[pull] main from AlphaGenes:main

.github/ISSUE_TEMPLATE/task-issue-template.md

@@ -0,0 +1,20 @@
+---
+name: Task issue template
+about: The actionable task template.
+title: ''
+labels: task
+assignees: ''
+
+---
+
+## Goal
+What are we trying to achieve?
+
+## Proposed approach
+(brief, not perfect)
+
+## Scope
+What files/modules are affected?
+
+## Done when
+Clear condition for completion

.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
@@ -36,7 +37,7 @@ jobs:
               run: python3 -m build
 
             - name: Install AlphaImpute2
-              run: pip install dist/alphaimpute2-0.0.3-py3-none-any.whl
+              run: pip install dist/alphaimpute2-0.0.4-py3-none-any.whl
 
             - name: Install pytest
               run: |

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 may be missing for the generation for the accuracy report. You can check tests/accuracy_tests/accu_report.txt for the recorded accuracies or rerun the tests. "
+            )
 
 
 @pytest.hookimpl()
@@ -88,7 +98,15 @@ def pytest_terminal_summary(terminalreporter):
         "Gen5 Accu",
     )
     dt = {"names": columns, "formats": ("U76", "U28", "U25") + ("f4",) * (nGen + 1)}
-    accu = np.loadtxt("tests/accuracy_tests/accu_report.txt", encoding=None, dtype=dt)
+    try:
+        accu = np.loadtxt(
+            "tests/accuracy_tests/accu_report.txt", encoding=None, dtype=dt
+        )
+    except ValueError:
+        warnings.warn(
+            "Some outputs may be missing for the generation for the accuracy report. You can check tests/accuracy_tests/accu_report.txt for the recorded accuracies or rerun the tests. "
+        )
+        return
 
     mkr_accu = list(
         filter(