Merge pull request #108 from xylar/fix_mypy

Various fixes to do with linting

Author: xylar

.pre-commit-config.yaml

@@ -33,4 +33,4 @@ repos:
       - id: mypy
         args: ["--config=setup.cfg", "--show-error-codes"]
         verbose: true
-        additional_dependencies: ['types-requests']
+        additional_dependencies: ['types-requests', 'types-PyYAML']

mache/__init__.py

@@ -1,4 +1,3 @@
-from mache.machine_info import MachineInfo
 from mache.discover import discover_machine
-
+from mache.machine_info import MachineInfo
 from mache.version import __version__, __version_info__

mache/__main__.py

@@ -1,5 +1,5 @@
-import sys
 import argparse
+import sys
 
 import mache.version
 from mache import sync

mache/discover.py

@@ -1,6 +1,6 @@
+import os
 import socket
 import warnings
-import os
 
 
 def discover_machine(quiet=False):

mache/machine_info.py

@@ -1,12 +1,17 @@
-from lxml import etree
-try:
-    from importlib import resources as importlib_resources
-except ImportError:
-    # python<=3.8
-    import importlib_resources
 import configparser
 import os
 import pwd
+import sys
+from typing import TYPE_CHECKING
+
+from lxml import etree
+
+if TYPE_CHECKING or sys.version_info > (3, 8, 0):
+    from importlib import resources as importlib_resources
+else:
+    # python <= 3.8
+    import importlib_resources
+
 
 from mache.discover import discover_machine
 
@@ -120,7 +125,8 @@ def __str__(self):
         info = f'Machine: {self.machine}\n' \
                f'  E3SM Supported Machine: {self.e3sm_supported}'
 
-        if self.e3sm_supported:
+        if self.e3sm_supported and self.compilers is not None and \
+                self.mpilibs is not None and self.os is not None:
             info = f'{info}\n' \
                    f'  Compilers: {", ".join(self.compilers)}\n' \
                    f'  MPI libraries: {", ".join(self.mpilibs)}\n' \
@@ -231,12 +237,12 @@ def _get_config(self):
         try:
             cfg_path = \
                 importlib_resources.files('mache.machines') / f'{machine}.cfg'
-            config.read(cfg_path)
+            config.read(str(cfg_path))
         except FileNotFoundError:
             # this isn't a known machine so use the default
             cfg_path = \
                 importlib_resources.files('mache.machines') / 'default.cfg'
-            config.read(cfg_path)
+            config.read(str(cfg_path))
 
         return config
 

mache/permissions.py

@@ -1,10 +1,11 @@
+import grp
 import os
 import stat
-import grp
+
 import progressbar
 
 
-def update_permissions(base_paths, group, show_progress=True,
+def update_permissions(base_paths, group, show_progress=True,  # noqa: C901
                        group_writable=False, other_readable=True):
     """
     Update the group that a directory belongs to along with the "group" and

mache/spack/__init__.py

@@ -1,14 +1,19 @@
 import os
 import subprocess
+import sys
+from typing import TYPE_CHECKING
+
 from jinja2 import Template
-try:
+
+if TYPE_CHECKING or sys.version_info > (3, 8, 0):
     from importlib import resources as importlib_resources
-except ImportError:
-    # python<=3.8
+else:
+    # python <= 3.8
     import importlib_resources
+
 import yaml
 
-from mache.machine_info import discover_machine, MachineInfo
+from mache.machine_info import MachineInfo, discover_machine
 from mache.version import __version__
 
 
@@ -99,7 +104,7 @@ def make_spack_env(spack_path, env_name, spack_specs, compiler, mpi,
         path = \
             importlib_resources.files('mache.spack') / shell_filename
         try:
-            with open(path) as fp:
+            with open(str(path)) as fp:
                 template = Template(fp.read())
         except FileNotFoundError:
             # there's nothing to add, which is fine
@@ -112,7 +117,7 @@ def make_spack_env(spack_path, env_name, spack_specs, compiler, mpi,
 
     path = \
         importlib_resources.files('mache.spack') / 'build_spack_env.template'
-    with open(path) as fp:
+    with open(str(path)) as fp:
         template = Template(fp.read())
     if tmpdir is not None:
         modules = f'{modules}\n' \
@@ -219,7 +224,7 @@ def get_spack_script(spack_path, env_name, compiler, mpi, shell, machine=None,
         path = \
             importlib_resources.files('mache.spack') / shell_filename
         try:
-            with open(path) as fp:
+            with open(str(path)) as fp:
                 template = Template(fp.read())
         except FileNotFoundError:
             # there's nothing to add, which is fine
@@ -321,7 +326,7 @@ def get_modules_env_vars_and_mpi_compilers(machine, compiler, mpi, shell,
         path = \
             importlib_resources.files('mache.spack') / shell_filename
         try:
-            with open(path) as fp:
+            with open(str(path)) as fp:
                 template = Template(fp.read())
         except FileNotFoundError:
             # there's nothing to add, which is fine
@@ -345,7 +350,7 @@ def _get_yaml_data(machine, compiler, mpi, include_e3sm_lapack,
         path = \
             importlib_resources.files('mache.spack') / template_filename
         try:
-            with open(path) as fp:
+            with open(str(path)) as fp:
                 template = Template(fp.read())
         except FileNotFoundError:
             raise ValueError(f'Spack template not available for {compiler} '
@@ -373,9 +378,9 @@ def _get_modules(yaml_string):
                         for mod in item['modules']:
                             mods.append(f'module load {mod}')
 
-    mods = '\n'.join(mods)
+    mods_str = '\n'.join(mods)
 
-    return mods
+    return mods_str
 
 
 def _get_mpi_compilers(machine, compiler, mpi, cray_compilers):

mache/sync/__init__.py

@@ -1,8 +1,9 @@
-import sys
 import argparse
+import sys
 
 from mache.sync import diags
 
+
 def main():
     """
     Defines the ``mache sync`` command
@@ -33,4 +34,4 @@ def main():
         exit(1)
 
     # call the function associated with the requested command
-    commands[args.command]()
+    commands[args.command]()

mache/sync/diags.py

@@ -1,13 +1,13 @@
-import sys
 import argparse
 import subprocess
+import sys
 
 from mache.machine_info import MachineInfo
 from mache.permissions import update_permissions
 
 
-def sync_diags(other, direction='to', machine=None, username=None,
-               config_filename=None):
+def sync_diags(other, direction='to', machine=None,  # noqa: C901
+               username=None, config_filename=None):
     """
     Synchronize diagnostics files between supported machines