Merge branch 'staging'

requirements/_requirements_base.txt

@@ -8,6 +8,8 @@ scikit-learn>=1.3.0
 fastcluster>=1.2.6
 matplotlib>=3.8.0
 imageio>=2.33.1
-imageio-ffmpeg>=0.4.9
+# ffmpeg binary >=0.6.0 breaks convert.
+# TODO fix convert to use latest binary
+imageio-ffmpeg>=0.4.9,<0.6.0
 ffmpy>=0.3.0
 pywin32>=305 ; sys_platform == "win32"

setup.py

@@ -13,7 +13,7 @@ import re
 import sys
 import typing as T
 from shutil import which
-from subprocess import list2cmdline, PIPE, Popen, run, STDOUT
+from subprocess import PIPE, Popen, run, STDOUT
 
 from pkg_resources import parse_requirements
 
@@ -1076,7 +1076,9 @@ class Install():  # pylint:disable=too-few-public-methods
         str
             The formatted full package and version string
         """
-        return f"{package}{','.join(''.join(spec) for spec in version)}"
+        retval = f"{package}{','.join(''.join(spec) for spec in version)}"
+        logger.debug("Formatted package \"%s\" version \"%s\" to \"%s'", package, version, retval)
+        return retval
 
     def _install_setup_packages(self) -> None:
         """ Install any packages that are required for the setup.py installer to work. This
@@ -1088,8 +1090,6 @@ class Install():  # pylint:disable=too-few-public-methods
             pkg_str = self._format_package(*pkg)
             if self._env.is_conda:
                 cmd = ["conda", "install", "-y"]
-                if any(char in pkg_str for char in (" ", "<", ">", "*", "|")):
-                    pkg_str = f"\"{pkg_str}\""
             else:
                 cmd = [sys.executable, "-m", "pip", "install", "--no-cache-dir"]
                 if self._env.is_admin:
@@ -1495,7 +1495,7 @@ class WinPTYInstaller(Installer):  # pylint:disable=too-few-public-methods
                  is_gui: bool) -> None:
         super().__init__(environment, package, command, is_gui)
         self._cmd = which(command[0], path=os.environ.get('PATH', os.defpath))
-        self._cmdline = list2cmdline(command)
+        self._cmdline = " ".join(command)
         logger.debug("cmd: '%s', cmdline: '%s'", self._cmd, self._cmdline)
 
         self._pbar = re.compile(r"(?:eta\s[\d\W]+)|(?:\s+\|\s+\d+%)\Z")

tools/alignments/jobs.py

@@ -327,7 +327,7 @@ class Check:
         """
         now = datetime.now().strftime("%Y%m%d_%H%M%S")
         folder_name = (f"{self._get_filename_prefix()}"
-                       f"{self.output_message.replace(' ','_').lower()}_{now}")
+                       f"{self.output_message.replace(' ', '_').lower()}_{now}")
         dst_dir = self._get_output_folder()
         output_folder = os.path.join(dst_dir, folder_name)
         logger.debug("Creating folder: '%s'", output_folder)