51 +0100
Subject: [PATCH 68/70] back to curly brackets

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 825d5db1d5..3f1de57c80 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -185,7 +185,7 @@ jobs:
 
           echo $num_main_errors
           #
-          # compared_errors=$(($((steps.improvement_lint.outputs.num_pr_errors))-$((steps.num_errors.outputs.num_main_errors))))
+          # compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - ${{ steps.num_errors.outputs.num_main_errors }}))
           # echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
           # echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors

From 9e33b563cade12289291dc318a16400c0c1b3351 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:55:12 +0100
Subject: [PATCH 69/70] whoops

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index 3f1de57c80..bafeeefad5 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -184,10 +184,10 @@ jobs:
           num_main_errors=${num_main_errors:-0}
 
           echo $num_main_errors
-          #
-          # compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - ${{ steps.num_errors.outputs.num_main_errors }}))
-          # echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
-          # echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
+
+          compared_errors=$(( ${{ steps.improvement_lint.outputs.num_pr_errors }} - ${{ steps.num_errors.outputs.num_main_errors }}))
+          echo "comp errors = $compared_errors" >> GITHUB_OUTPUT
+          echo "pr errors ${{ steps.improvement_lint.outputs.num_pr_errors }}" >> GITHUB_OUTPUT
         id: num_errors
 
       - name: Find warning report comment

From e4905548e200d3af9871b86b3d678df06a32b5c3 Mon Sep 17 00:00:00 2001
From: Clair Mould <86794332+clmould@users.noreply.github.com>
Date: Mon, 28 Sep 2026 17:59:46 +0100
Subject: [PATCH 70/70] print number

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

diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index bafeeefad5..d2e840ddba 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -206,7 +206,7 @@ jobs:
           comment-id: ${{ steps.find-warning-report-comment.outputs.comment-id }}
           issue-number: ${{ steps.workflow-run-info.outputs.pullRequestNumber }}
           body: |
-            Files changed by this PR have introduced ${{ steps.num_errors.outputs.compared_errors }} more linting errors when compared to main.
+            Files changed by this PR have introduced $"{{ steps.num_errors.outputs.compared_errors }}" more linting errors when compared to main.
             Please fix these
           edit-mode: replace