Windows compatibility

cli/medperf/entities/cube.py

@@ -1,11 +1,16 @@
 import os
+import sys
 import yaml
-import pexpect
 import logging
 from typing import List, Dict, Optional, Union
 from pydantic import Field
 from pathlib import Path
 
+if sys.platform == "win32":
+    import wexpect as pexpect
+else:
+    import pexpect
+
 from medperf.utils import untar, combine_proc_sp_text, list_files, storage_path, cleanup
 from medperf.entities.interface import Entity, Uploadable
 from medperf.entities.schemas import MedperfSchema, DeployableSchema
@@ -228,7 +233,7 @@ def download_image(self):
             # Retrieve image from image registry
             logging.debug(f"Retrieving {self.id} image")
             cmd = f"mlcube configure --mlcube={self.cube_path}"
-            proc = pexpect.spawn(cmd)
+            proc = pexpect.spawn(cmd, timeout=None)
             proc_out = combine_proc_sp_text(proc)
             logging.debug(proc_out)
             proc.close()
@@ -295,7 +300,7 @@ def run(
         proc_out = combine_proc_sp_text(proc)
         proc.close()
         logging.debug(proc_out)
-        if proc.exitstatus != 0:
+        if proc.exitstatus and proc.exitstatus != 0:
             raise ExecutionError("There was an error while executing the cube")
 
         logging.debug(list_files(config.storage))

cli/medperf/tests/entities/test_cube.py

@@ -13,10 +13,7 @@
     setup_cube_comms_downloads,
 )
 from medperf.tests.mocks.pexpect import MockPexpect
-from medperf.exceptions import (
-    ExecutionError,
-    InvalidEntityError
-)
+from medperf.exceptions import ExecutionError, InvalidEntityError
 
 PATCH_CUBE = "medperf.entities.cube.{}"
 DEFAULT_CUBE = {"id": 37}
@@ -132,7 +129,7 @@ def test_get_cube_without_image_configures_mlcube(self, mocker, setup):
         Cube.get(self.id)
 
         # Assert
-        spy.assert_called_once_with(expected_cmd)
+        spy.assert_called_once_with(expected_cmd, timeout=None)
 
     @pytest.mark.parametrize("setup", [{"remote": [DEFAULT_CUBE]}], indirect=True)
     def test_get_cube_with_image_isnt_configured(self, mocker, setup):

cli/medperf/utils.py

@@ -15,12 +15,16 @@
 import json
 from pathlib import Path
 from shutil import rmtree
-from pexpect import spawn
 from datetime import datetime
 from typing import List
 from colorama import Fore, Style
 from pexpect.exceptions import TIMEOUT
 
+if sys.platform == "win32":
+    from wexpect import spawn
+else:
+    from pexpect import spawn
+
 import medperf.config as config
 from medperf.logging.filters.redacting_filter import RedactingFilter
 from medperf.exceptions import ExecutionError, InvalidEntityError, MedperfException
@@ -29,7 +33,12 @@
 def setup_logging(log_lvl):
     log_fmt = "%(asctime)s | %(levelname)s: %(message)s"
     log_file = storage_path(config.log_file)
-    handler = handlers.RotatingFileHandler(log_file, maxBytes=10000000, backupCount=5)
+    handler = handlers.RotatingFileHandler(
+        log_file,
+        maxBytes=10000000,
+        backupCount=5,
+        encoding="utf-8"
+    )
     handler.setFormatter(logging.Formatter(log_fmt))
     logging.basicConfig(
         level=log_lvl,
@@ -452,12 +461,18 @@ def combine_proc_sp_text(proc: spawn) -> str:
             logging.error("Process timed out")
             raise ExecutionError("Process timed out")
 
-        while byte and not re.match(b"[\r\n]", byte):
+        if type(byte) == str:
+            pattern = "[\r\n]"
+        else:
+            pattern = b"[\r\n]"
+
+        while byte and not re.match(pattern, byte):
             byte = proc.read(1)
             line += byte
         if not byte:
             break
-        line = line.decode("utf-8", "ignore")
+        if type(line) != str:
+            line = line.decode("utf-8", "ignore")
         if line:
             # add to proc_out list for logging
             proc_out += line

cli/requirements.txt

@@ -1,18 +1,20 @@
-typer~=0.6.0
+typer~=0.6.0; sys_platform != "win32"
+typer<0.5.0; sys_platform == "win32"
 rich~=12.5.0
 PyYAML>=5.4,<6
 requests>=2.26.0
 pydantic==1.10.2
 yaspin==2.1.0
 tabulate==0.8.9
 pexpect==4.8.0
+wexpect==4.0.0; sys_platform == "win32"
 colorama==0.4.4
 time-machine==2.4.0
 pytest-mock==1.13.0
 pyfakefs==5.0.0
 mlcube==0.0.9
 mlcube-docker==0.0.9
-mlcube-singularity==0.0.9
+mlcube-singularity==0.0.9; sys_platform != "win32"
 validators==0.18.2
 merge-args==0.1.4
 synapseclient==2.7.0