[med-svn] [Git][med-team/qiime][master] Added patch to finish migration to platformdirs from appdirs. Closes: #1068006

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / qiime


Commits:
9ac56e0a by Michael R. Crusoe at 2024-06-24T16:26:38+02:00
Added patch to finish migration to platformdirs from appdirs. Closes: #1068006

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/platformdirs
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -10,6 +10,9 @@ qiime (2024.5.0-1) UNRELEASED; urgency=medium
   [ Athos Ribeiro ]
   * d/p/configparser.patch: support python 3.12 configparser
 
+  [ Michael R. Crusoe ]
+  * Added patch to finish migration to platformdirs from appdirs.
+
  -- Andreas Tille <tille at debian.org>  Thu, 06 Jun 2024 15:33:01 +0200
 
 qiime (2024.2.0-1) unstable; urgency=medium


=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
                python3,
                python3-setuptools,
                python3-pytest <!nocheck>,
-               python3-appdirs <!nocheck>,
+               python3-platformdirs <!nocheck>,
                python3-bibtexparser <!nocheck>,
                python3-decorator <!nocheck>,
                python3-dill <!nocheck>,


=====================================
debian/patches/platformdirs
=====================================
@@ -0,0 +1,59 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Switch to platform dirs from appdirs
+Debian-Bug:1068006
+
+> python3-appdirs is dead upstream[1] and its Debian maintainer has indicated
+> that it should not be included in trixie[2]. A recommended replacement is
+> python3-platformdirs[3], which is a fork of appdirs with a very similar API.
+> [1] https://github.com/ActiveState/appdirs/commit/8734277956c1df3b85385e6b308e954910533884
+> [2] https://bugs.debian.org/1060427
+> [3] https://pypi.org/project/platformdirs/
+
+--- qiime.orig/qiime2/sdk/parallel_config.py
++++ qiime/qiime2/sdk/parallel_config.py
+@@ -8,12 +8,12 @@
+ 
+ import os
+ import psutil
+-import appdirs
+ import threading
+ import importlib
+ 
+ import parsl
+ import tomlkit
++from platformdirs import user_config_dir
+ 
+ PARALLEL_CONFIG = threading.local()
+ PARALLEL_CONFIG.dfk = None
+@@ -161,16 +161,16 @@
+ 
+     if config_fp is None:
+         # 2. Check in user writable location
+-        # appdirs.user_config_dir(appname='qiime2', author='...')
++        # user_config_dir(appname='qiime2', author='...')
+         if os.path.exists(fp_ := os.path.join(
+-                appdirs.user_config_dir('qiime2'), 'qiime2_config.toml')):
++                user_config_dir('qiime2'), 'qiime2_config.toml')):
+             config_fp = fp_
+         # 3. Check in admin writable location
+         # /etc/
+         # site_config_dir
+-        # appdirs.site_config_dir(appname='qiime2, author='...')
++        # site_config_dir(appname='qiime2, author='...')
+         elif os.path.exists(fp_ := os.path.join(
+-                appdirs.site_config_dir('qiime2'), 'qiime2_config.toml')):
++                site_config_dir('qiime2'), 'qiime2_config.toml')):
+             config_fp = fp_
+         # NOTE: These next two are dependent on us being in a conda environment
+         # 4. Check in conda env
+--- qiime.orig/ci/recipe/meta.yaml
++++ qiime/ci/recipe/meta.yaml
+@@ -35,7 +35,7 @@
+     - psutil
+     - flufl.lock
+     - parsl {{ parsl }}
+-    - appdirs
++    - platformdirs
+     - tomlkit
+     - lxml
+ 


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+platformdirs
 python3.8.patch
 enable_decorator_5.patch
 python3.10.patch



View it on GitLab: https://salsa.debian.org/med-team/qiime/-/commit/9ac56e0a3dac450678efcafc3b4c6c51d7760778

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