Cleanup issues AlphaGenes/AlphaImpute2#64

.github/workflows/tests.yml

@@ -7,6 +7,7 @@ jobs:
         strategy:
           matrix:
             os: [ubuntu-latest, Windows-latest, macos-latest]
+            python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
         runs-on: ${{ matrix.os }}
         permissions:
             contents: read

conftest.py

@@ -2,6 +2,7 @@
 import operator
 import os
 import shutil
+import warnings
 import numpy as np
 
 
@@ -50,13 +51,22 @@ def pytest_runtest_makereport():
             num_file = 3
         else:
             num_file = 2
-        accu = stdout[-1][-1].split("\n")[-(2 + 3 * num_file) :]
-        name = accu[0].split()[-1]
-        with open("tests/accuracy_tests/accu_report.txt", "a") as file:
-            for i in range(num_file):
-                assessed_file = accu[i * 3 + 1].split()[-1]
-                file.write(name + " " + assessed_file + " " + accu[i * 3 + 2] + "\n")
-                file.write(name + " " + assessed_file + " " + accu[i * 3 + 3] + "\n")
+        try:
+            accu = stdout[-1][-1].split("\n")[-(2 + 3 * num_file) :]
+            name = accu[0].split()[-1]
+            with open("tests/accuracy_tests/accu_report.txt", "a") as file:
+                for i in range(num_file):
+                    assessed_file = accu[i * 3 + 1].split()[-1]
+                    file.write(
+                        name + " " + assessed_file + " " + accu[i * 3 + 2] + "\n"
+                    )
+                    file.write(
+                        name + " " + assessed_file + " " + accu[i * 3 + 3] + "\n"
+                    )
+        except IndexError:
+            warnings.warn(
+                "Some outputs are missing in the accuracy report. If you are using Linux system, you can rerun the tests, or check the test outputs directly with pytest -s for more details."
+            )
 
 
 @pytest.hookimpl()

pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "numpy>=1.19",
     "numba>=0.49.0"
 ]
-requires-python = "!= 3.12, !=3.14"
+requires-python = ">= 3.6, < 3.14"
 
 [project.scripts]
 # correspond to entry_points

src/alphaimpute2/alphaimpute2.py

@@ -1,4 +1,5 @@
 import argparse
+import sys
 import numpy as np
 
 from .tinyhouse import Pedigree
@@ -13,10 +14,9 @@
 
 from .tinyhouse.Utils import time_func
 
-# try:
 from .Imputation import version
 
-version_verion = version.version
+version_version = version.version
 
 if not ("profile" in globals()):
 
@@ -240,6 +240,21 @@ def getArgs():
         help=argparse.SUPPRESS,
     )  # help='Flag to prioritze pedigree imputation for individuals at the same genotyping density as their parents.')
 
+    # special handle for version argument to allow it to be called with just -version
+    parser.add_argument(
+        "-version",
+        default=None,
+        action="version",
+        version="%(prog)s " + version_version,
+        help="Show program's version number and exit.",
+    )
+
+    args = sys.argv[1:]
+
+    if "-version" in args:
+        parser.parse_args(args)
+        sys.exit(0)
+
     return InputOutput.parseArgs("AlphaImpute", parser)
 
 
@@ -472,9 +487,15 @@ def write_seg(pedigree, outputFile):
 
 @time_func("Full Program Run")
 def main():
-    InputOutput.print_boilerplate("AlphaImpute2", version_verion)
     args = getArgs()
 
+    # commenting out as AlphaImpute2 does not have recent changes for x-chr and metafounder
+    # therefore cannot use the boilerplate as the commit with updated boilerplate also has
+    # the changes for x-chr and metafounder and cause issues
+    # remove comment once AlphaImpute2 has been updated to work with x-chr and metafounder
+
+    # InputOutput.print_boilerplate("AlphaImpute2", version_version)
+
     InputOutput.setNumbaSeeds(12345)
     pedigree = Pedigree.Pedigree(constructor=ImputationIndividual.AlphaImputeIndividual)
     read_in_data(pedigree, args)