From eb9bbfc9b4a278cc7713689a0040021c0925ac13 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <47090312+singiamtel@users.noreply.github.com>
Date: Mon, 30 Jun 2025 16:46:54 +0200
Subject: [PATCH 01/30] Fix release action (#940)

---
 .github/workflows/release.yml | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 724452bc..37234781 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,30 +1,32 @@
 ---
 name: Release
 
-'on':
+"on":
   release:
     types: [published]
 
 permissions:
-  contents: read  # required for github.ref to be set
+  contents: read # required for github.ref to be set
 
 jobs:
   pypi-publish:
     name: Upload release to PyPI
     runs-on: ubuntu-latest
     environment:
-      name: pypi
-      url: https://pypi.org/p/alibuild
+      name: release
+      url: https://pypi.org/p/bits # TODO: update with actual package name
     permissions:
-      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-    # retrieve your distributions here
-    - name: Install build dependencies
-      run: python -m pip install --upgrade setuptools build pip
-    - name: Build the Python distribution
-      run: python -m build
-    - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Install build dependencies
+        run: python -m pip install --upgrade setuptools build pip
+      - name: Build the Python distribution
+        run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
 
   brew:
     name: Update Homebrew formula
@@ -39,15 +41,14 @@ jobs:
       - name: Update bits formula with new version
         run: |
           set -x
-          json=$(curl -fSsL "https://pypi.org/pypi/bits/${GITHUB_REF#refs/tags/}/json")
-          sha=$(echo "$json" | jq -r '.urls[0].digests.sha256')
-          url=$(echo "$json" | jq -r '.urls[0].url')
+          json=$(curl -fSsL "https://pypi.org/pypi/bits/${GITHUB_REF#refs/tags/}/json") # TODO: update with actual package name
+          sha=$(echo "$json" | jq -r '.urls.[] | select(.filename | endswith(".tar.gz")) | .digests.sha256')
+          url=$(echo "$json" | jq -r '.urls.[] | select(.filename | endswith(".tar.gz")) | .url')
           # Replace keys with two leading spaces only, so we get the toplevel
           # ones applying to bits, not those for dependencies.
           sed -i.bak "
           s|^  url .*|  url \"$url\"|;
           s|^  sha256 .*|  sha256 \"$sha\"|;
-          s|^  version .*|  version \"${GITHUB_REF#refs/tags/v}\"|
           " "$(brew formula bits)"
           rm -f "$(brew formula bits).bak"
       - name: Regenerate bits formula
@@ -70,6 +71,6 @@ jobs:
           git add bits.rb
           git commit -m "Update bits to ${GITHUB_REF#refs/tags/}"
           git show
-          git push "https://bits:$GITHUB_TOKEN@github.com/bitsorg/homebrew-system-deps" master
+          git push "https://bits:$GITHUB_TOKEN@github.com/bits/homebrew-system-deps" master # TODO: update user and repo
         env:
           GITHUB_TOKEN: ${{ secrets.homebrew_repo_token }}

From 5a55f854b0073f9cb8a0bda0d911c7bd9e5ff881 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <47090312+singiamtel@users.noreply.github.com>
Date: Mon, 30 Jun 2025 17:31:22 +0200
Subject: [PATCH 02/30] Fix readme syntax error (#942)

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index fd12a08c..3d44aaf9 100644
--- a/README.rst
+++ b/README.rst
@@ -39,7 +39,7 @@ you have the dependencies installed. The easiest way to do this is to run::
 
 
 For developers
-==========
+==============
 
 If you want to contribute to bits, you can run the tests with::
 

From f2bad8c6ecab2d0a784c0fa046c1764676a23b35 Mon Sep 17 00:00:00 2001
From: sfayer <sfayer@users.noreply.github.com>
Date: Wed, 2 Jul 2025 16:58:06 +0100
Subject: [PATCH 03/30] Fix Rocky Linux detection (#938)

---
 bits_helpers/utilities.py |  4 +-
 tests/test_utilities.py   | 90 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 92 insertions(+), 2 deletions(-)

diff --git a/bits_helpers/utilities.py b/bits_helpers/utilities.py
index c5335d68..cb07a752 100644
--- a/bits_helpers/utilities.py
+++ b/bits_helpers/utilities.py
@@ -246,7 +246,7 @@ def doDetectArch(hasOsRelease, osReleaseLines, platformTuple, platformSystem, pl
   distribution = distribution.lower()
   # If platform.dist does not return something sensible,
   # let's try with /etc/os-release
-  if distribution not in ["ubuntu", "red hat enterprise linux", "redhat", "centos", "almalinux", "rockylinux"] and hasOsRelease:
+  if distribution not in ["ubuntu", "red hat enterprise linux", "redhat", "centos", "almalinux", "rocky linux"] and hasOsRelease:
     for x in osReleaseLines:
       key, is_prop, val = x.partition("=")
       if not is_prop:
@@ -266,7 +266,7 @@ def doDetectArch(hasOsRelease, osReleaseLines, platformTuple, platformSystem, pl
     if version in debian_ubuntu:
       distribution = "ubuntu"
       version = debian_ubuntu[version]
-  elif distribution in ["redhat", "red hat enterprise linux", "centos", "almalinux", "rockylinux"]:
+  elif distribution in ["redhat", "red hat enterprise linux", "centos", "almalinux", "rocky linux"]:
     distribution = "slc"
 
   processor = platformProcessor
diff --git a/tests/test_utilities.py b/tests/test_utilities.py
index c8d14220..2c781606 100644
--- a/tests/test_utilities.py
+++ b/tests/test_utilities.py
@@ -114,12 +114,102 @@
 BUG_REPORT_URL="https://bugs.sabayon.org/"
 """
 
+ALMA_8_OS_RELEASE = """
+NAME="AlmaLinux"
+VERSION="8.10 (Cerulean Leopard)"
+ID="almalinux"
+ID_LIKE="rhel centos fedora"
+VERSION_ID="8.10"
+PLATFORM_ID="platform:el8"
+PRETTY_NAME="AlmaLinux 8.10 (Cerulean Leopard)"
+ANSI_COLOR="0;34"
+LOGO="fedora-logo-icon"
+CPE_NAME="cpe:/o:almalinux:almalinux:8::baseos"
+HOME_URL="https://almalinux.org/"
+DOCUMENTATION_URL="https://wiki.almalinux.org/"
+BUG_REPORT_URL="https://bugs.almalinux.org/"
+
+ALMALINUX_MANTISBT_PROJECT="AlmaLinux-8"
+ALMALINUX_MANTISBT_PROJECT_VERSION="8.10"
+REDHAT_SUPPORT_PRODUCT="AlmaLinux"
+REDHAT_SUPPORT_PRODUCT_VERSION="8.10"
+SUPPORT_END=2029-06-01
+"""
+
+ALMA_9_OS_RELEASE = """
+NAME="AlmaLinux"
+VERSION="9.6 (Sage Margay)"
+ID="almalinux"
+ID_LIKE="rhel centos fedora"
+VERSION_ID="9.6"
+PLATFORM_ID="platform:el9"
+PRETTY_NAME="AlmaLinux 9.6 (Sage Margay)"
+ANSI_COLOR="0;34"
+LOGO="fedora-logo-icon"
+CPE_NAME="cpe:/o:almalinux:almalinux:9::baseos"
+HOME_URL="https://almalinux.org/"
+DOCUMENTATION_URL="https://wiki.almalinux.org/"
+BUG_REPORT_URL="https://bugs.almalinux.org/"
+
+ALMALINUX_MANTISBT_PROJECT="AlmaLinux-9"
+ALMALINUX_MANTISBT_PROJECT_VERSION="9.6"
+REDHAT_SUPPORT_PRODUCT="AlmaLinux"
+REDHAT_SUPPORT_PRODUCT_VERSION="9.6"
+SUPPORT_END=2032-06-01
+"""
+
+ROCKY_8_OS_RELEASE = """
+NAME="Rocky Linux"
+VERSION="8.10 (Green Obsidian)"
+ID="rocky"
+ID_LIKE="rhel centos fedora"
+VERSION_ID="8.10"
+PLATFORM_ID="platform:el8"
+PRETTY_NAME="Rocky Linux 8.10 (Green Obsidian)"
+ANSI_COLOR="0;32"
+LOGO="fedora-logo-icon"
+CPE_NAME="cpe:/o:rocky:rocky:8:GA"
+HOME_URL="https://rockylinux.org/"
+BUG_REPORT_URL="https://bugs.rockylinux.org/"
+SUPPORT_END="2029-05-31"
+ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8"
+ROCKY_SUPPORT_PRODUCT_VERSION="8.10"
+REDHAT_SUPPORT_PRODUCT="Rocky Linux"
+REDHAT_SUPPORT_PRODUCT_VERSION="8.10"
+"""
+
+ROCKY_9_OS_RELEASE = """
+NAME="Rocky Linux"
+VERSION="9.6 (Blue Onyx)"
+ID="rocky"
+ID_LIKE="rhel centos fedora"
+VERSION_ID="9.6"
+PLATFORM_ID="platform:el9"
+PRETTY_NAME="Rocky Linux 9.6 (Blue Onyx)"
+ANSI_COLOR="0;32"
+LOGO="fedora-logo-icon"
+CPE_NAME="cpe:/o:rocky:rocky:9::baseos"
+HOME_URL="https://rockylinux.org/"
+VENDOR_NAME="RESF"
+VENDOR_URL="https://resf.org/"
+BUG_REPORT_URL="https://bugs.rockylinux.org/"
+SUPPORT_END="2032-05-31"
+ROCKY_SUPPORT_PRODUCT="Rocky-Linux-9"
+ROCKY_SUPPORT_PRODUCT_VERSION="9.6"
+REDHAT_SUPPORT_PRODUCT="Rocky Linux"
+REDHAT_SUPPORT_PRODUCT_VERSION="9.6"
+"""
+
 architecturePayloads = [
   ['osx_x86-64', False, [], ('','',''), 'Darwin', 'x86-64'],
   ['osx_arm64', False, [], ('','',''), 'Darwin', 'arm64'],
   ['slc5_x86-64', False, [], ('redhat', '5.XX', 'Boron'), 'Linux', 'x86-64'],
   ['slc6_x86-64', False, [], ('centos', '6.X', 'Carbon'), 'Linux', 'x86-64'],
   ['slc7_x86-64', False, [], ('centos', '7.X', 'Ptor'), 'Linux', 'x86-64'],
+  ['slc8_x86-64', True, ALMA_8_OS_RELEASE.split("\n"), ('AlmaLinux', '8.10', 'Cerulean Leopard'), 'Linux', 'x86_64'],
+  ['slc8_x86-64', True, ROCKY_8_OS_RELEASE.split("\n"), ('Rocky Linux', '8.10', 'Green Obsidian'), 'Linux', 'x86_64'],
+  ['slc9_x86-64', True, ALMA_9_OS_RELEASE.split("\n"), ('AlmaLinux', '9.6', 'Sage Margay'), 'Linux', 'x86_64'],
+  ['slc9_x86-64', True, ROCKY_9_OS_RELEASE.split("\n"), ('Rocky Linux', '9.6', 'Blue Onyx'), 'Linux', 'x86_64'],
   ['ubuntu1804_x86-64', True, UBUNTU_1804_OS_RELEASE.split("\n"), ('Ubuntu', '18.04', 'bionic'), 'Linux', 'x86-64'],
   ['ubuntu1604_x86-64', True, UBUNTU_1604_OS_RELEASE.split("\n"), ('Ubuntu', '16.04', 'xenial'), 'Linux', 'x86-64'],
   ['ubuntu1510_x86-64', False, [], ('Ubuntu', '15.10', 'wily'), 'Linux', 'x86-64'],

From 73f34a7f06ac75546bffc6666f22d3a40a2f3401 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <47090312+singiamtel@users.noreply.github.com>
Date: Thu, 3 Jul 2025 13:03:00 +0200
Subject: [PATCH 04/30] Add job to check readme before merge (#946)

Seems like a requirement from pypi. It can make the release fail to
publish, so it's better to check early
---
 .github/workflows/pr-check.yml | 19 +++++++++++++++++++
 tox.ini                        |  8 ++++++++
 2 files changed, 27 insertions(+)

diff --git a/.github/workflows/pr-check.yml b/.github/workflows/pr-check.yml
index 056dd11b..0ca7ef52 100644
--- a/.github/workflows/pr-check.yml
+++ b/.github/workflows/pr-check.yml
@@ -134,3 +134,22 @@ jobs:
   #
   #     - name: Run linters
   #       run: tox -e lint
+    
+  check-readme:
+    name: Check README
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Install dependencies
+        run: python -m pip install --upgrade tox tox-gh-actions
+
+      - name: Run README check
+        run: tox -e check-readme
+
diff --git a/tox.ini b/tox.ini
index ed18b650..710a7e64 100644
--- a/tox.ini
+++ b/tox.ini
@@ -139,3 +139,11 @@ exclude_lines =
     raise NotImplementedError
     # Don't complain if non-runnable code isn't run:
     if __name__ == .__main__.:
+
+[testenv:check-readme]
+# Check the README.rst file for common issues.
+# The pypa publishing job fails if this fails.
+deps =
+    rstcheck
+commands =
+    rstcheck {toxinidir}/README.rst

From 89df1d105baff5ffb6043feb26d40330de60a7e4 Mon Sep 17 00:00:00 2001
From: Chunzheng Wang <83008337+ChunzhengLab@users.noreply.github.com>
Date: Sun, 6 Jul 2025 16:20:14 +0200
Subject: [PATCH 05/30] Fix escaping issue in find -exec by properly escaping
 \; (#948)

---
 bits_helpers/sync.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bits_helpers/sync.py b/bits_helpers/sync.py
index 311e8919..8a0399b2 100644
--- a/bits_helpers/sync.py
+++ b/bits_helpers/sync.py
@@ -357,7 +357,7 @@ def fetch_symlinks(self, spec) -> None:
       # Create the dummy tarball, if it does not exists
       test -f "{workDir}/{architecture}/store/${{pkg_hash:0:2}}/$pkg_hash/$tarball" && continue
       mkdir -p "{workDir}/INSTALLROOT/$pkg_hash/{architecture}/{package}"
-      find "{remote_store}/{cvmfs_architecture}/Packages/{package}/$full_version" ! -name etc -maxdepth 1 -mindepth 1 -exec ln -sf {} "{workDir}/INSTALLROOT/$pkg_hash/{architecture}/{package}/" \;
+      find "{remote_store}/{cvmfs_architecture}/Packages/{package}/$full_version" ! -name etc -maxdepth 1 -mindepth 1 -exec ln -sf {} "{workDir}/INSTALLROOT/$pkg_hash/{architecture}/{package}/" \\;
       cp -fr "{remote_store}/{cvmfs_architecture}/Packages/{package}/$full_version/etc" "{workDir}/INSTALLROOT/$pkg_hash/{architecture}/{package}/etc"
       mkdir -p "{workDir}/TARS/{architecture}/store/${{pkg_hash:0:2}}/$pkg_hash"
       tar -C "{workDir}/INSTALLROOT/$pkg_hash" -czf "{workDir}/TARS/{architecture}/store/${{pkg_hash:0:2}}/$pkg_hash/$tarball" .

From f0cc8f403e0bf51e7be9ec537581ef440a0fa248 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Mon, 14 Jul 2025 17:55:53 +0200
Subject: [PATCH 06/30] Print progress only every 1s (#950)

---
 bits_helpers/log.py  | 9 ++++++++-
 bits_helpers/sync.py | 4 ++--
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/bits_helpers/log.py b/bits_helpers/log.py
index 35291ccd..6f0e3434 100644
--- a/bits_helpers/log.py
+++ b/bits_helpers/log.py
@@ -53,14 +53,21 @@ def log_current_package(package, main_package, specs, devel_prefix) -> None:
 
 
 class ProgressPrint:
-  def __init__(self, begin_msg="") -> None:
+  def __init__(self, begin_msg="", min_interval=0.) -> None:
     self.count = -1
     self.lasttime = 0
     self.STAGES = ".", "..", "...", "....", ".....", "....", "...", ".."
     self.begin_msg = begin_msg
     self.percent = -1
+    self.min_interval = min_interval
+    self.last_update = 0
 
   def __call__(self, txt, *args) -> None:
+    now = time.time()
+    if (now - self.last_update) < self.min_interval:
+      return
+    self.last_update = now
+
     if logger.level <= logging.DEBUG or not sys.stdout.isatty():
       debug(txt, *args)
       return
diff --git a/bits_helpers/sync.py b/bits_helpers/sync.py
index 8a0399b2..09e472c3 100644
--- a/bits_helpers/sync.py
+++ b/bits_helpers/sync.py
@@ -178,7 +178,7 @@ def fetch_tarball(self, spec) -> None:
       destPath = os.path.join(self.workdir, store_path, use_tarball)
       if not os.path.isfile(destPath):   # do not download twice
         progress = ProgressPrint("Downloading tarball for %s@%s" %
-                                 (spec["package"], spec["version"]))
+                                 (spec["package"], spec["version"]), min_interval=5.0)
         progress("[0%%] Starting download of %s", use_tarball)  # initialise progress bar
         self.getRetry("/".join((self.remoteStore, store_path, use_tarball)),
                       destPath, session=session, progress=progress)
@@ -552,7 +552,7 @@ def fetch_tarball(self, spec) -> None:
       for tarball in self._s3_listdir(store_path):
         debug("Fetching tarball %s", tarball)
         progress = ProgressPrint("Downloading tarball for %s@%s" %
-                                 (spec["package"], spec["version"]))
+                                 (spec["package"], spec["version"]), min_interval=5.0)
         progress("[0%%] Starting download of %s", tarball)   # initialise progress bar
         # Create containing directory locally. (exist_ok= is python3-specific.)
         os.makedirs(os.path.join(self.workdir, store_path), exist_ok=True)

From 7d3cb82203d4edf2a54127c6c5f5bc1e1716388d Mon Sep 17 00:00:00 2001
From: Sergio Garcia <47090312+singiamtel@users.noreply.github.com>
Date: Tue, 15 Jul 2025 14:13:39 +0200
Subject: [PATCH 07/30] Fix BUILD folder symlinks (#951)

Oversight from #924
---
 bits_helpers/build_template.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bits_helpers/build_template.sh b/bits_helpers/build_template.sh
index 74e5f461..c41bc399 100644
--- a/bits_helpers/build_template.sh
+++ b/bits_helpers/build_template.sh
@@ -112,9 +112,9 @@ unset DYLD_LIBRARY_PATH
 EOF
 
 cd "$BUILDROOT"
-ln -snf $PKGHASH "${BUILDROOT}-latest"
+ln -snf "$PKGHASH" "$ALIBUILD_BUILD_WORK_DIR/BUILD/$PKGNAME-latest"
 if [[ $DEVEL_PREFIX ]]; then
-  ln -snf $PKGHASH "${BUILDROOT}-latest-$DEVEL_PREFIX"
+  ln -snf "$PKGHASH" "$ALIBUILD_BUILD_WORK_DIR/BUILD/$PKGNAME-latest-$DEVEL_PREFIX"
 fi
 
 cd "$BUILDDIR"

From b1384f5005989767e03a2c2bb046c1d28b0b2de4 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <47090312+singiamtel@users.noreply.github.com>
Date: Tue, 15 Jul 2025 19:52:41 +0200
Subject: [PATCH 08/30] Log the time it takes to upload the symlinks (#952)

---
 bits_helpers/sync.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/bits_helpers/sync.py b/bits_helpers/sync.py
index 09e472c3..b0b592fc 100644
--- a/bits_helpers/sync.py
+++ b/bits_helpers/sync.py
@@ -680,6 +680,7 @@ def upload_symlinks_and_tarball(self, spec) -> None:
 
     # Second, upload dist symlinks. These should be in place before the main
     # tarball, to avoid races in the publisher.
+    start_time = time.time()
     for link_dir, symlinks in dist_symlinks.items():
       for link_key, hash_path in symlinks:
         self.s3.put_object(Bucket=self.writeStore,
@@ -689,6 +690,10 @@ def upload_symlinks_and_tarball(self, spec) -> None:
                            WebsiteRedirectLocation=hash_path)
       debug("Uploaded %d dist symlinks to S3 from %s",
             len(symlinks), link_dir)
+    end_time = time.time()
+    debug("Uploaded %d dist symlinks in %.2f seconds",
+          sum(len(symlinks) for _, symlinks in dist_symlinks.items()),
+          end_time - start_time)
 
     self.s3.upload_file(Bucket=self.writeStore, Key=tar_path,
                         Filename=os.path.join(self.workdir, tar_path))

From 62852d9104bd5cf31e15c6adb1173978bbd28211 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Wed, 16 Jul 2025 16:13:49 +0200
Subject: [PATCH 09/30] Escape fetching of symlinks (#953)

---
 bits_helpers/sync.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bits_helpers/sync.py b/bits_helpers/sync.py
index b0b592fc..4d6df503 100644
--- a/bits_helpers/sync.py
+++ b/bits_helpers/sync.py
@@ -8,6 +8,7 @@
 import time
 import requests
 from requests.exceptions import RequestException
+from urllib.parse import quote
 
 from bits_helpers.cmd import execute
 from bits_helpers.log import debug, info, error, dieOnError, ProgressPrint
@@ -225,7 +226,7 @@ def fetch_symlinks(self, spec) -> None:
         # This symlink isn't in the manifest yet, and we don't have it locally,
         # so download it individually.
         symlinks[linkname] = \
-            self.getRetry("/".join((self.remoteStore, links_path, linkname)),
+            self.getRetry("/".join((self.remoteStore, links_path, quote(linkname))),
                           returnResult=True, log=False, session=session) \
                 .decode("utf-8").rstrip("\r\n")
     for linkname, target in symlinks.items():

From f43438cfa6aafdf2890516cb9da8dafcc3f83f7f Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Thu, 17 Jul 2025 11:02:50 +0200
Subject: [PATCH 10/30] Revert "Escape fetching of symlinks (#953)"

This reverts commit 42f05f6e265cbd52f62dd66e97c5fbfca07803fe.
---
 bits_helpers/sync.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/bits_helpers/sync.py b/bits_helpers/sync.py
index 4d6df503..b0b592fc 100644
--- a/bits_helpers/sync.py
+++ b/bits_helpers/sync.py
@@ -8,7 +8,6 @@
 import time
 import requests
 from requests.exceptions import RequestException
-from urllib.parse import quote
 
 from bits_helpers.cmd import execute
 from bits_helpers.log import debug, info, error, dieOnError, ProgressPrint
@@ -226,7 +225,7 @@ def fetch_symlinks(self, spec) -> None:
         # This symlink isn't in the manifest yet, and we don't have it locally,
         # so download it individually.
         symlinks[linkname] = \
-            self.getRetry("/".join((self.remoteStore, links_path, quote(linkname))),
+            self.getRetry("/".join((self.remoteStore, links_path, linkname)),
                           returnResult=True, log=False, session=session) \
                 .decode("utf-8").rstrip("\r\n")
     for linkname, target in symlinks.items():

From b810e4921394a2822f20742948fa5599d9418b4b Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Thu, 17 Jul 2025 11:01:56 +0200
Subject: [PATCH 11/30] Sanitize getRetry

---
 bits_helpers/sync.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bits_helpers/sync.py b/bits_helpers/sync.py
index b0b592fc..d2dae867 100644
--- a/bits_helpers/sync.py
+++ b/bits_helpers/sync.py
@@ -8,6 +8,7 @@
 import time
 import requests
 from requests.exceptions import RequestException
+from urllib.parse import quote
 
 from bits_helpers.cmd import execute
 from bits_helpers.log import debug, info, error, dieOnError, ProgressPrint
@@ -59,6 +60,7 @@ def __init__(self, remoteStore, architecture, workdir, insecure) -> None:
 
   def getRetry(self, url, dest=None, returnResult=False, log=True, session=None, progress=debug):
     get = session.get if session is not None else requests.get
+    url = quote(url, safe=":/")
     for i in range(0, self.httpConnRetries):
       if i > 0:
         pauseSec = self.httpBackoff * (2 ** (i - 1))

From bf393df573f4c690a96c20863fe0d7b0d2122c50 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Fri, 29 Aug 2025 09:22:10 +0200
Subject: [PATCH 12/30] Add back setup.py and requirements.txt

Until pyp2rpm supports not having them. See:

https://github.com/fedora-python/pyp2rpm/issues/286
---
 requirements.txt | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 requirements.txt

diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..12a7d59a
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,6 @@
+requests
+pyyaml
+distro
+jinja2
+# https://github.com/boto/boto3/issues/4398
+boto3<1.36.0

From 5529aee7ac8c56b4a4539f616241926259a45ae1 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Fri, 29 Aug 2025 10:19:25 +0200
Subject: [PATCH 13/30] Fix the license metadata

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2225ccf3..eed303fb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,8 @@ name = 'bits'
 dynamic = ['readme', 'version']
 description = 'Build Tool'
 keywords = ['HEP', 'ALICE']
-license = { file = 'LICENSE' }
+license = "GPL-3.0-only"
+license-files = ["LICENSE[.]md"]
 authors = [
   {name = 'Giulio Eulisse', email = 'giulio.eulisse@cern.ch'},
   {name = 'Timo Wilken', email = 'timo.wilken@cern.ch'},

From c509b729bfbcc192bd38e0aa4c8577638eca4263 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Wed, 3 Sep 2025 13:26:57 +0200
Subject: [PATCH 14/30] Revert "Fix the license metadata"

This reverts commit d0b6a7065146de333536d07274aa5ad842d449d1.
---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index eed303fb..2225ccf3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,8 +8,7 @@ name = 'bits'
 dynamic = ['readme', 'version']
 description = 'Build Tool'
 keywords = ['HEP', 'ALICE']
-license = "GPL-3.0-only"
-license-files = ["LICENSE[.]md"]
+license = { file = 'LICENSE' }
 authors = [
   {name = 'Giulio Eulisse', email = 'giulio.eulisse@cern.ch'},
   {name = 'Timo Wilken', email = 'timo.wilken@cern.ch'},

From ce881d676f388bc5dbbcadbf419f216656fce1b8 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Wed, 17 Sep 2025 15:08:39 +0200
Subject: [PATCH 15/30] Auto prune on fetch

Fixes situations like the remote repository deleting a branch `a` and
creating a branch `a/b`. Otherwise we have situations like the
following:

```
error: cannot lock ref 'refs/remotes/origin/a/b': 'refs/remotes/a' exists; cannot create 'refs/remotes/origin/a/b'
```

Solution adapted from https://stackoverflow.com/a/67060742/20041091
---
 bits_helpers/git.py    | 2 +-
 tests/test_build.py    | 2 +-
 tests/test_workarea.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bits_helpers/git.py b/bits_helpers/git.py
index c0e86765..000b7e2d 100644
--- a/bits_helpers/git.py
+++ b/bits_helpers/git.py
@@ -68,7 +68,7 @@ def checkoutCmd(self, tag):
     return ["checkout", "-f", tag]
 
   def fetchCmd(self, remote, *refs):
-    return ["fetch", "-f"] + clone_speedup_options() + [remote, *refs]
+    return ["fetch", "-f", "--prune"] + clone_speedup_options() + [remote, *refs]
 
   def setWriteUrlCmd(self, url):
     return ["remote", "set-url", "--push", "origin", url]
diff --git a/tests/test_build.py b/tests/test_build.py
index 82bab377..f2794525 100644
--- a/tests/test_build.py
+++ b/tests/test_build.py
@@ -101,7 +101,7 @@
 GIT_CHECKOUT_ZLIB_ARGS = ("checkout", "-f", "master"), \
     "/sw/SOURCES/zlib/v1.2.3/8822efa61f", False
 
-GIT_FETCH_REF_ROOT_ARGS = ("fetch", "-f", "--filter=blob:none", "https://github.com/root-mirror/root", "+refs/tags/*:refs/tags/*",
+GIT_FETCH_REF_ROOT_ARGS = ("fetch", "-f", "--prune", "--filter=blob:none", "https://github.com/root-mirror/root", "+refs/tags/*:refs/tags/*",
                            "+refs/heads/*:refs/heads/*"), "/sw/MIRROR/root", False
 GIT_CLONE_SRC_ROOT_ARGS = ("clone", "-n", "https://github.com/root-mirror/root",
                            "/sw/SOURCES/ROOT/v6-08-30/f7b3366117",
diff --git a/tests/test_workarea.py b/tests/test_workarea.py
index a16c6b58..7dc2eb30 100644
--- a/tests/test_workarea.py
+++ b/tests/test_workarea.py
@@ -57,7 +57,7 @@ def test_reference_sources_updated(self, mock_git, mock_open, mock_makedirs, moc
         mock_exists.assert_has_calls([])
         mock_makedirs.assert_called_with("%s/sw/MIRROR" % getcwd(), exist_ok=True)
         mock_git.assert_called_once_with([
-            "fetch", "-f", "--filter=blob:none", spec["source"], "+refs/tags/*:refs/tags/*", "+refs/heads/*:refs/heads/*",
+            "fetch", "-f", "--prune", "--filter=blob:none", spec["source"], "+refs/tags/*:refs/tags/*", "+refs/heads/*:refs/heads/*",
         ], directory="%s/sw/MIRROR/aliroot" % getcwd(), check=False, prompt=True)
         self.assertEqual(spec.get("reference"), "%s/sw/MIRROR/aliroot" % getcwd())
 

From 3e3c9fef688d5165c5052387a7bb2d804796bfe3 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Thu, 25 Sep 2025 15:35:59 +0200
Subject: [PATCH 16/30] Fix track_env command execution in aliBuild init

The performPreferCheck function in init.py was hardcoded to always return
(1, "") which caused all track_env commands to fail during initialization.

Fixes error: "Error while executing track_env for O2PhysicsO2PHYSICS_COMPONENTS: echo
${O2PHYSICS_COMPONENTS:-install} =>"

Regression spotted in alisw/alidist#5888
---
 bits_helpers/init.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bits_helpers/init.py b/bits_helpers/init.py
index c9d68c5b..d5d2027b 100644
--- a/bits_helpers/init.py
+++ b/bits_helpers/init.py
@@ -3,6 +3,7 @@
 from bits_helpers.log import debug, error, warning, banner, info
 from bits_helpers.log import dieOnError
 from bits_helpers.workarea import updateReferenceRepoSpec
+from bits_helpers.cmd import getstatusoutput
 
 from os.path import join
 import os.path as path
@@ -54,7 +55,7 @@ def doInit(args):
                                          architecture="",
                                          disable=[],
                                          defaults=args.defaults,
-                                         performPreferCheck=lambda *x, **y: (1, ""),
+                                         performPreferCheck=lambda pkg, cmd: getstatusoutput(["bash", "-c", cmd]),
                                          performRequirementCheck=lambda *x, **y: (0, ""),
                                          performValidateDefaults=lambda spec : validateDefaults(spec, args.defaults),
                                          overrides=overrides,

From 75cf26a05171c40bf256845ee56bd50b2ab05d32 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Thu, 25 Sep 2025 16:20:49 +0200
Subject: [PATCH 17/30] Handle the case sapling is in git mode

---
 bits_helpers/build.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bits_helpers/build.py b/bits_helpers/build.py
index cff5025e..209dad48 100644
--- a/bits_helpers/build.py
+++ b/bits_helpers/build.py
@@ -60,7 +60,7 @@ def update_repo(package, git_prompt):
         specs[package]["scm"] = Git()
         if specs[package]["is_devel_pkg"]:
             specs[package]["source"] = os.path.join(os.getcwd(), specs[package]["package"])
-            if exists(os.path.join(specs[package]["source"], ".sl")):
+            if exists(os.path.join(specs[package]["source"], ".sl")) or exists(os.path.join(specs[package]["source"], ".git/sl")):
                 specs[package]["scm"] = Sapling()
         updateReferenceRepoSpec(args.referenceSources, package, specs[package],
                                 fetch=args.fetchRepos, allowGitPrompt=git_prompt)

From c8370ac8734f0a746593bed1d1253730298a5a83 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Thu, 25 Sep 2025 17:32:53 +0200
Subject: [PATCH 18/30] Improve sapling behavior with devel packages

* If no bookmarks are found, consider always the same branchOrRef,
  as if you where on a branch called "none".
* If a bookmark is there, use the bookmark as identifier for branchOrRef.
---
 bits_helpers/sl.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/bits_helpers/sl.py b/bits_helpers/sl.py
index 5afee89e..3ac6cb2e 100644
--- a/bits_helpers/sl.py
+++ b/bits_helpers/sl.py
@@ -20,9 +20,22 @@ def checkedOutCommitName(self, directory):
     return sapling(("whereami", ), directory)
 
   def branchOrRef(self, directory):
-    # Format is <hash>[+] <branch>
-    identity = sapling(("identify", ), directory)
-    return identity.split(" ")[-1]
+    # Format is * branch     ref or nothing
+    err, output = getstatusoutput("""\
+    set -e +x
+    sl -R {directory} bookmark -r . 2>/dev/null | grep -- "*"
+    """.format(
+        directory=quote(directory),
+    ), timeout=SL_COMMAND_TIMEOUT_SEC)
+    if err > 1:
+        raise SCMError("Error {} from sl bookmark -r . : {}".format(err, output))
+    # We use "none" to indicate there are no bookmarks. This means
+    # that a devel package will act as a single branch, regardless of where we are.
+    if not output.strip():
+      return "none"
+    # If a bookmark is there, we use it to determine that we should rebuild
+    # when we move to it
+    return output.split(" ")[2]
 
   def exec(self, *args, **kwargs):
     return sapling(*args, **kwargs)

From f1f291d0a7db71de1290c76f8c47887bc5dcc480 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Thu, 9 Oct 2025 15:05:52 +0200
Subject: [PATCH 19/30] Fix darwin tests in new macos

zlib<1.3.1 doesn't build in the newer XCode. I'm bumping the zlib
version and fixing the architecture for the macOS ARM tests in general
---
 tests/test_build.py | 71 ++++++++++++++++++++++++++-------------------
 tests/test_sync.py  |  6 ++--
 tox.ini             |  2 +-
 3 files changed, 45 insertions(+), 34 deletions(-)

diff --git a/tests/test_build.py b/tests/test_build.py
index f2794525..27f7f3f9 100644
--- a/tests/test_build.py
+++ b/tests/test_build.py
@@ -1,6 +1,7 @@
 from argparse import Namespace
 import os
 import os.path
+import platform
 import re
 import sys
 import unittest
@@ -12,6 +13,19 @@
 from bits_helpers.utilities import parseRecipe, resolve_tag
 from bits_helpers.build import doBuild, storeHashes, generate_initdotsh
 
+# Determine architecture based on platform
+def get_test_architecture():
+    if sys.platform == 'darwin':
+        machine = platform.machine()
+        if machine == 'arm64':
+            return 'osx_arm64'
+        else:
+            return 'osx_x86-64'
+    else:
+        return 'slc7_x86-64'
+
+TEST_ARCHITECTURE = os.environ.get('ARCHITECTURE', get_test_architecture())
+
 
 TEST_DEFAULT_RELEASE = """\
 package: defaults-release
@@ -23,7 +37,7 @@
 
 TEST_ZLIB_RECIPE = """\
 package: zlib
-version: v1.2.3
+version: v1.3.1
 source: https://github.com/madler/zlib
 tag: master
 ---
@@ -32,7 +46,7 @@
 make install
 """
 TEST_ZLIB_GIT_REFS = "8822efa61f2a385e0bc83ca5819d608111b2168a\trefs/heads/master"
-TEST_ZLIB_BUILD_HASH = "8cd1f56c450f05ffbba3276bad08eae30f814999"
+TEST_ZLIB_BUILD_HASH = "4d6a75f214dc7931a2a7d5ba82ea0568e652cd84"
 
 TEST_ROOT_RECIPE = """\
 package: ROOT
@@ -71,7 +85,7 @@
 87b87c4322d2a3fad315c919cb2e2dd73f2154dc\trefs/heads/master
 f7b336611753f1f4aaa94222b0d620748ae230c0\trefs/heads/v6-08-00-patches
 f7b336611753f1f4aaa94222b0d620748ae230c0\trefs/tags/test-tag"""
-TEST_ROOT_BUILD_HASH = ("8ec3f41b6b585ef86a02e9c595eed67f34d63f08")
+TEST_ROOT_BUILD_HASH = ("1f3c771080f71b6c0d2e3d7a285698a20035da12")
 
 
 TEST_EXTRA_RECIPE = """\
@@ -88,18 +102,18 @@
 ba22\trefs/tags/v1
 ba22\trefs/tags/v2
 baad\trefs/tags/v3"""
-TEST_EXTRA_BUILD_HASH = ("5afae57bfc6a374e74c1c4427698ab5edebce0bc")
+TEST_EXTRA_BUILD_HASH = ("6e7bc4976abf77b558cf7faf575ec51670f8d0e5")
 
 
 GIT_CLONE_REF_ZLIB_ARGS = ("clone", "--bare", "https://github.com/madler/zlib",
                            "/sw/MIRROR/zlib", "--filter=blob:none"), ".", False
 GIT_CLONE_SRC_ZLIB_ARGS = ("clone", "-n", "https://github.com/madler/zlib",
-                           "/sw/SOURCES/zlib/v1.2.3/8822efa61f",
+                           "/sw/SOURCES/zlib/v1.3.1/8822efa61f",
                            "--dissociate", "--reference", "/sw/MIRROR/zlib", "--filter=blob:none"), ".", False
 GIT_SET_URL_ZLIB_ARGS = ("remote", "set-url", "--push", "origin", "https://github.com/madler/zlib"), \
-    "/sw/SOURCES/zlib/v1.2.3/8822efa61f", False
+    "/sw/SOURCES/zlib/v1.3.1/8822efa61f", False
 GIT_CHECKOUT_ZLIB_ARGS = ("checkout", "-f", "master"), \
-    "/sw/SOURCES/zlib/v1.2.3/8822efa61f", False
+    "/sw/SOURCES/zlib/v1.3.1/8822efa61f", False
 
 GIT_FETCH_REF_ROOT_ARGS = ("fetch", "-f", "--prune", "--filter=blob:none", "https://github.com/root-mirror/root", "+refs/tags/*:refs/tags/*",
                            "+refs/heads/*:refs/heads/*"), "/sw/MIRROR/root", False
@@ -143,9 +157,9 @@ def dummy_open(x, mode="r", encoding=None, errors=None):
                 "/sw/BUILD/%s/defaults-release/.build_succeeded" % TEST_DEFAULT_RELEASE_BUILD_HASH: (0, StringIO("0")),
                 "/sw/BUILD/%s/zlib/.build_succeeded" % TEST_ZLIB_BUILD_HASH: (0, StringIO("0")),
                 "/sw/BUILD/%s/ROOT/.build_succeeded" % TEST_ROOT_BUILD_HASH: (0, StringIO("0")),
-                "/sw/osx_x86-64/defaults-release/v1-1/.build-hash": (1, StringIO(TEST_DEFAULT_RELEASE_BUILD_HASH)),
-                "/sw/osx_x86-64/zlib/v1.2.3-local1/.build-hash": (1, StringIO(TEST_ZLIB_BUILD_HASH)),
-                "/sw/osx_x86-64/ROOT/v6-08-30-local1/.build-hash": (1, StringIO(TEST_ROOT_BUILD_HASH))
+                f"/sw/{TEST_ARCHITECTURE}/defaults-release/v1-1/.build-hash": (1, StringIO(TEST_DEFAULT_RELEASE_BUILD_HASH)),
+                f"/sw/{TEST_ARCHITECTURE}/zlib/v1.3.1-local1/.build-hash": (1, StringIO(TEST_ZLIB_BUILD_HASH)),
+                f"/sw/{TEST_ARCHITECTURE}/ROOT/v6-08-30-local1/.build-hash": (1, StringIO(TEST_ROOT_BUILD_HASH))
             }[x]
         except KeyError:
             return DEFAULT
@@ -163,17 +177,16 @@ def dummy_execute(x, **kwds):
     if re.match(".*ln -sfn.*TARS", s):
         return 0
     return {
-        "/bin/bash -e -x /sw/SPECS/osx_x86-64/defaults-release/v1-1/build.sh 2>&1": 0,
-        '/bin/bash -e -x /sw/SPECS/osx_x86-64/zlib/v1.2.3-local1/build.sh 2>&1': 0,
-        '/bin/bash -e -x /sw/SPECS/osx_x86-64/ROOT/v6-08-30-local1/build.sh 2>&1': 0,
+        f"/bin/bash -e -x /sw/SPECS/{TEST_ARCHITECTURE}/defaults-release/v1-1/build.sh 2>&1": 0,
+        f'/bin/bash -e -x /sw/SPECS/{TEST_ARCHITECTURE}/zlib/v1.3.1-local1/build.sh 2>&1': 0,
+        f'/bin/bash -e -x /sw/SPECS/{TEST_ARCHITECTURE}/ROOT/v6-08-30-local1/build.sh 2>&1': 0,
     }[s]
 
 
 def dummy_readlink(x):
     return {
-        "/sw/TARS/osx_x86-64/defaults-release/defaults-release-v1-1.osx_x86-64.tar.gz":
-        "../../osx_x86-64/store/%s/%s/defaults-release-v1-1.osx_x86-64.tar.gz" %
-        (TEST_DEFAULT_RELEASE_BUILD_HASH[:2], TEST_DEFAULT_RELEASE_BUILD_HASH)
+        f"/sw/TARS/{TEST_ARCHITECTURE}/defaults-release/defaults-release-v1-1.{TEST_ARCHITECTURE}.tar.gz":
+        f"../../{TEST_ARCHITECTURE}/store/{TEST_DEFAULT_RELEASE_BUILD_HASH[:2]}/{TEST_DEFAULT_RELEASE_BUILD_HASH}/defaults-release-v1-1.{TEST_ARCHITECTURE}.tar.gz"
     }[x]
 
 
@@ -225,13 +238,11 @@ class BuildTestCase(unittest.TestCase):
     @patch("os.listdir")
     @patch("bits_helpers.build.glob", new=lambda pattern: {
         "*": ["zlib"],
-        "/sw/TARS/osx_x86-64/store/%s/%s/*gz" % (TEST_DEFAULT_RELEASE_BUILD_HASH[:2],
-                                                 TEST_DEFAULT_RELEASE_BUILD_HASH): [],
-        "/sw/TARS/osx_x86-64/store/%s/%s/*gz" % (TEST_ZLIB_BUILD_HASH[:2], TEST_ZLIB_BUILD_HASH): [],
-        "/sw/TARS/osx_x86-64/store/%s/%s/*gz" % (TEST_ROOT_BUILD_HASH[:2], TEST_ROOT_BUILD_HASH): [],
-        "/sw/TARS/osx_x86-64/defaults-release/defaults-release-v1-1.osx_x86-64.tar.gz":
-        ["../../osx_x86-64/store/%s/%s/defaults-release-v1-1.osx_x86-64.tar.gz" %
-         (TEST_DEFAULT_RELEASE_BUILD_HASH[:2], TEST_DEFAULT_RELEASE_BUILD_HASH)],
+        f"/sw/TARS/{TEST_ARCHITECTURE}/store/{TEST_DEFAULT_RELEASE_BUILD_HASH[:2]}/{TEST_DEFAULT_RELEASE_BUILD_HASH}/*gz": [],
+        f"/sw/TARS/{TEST_ARCHITECTURE}/store/{TEST_ZLIB_BUILD_HASH[:2]}/{TEST_ZLIB_BUILD_HASH}/*gz": [],
+        f"/sw/TARS/{TEST_ARCHITECTURE}/store/{TEST_ROOT_BUILD_HASH[:2]}/{TEST_ROOT_BUILD_HASH}/*gz": [],
+        f"/sw/TARS/{TEST_ARCHITECTURE}/defaults-release/defaults-release-v1-1.{TEST_ARCHITECTURE}.tar.gz":
+        [f"../../{TEST_ARCHITECTURE}/store/{TEST_DEFAULT_RELEASE_BUILD_HASH[:2]}/{TEST_DEFAULT_RELEASE_BUILD_HASH}/defaults-release-v1-1.{TEST_ARCHITECTURE}.tar.gz"],
     }[pattern])
     @patch("bits_helpers.build.readlink", new=dummy_readlink)
     @patch("bits_helpers.build.banner", new=MagicMock(return_value=None))
@@ -244,9 +255,9 @@ def test_coverDoBuild(self, mock_debug, mock_listdir, mock_warning, mock_git_git
         mock_debug.side_effect = lambda *args: None
         mock_warning.side_effect = lambda *args: None
         mock_listdir.side_effect = lambda directory: {
-            "/sw/TARS/osx_x86-64/defaults-release": ["defaults-release-v1-1.osx_x86-64.tar.gz"],
-            "/sw/TARS/osx_x86-64/zlib": [],
-            "/sw/TARS/osx_x86-64/ROOT": [],
+            f"/sw/TARS/{TEST_ARCHITECTURE}/defaults-release": [f"defaults-release-v1-1.{TEST_ARCHITECTURE}.tar.gz"],
+            f"/sw/TARS/{TEST_ARCHITECTURE}/zlib": [],
+            f"/sw/TARS/{TEST_ARCHITECTURE}/ROOT": [],
         }.get(directory, DEFAULT)
         os.environ["BITS_NO_ANALYTICS"] = "1"
 
@@ -258,7 +269,7 @@ def test_coverDoBuild(self, mock_debug, mock_listdir, mock_warning, mock_git_git
             docker=False,
             dockerImage=None,
             docker_extra_args=["--network=host"],
-            architecture="osx_x86-64",
+            architecture=TEST_ARCHITECTURE,
             workDir="/sw",
             pkgname=["root"],
             configDir="/alidist",
@@ -321,7 +332,7 @@ def mkcall(args):
         doBuild(args, mock_parser)
         mock_warning.assert_called_with("%s.sh contains a recipe, which will be ignored", "defaults-release")
         mock_debug.assert_called_with("Everything done")
-        mock_listdir.assert_called_with("/sw/TARS/osx_x86-64/ROOT")
+        mock_listdir.assert_called_with(f"/sw/TARS/{TEST_ARCHITECTURE}/ROOT")
         # We can't compare directly against the list of calls here as they
         # might happen in any order.
         mock_git_git.assert_has_calls(common_calls + [
@@ -408,8 +419,8 @@ def test_initdotsh(self) -> None:
         self.assertNotIn("Extra", complete_initdotsh)
 
         # Dependencies must be loaded both for this build and for subsequent ones.
-        self.assertIn('. "$WORK_DIR/$BITS_ARCH_PREFIX"/zlib/v1.2.3-1/etc/profile.d/init.sh', setup_initdotsh)
-        self.assertIn('. "$WORK_DIR/$BITS_ARCH_PREFIX"/zlib/v1.2.3-1/etc/profile.d/init.sh', complete_initdotsh)
+        self.assertIn('. "$WORK_DIR/$BITS_ARCH_PREFIX"/zlib/v1.3.1-1/etc/profile.d/init.sh', setup_initdotsh)
+        self.assertIn('. "$WORK_DIR/$BITS_ARCH_PREFIX"/zlib/v1.3.1-1/etc/profile.d/init.sh', complete_initdotsh)
 
         # ROOT-specific variables must not be set during ROOT's build yet...
         self.assertNotIn("export ROOT_VERSION=", setup_initdotsh)
diff --git a/tests/test_sync.py b/tests/test_sync.py
index af898261..2fa1d7ac 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -16,19 +16,19 @@
 BAD_HASH = "baadf00dbaadf00dbaadf00dbaadf00dbaadf00d"
 NONEXISTENT_HASH = "TRIGGERS_A_404"
 GOOD_SPEC = {    # fully present on the remote store
-    "package": PACKAGE, "version": "v1.2.3", "revision": "1",
+    "package": PACKAGE, "version": "v1.3.1", "revision": "1",
     "hash": GOOD_HASH,
     "remote_revision_hash": GOOD_HASH,
     "remote_hashes": [GOOD_HASH],
 }
 BAD_SPEC = {     # partially present on the remote store
-    "package": PACKAGE, "version": "v1.2.3", "revision": "2",
+    "package": PACKAGE, "version": "v1.3.1", "revision": "2",
     "hash": BAD_HASH,
     "remote_revision_hash": BAD_HASH,
     "remote_hashes": [BAD_HASH],
 }
 MISSING_SPEC = {    # completely absent from the remote store
-    "package": PACKAGE, "version": "v1.2.3", "revision": "3",
+    "package": PACKAGE, "version": "v1.3.1", "revision": "3",
     "hash": NONEXISTENT_HASH,
     "remote_revision_hash": NONEXISTENT_HASH,
     "remote_hashes": [NONEXISTENT_HASH],
diff --git a/tox.ini b/tox.ini
index 710a7e64..0dab5d28 100644
--- a/tox.ini
+++ b/tox.ini
@@ -121,7 +121,7 @@ commands =
     darwin: sl clone https://github.com/alisw/alidist alidist-sapling
     darwin: coverage run --source={toxinidir} -a {toxinidir}/bitsBuild -a {env:ARCHITECTURE} -c alidist-sapling --no-system --disable GCC-Toolchain build zlib
     darwin: rm -fr zlib
-    darwin: sl clone https://github.com/alisw/zlib
+    darwin: sl clone https://github.com/madler/zlib
     darwin: coverage run --source={toxinidir} -a {toxinidir}/bitsBuild -a {env:ARCHITECTURE} --no-system --disable GCC-Toolchain build zlib
     touch zlib/foo
     darwin: coverage run --source={toxinidir} -a {toxinidir}/bitsBuild -a {env:ARCHITECTURE} --no-system --disable GCC-Toolchain build zlib

From d349da0a237f690024ef021dd48f77a426d0ce0c Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Wed, 8 Oct 2025 13:03:41 +0200
Subject: [PATCH 20/30] Add Python tests for 3.14

---
 .github/workflows/pr-check.yml | 2 ++
 tox.ini                        | 3 ++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr-check.yml b/.github/workflows/pr-check.yml
index 0ca7ef52..1f5c3fda 100644
--- a/.github/workflows/pr-check.yml
+++ b/.github/workflows/pr-check.yml
@@ -31,6 +31,7 @@ jobs:
           - '3.11'
           - '3.12'
           - '3.13'
+          - '3.14'
 
     steps:
       - uses: actions/checkout@v4
@@ -78,6 +79,7 @@ jobs:
           - '3.11'
           - '3.12'
           - '3.13'
+          - '3.14'
 
     steps:
       - uses: actions/checkout@v4
diff --git a/tox.ini b/tox.ini
index 0dab5d28..fbeef159 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,6 +1,6 @@
 [tox]
 minversion = 3.20
-envlist = lint, py{37, 38, 39, 310, 311, 312, 313}, darwin
+envlist = lint, py{37, 38, 39, 310, 311, 312, 313, 314}, darwin
 
 [gh-actions]
 # The "lint" job is run separately.
@@ -12,6 +12,7 @@ python =
     3.11: py311
     3.12: py312
     3.13: py313
+    3.14: py314
 
 ; [testenv:lint]
 ; # Warning: This environment inherits settings from the main [testenv] section.

From 652a46181606478e396fe25b8b0c10a49104cd41 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Wed, 17 Sep 2025 10:52:17 +0200
Subject: [PATCH 21/30] Parallelize symlinks

---
 bits_helpers/sync.py | 48 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 37 insertions(+), 11 deletions(-)

diff --git a/bits_helpers/sync.py b/bits_helpers/sync.py
index d2dae867..c40192a0 100644
--- a/bits_helpers/sync.py
+++ b/bits_helpers/sync.py
@@ -7,6 +7,7 @@
 import sys
 import time
 import requests
+from concurrent.futures import ThreadPoolExecutor, as_completed
 from requests.exceptions import RequestException
 from urllib.parse import quote
 
@@ -683,19 +684,44 @@ def upload_symlinks_and_tarball(self, spec) -> None:
     # Second, upload dist symlinks. These should be in place before the main
     # tarball, to avoid races in the publisher.
     start_time = time.time()
-    for link_dir, symlinks in dist_symlinks.items():
-      for link_key, hash_path in symlinks:
-        self.s3.put_object(Bucket=self.writeStore,
-                           Key=link_key,
-                           Body=os.fsencode(hash_path),
-                           ACL="public-read",
-                           WebsiteRedirectLocation=hash_path)
-      debug("Uploaded %d dist symlinks to S3 from %s",
-            len(symlinks), link_dir)
+    total_symlinks = 0
+
+    # Limit concurrency to avoid overwhelming S3 with too many simultaneous requests
+    max_workers = min(32, (len(dist_symlinks) * 10) or 1)
+
+    def _upload_single_symlink(link_key, hash_path):
+      self.s3.put_object(Bucket=self.writeStore,
+                         Key=link_key,
+                         Body=os.fsencode(hash_path),
+                         ACL="public-read",
+                         WebsiteRedirectLocation=hash_path)
+      return link_key
+
+    with ThreadPoolExecutor(max_workers=max_workers) as executor:
+      future_to_info = {}
+      for link_dir, symlinks in dist_symlinks.items():
+        for link_key, hash_path in symlinks:
+          future = executor.submit(_upload_single_symlink, link_key, hash_path)
+          future_to_info[future] = (link_dir, link_key)
+          total_symlinks += 1
+
+      dir_counts = {link_dir: 0 for link_dir in dist_symlinks.keys()}
+      for future in as_completed(future_to_info):
+        link_dir, link_key = future_to_info[future]
+        try:
+          future.result()
+          dir_counts[link_dir] += 1
+        except Exception as e:
+          error("Failed to upload symlink %s: %s", link_key, e)
+          raise
+
+      for link_dir, count in dir_counts.items():
+        if count > 0:
+          debug("Uploaded %d dist symlinks to S3 from %s", count, link_dir)
+
     end_time = time.time()
     debug("Uploaded %d dist symlinks in %.2f seconds",
-          sum(len(symlinks) for _, symlinks in dist_symlinks.items()),
-          end_time - start_time)
+          total_symlinks, end_time - start_time)
 
     self.s3.upload_file(Bucket=self.writeStore, Key=tar_path,
                         Filename=os.path.join(self.workdir, tar_path))

From fe30bed6b4946746c8759e12c41534e2889f0e78 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Mon, 27 Oct 2025 14:59:37 +0100
Subject: [PATCH 22/30] Improve README documentation

---
 README.rst     | 19 +++++++++++++++++--
 docs/README.md |  1 -
 2 files changed, 17 insertions(+), 3 deletions(-)
 delete mode 100644 docs/README.md

diff --git a/README.rst b/README.rst
index 3d44aaf9..c6e2c8a2 100644
--- a/README.rst
+++ b/README.rst
@@ -35,14 +35,22 @@ Pre-requisites
 If you are using bits directly from git clone, you should make sure
 you have the dependencies installed. The easiest way to do this is to run::
 
+    # Optional, make a venv so the dependencies are not installed globally
+    python -m venv .venv
+    source .venv/bin/activate
     pip install -e .
 
 
-For developers
-==============
+Contributing
+============
+
 
 If you want to contribute to bits, you can run the tests with::
 
+    # Optional, make a venv so the dependencies are not installed globally
+    python -m venv .venv
+    source .venv/bin/activate
+
     pip install -e .[test] # Only needed once
     tox
 
@@ -56,6 +64,13 @@ You can also run only the unit tests (it's a lot faster than the full suite) wit
 
 To run the documentation locally, you can use::
 
+    # Optional, make a venv so the dependencies are not installed globally
+    python -m venv .venv
+    source .venv/bin/activate
+
+    # Install dependencies for the docs, check pyproject.toml for more info
     pip install -e .[docs]
+
+    # Run the docs
     cd docs
     mkdocs serve
diff --git a/docs/README.md b/docs/README.md
deleted file mode 100644
index 6c4730db..00000000
--- a/docs/README.md
+++ /dev/null
@@ -1 +0,0 @@
-Read the documentation here: <http://alisw.github.io/alibuild/>

From 90d39d61d8b4a6f437134a76671aed8ba8317ffc Mon Sep 17 00:00:00 2001
From: Andre Sailer <andre.philippe.sailer@cern.ch>
Date: Wed, 29 Oct 2025 11:29:43 +0100
Subject: [PATCH 23/30] docs/references: fix syntax for bullet lists (#975)

---
 docs/docs/reference.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/docs/docs/reference.md b/docs/docs/reference.md
index aac8c23c..0eed8a7b 100644
--- a/docs/docs/reference.md
+++ b/docs/docs/reference.md
@@ -79,13 +79,16 @@ The following entries are optional in the header:
   - `source`: URL of a Git repository from which the source is downloaded.
     It's good practice to make sure that they are already patched, so that you
     can easily point to the actual sources used by the software.
+
   - `write_repo`: in case the repository URL to be used for developing is
     different from the `source`, set this key. It is used by `bits init`,
     which will initialise your local repository with the `upstream` remote
     pointing at this URL instead of the one in `source`.
+
   - `tag`: git reference in the above mentioned repository which points to the
     software to be built. This can be a tag name, a branch name or a commit
     hash.
+
   - `env`: dictionary whose key-value pairs are environment variables to be set
     after the recipe is built. The values are interpreted as the contents of a
     double-quoted shell string, so you can reference other environment variables
@@ -101,6 +104,7 @@ The following entries are optional in the header:
     intended to be used to point to build products of the current recipe. If you
     need to set an environment variable for use in the recipe, use
     `export VARIABLE=value` in the recipe body.
+
   - `prepend_path`: dictionary whose key-value pairs are an environment variable
     name and a path to be prepended to it, as it happens in `LD_LIBRARY_PATH`.
     This happens only after the package declaring the `prepend_path` in question
@@ -116,9 +120,11 @@ The following entries are optional in the header:
 
     will result in prepending `$FOO_ROOT/binexec/foobar` to `$PATH`, and both
     `$FOO_ROOT/sub/lib` and `lib64` to `LD_LIBRARY_PATH`.
+
   - `append_path`: same as `prepend_path` but paths are appended rather than
     prepended. Like `append_path` and `env`, this **does not** affect the
     environment of the current recipe.
+
   - `requires`: a list of run-time dependencies for the package, *e.g.*:
 
     ```yaml
@@ -145,6 +151,7 @@ The following entries are optional in the header:
 
     will make sure that `IgProf` is only built on platforms whose name does not
     begin with `osx`.
+
   - `build_requires`: a list of build-time dependencies for the package. Like
     `requires`, these packages will be built before the current package is
     built.
@@ -154,8 +161,10 @@ The following entries are optional in the header:
     `requires`: for instance, RPMs produced for a package won't depend on its
     `build_requires`, and `alibuild-generate-module` won't pull in build
     requirements' modulefiles.
+
   - `force_rebuild`: set it to `true` to force re-running the build recipe every
     time you invoke bits on it.
+
   - `prefer_system_check`: a script which is used to determine whether
     or not the system equivalent of the package can be used. See also
     `prefer_system`. If the `--no-system` option is specified, this key is not
@@ -170,6 +179,7 @@ The following entries are optional in the header:
     does not match, the check is skipped and the recipe is run. Using the switch
     `--always-prefer-system` runs the check always (even when the regular
     expression for the architecture does not match).
+
   - `relocate_paths`: a list of toplevel paths scanned recursively to perform
     relocation of executables and dynamic libraries **on macOS only**. If not
     specified, defaults to `bin`, `lib` and `lib64`.

From e393e4e46038d25af4511d5791db491d0ddc91b7 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Wed, 29 Oct 2025 11:36:27 +0100
Subject: [PATCH 24/30] Update the documentation

Adding some missing flags, updating some tables, supported archs, etc
---
 docs/docs/user.md | 121 +++++++++++++++++++++++++++++++---------------
 1 file changed, 81 insertions(+), 40 deletions(-)

diff --git a/docs/docs/user.md b/docs/docs/user.md
index b474984d..c51f8052 100644
--- a/docs/docs/user.md
+++ b/docs/docs/user.md
@@ -9,15 +9,17 @@ For a quick start introduction, please look [here](quick.md).
 
 ```
 bits build [-h] [--defaults DEFAULT]
-           [-a ARCH] [--force-unknown-architecture]
-           [-z [DEVELPREFIX]] [-e ENVIRONMENT] [-j JOBS] [-u]
-           [--no-local PKGLIST] [--disable PACKAGE]
-           [--always-prefer-system | --no-system]
-           [--docker] [--docker-image IMAGE] [--docker-extra-args ARGLIST] [-v VOLUMES]
-           [--no-remote-store] [--remote-store STORE] [--write-store STORE] [--insecure] 
-           [-C DIR] [-w WORKDIR] [-c CONFIGDIR] [--reference-sources MIRRORDIR]
-           [--aggressive-cleanup] [--no-auto-cleanup]
-           PACKAGE [PACKAGE ...]
+               [-a ARCH] [--force-unknown-architecture]
+               [-z [DEVELPREFIX]] [-e ENVIRONMENT] [-j JOBS] [-u]
+               [--no-local PKGLIST] [--force-tracked] [--disable PACKAGE]
+               [--force-rebuild PACKAGE] [--annotate PACKAGE=COMMENT]
+               [--only-deps] [--plugin PLUGIN]
+               [--always-prefer-system | --no-system]
+               [--docker] [--docker-image IMAGE] [--docker-extra-args ARGLIST] [-v VOLUMES]
+               [--no-remote-store] [--remote-store STORE] [--write-store STORE] [--insecure] 
+               [-C DIR] [-w WORKDIR] [-c CONFIGDIR] [--reference-sources MIRRORDIR]
+               [--aggressive-cleanup] [--no-auto-cleanup]
+               PACKAGE [PACKAGE ...]
 ```
 
 - `PACKAGE`: One of the packages in `CONFIGDIR`. May be specified multiple
@@ -39,7 +41,18 @@ bits build [-h] [--defaults DEFAULT]
   given.
 - `--no-local PKGLIST`: Do not pick up the following packages from a local
   checkout. `PKGLIST` is a comma-separated list.
+- `--force-tracked`: Do not pick up any packages from a local checkout.
 - `--disable PACKAGE`: Do not build `PACKAGE` and all its (unique) dependencies.
+- `--force-rebuild PACKAGE`: Always rebuild the specified packages from scratch,
+  even if they were built before. Has the same effect as adding
+  `force_rebuild: true` to the recipe. May be specified multiple times or
+  separate multiple arguments with commas.
+- `--annotate PACKAGE=COMMENT`: Store `COMMENT` in the build metadata for
+  `PACKAGE`. The comment will only be stored if the package is compiled or
+  downloaded during this run. May be specified multiple times.
+- `--only-deps`: Only build dependencies, not the main package. Useful for
+  populating a build cache.
+- `--plugin PLUGIN`: Plugin to use for the build. Default is `legacy`.
 - `--always-prefer-system`: Always use system packages when compatible.
 - `--no-system`: Never use system packages, even if compatible.
 
@@ -102,8 +115,8 @@ provides tarballs for the most common supported architectures.
 
 ## Using precompiled packages
 
-By running bits with no special option on CentOS/Alma 7, 8 or 9, or on
-Ubuntu 20.04, 22.04 or 24.04, it will automatically try to
+By running bits with no special option on CentOS/Alma 7, 8 or 9 (x86-64 or ARM),
+or on Ubuntu 20.04, 22.04 or 24.04 (x86-64), it will automatically try to
 use as many precompiled packages as possible by downloading them from a default
 central server. By using precompiled packages you lose the ability to pick some
 of them from your system. If you do not want to use precompiled packages and you
@@ -199,16 +212,30 @@ case the incremental recipe will always be executed.
 
 While bits does its best to find out which OS / distribution you are
 using, sometimes it might fail to do so, for example in the case you
-start using a new *buntu flavour or a bleeding edge version of Centos.
-In order to force the the correct architecture for the build you can use
+start using a new *buntu flavour or a bleeding edge version of a distribution.
+In order to force the correct architecture for the build you can use
 the `--architecture` (`-a`) flag with one of the supported options:
 
-- `slc5_x86-64`: Scientific Linux 5 and compatibles, on Intel / AMD x86-64.
-- `slc6_x86-64`: Scientific Linux 6 and compatibles, on Intel / AMD x86-64.
-- `slc7_x86-64`: CERN Centos 7 and compatibles, on Intel / AMD x86-64.
-- `ubuntu1404_x86-64`: Ubuntu 1404 and compatibles, on Intel / AMD x86-64.
-- `osx_x86-64`: OSX, on Intel / AMD x86-64.
-- `slc7_ppc64`: RHEL7 on POWER8 (LE only for now).
+On Linux, x86-64:
+- `slc6_x86-64`: RHEL6 / SLC6 compatible
+- `slc7_x86-64`: RHEL7 / CC7 compatible
+- `slc8_x86-64`: RHEL8 / CC8 compatible
+- `slc9_x86-64`: RHEL9 / ALMA9 compatible
+- `ubuntu2004_x86-64`: Ubuntu 20.04 compatible
+- `ubuntu2204_x86-64`: Ubuntu 22.04 compatible
+- `ubuntu2404_x86-64`: Ubuntu 24.04 compatible
+- `fedora33_x86-64`: Fedora 33 compatible
+- `fedora34_x86-64`: Fedora 34 compatible
+
+On Linux, ARM:
+- `slc9_aarch64`: RHEL9 / ALMA9 compatible
+
+On Linux, POWER8 / PPC64 (little endian):
+- `slc7_ppc64`: RHEL7 / CC7 compatible
+
+On Mac:
+- `osx_x86-64`: Intel
+- `osx_arm64`: Apple Silicon
 
 ### Running in Docker
 
@@ -234,15 +261,22 @@ option using the same syntax used by Docker.
 
 ## Defaults
 
-By default `bits` is tuned to build the production version of ALICE
-Offline software, as deployed on the Grid, so some of the choices in
-terms of version of the packages and compilation flags are tweaked for
-that. For example, ROOT5 is used because that's what is what has been
-validated for datataking and the choice will not change until the end of
-RUN2 of LHC. In order to change that and use, for example, a more recent
-version of ROOT you can use the `--default root6` option which will
-enable ROOT6 based builds. For a more complete description of how defaults
-works please look at [the reference manual](reference.md#defaults).
+By default, `bits` uses the `o2` defaults (`--defaults o2`), which are
+optimized for building the ALICE O2 software stack. The defaults system
+allows you to specify different sets of build configurations, compiler
+flags, and package versions through the `--defaults` option.
+
+Different defaults can be used to:
+- Use different package versions (e.g., different ROOT versions)
+- Apply specific compiler flags (e.g., debug builds, optimization levels)
+- Enable or disable certain features or packages
+
+To use a different set of defaults, use the `--defaults <name>` option,
+which will load settings from `CONFIGDIR/defaults-<name>.sh`. For example,
+`--defaults o2-epn` would use the `defaults-o2-epn.sh` file.
+
+For a more complete description of how the defaults system works and how to
+create custom defaults, please look at [the reference manual](reference.md#defaults).
 
 ## Disabling packages
 
@@ -252,8 +286,8 @@ separated list with the `--disable` option.
 It is possible to disable packages by adding them to the `disable`
 keyword of your defaults file (see previous paragraph). See the
 [defaults-o2.sh](https://github.com/alisw/alidist/blob/master/defaults-o2.sh)
-file for an example of how to disable `AliEn-Runtime` and `AliRoot`
-when passing `--defaults o2`.
+file for an example of how to disable `mesos` and `MySQL` when
+passing `--defaults o2`.
 
 ## Controlling which system packages are picked up
 
@@ -293,15 +327,12 @@ installation area.
 
 ## Upgrading bits
 
-bits is installed via `pip`. In order to upgrade it on most laptops (in
-particular Macs) do:
+bits can be installed either via `pip`, or by your OS package manager (more info [here](https://alice-doc.github.io/alice-analysis-tutorial/building/custom.html). 
 
-    pip install --upgrade bits
+The way to upgrade it depends on your installation method. If you installed it
+via `pip`, you can upgrade it by running:
 
-or in case you need to be root (_e.g._ on Ubuntu and most Linux distributions
-for convenience):
-
-    sudo pip install --upgrade bits
+    pip install --upgrade bits
 
 In general updating bits is safe and it should never trigger a rebuild or
 break compilation of older versions of alidist (i.e. we do try to guarantee
@@ -314,10 +345,8 @@ when running the command.
 You can also upgrade / install a specific version of bits by specifying it on the 
 command line. E.g.:
 
-    pip install bits=1.5.5.rc1
+    pip install bits=1.17.23
     
-this is in particular required when you want to try out release candidates (rc) builds which
-are masked out by default.
 
 ## Rebuilding packages from branches instead of tags
 
@@ -362,6 +391,18 @@ you may want to use:
 
     bitsDeps O2 --no-system --outgraph graph.pdf
 
+Additional useful options for `bitsDeps` include:
+
+- `--neat`: Produce a graph with transitive reduction, removing edges that are
+  implied by other paths in the graph. This can make complex dependency graphs
+  easier to read.
+- `--outdot FILE`: Keep the intermediate Graphviz dot file in `FILE`. Useful if
+  you want to manually modify the graph or generate output in different formats.
+
+For example, to generate a simplified graph and keep the dot file:
+
+    bitsDeps O2 --neat --outdot graph.dot --outgraph graph.pdf
+
 Please run `bitsDeps --help` for further information.
 
 ## Using the packages you have built

From 203ec434f123d620739b8a0692285e4dfa3f1565 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Thu, 5 Jun 2025 09:50:24 +0200
Subject: [PATCH 25/30] Add location of alidist as BITS_CONFIG_DIR variable
 (#934)

---
 bits_helpers/build.py          | 5 +++--
 bits_helpers/build_template.sh | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/bits_helpers/build.py b/bits_helpers/build.py
index 209dad48..0b73a95c 100644
--- a/bits_helpers/build.py
+++ b/bits_helpers/build.py
@@ -1151,12 +1151,13 @@ def performPreferCheckWithTempDir(pkg, cmd):
     if args.docker:
       build_command = (
         "docker run --rm --entrypoint= --user $(id -u):$(id -g) "
-        "-v {workdir}:/sw -v {scriptDir}/build.sh:/build.sh:ro "
+        "-v {workdir}:/sw -v{configDir}:/alidist:ro -v {scriptDir}/build.sh:/build.sh:ro "
         "{mirrorVolume} {develVolumes} {additionalEnv} {additionalVolumes} "
-        "-e WORK_DIR_OVERRIDE=/sw {extraArgs} {image} bash -ex /build.sh"
+        "-e WORK_DIR_OVERRIDE=/sw -e BITS_CONFIG_DIR_OVERRIDE=/alidist {extraArgs} {image} bash -ex /build.sh"
       ).format(
         image=quote(args.dockerImage),
         workdir=quote(abspath(args.workDir)),
+        configDir=quote(abspath(args.configDir)),
         scriptDir=quote(scriptDir),
         extraArgs=" ".join(map(quote, args.docker_extra_args)),
         additionalEnv=" ".join(
diff --git a/bits_helpers/build_template.sh b/bits_helpers/build_template.sh
index c41bc399..b73676e6 100644
--- a/bits_helpers/build_template.sh
+++ b/bits_helpers/build_template.sh
@@ -20,6 +20,7 @@ cpath=$(which gcc)
 function hash() { true; }
 
 export WORK_DIR="${WORK_DIR_OVERRIDE:-%(workDir)s}"
+export BITS_CONFIG_DIR="${BITS_CONFIG_DIR_OVERRIDE:-%(configDir)s}"
 
 # Insert our own wrapper scripts into $PATH, patched to use the system OpenSSL,
 # instead of the one we build ourselves.

From 6bb521605b027fa90af9d1291fdbeb05a5a9aeb6 Mon Sep 17 00:00:00 2001
From: Giulio Eulisse <10544+ktf@users.noreply.github.com>
Date: Mon, 30 Jun 2025 16:09:23 +0200
Subject: [PATCH 26/30] Allow for extra variables, volumes in the docker runner
 (#935)

* Allow for extra variables, volumes in the docker runner
* Also inject variables when using docker
* Pass ALIBUILD_CONFIG_DIR to the prefer_system_check
* Mount alidist as volume

---------

Co-authored-by: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
---
 bits_helpers/build.py  |  2 +-
 bits_helpers/cmd.py    | 29 +++++++++++++++++++++++------
 bits_helpers/deps.py   | 11 +++++++----
 bits_helpers/doctor.py |  4 ++--
 tests/test_cmd.py      | 32 +++++++++++++++++++++++++++++++-
 5 files changed, 64 insertions(+), 14 deletions(-)

diff --git a/bits_helpers/build.py b/bits_helpers/build.py
index 0b73a95c..7b606fc4 100644
--- a/bits_helpers/build.py
+++ b/bits_helpers/build.py
@@ -516,7 +516,7 @@ def doBuild(args, parser):
 
   install_wrapper_script("git", workDir)
 
-  with DockerRunner(args.dockerImage, args.docker_extra_args) as getstatusoutput_docker:
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
     def performPreferCheckWithTempDir(pkg, cmd):
       with tempfile.TemporaryDirectory(prefix=f"bits_prefer_check_{pkg['package']}_") as temp_dir:
         return getstatusoutput_docker(cmd, cwd=temp_dir)
diff --git a/bits_helpers/cmd.py b/bits_helpers/cmd.py
index 65adf6e7..0b1dbc5e 100644
--- a/bits_helpers/cmd.py
+++ b/bits_helpers/cmd.py
@@ -78,25 +78,42 @@ class DockerRunner:
   instead.
   """
 
-  def __init__(self, docker_image, docker_run_args=()) -> None:
+  def __init__(self, docker_image, docker_run_args=(), extra_env={}, extra_volumes=[]) -> None:
     self._docker_image = docker_image
     self._docker_run_args = docker_run_args
     self._container = None
+    self._extra_env = extra_env
+    self._extra_volumes = extra_volumes
 
   def __enter__(self):
     if self._docker_image:
       # "sleep inf" pauses forever, until we kill it.
-      cmd = ["docker", "run", "--detach", "--rm", "--entrypoint="]
+      envOpts = []
+      volumes = []
+      for env in self._extra_env.items():
+        envOpts.append("-e")
+        envOpts.append(f"{env[0]}={env[1]}")
+      for v in self._extra_volumes:
+        volumes.append("-v")
+        volumes.append(v)
+      cmd = ["docker", "run", "--detach"] + envOpts + volumes + ["--rm", "--entrypoint="]
       cmd += self._docker_run_args
       cmd += [self._docker_image, "sleep", "inf"]
       self._container = getoutput(cmd).strip()
 
     def getstatusoutput_docker(cmd, cwd=None):
       if self._container is None:
-        return getstatusoutput("{} -c {}".format(BASH, quote(cmd)), cwd=cwd)
-      return getstatusoutput("docker container exec {} bash -c {}"
-                             .format(quote(self._container), quote(cmd)),
-                             cwd=cwd)
+        command_prefix=""
+        if self._extra_env:
+          command_prefix="env " + " ".join("{}={}".format(k, v) for (k,v) in self._extra_env.items()) + " "
+        return getstatusoutput("{}{} -c {}".format(command_prefix, BASH, quote(cmd))
+                             , cwd=cwd)
+      envOpts = []
+      for env in self._extra_env.items():
+        envOpts.append("-e")
+        envOpts.append("{}={}".format(env[0], env[1]))
+      exec_cmd = ["docker", "container", "exec"] + envOpts + [self._container, "bash", "-c", cmd]
+      return getstatusoutput(exec_cmd, cwd=cwd)
 
     return getstatusoutput_docker
 
diff --git a/bits_helpers/deps.py b/bits_helpers/deps.py
index 3ee504a2..b7e48a3a 100644
--- a/bits_helpers/deps.py
+++ b/bits_helpers/deps.py
@@ -4,7 +4,7 @@
 from bits_helpers.utilities import parseDefaults, readDefaults, getPackageList, validateDefaults
 from bits_helpers.cmd import DockerRunner, execute
 from tempfile import NamedTemporaryFile
-from os import remove
+from os import remove, path
 
 def doDeps(args, parser):
 
@@ -16,7 +16,10 @@ def doDeps(args, parser):
   specs = {}
   defaultsReader = lambda: readDefaults(args.configDir, args.defaults, parser.error, args.architecture. args.xdefaults)
   (err, overrides, taps) = parseDefaults(args.disable, defaultsReader, debug)
-  with DockerRunner(args.dockerImage, args.docker_extra_args) as getstatusoutput_docker:
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else path.abspath(args.configDir)}, extra_volumes=[f"{path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
+    def performCheck(pkg, cmd):
+      return getstatusoutput_docker(cmd)
+    
     systemPackages, ownPackages, failed, validDefaults = \
       getPackageList(packages                = [args.package],
                      specs                   = specs,
@@ -26,8 +29,8 @@ def doDeps(args, parser):
                      architecture            = args.architecture,
                      disable                 = args.disable,
                      defaults                = args.defaults,
-                     performPreferCheck      = lambda pkg, cmd: getstatusoutput_docker(cmd),
-                     performRequirementCheck = lambda pkg, cmd: getstatusoutput_docker(cmd),
+                     performPreferCheck      = performCheck,
+                     performRequirementCheck = performCheck,
                      performValidateDefaults = lambda spec: validateDefaults(spec, args.defaults),
                      overrides               = overrides,
                      taps                    = taps,
diff --git a/bits_helpers/doctor.py b/bits_helpers/doctor.py
index 0f5a5b7e..d79ce2f2 100644
--- a/bits_helpers/doctor.py
+++ b/bits_helpers/doctor.py
@@ -83,7 +83,7 @@ def doDoctor(args, parser):
   # Decide if we can use homebrew. If not, we replace it with "true" so
   # that we do not get spurious messages on linux
   homebrew_replacement = ""
-  with DockerRunner(args.dockerImage, args.docker_extra_args) as getstatusoutput_docker:
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
     err, output = getstatusoutput_docker("type c++")
   if err:
     warning("Unable to find system compiler.\n"
@@ -140,7 +140,7 @@ def performValidateDefaults(spec):
       error("%s", msg)
     return (ok,msg,valid)
 
-  with DockerRunner(args.dockerImage, args.docker_extra_args) as getstatusoutput_docker:
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
     def performPreferCheckWithTempDir(pkg, cmd):
       with tempfile.TemporaryDirectory(prefix=f"bits_prefer_check_{pkg['package']}_") as temp_dir:
         return getstatusoutput_docker(cmd, cwd=temp_dir)
diff --git a/tests/test_cmd.py b/tests/test_cmd.py
index 2934f425..d3676ff6 100644
--- a/tests/test_cmd.py
+++ b/tests/test_cmd.py
@@ -26,7 +26,7 @@ def test_DockerRunner(self, mock_getstatusoutput, mock_getoutput):
             mock_getoutput.assert_called_with(["docker", "run", "--detach", "--rm", "--entrypoint=",
                                                "extra arg", "image", "sleep", "inf"])
             getstatusoutput_docker("echo foo")
-            mock_getstatusoutput.assert_called_with("docker container exec container-id bash -c 'echo foo'", cwd=None)
+            mock_getstatusoutput.assert_called_with(["docker", "container", "exec", "container-id", "bash", "-c", "echo foo"], cwd=None)
         mock_getstatusoutput.assert_called_with("docker container kill container-id")
 
         mock_getoutput.reset_mock()
@@ -38,6 +38,36 @@ def test_DockerRunner(self, mock_getstatusoutput, mock_getoutput):
             mock_getstatusoutput.reset_mock()
         mock_getstatusoutput.assert_not_called()
 
+    @mock.patch("alibuild_helpers.cmd.getoutput")
+    @mock.patch("alibuild_helpers.cmd.getstatusoutput")
+    def test_DockerRunner_with_env_vars(self, mock_getstatusoutput, mock_getoutput):
+        # Test that environment variables are properly injected into docker exec commands.
+        mock_getoutput.side_effect = lambda cmd: "container-id\n"
+        
+        # Test with environment variables
+        extra_env = {"TEST_VAR": "test_value", "ANOTHER_VAR": "another_value"}
+        with DockerRunner("image", extra_env=extra_env) as getstatusoutput_docker:
+            # Verify container creation includes environment variables
+            mock_getoutput.assert_called_with(["docker", "run", "--detach", 
+                                               "-e", "TEST_VAR=test_value",
+                                               "-e", "ANOTHER_VAR=another_value",
+                                               "--rm", "--entrypoint=", "image", "sleep", "inf"])
+            
+            # Test that exec command includes environment variables
+            getstatusoutput_docker("echo test")
+            mock_getstatusoutput.assert_called_with(["docker", "container", "exec", 
+                                                     "-e", "TEST_VAR=test_value",
+                                                     "-e", "ANOTHER_VAR=another_value", 
+                                                     "container-id", "bash", "-c", "echo test"], cwd=None)
+
+        # Test host execution with environment variables
+        mock_getoutput.reset_mock()
+        mock_getstatusoutput.reset_mock()
+        with DockerRunner("", extra_env=extra_env) as getstatusoutput_docker:
+            mock_getoutput.assert_not_called()
+            getstatusoutput_docker("echo test")
+            mock_getstatusoutput.assert_called_with("env TEST_VAR=test_value ANOTHER_VAR=another_value /bin/bash -c 'echo test'", cwd=None)
+
 
 if __name__ == '__main__':
     unittest.main()

From b6c13cc4ada88a352d7d49a9ec30d60e4db6f1e3 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <47090312+singiamtel@users.noreply.github.com>
Date: Mon, 7 Jul 2025 09:41:41 +0200
Subject: [PATCH 27/30] Load CLI environment variables in prefer_system_check
 (#947)

---
 bits_helpers/args.py   |  2 ++
 bits_helpers/build.py  |  5 ++++-
 bits_helpers/deps.py   |  6 +++++-
 bits_helpers/doctor.py | 11 +++++++++--
 tests/test_build.py    |  2 +-
 tests/test_deps.py     |  7 ++++++-
 tests/test_doctor.py   |  3 ++-
 tests/test_init.py     |  6 ++++--
 8 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/bits_helpers/args.py b/bits_helpers/args.py
index 5db07155..722ea1f6 100644
--- a/bits_helpers/args.py
+++ b/bits_helpers/args.py
@@ -262,6 +262,8 @@ def doParseArgs():
                              help=("Assume we're not building %(metavar)s and all its (unique) dependencies. "
                                    "You can specify this option multiple times or separate multiple arguments "
                                    "with commas."))
+  doctor_parser.add_argument("-e", dest="environment", action="append", default=[],
+                            help="KEY=VALUE binding to add to the build environment. May be specified multiple times.")
 
   doctor_system = doctor_parser.add_mutually_exclusive_group()
   doctor_system.add_argument("--always-prefer-system", dest="preferSystem", action="store_true",
diff --git a/bits_helpers/build.py b/bits_helpers/build.py
index 7b606fc4..bf5a280c 100644
--- a/bits_helpers/build.py
+++ b/bits_helpers/build.py
@@ -516,7 +516,10 @@ def doBuild(args, parser):
 
   install_wrapper_script("git", workDir)
 
-  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
+  extra_env = {"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}
+  extra_env.update(dict([e.partition('=')[::2] for e in args.environment]))
+
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env=extra_env, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
     def performPreferCheckWithTempDir(pkg, cmd):
       with tempfile.TemporaryDirectory(prefix=f"bits_prefer_check_{pkg['package']}_") as temp_dir:
         return getstatusoutput_docker(cmd, cwd=temp_dir)
diff --git a/bits_helpers/deps.py b/bits_helpers/deps.py
index b7e48a3a..01d8d08a 100644
--- a/bits_helpers/deps.py
+++ b/bits_helpers/deps.py
@@ -16,7 +16,11 @@ def doDeps(args, parser):
   specs = {}
   defaultsReader = lambda: readDefaults(args.configDir, args.defaults, parser.error, args.architecture. args.xdefaults)
   (err, overrides, taps) = parseDefaults(args.disable, defaultsReader, debug)
-  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else path.abspath(args.configDir)}, extra_volumes=[f"{path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
+
+  extra_env = {"BITS_CONFIG_DIR": "/alidist" if args.docker else path.abspath(args.configDir)}
+  extra_env.update(dict([e.partition('=')[::2] for e in args.environment]))
+  
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env=extra_env, extra_volumes=[f"{path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
     def performCheck(pkg, cmd):
       return getstatusoutput_docker(cmd)
     
diff --git a/bits_helpers/doctor.py b/bits_helpers/doctor.py
index d79ce2f2..7af84d54 100644
--- a/bits_helpers/doctor.py
+++ b/bits_helpers/doctor.py
@@ -83,7 +83,11 @@ def doDoctor(args, parser):
   # Decide if we can use homebrew. If not, we replace it with "true" so
   # that we do not get spurious messages on linux
   homebrew_replacement = ""
-  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
+
+  extra_env = {"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}
+  extra_env.update(dict([e.partition('=')[::2] for e in args.environment]))
+
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env=extra_env, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
     err, output = getstatusoutput_docker("type c++")
   if err:
     warning("Unable to find system compiler.\n"
@@ -140,7 +144,10 @@ def performValidateDefaults(spec):
       error("%s", msg)
     return (ok,msg,valid)
 
-  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env={"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
+  extra_env = {"BITS_CONFIG_DIR": "/alidist" if args.docker else os.path.abspath(args.configDir)}
+  extra_env.update(dict([e.partition('=')[::2] for e in args.environment]))
+  
+  with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env=extra_env, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
     def performPreferCheckWithTempDir(pkg, cmd):
       with tempfile.TemporaryDirectory(prefix=f"bits_prefer_check_{pkg['package']}_") as temp_dir:
         return getstatusoutput_docker(cmd, cwd=temp_dir)
diff --git a/tests/test_build.py b/tests/test_build.py
index 27f7f3f9..51993dca 100644
--- a/tests/test_build.py
+++ b/tests/test_build.py
@@ -283,7 +283,7 @@ def test_coverDoBuild(self, mock_debug, mock_listdir, mock_warning, mock_git_git
             debug=True,
             dryRun=False,
             aggressiveCleanup=False,
-            environment={},
+            environment=[],
             autoCleanup=False,
             noDevel=[],
             onlyDeps=False,
diff --git a/tests/test_deps.py b/tests/test_deps.py
index 6f910152..ea10b85b 100644
--- a/tests/test_deps.py
+++ b/tests/test_deps.py
@@ -65,7 +65,12 @@ def depsOpen(fn, mode):
                          outdot="/tmp/out.dot",
                          outgraph="/tmp/outgraph.pdf",
                          package="AliRoot",
-                         defaults="release")
+                         defaults="release",
+                         environment=[])
+        def fake_exists(n):
+            return {"/alidist/aliroot.sh": True}
+        with patch.object(os.path, "exists", fake_exists):
+            doDeps(args, MagicMock())
 
 
         def fake_exists(n):
diff --git a/tests/test_doctor.py b/tests/test_doctor.py
index b0f29321..0412ddbe 100644
--- a/tests/test_doctor.py
+++ b/tests/test_doctor.py
@@ -90,7 +90,8 @@ def resetOut():
                      noSystem="*",
                      architecture="osx_x86-64",
                      disable=[],
-                     defaults="release")
+                     defaults="release",
+                     environment=[])
 
     # What to call (longer names deprecated in Python 3.5+)
     if not hasattr(self, "assertRegex"):
diff --git a/tests/test_init.py b/tests/test_init.py
index 15c00429..cf748fd6 100644
--- a/tests/test_init.py
+++ b/tests/test_init.py
@@ -47,7 +47,8 @@ def test_doDryRunInit(self, mock_os, mock_path,  mock_info) -> None:
         defaults = "release",
         dryRun = True,
         fetchRepos = False,
-        architecture = "slc7_x86-64"
+        architecture = "slc7_x86-64",
+        environment = {},
       )
       self.assertRaises(SystemExit, doInit, args)
       self.assertEqual(mock_info.mock_calls, [call('This will initialise local checkouts for %s\n--dry-run / -n specified. Doing nothing.', 'zlib,AliRoot')])
@@ -86,7 +87,8 @@ def test_doRealInit(self, mock_read_defaults, mock_open, mock_update_reference,
         defaults = "release",
         dryRun = False,
         fetchRepos = False,
-        architecture = "slc7_x86-64"
+        architecture = "slc7_x86-64",
+        environment = {},
       )
       doInit(args)
       self.assertEqual(mock_git.mock_calls, CLONE_EVERYTHING)

From ce44692aa5620fe10ded6eaffdc746cccc892f6e Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Tue, 22 Jul 2025 10:49:42 +0200
Subject: [PATCH 28/30] Fix multiline env variables

Regression in #947
---
 bits_helpers/cmd.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bits_helpers/cmd.py b/bits_helpers/cmd.py
index 0b1dbc5e..ac5a0119 100644
--- a/bits_helpers/cmd.py
+++ b/bits_helpers/cmd.py
@@ -105,7 +105,7 @@ def getstatusoutput_docker(cmd, cwd=None):
       if self._container is None:
         command_prefix=""
         if self._extra_env:
-          command_prefix="env " + " ".join("{}={}".format(k, v) for (k,v) in self._extra_env.items()) + " "
+          command_prefix="env " + " ".join("{}={}".format(k, quote(v)) for (k,v) in self._extra_env.items()) + " "
         return getstatusoutput("{}{} -c {}".format(command_prefix, BASH, quote(cmd))
                              , cwd=cwd)
       envOpts = []

From 66de1714e2c3fe0d35f06ef153295d851d61171e Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Mon, 28 Jul 2025 14:50:35 +0200
Subject: [PATCH 29/30] Add tests for multiline env variables

---
 tests/test_cmd.py | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/tests/test_cmd.py b/tests/test_cmd.py
index d3676ff6..f1f604f4 100644
--- a/tests/test_cmd.py
+++ b/tests/test_cmd.py
@@ -38,8 +38,8 @@ def test_DockerRunner(self, mock_getstatusoutput, mock_getoutput):
             mock_getstatusoutput.reset_mock()
         mock_getstatusoutput.assert_not_called()
 
-    @mock.patch("alibuild_helpers.cmd.getoutput")
-    @mock.patch("alibuild_helpers.cmd.getstatusoutput")
+    @mock.patch("bits_helpers.cmd.getoutput")
+    @mock.patch("bits_helpers.cmd.getstatusoutput")
     def test_DockerRunner_with_env_vars(self, mock_getstatusoutput, mock_getoutput):
         # Test that environment variables are properly injected into docker exec commands.
         mock_getoutput.side_effect = lambda cmd: "container-id\n"
@@ -68,6 +68,28 @@ def test_DockerRunner_with_env_vars(self, mock_getstatusoutput, mock_getoutput):
             getstatusoutput_docker("echo test")
             mock_getstatusoutput.assert_called_with("env TEST_VAR=test_value ANOTHER_VAR=another_value /bin/bash -c 'echo test'", cwd=None)
 
+    @mock.patch("bits_helpers.cmd.getoutput")
+    @mock.patch("bits_helpers.cmd.getstatusoutput")
+    def test_DockerRunner_multiline_env_var(self, mock_getstatusoutput, mock_getoutput):
+        multiline_value = "line1\nline2\nline3"
+        extra_env = {"MULTILINE_VAR": multiline_value}
+        
+        with DockerRunner("", extra_env=extra_env) as getstatusoutput_docker:
+            mock_getoutput.assert_not_called()
+            getstatusoutput_docker("echo test")
+            mock_getstatusoutput.assert_called_with("env MULTILINE_VAR='line1\nline2\nline3' /bin/bash -c 'echo test'", cwd=None)
+
+    @mock.patch("bits_helpers.cmd.getoutput")
+    @mock.patch("bits_helpers.cmd.getstatusoutput")
+    def test_DockerRunner_env_var_with_semicolon(self, mock_getstatusoutput, mock_getoutput):
+        semicolon_value = "value1;value2;value3"
+        extra_env = {"SEMICOLON_VAR": semicolon_value}
+        
+        with DockerRunner("", extra_env=extra_env) as getstatusoutput_docker:
+            mock_getoutput.assert_not_called()
+            getstatusoutput_docker("echo test")
+            mock_getstatusoutput.assert_called_with("env SEMICOLON_VAR='value1;value2;value3' /bin/bash -c 'echo test'", cwd=None)
+
 
 if __name__ == '__main__':
     unittest.main()

From 2d55d24dc19b1f2057ffcaf962a891b10cb476c7 Mon Sep 17 00:00:00 2001
From: Sergio Garcia <sergio.garcia.de.la.cruz@cern.ch>
Date: Tue, 2 Sep 2025 12:03:41 +0200
Subject: [PATCH 30/30] Fix aliDoctor logs

---
 bits_helpers/doctor.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/bits_helpers/doctor.py b/bits_helpers/doctor.py
index 7af84d54..ddee9ae0 100644
--- a/bits_helpers/doctor.py
+++ b/bits_helpers/doctor.py
@@ -22,7 +22,8 @@ def checkPreferSystem(spec, cmd, homebrew_replacement, getstatusoutput_docker):
       debug("Package %s can only be managed via bits.", spec["package"])
       return (1, "")
     cmd = homebrew_replacement + cmd
-    err, out = getstatusoutput_docker(cmd)
+    with tempfile.TemporaryDirectory(prefix=f"bits_prefer_check_{spec['package']}_") as temp_dir:
+        err, out = getstatusoutput_docker(cmd, cwd=temp_dir)
     if not err:
       success("Package %s will be picked up from the system.", spec["package"])
       for x in out.split("\n"):
@@ -40,7 +41,8 @@ def checkRequirements(spec, cmd, homebrew_replacement, getstatusoutput_docker):
       debug("Package %s is not a system requirement.", spec["package"])
       return (0, "")
     cmd = homebrew_replacement + cmd
-    err, out = getstatusoutput_docker(cmd)
+    with tempfile.TemporaryDirectory(prefix=f"bits_prefer_check_{spec['package']}_") as temp_dir:
+        err, out = getstatusoutput_docker(cmd, cwd=temp_dir)
     if not err:
       success("Required package %s will be picked up from the system.", spec["package"])
       debug("%s", cmd)
@@ -148,9 +150,6 @@ def performValidateDefaults(spec):
   extra_env.update(dict([e.partition('=')[::2] for e in args.environment]))
   
   with DockerRunner(args.dockerImage, args.docker_extra_args, extra_env=extra_env, extra_volumes=[f"{os.path.abspath(args.configDir)}:/alidist:ro"] if args.docker else []) as getstatusoutput_docker:
-    def performPreferCheckWithTempDir(pkg, cmd):
-      with tempfile.TemporaryDirectory(prefix=f"bits_prefer_check_{pkg['package']}_") as temp_dir:
-        return getstatusoutput_docker(cmd, cwd=temp_dir)
     fromSystem, own, failed, validDefaults = \
       getPackageList(packages                = packages,
                      specs                   = specs,
@@ -160,8 +159,8 @@ def performPreferCheckWithTempDir(pkg, cmd):
                      architecture            = args.architecture,
                      disable                 = args.disable,
                      defaults                = args.defaults,
-                     performPreferCheck      = performPreferCheckWithTempDir,
-                     performRequirementCheck = performPreferCheckWithTempDir,
+                     performPreferCheck      = lambda pkg, cmd: checkPreferSystem(pkg, cmd, homebrew_replacement, getstatusoutput_docker),
+                     performRequirementCheck = lambda pkg, cmd: checkRequirements(pkg, cmd, homebrew_replacement, getstatusoutput_docker),
                      performValidateDefaults = performValidateDefaults,
                      overrides               = overrides,
                      taps                    = taps,