Merge pull request #530 from Ecogenomics/staging

Merge staging to fix pydantic depencies

gtdbtk/external/mash.py

@@ -234,14 +234,17 @@ def _generate(self):
             args = list(map(str, args))
             proc = subprocess.Popen(args, stdout=subprocess.PIPE,
                                     stderr=subprocess.PIPE, encoding='utf-8')
+            stderr_lines = []
             with tqdm_log(total=len(self.genomes), unit='genome') as p_bar:
                 for line in iter(proc.stderr.readline, ''):
+                    stderr_lines.append(line)
                     if line.startswith('Sketching'):
                         p_bar.update()
             proc.wait()
 
             if proc.returncode != 0 or not os.path.isfile(self.path):
-                raise GTDBTkExit(f'Error generating Mash sketch: {proc.stderr.read()}')
+                raise GTDBTkExit(f'Error generating Mash sketch:\n'
+                                 f'{"".join(stderr_lines)}')
 
 
 class QrySketchFile(SketchFile):

setup.py

@@ -45,7 +45,7 @@ def readme():
             'gtdbtk = gtdbtk.__main__:main'
         ]
     },
-    install_requires=["dendropy>=4.1.0", 'numpy>=1.9.0', 'tqdm>=4.35.0', 'pydantic'],
+    install_requires=["dendropy>=4.1.0", 'numpy>=1.9.0', 'tqdm>=4.35.0', 'pydantic>=1.9.2,<2'],
     license=meta['license'],
     long_description=readme(),
     long_description_content_type='text/markdown',