add unit test for [Sequence] AnthonyNolan filter (#243)

* move MSF files into the unit tests data area

* restore the associated .pop file and .ini file for the `sequence-nopoptests.ini`

src/PyPop/Main.py

@@ -33,6 +33,7 @@
 
 """Python population genetics statistics."""
 
+import os
 import sys
 import time
 from configparser import ConfigParser, NoOptionError, NoSectionError
@@ -624,13 +625,41 @@ def _runFilters(self):
                 except Exception:
                     sequenceFileSuffix = "_prot"
                 try:
-                    anthonynolanPath = self.config.get(filterCall, "directory")
-                except Exception:
-                    anthonynolanPath = Path(self.datapath) / "anthonynolan" / "msf"
-                    if self.debug:
-                        print(
-                            f"LOG: Defaulting to system datapath {anthonynolanPath} for anthonynolanPath data"
+                    path_obj = Path(self.config.get(filterCall, "directory"))
+
+                    # if the path is relative, resolve it to an absolute path if it exists
+                    if not path_obj.is_absolute():
+                        if path_obj.exists() and path_obj.is_dir():
+                            path_obj = path_obj.resolve()
+                        elif os.environ.get(
+                            "CURRENT_TEST_DIRECTORY"
+                        ) and os.environ.get("PYTEST_VERSION"):
+                            # if we're running in a test environment, resolve paths relative to the parent of the "tests" directory
+                            path_obj = (
+                                Path(os.environ.get("CURRENT_TEST_DIRECTORY")).parent
+                                / path_obj
+                            )
+                        else:
+                            sys.exit(
+                                f"Relative path {path_obj} for AnthonyNolan sequence files does not exist or is not a directory."
+                            )
+
+                    # at this point, the path is absolute, now we need to check it exits
+                    if path_obj.exists() and path_obj.is_dir():
+                        anthonynolanPath = str(path_obj)
+                        if self.debug:
+                            print(
+                                f"Using  {anthonynolanPath} for AnthonyNolan data files"
+                            )
+                    else:
+                        sys.exit(
+                            f"Absolute path {path_obj} for Anthony Nolan sequence files does not exist or is not a directory"
                         )
+
+                except Exception:
+                    sys.exit(
+                        "Need to provide a path to the Anthony Nolan sequence files: no default"
+                    )
                 try:
                     sequenceFilterMethod = self.config.get(
                         filterCall, "sequenceConsensusMethod"

data/samples/sequence-nopoptests.ini → tests/data/sequence-nopoptests.ini

@@ -49,7 +49,5 @@ validSampleFields=+populat
 filtersToApply=Sequence
 
 [Sequence]
-;;alleleFileFormat=msf
-;; alternative location of msf sequence alignment files (available
-;; from ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/
-directory=/home/alex/ihwg/src/data/anthonynolan/msf/
+# relative location of msf sequence alignment files (available from ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/)
+directory=tests/data/anthonynolan/msf/

tests/test_Filters.py

@@ -1,3 +1,6 @@
+import os
+from pathlib import Path
+
 from base import (
     DEFAULT_GOLD_OUTPUT_DIR,
     abspath_test_data,
@@ -87,3 +90,17 @@ def test_Filters_CustomBinning_P_Filter():
             DEFAULT_GOLD_OUTPUT_DIR / "custom-binning-P-Filter" / out_filename
         )
         assert filecmp_ignore_newlines(out_filename, gold_out_filename)
+
+
+def test_Filters_Sequence_AnthonyNolan():
+    # FIXME: a bit hacky
+    # set an environment variable for the current test directory
+    current_dir = Path(__file__).parent  # get the current test script directory
+    os.environ["CURRENT_TEST_DIRECTORY"] = str(current_dir)
+
+    exit_code = run_pypop_process(
+        "./tests/data/sequence-nopoptests.ini",
+        "./tests/data/USAFEL-UchiTelle.pop",
+    )
+    # check exit code
+    assert exit_code == 0