Drop Python 3.6 and 3.7 support, add 3.12 (#2121)

* Fix python python 3.12: use shutil instead of removed distuil to copy tree with time and mode unpreserved

* [automated] Update CHANGELOG.md

* Remove more disutils from modules

* Replace more distutil.copy_tree with shutil.copytree

* Fix overriding parent template

* [automated] Update CHANGELOG.md

* [automated] Fix code linting

* Move strtobool into utils

* Fix

* Bundle lzstring to fix Python 3.12

* [automated] Update CHANGELOG.md

* [automated] Update CHANGELOG.md

* Same style of bundling packages

* dirs_exist_ok missing for Py 3.6 and 3.7

* Drop Python 3.6 and 3.7 support, add 3.12

* [automated] Update CHANGELOG.md

---------

Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

.github/workflows/multiqc.yml

@@ -15,7 +15,7 @@ env:
   # To reduce code duplication between Win and Linux jobs
   core_python_dependencies: "pip setuptools beautifulsoup4"
   # No need to run test variations across all Python versions
-  latest_python: "3.11"
+  latest_python: "3.12"
 
 jobs:
   changes:
@@ -56,7 +56,7 @@ jobs:
     strategy:
       matrix:
         # Just test the oldest and newest supported Python versions
-        python-version: ["3.6", "3.11"]
+        python-version: ["3.8", "3.12"]
     timeout-minutes: 10
 
     steps:
@@ -155,7 +155,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       # Update core packages
       - name: Install dependencies for CI tests

CHANGELOG.md

@@ -14,6 +14,7 @@
 - Fix adding changelog entries with backticks from PR titles ([#2115](https://github.com/ewels/MultiQC/pull/2115))
 - Fix for python 3.12: replace removed `distutils` ([#2113](https://github.com/ewels/MultiQC/pull/2113))
 - Bundle lzstring to fix Python 3.12 ([#2119](https://github.com/ewels/MultiQC/pull/2119))
+- Drop Python 3.6 and 3.7 support, add 3.12 ([#2121](https://github.com/ewels/MultiQC/pull/2121))
 - <img src="./multiqc/templates/default/assets/img/favicon-16x16.png" alt="///" width="10px"/> New logo
 
 ### New Modules

multiqc/multiqc.py

@@ -1049,8 +1049,9 @@ def __rich_measure__(self, console: rich.console.Console, options: rich.console.
         except AttributeError:
             pass  # Not a child theme
 
-        # Copy the template files to the tmp directory
-        util_functions.copytree_overwrite(template_mod.template_dir, tmp_dir)
+        # Copy the template files to the tmp directory (`dirs_exist_ok` makes sure
+        # parent template files are overwritten)
+        shutil.copytree(template_mod.template_dir, tmp_dir, dirs_exist_ok=True)
 
         # Function to include file contents in Jinja template
         def include_file(name, fdir=tmp_dir, b64=False):

multiqc/utils/util_functions.py

@@ -162,18 +162,3 @@ def strtobool(val):
         return 0
     else:
         raise ValueError("invalid truth value %r" % (val,))
-
-
-def copytree_overwrite(parent_dir, child_dir):
-    """
-    Replicates the behaviour of `shutil.copytree(..., dirs_exist_ok=True)` (which is
-    not available before Python 3.8) to overwrite files in `parent_dir` with files
-    in `child_dir`.
-    """
-    # Copy files from src to dst that already exist in dst (i.e., overwrite them)
-    for dir_name, sub_dirs, filenames in os.walk(parent_dir):
-        for filename in filenames:
-            src_file_path = os.path.join(dir_name, filename)
-            dst_file_path = os.path.join(child_dir, os.path.relpath(src_file_path, parent_dir))
-            os.makedirs(os.path.dirname(dst_file_path), exist_ok=True)
-            shutil.copy2(src_file_path, dst_file_path)