From d550002d20852c2592e01ed3cc3a9d5818222d37 Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Wed, 22 Oct 2025 20:22:35 +0200
Subject: [PATCH 01/15] Add workflow to fix outdated tools and implement script
 for uninstallable revisions

---
 .github/workflows/fix-outdated-tools.yml | 105 ++++++++++++++++++
 scripts/fix_outdated.py                  | 131 +++++++++++++++++++++++
 2 files changed, 236 insertions(+)
 create mode 100644 .github/workflows/fix-outdated-tools.yml
 create mode 100644 scripts/fix_outdated.py

diff --git a/.github/workflows/fix-outdated-tools.yml b/.github/workflows/fix-outdated-tools.yml
new file mode 100644
index 00000000..ec39ceb3
--- /dev/null
+++ b/.github/workflows/fix-outdated-tools.yml
@@ -0,0 +1,105 @@
+name: Fix Outdated Tools
+
+on:
+  workflow_dispatch:
+
+jobs:
+  get-lockfiles:
+    runs-on: ubuntu-latest
+    outputs:
+      lockfiles: ${{ steps.set-matrix.outputs.lockfiles }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Get all lock files
+        id: set-matrix
+        run: |
+          lockfiles=$(ls *.yaml.lock | jq -R -s -c 'split("\n")[:-1]')
+          echo "lockfiles=$lockfiles" >> $GITHUB_OUTPUT
+
+  fix-outdated:
+    needs: get-lockfiles
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        lockfile: ${{ fromJson(needs.get-lockfiles.outputs.lockfiles) }}
+      fail-fast: false
+    permissions:
+      contents: write
+      pull-requests: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Install dependencies
+        run: uv pip install --system -r requirements.txt
+
+      - name: Fix ${{ matrix.lockfile }}
+        run: python scripts/fix_outdated.py "${{ matrix.lockfile }}"
+
+      - name: Upload changes
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: ${{ matrix.lockfile }}
+          path: ${{ matrix.lockfile }}
+
+  create-pr:
+    needs: fix-outdated
+    if: always()
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+            fetch-depth: 0
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@v5
+        with:
+          merge-multiple: true
+
+      - name: Check for changes
+        id: check_changes
+        run: |
+          if [[ -n $(git status --porcelain) ]]; then
+            echo "changes=true" >> $GITHUB_OUTPUT
+            echo "Changes detected in lock files"
+          else
+            echo "changes=false" >> $GITHUB_OUTPUT
+            echo "No changes detected"
+          fi
+
+      - name: Create or update Pull Request
+        id: cpr
+        if: steps.check_changes.outputs.changes == 'true'
+        uses: peter-evans/create-pull-request@v7
+        with:
+          branch: fix-outdated-tools
+          commit-message: Fix uninstallable tool revisions
+          title: 'Fix uninstallable tool revisions'
+          body: |
+            This PR was automatically generated by the `fix-outdated-tools` workflow.
+            Workflow run: [${{ github.run_id }}](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})
+          delete-branch: true
+
+      - name: Comment on updated PR
+        if: steps.cpr.outputs.pull-request-operation == 'update'
+        uses: peter-evans/create-or-update-comment@v5
+        with:
+          issue-number: ${{ steps.cpr.outputs.pull-request-number }}
+          body: |
+            🔄 This PR was automatically updated with new lockfile changes.
+            Workflow run: [${{ github.run_id }}](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})
diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
new file mode 100644
index 00000000..04725fc2
--- /dev/null
+++ b/scripts/fix_outdated.py
@@ -0,0 +1,131 @@
+import argparse
+import logging
+import yaml
+from concurrent.futures import ThreadPoolExecutor, as_completed
+
+from bioblend import toolshed
+
+logging.basicConfig(
+    level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s"
+)
+logger = logging.getLogger(__name__)
+
+
+def get_tool_versions(ts, name, owner, revision):
+    versions = set()
+
+    try:
+        repo_metadata = ts.repositories.get_repository_revision_install_info(
+            name, owner, revision
+        )
+        if isinstance(repo_metadata, list) and len(repo_metadata) > 1:
+            for tool in repo_metadata[1].get("valid_tools", []):
+                if "id" in tool and "version" in tool:
+                    versions.add((tool["id"], tool["version"]))
+    except Exception as e:
+        logger.warning(f"{name},{owner}: failed to fetch {revision} ({e})")
+    return versions
+
+
+def fetch_versions_parallel(ts, name, owner, revisions, max_workers=10):
+    version_cache = {}
+    with ThreadPoolExecutor(max_workers=max_workers) as executor:
+        futures = {
+            executor.submit(get_tool_versions, ts, name, owner, rev): rev
+            for rev in revisions
+        }
+        for future in as_completed(futures):
+            rev = futures[future]
+            try:
+                version_cache[rev] = future.result()
+            except Exception as e:
+                logger.warning(f"{name},{owner}: error fetching {rev} ({e})")
+                version_cache[rev] = set()
+    return version_cache
+
+
+def fix_uninstallable(lockfile_name, toolshed_url):
+    ts = toolshed.ToolShedInstance(url=toolshed_url)
+    with open(lockfile_name) as f:
+        lockfile = yaml.safe_load(f) or {}
+    locked_tools = lockfile.get("tools", [])
+    total = len(locked_tools)
+
+    logger.info(f"Processing {total} tools from {lockfile_name}...")
+    changed, skipped = 0, 0
+
+    for i, tool in enumerate(locked_tools):
+        if i % 10 == 0:
+            logger.info(
+                f"Progress: {i}/{total} tools ({skipped} skipped, {changed} changed)"
+            )
+
+        name, owner = tool.get("name"), tool.get("owner")
+        revisions = tool.get("revisions", [])
+        try:
+            installable = ts.repositories.get_ordered_installable_revisions(name, owner)
+        except Exception as e:
+            logger.warning(f"{name},{owner}: could not get installable revisions ({e})")
+            continue
+
+        uninstallable = set(revisions) - set(installable)
+        if not uninstallable:
+            skipped += 1
+            continue
+
+        all_revs = list(uninstallable) + list(installable)
+        version_cache = fetch_versions_parallel(ts, name, owner, all_revs)
+
+        to_remove = []
+        for cur in uninstallable:
+            cur_versions = version_cache.get(cur, set())
+            if not cur_versions:
+                if installable:
+                    nxt = installable[0]
+                    logger.info(f"{name},{owner}: unverifiable {cur}, keeping {nxt}")
+                    to_remove.append(cur)
+                continue
+
+            nxt = next(
+                (
+                    cand
+                    for cand in installable
+                    if version_cache.get(cand) == cur_versions
+                ),
+                None,
+            )
+
+            if not nxt:
+                logger.warning(
+                    f"{name},{owner}: no matching installable revision for {cur}"
+                )
+                continue
+
+            logger.info(
+                f"{name},{owner}: removing {cur} {'in favor of ' + nxt if nxt in revisions else 'with no installable alternative found'}"
+            )
+            to_remove.append(cur)
+
+        if to_remove:
+            changed += 1
+            tool["revisions"] = sorted(set(r for r in revisions if r not in to_remove))
+
+    logger.info(
+        f"Completed: {total} tools processed, {skipped} skipped, {changed} changed"
+    )
+
+    with open(lockfile_name, "w") as f:
+        yaml.dump(lockfile, f, sort_keys=False, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "lockfile", type=argparse.FileType("r"), help="Tool.yaml.lock file"
+    )
+    parser.add_argument(
+        "--toolshed", default="https://toolshed.g2.bx.psu.edu", help="Toolshed base URL"
+    )
+    args = parser.parse_args()
+
+    fix_uninstallable(args.lockfile.name, args.toolshed)

From 0b0e5a64e6a761b0220448c9df568a443e59f59e Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Thu, 23 Oct 2025 11:15:05 +0200
Subject: [PATCH 02/15] Handle errors by exiting the script in fix_outdated.py

---
 ephemeris               | 1 +
 scripts/fix_outdated.py | 8 +++++---
 2 files changed, 6 insertions(+), 3 deletions(-)
 create mode 160000 ephemeris

diff --git a/ephemeris b/ephemeris
new file mode 160000
index 00000000..ea30c38e
--- /dev/null
+++ b/ephemeris
@@ -0,0 +1 @@
+Subproject commit ea30c38ed570455fe8c6d699305977b49068b5d9
diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index 04725fc2..b698dc20 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -1,8 +1,9 @@
 import argparse
 import logging
-import yaml
+import sys
 from concurrent.futures import ThreadPoolExecutor, as_completed
 
+import yaml
 from bioblend import toolshed
 
 logging.basicConfig(
@@ -24,6 +25,7 @@ def get_tool_versions(ts, name, owner, revision):
                     versions.add((tool["id"], tool["version"]))
     except Exception as e:
         logger.warning(f"{name},{owner}: failed to fetch {revision} ({e})")
+        sys.exit(1)
     return versions
 
 
@@ -40,7 +42,7 @@ def fetch_versions_parallel(ts, name, owner, revisions, max_workers=10):
                 version_cache[rev] = future.result()
             except Exception as e:
                 logger.warning(f"{name},{owner}: error fetching {rev} ({e})")
-                version_cache[rev] = set()
+                sys.exit(1)
     return version_cache
 
 
@@ -99,7 +101,7 @@ def fix_uninstallable(lockfile_name, toolshed_url):
                 logger.warning(
                     f"{name},{owner}: no matching installable revision for {cur}"
                 )
-                continue
+                sys.exit(1)
 
             logger.info(
                 f"{name},{owner}: removing {cur} {'in favor of ' + nxt if nxt in revisions else 'with no installable alternative found'}"

From 9d953a35047e771f19e7a1ca7957cabd6d5b38cd Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Fri, 24 Oct 2025 10:25:09 +0200
Subject: [PATCH 03/15] Remove ephemeris subproject reference

---
 ephemeris | 1 -
 1 file changed, 1 deletion(-)
 delete mode 160000 ephemeris

diff --git a/ephemeris b/ephemeris
deleted file mode 160000
index ea30c38e..00000000
--- a/ephemeris
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ea30c38ed570455fe8c6d699305977b49068b5d9

From 6263fb601a231f38892f7d4988e2865238966e68 Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Fri, 24 Oct 2025 11:05:58 +0200
Subject: [PATCH 04/15] Implement retry logic with exponential backoff for
 repository fetch operations

---
 scripts/fix_outdated.py | 40 +++++++++++++++++++++++++++++++++++++---
 1 file changed, 37 insertions(+), 3 deletions(-)

diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index b698dc20..fdaed895 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -1,6 +1,7 @@
 import argparse
 import logging
 import sys
+import time
 from concurrent.futures import ThreadPoolExecutor, as_completed
 
 import yaml
@@ -12,12 +13,43 @@
 logger = logging.getLogger(__name__)
 
 
+def retry_with_backoff(func, *args, **kwargs):
+    MAX_RETRIES = 5
+    backoff = 2
+    last_exception = None
+
+    for attempt in range(MAX_RETRIES):
+        try:
+            return func(*args, **kwargs)
+        except Exception as e:
+            last_exception = e
+            error_msg = str(e)
+            if any(
+                code in error_msg
+                for code in ["502", "503", "504", "timed out", "timeout", "Connection"]
+            ):
+                if attempt < MAX_RETRIES - 1:
+                    logger.warning(
+                        f"Attempt {attempt + 1}/{MAX_RETRIES} failed: {error_msg}. Retrying in {backoff}s..."
+                    )
+                    time.sleep(backoff)
+                    backoff = min(backoff * 2, 60)
+                else:
+                    logger.error(f"All {MAX_RETRIES} attempts failed")
+            else:
+                raise
+
+    if last_exception:
+        raise last_exception
+    raise Exception("Retry failed with no exception captured")
+
+
 def get_tool_versions(ts, name, owner, revision):
     versions = set()
 
     try:
-        repo_metadata = ts.repositories.get_repository_revision_install_info(
-            name, owner, revision
+        repo_metadata = retry_with_backoff(
+            ts.repositories.get_repository_revision_install_info, name, owner, revision
         )
         if isinstance(repo_metadata, list) and len(repo_metadata) > 1:
             for tool in repo_metadata[1].get("valid_tools", []):
@@ -65,7 +97,9 @@ def fix_uninstallable(lockfile_name, toolshed_url):
         name, owner = tool.get("name"), tool.get("owner")
         revisions = tool.get("revisions", [])
         try:
-            installable = ts.repositories.get_ordered_installable_revisions(name, owner)
+            installable = retry_with_backoff(
+                ts.repositories.get_ordered_installable_revisions, name, owner
+            )
         except Exception as e:
             logger.warning(f"{name},{owner}: could not get installable revisions ({e})")
             continue

From f926b662dd8f76acb6a79cb5b4addbffaca199eb Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Fri, 24 Oct 2025 12:26:37 +0200
Subject: [PATCH 05/15] Remove comment step from PR update workflow in
 fix-outdated-tools.yml

---
 .github/workflows/fix-outdated-tools.yml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/.github/workflows/fix-outdated-tools.yml b/.github/workflows/fix-outdated-tools.yml
index ec39ceb3..b32bc8f9 100644
--- a/.github/workflows/fix-outdated-tools.yml
+++ b/.github/workflows/fix-outdated-tools.yml
@@ -94,12 +94,3 @@ jobs:
             This PR was automatically generated by the `fix-outdated-tools` workflow.
             Workflow run: [${{ github.run_id }}](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})
           delete-branch: true
-
-      - name: Comment on updated PR
-        if: steps.cpr.outputs.pull-request-operation == 'update'
-        uses: peter-evans/create-or-update-comment@v5
-        with:
-          issue-number: ${{ steps.cpr.outputs.pull-request-number }}
-          body: |
-            🔄 This PR was automatically updated with new lockfile changes.
-            Workflow run: [${{ github.run_id }}](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})

From 732e484b0e7bc6f7d92ae5645fb3badb202cdd20 Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Tue, 28 Oct 2025 12:24:22 +0100
Subject: [PATCH 06/15] Refactor tool removal logic to ensure revisions are
 updated correctly and improve logging clarity

---
 scripts/fix_outdated.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index fdaed895..5b716017 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -137,14 +137,14 @@ def fix_uninstallable(lockfile_name, toolshed_url):
                 )
                 sys.exit(1)
 
-            logger.info(
-                f"{name},{owner}: removing {cur} {'in favor of ' + nxt if nxt in revisions else 'with no installable alternative found'}"
-            )
+            logger.info(f"{name},{owner}: removing {cur} in favor of {nxt}")
+            if nxt not in revisions:
+                revisions.append(nxt)
             to_remove.append(cur)
 
         if to_remove:
             changed += 1
-            tool["revisions"] = sorted(set(r for r in revisions if r not in to_remove))
+            tool["revisions"] = sorted(set(revisions) - set(to_remove))
 
     logger.info(
         f"Completed: {total} tools processed, {skipped} skipped, {changed} changed"

From ac1664cebd17b1297168d6802de42bd07339677d Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Fri, 7 Nov 2025 12:54:47 +0100
Subject: [PATCH 07/15] reverse over installable to get the latest revisions

---
 scripts/fix_outdated.py | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index 5b716017..1a1cdec4 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -122,14 +122,11 @@ def fix_uninstallable(lockfile_name, toolshed_url):
                     to_remove.append(cur)
                 continue
 
-            nxt = next(
-                (
-                    cand
-                    for cand in installable
-                    if version_cache.get(cand) == cur_versions
-                ),
-                None,
-            )
+            nxt = None
+            for cand in reversed(installable):
+                if version_cache.get(cand) == cur_versions:
+                    nxt = cand
+                    break
 
             if not nxt:
                 logger.warning(

From 8c920f8b2bef0e070e9a64cc275219794213ac0c Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Mon, 24 Nov 2025 12:19:29 +0100
Subject: [PATCH 08/15] Fix: Add missing github-token to uv installation step

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

diff --git a/.github/workflows/fix-outdated-tools.yml b/.github/workflows/fix-outdated-tools.yml
index b32bc8f9..b361fac7 100644
--- a/.github/workflows/fix-outdated-tools.yml
+++ b/.github/workflows/fix-outdated-tools.yml
@@ -39,6 +39,8 @@ jobs:
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install dependencies
         run: uv pip install --system -r requirements.txt

From c7696df83c9a494c6ca3da26a7d5285f171009d2 Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Mon, 24 Nov 2025 17:05:23 +0100
Subject: [PATCH 09/15] Fix: Refactor fix_uninstallable function for improved
 error handling and path management

---
 scripts/fix_outdated.py | 95 +++++++++++++++++++++++++----------------
 1 file changed, 58 insertions(+), 37 deletions(-)

diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index 1a1cdec4..d05537df 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -2,7 +2,9 @@
 import logging
 import sys
 import time
+from pathlib import Path
 from concurrent.futures import ThreadPoolExecutor, as_completed
+from collections import defaultdict
 
 import yaml
 from bioblend import toolshed
@@ -16,13 +18,11 @@
 def retry_with_backoff(func, *args, **kwargs):
     MAX_RETRIES = 5
     backoff = 2
-    last_exception = None
 
     for attempt in range(MAX_RETRIES):
         try:
             return func(*args, **kwargs)
         except Exception as e:
-            last_exception = e
             error_msg = str(e)
             if any(
                 code in error_msg
@@ -34,14 +34,9 @@ def retry_with_backoff(func, *args, **kwargs):
                     )
                     time.sleep(backoff)
                     backoff = min(backoff * 2, 60)
-                else:
-                    logger.error(f"All {MAX_RETRIES} attempts failed")
-            else:
-                raise
-
-    if last_exception:
-        raise last_exception
-    raise Exception("Retry failed with no exception captured")
+                    continue
+            raise e
+    raise Exception("Retry failed after max attempts")
 
 
 def get_tool_versions(ts, name, owner, revision):
@@ -80,12 +75,28 @@ def fetch_versions_parallel(ts, name, owner, revisions, max_workers=10):
 
 def fix_uninstallable(lockfile_name, toolshed_url):
     ts = toolshed.ToolShedInstance(url=toolshed_url)
-    with open(lockfile_name) as f:
+    lockfile_path = Path(lockfile_name)
+    with open(lockfile_path) as f:
         lockfile = yaml.safe_load(f) or {}
     locked_tools = lockfile.get("tools", [])
     total = len(locked_tools)
 
-    logger.info(f"Processing {total} tools from {lockfile_name}...")
+    uninstallable_file = lockfile_path.with_name(
+        lockfile_path.name.replace(".yaml.lock", ".uninstallable_revisions.yaml")
+    )
+
+    removed_map = defaultdict(set)
+    try:
+        with open(uninstallable_file) as f:
+            uninstallable_data = yaml.safe_load(f) or {}
+            for t in uninstallable_data.get("tools", []):
+                removed_map[(t["name"], t["owner"])] = set(
+                    t.get("removed_revisions", [])
+                )
+    except FileNotFoundError:
+        pass
+
+    logger.info(f"Processing {total} tools from {lockfile_path.name}...")
     changed, skipped = 0, 0
 
     for i, tool in enumerate(locked_tools):
@@ -95,38 +106,40 @@ def fix_uninstallable(lockfile_name, toolshed_url):
             )
 
         name, owner = tool.get("name"), tool.get("owner")
-        revisions = tool.get("revisions", [])
+        current_revisions = set(tool.get("revisions", []))
         try:
-            installable = retry_with_backoff(
+            installable_list = retry_with_backoff(
                 ts.repositories.get_ordered_installable_revisions, name, owner
             )
         except Exception as e:
             logger.warning(f"{name},{owner}: could not get installable revisions ({e})")
             continue
 
-        uninstallable = set(revisions) - set(installable)
+        uninstallable = current_revisions - set(installable_list)
         if not uninstallable:
             skipped += 1
             continue
 
-        all_revs = list(uninstallable) + list(installable)
+        all_revs = list(uninstallable) + installable_list
         version_cache = fetch_versions_parallel(ts, name, owner, all_revs)
 
-        to_remove = []
+        installable_signatures = {}
+        for rev in installable_list:
+            sig = frozenset(version_cache.get(rev, []))
+            if sig:
+                installable_signatures[sig] = rev
+        to_remove = set()
+
         for cur in uninstallable:
-            cur_versions = version_cache.get(cur, set())
-            if not cur_versions:
-                if installable:
-                    nxt = installable[0]
+            cur_sig = frozenset(version_cache.get(cur, []))
+            if not cur_sig:
+                if installable_list:
+                    nxt = installable_list[-1]
                     logger.info(f"{name},{owner}: unverifiable {cur}, keeping {nxt}")
-                    to_remove.append(cur)
-                continue
+                    to_remove.add(cur)
+                    continue
 
-            nxt = None
-            for cand in reversed(installable):
-                if version_cache.get(cand) == cur_versions:
-                    nxt = cand
-                    break
+            nxt = installable_signatures.get(cur_sig)
 
             if not nxt:
                 logger.warning(
@@ -135,30 +148,38 @@ def fix_uninstallable(lockfile_name, toolshed_url):
                 sys.exit(1)
 
             logger.info(f"{name},{owner}: removing {cur} in favor of {nxt}")
-            if nxt not in revisions:
-                revisions.append(nxt)
-            to_remove.append(cur)
+            if nxt not in current_revisions:
+                tool["revisions"].append(nxt)
+            to_remove.add(cur)
 
         if to_remove:
             changed += 1
-            tool["revisions"] = sorted(set(revisions) - set(to_remove))
+            tool["revisions"] = sorted(set(tool["revisions"]) - to_remove)
+            removed_map[(name, owner)].update(to_remove)
 
     logger.info(
         f"Completed: {total} tools processed, {skipped} skipped, {changed} changed"
     )
 
-    with open(lockfile_name, "w") as f:
+    with open(lockfile_path, "w") as f:
         yaml.dump(lockfile, f, sort_keys=False, default_flow_style=False)
 
+    uninstallable_output = {
+        "tools": [
+            {"name": n, "owner": o, "removed_revisions": sorted(revs)}
+            for (n, o), revs in removed_map.items()
+        ]
+    }
+    with open(uninstallable_file, "w") as f:
+        yaml.dump(uninstallable_output, f, sort_keys=False, default_flow_style=False)
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument(
-        "lockfile", type=argparse.FileType("r"), help="Tool.yaml.lock file"
-    )
+    parser.add_argument("lockfile", help="Tool.yaml.lock file path")
     parser.add_argument(
         "--toolshed", default="https://toolshed.g2.bx.psu.edu", help="Toolshed base URL"
     )
     args = parser.parse_args()
 
-    fix_uninstallable(args.lockfile.name, args.toolshed)
+    fix_uninstallable(args.lockfile, args.toolshed)

From 84418c8e199f4a7b65e56a796ef2c2b9bc7f961a Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Tue, 25 Nov 2025 11:16:05 +0100
Subject: [PATCH 10/15] Fix: Update upload artifact step to include
 uninstallable revisions and ignore if no files found

---
 .github/workflows/fix-outdated-tools.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/fix-outdated-tools.yml b/.github/workflows/fix-outdated-tools.yml
index b361fac7..6b619912 100644
--- a/.github/workflows/fix-outdated-tools.yml
+++ b/.github/workflows/fix-outdated-tools.yml
@@ -53,7 +53,10 @@ jobs:
         if: always()
         with:
           name: ${{ matrix.lockfile }}
-          path: ${{ matrix.lockfile }}
+          path: |
+            ${{ matrix.lockfile }}
+            *.uninstallable_revisions.yaml
+          if-no-files-found: ignore
 
   create-pr:
     needs: fix-outdated

From 7991eb4e1b460ba01f009d6670235c6f4eaee392 Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Tue, 25 Nov 2025 13:10:06 +0100
Subject: [PATCH 11/15] Fix: Only write uninstallable revisions file if there
 are removed revisions

---
 scripts/fix_outdated.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index d05537df..ac15c462 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -164,14 +164,17 @@ def fix_uninstallable(lockfile_name, toolshed_url):
     with open(lockfile_path, "w") as f:
         yaml.dump(lockfile, f, sort_keys=False, default_flow_style=False)
 
-    uninstallable_output = {
-        "tools": [
-            {"name": n, "owner": o, "removed_revisions": sorted(revs)}
-            for (n, o), revs in removed_map.items()
-        ]
-    }
-    with open(uninstallable_file, "w") as f:
-        yaml.dump(uninstallable_output, f, sort_keys=False, default_flow_style=False)
+    if removed_map:
+        uninstallable_output = {
+            "tools": [
+                {"name": n, "owner": o, "removed_revisions": sorted(revs)}
+                for (n, o), revs in removed_map.items()
+            ]
+        }
+        with open(uninstallable_file, "w") as f:
+            yaml.dump(
+                uninstallable_output, f, sort_keys=False, default_flow_style=False
+            )
 
 
 if __name__ == "__main__":

From d30bb8d4c6121393aa626688311845df2b429e5f Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Fri, 28 Nov 2025 12:08:28 +0100
Subject: [PATCH 12/15] Add scheduled trigger for the fix outdated tools
 workflow

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

diff --git a/.github/workflows/fix-outdated-tools.yml b/.github/workflows/fix-outdated-tools.yml
index 6b619912..d63408e7 100644
--- a/.github/workflows/fix-outdated-tools.yml
+++ b/.github/workflows/fix-outdated-tools.yml
@@ -2,6 +2,8 @@ name: Fix Outdated Tools
 
 on:
   workflow_dispatch:
+  schedule:
+    - cron: '0 9 1 * *'
 
 jobs:
   get-lockfiles:

From 7548fad8ac66b275289f5aff512ec8f445a24063 Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Wed, 3 Dec 2025 12:44:12 +0100
Subject: [PATCH 13/15] Rename uninstallable revisions to not-installable
 revisions in workflow and script

---
 .github/workflows/fix-outdated-tools.yml |  6 +++---
 scripts/fix_outdated.py                  | 22 ++++++++++------------
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/fix-outdated-tools.yml b/.github/workflows/fix-outdated-tools.yml
index d63408e7..447d1580 100644
--- a/.github/workflows/fix-outdated-tools.yml
+++ b/.github/workflows/fix-outdated-tools.yml
@@ -57,7 +57,7 @@ jobs:
           name: ${{ matrix.lockfile }}
           path: |
             ${{ matrix.lockfile }}
-            *.uninstallable_revisions.yaml
+            *.not-installable-revisions.yaml
           if-no-files-found: ignore
 
   create-pr:
@@ -95,8 +95,8 @@ jobs:
         uses: peter-evans/create-pull-request@v7
         with:
           branch: fix-outdated-tools
-          commit-message: Fix uninstallable tool revisions
-          title: 'Fix uninstallable tool revisions'
+          commit-message: Remove not-installable tool revisions
+          title: 'Remove not-installable tool revisions'
           body: |
             This PR was automatically generated by the `fix-outdated-tools` workflow.
             Workflow run: [${{ github.run_id }}](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }})
diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index ac15c462..ae4e25aa 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -81,18 +81,16 @@ def fix_uninstallable(lockfile_name, toolshed_url):
     locked_tools = lockfile.get("tools", [])
     total = len(locked_tools)
 
-    uninstallable_file = lockfile_path.with_name(
-        lockfile_path.name.replace(".yaml.lock", ".uninstallable_revisions.yaml")
+    not_installable_file = lockfile_path.with_name(
+        lockfile_path.name.replace(".yaml.lock", ".not-installable-revisions.yaml")
     )
 
     removed_map = defaultdict(set)
     try:
-        with open(uninstallable_file) as f:
-            uninstallable_data = yaml.safe_load(f) or {}
-            for t in uninstallable_data.get("tools", []):
-                removed_map[(t["name"], t["owner"])] = set(
-                    t.get("removed_revisions", [])
-                )
+        with open(not_installable_file) as f:
+            not_installable_data = yaml.safe_load(f) or {}
+            for t in not_installable_data.get("tools", []):
+                removed_map[(t["name"], t["owner"])] = set(t.get("revisions", []))
     except FileNotFoundError:
         pass
 
@@ -165,15 +163,15 @@ def fix_uninstallable(lockfile_name, toolshed_url):
         yaml.dump(lockfile, f, sort_keys=False, default_flow_style=False)
 
     if removed_map:
-        uninstallable_output = {
+        not_installable_output = {
             "tools": [
-                {"name": n, "owner": o, "removed_revisions": sorted(revs)}
+                {"name": n, "owner": o, "revisions": sorted(revs)}
                 for (n, o), revs in removed_map.items()
             ]
         }
-        with open(uninstallable_file, "w") as f:
+        with open(not_installable_file, "w") as f:
             yaml.dump(
-                uninstallable_output, f, sort_keys=False, default_flow_style=False
+                not_installable_output, f, sort_keys=False, default_flow_style=False
             )
 
 

From b976dbccf30330870681110216d833fa29b72332 Mon Sep 17 00:00:00 2001
From: Arash Kadkhodaei <arash77.kad@gmail.com>
Date: Wed, 7 Jan 2026 14:09:43 +0100
Subject: [PATCH 14/15] Apply suggestions from code review

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 scripts/fix_outdated.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index ae4e25aa..4c4f18dc 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -15,8 +15,9 @@
 logger = logging.getLogger(__name__)
 
 
+MAX_RETRIES = 5
+
 def retry_with_backoff(func, *args, **kwargs):
-    MAX_RETRIES = 5
     backoff = 2
 
     for attempt in range(MAX_RETRIES):

From c499cd02f36d8c6fa2c4fbc287419ff21bbbbfbc Mon Sep 17 00:00:00 2001
From: Arash <arash77.kad@gmail.com>
Date: Wed, 7 Jan 2026 15:22:47 +0100
Subject: [PATCH 15/15] Refactor retry_with_backoff to use a local max_retries
 variable instead of a global constant

---
 scripts/fix_outdated.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/scripts/fix_outdated.py b/scripts/fix_outdated.py
index 4c4f18dc..0e540633 100644
--- a/scripts/fix_outdated.py
+++ b/scripts/fix_outdated.py
@@ -15,12 +15,11 @@
 logger = logging.getLogger(__name__)
 
 
-MAX_RETRIES = 5
-
 def retry_with_backoff(func, *args, **kwargs):
     backoff = 2
+    max_retries = 5
 
-    for attempt in range(MAX_RETRIES):
+    for attempt in range(max_retries):
         try:
             return func(*args, **kwargs)
         except Exception as e:
@@ -29,9 +28,9 @@ def retry_with_backoff(func, *args, **kwargs):
                 code in error_msg
                 for code in ["502", "503", "504", "timed out", "timeout", "Connection"]
             ):
-                if attempt < MAX_RETRIES - 1:
+                if attempt < max_retries - 1:
                     logger.warning(
-                        f"Attempt {attempt + 1}/{MAX_RETRIES} failed: {error_msg}. Retrying in {backoff}s..."
+                        f"Attempt {attempt + 1}/{max_retries} failed: {error_msg}. Retrying in {backoff}s..."
                     )
                     time.sleep(backoff)
                     backoff = min(backoff * 2, 60)