pypop-genomics 1.2.2__cp310-cp310-macosx_10_15_x86_64.whl → 1.3.0__cp310-cp310-macosx_10_15_x86_64.whl

PyPop/CommandLineInterface.py

@@ -34,7 +34,6 @@ from argparse import (
     Action,
     ArgumentDefaultsHelpFormatter,
     ArgumentParser,
-    FileType,
     RawDescriptionHelpFormatter,
 )
 from pathlib import Path
@@ -238,8 +237,7 @@ current directory""",
     add_input(
         "-f",
         "--filelist",
-        help="file containing list of files (one per line) to process\n(mutually exclusive with supplying POPFILEs)",
-        type=FileType("r"),
+        help="file containing list of files (one per line) to process. files are resolved relative to FILELIST, unless absolute. mutually exclusive with supplying POPFILEs)",
         default=None,
     )
     add_input(

PyPop/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '1.2.2'
-__version_tuple__ = version_tuple = (1, 2, 2)
+__version__ = version = '1.3.0'
+__version_tuple__ = version_tuple = (1, 3, 0)
+
+__commit_id__ = commit_id = None

PyPop/citation/CITATION.apalike

@@ -1 +1 @@
-Lancaster A.K., Nelson M.P., Single R., Solberg O., Tsai Y., Meyer D., Webster G., Mariani M.P., Sochat V., Kornel K., Spaaks J.H., Mack S.J., and Thomson G. PyPop: Python for Population Genomics (version v1.2.2). DOI: 10.5281/zenodo.16555858 URL: http://pypop.org/
+Lancaster A.K., Nelson M.P., Single R., Solberg O., Tsai Y., Meyer D., Webster G., Mariani M.P., Sochat V., Kornel K., Spaaks J.H., Mack S.J., and Thomson G. PyPop: Python for Population Genomics (version v1.3.0). DOI: 10.5281/zenodo.17081295 URL: http://pypop.org/

PyPop/citation/CITATION.bibtex

@@ -1,6 +1,6 @@
 @misc{YourReferenceHere,
 author = {Lancaster, Alexander K. and Nelson, Mark P. and Single, Richard and Solberg, Owen and Tsai, Yingsu and Meyer, Diogo and Webster, Gordon and Mariani, Michael P. and Sochat, Vanessa and Kornel, Karl and Spaaks, Jurriaan H. and Mack, Steven J. and Thomson, Glenys},
-doi = {10.5281/zenodo.16555858},
+doi = {10.5281/zenodo.17081295},
 title = {PyPop: Python for Population Genomics},
 url = {http://pypop.org/},
 note = {If you use this software, please cite both the software itself, as well as the article Lancaster AK et al. (2024) <a href="https://doi.org/10.3389/fimmu.2024.1378512">PyPop: A mature open-source software pipeline for population genomics</a>. <i>Front. Immunol.</i> <b>15</b>:1378512. doi: 10.3389/fimmu.2024.1378512}

PyPop/citation/CITATION.cff

@@ -98,7 +98,7 @@ title: 'PyPop: Python for Population Genomics'
 repository-artifact: https://pypi.org/project/pypop-genomics/
 repository-code: https://github.com/alexlancaster/pypop/
 license: GPL-2.0-or-later
-version: v1.2.2
+version: v1.3.0
 type: software
 url: http://pypop.org/
 identifiers:
@@ -120,11 +120,11 @@ identifiers:
     relation: Continues
   - description: GitHub tag for repository
     type: url
-    value: https://github.com/alexlancaster/pypop/tree/v1.2.2
+    value: https://github.com/alexlancaster/pypop/tree/v1.3.0
     relation: IsSupplementTo
   - description: PyPI package
     type: url
-    value: https://pypi.org/project/pypop-genomics/1.2.2
+    value: https://pypi.org/project/pypop-genomics/1.3.0
     relation: IsSourceOf
   - description: DOI concept identifier for all versions of PyPop
     type: doi
@@ -140,4 +140,4 @@ keywords:
   - Major histocompatibility complex
   - HLA
   - MHC
-doi: 10.5281/zenodo.16555858
+doi: 10.5281/zenodo.17081295

PyPop/citation/CITATION.codemeta

@@ -192,7 +192,7 @@
   ],
   "codeRepository": "https://github.com/alexlancaster/pypop/",
   "description": "<p>PyPop for Population Genomics (<a href=\"http://pypop.org/\">PyPop</a>) is a Python program for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium (LD).&nbsp;Output of analyses are stored in XML format for maximum downstream flexibility. PyPop also has an internal facility for additionally aggregating the output XML and generating output tab-separated values (TSV) files, as well as default plain text files for each population. Although it can be run on any kind of genotype data, it has additional support for analyzing population genotype with allelic nomenclature from the human leukocyte antigen (HLA) region.</p>",
-  "identifier": "https://doi.org/10.5281/zenodo.16555858",
+  "identifier": "https://doi.org/10.5281/zenodo.17081295",
   "keywords": [
     "population genetics",
     "population genomics",
@@ -207,5 +207,5 @@
   "license": "https://spdx.org/licenses/GPL-2.0-or-later",
   "name": "PyPop: Python for Population Genomics",
   "url": "http://pypop.org/",
-  "version": "v1.2.2"
+  "version": "v1.3.0"
 }

PyPop/citation/CITATION.endnote

@@ -21,6 +21,6 @@
 %K Major histocompatibility complex
 %K HLA
 %K MHC
-%R 10.5281/zenodo.16555858
+%R 10.5281/zenodo.17081295
 %T PyPop: Python for Population Genomics
 %U http://pypop.org/

PyPop/citation/CITATION.ris

@@ -13,7 +13,7 @@ AU  - Kornel, Karl
 AU  - Spaaks, Jurriaan H.
 AU  - Mack, Steven J.
 AU  - Thomson, Glenys
-DO  - 10.5281/zenodo.16555858
+DO  - 10.5281/zenodo.17081295
 KW  - population genetics
 KW  - population genomics
 KW  - bioinformatics

PyPop/citation/CITATION.schema.org

@@ -192,7 +192,7 @@
   ],
   "codeRepository": "https://github.com/alexlancaster/pypop/",
   "description": "<p>PyPop for Population Genomics (<a href=\"http://pypop.org/\">PyPop</a>) is a Python program for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium (LD).&nbsp;Output of analyses are stored in XML format for maximum downstream flexibility. PyPop also has an internal facility for additionally aggregating the output XML and generating output tab-separated values (TSV) files, as well as default plain text files for each population. Although it can be run on any kind of genotype data, it has additional support for analyzing population genotype with allelic nomenclature from the human leukocyte antigen (HLA) region.</p>",
-  "identifier": "https://doi.org/10.5281/zenodo.16555858",
+  "identifier": "https://doi.org/10.5281/zenodo.17081295",
   "keywords": [
     "population genetics",
     "population genomics",
@@ -207,5 +207,5 @@
   "license": "https://spdx.org/licenses/GPL-2.0-or-later",
   "name": "PyPop: Python for Population Genomics",
   "url": "http://pypop.org/",
-  "version": "v1.2.2"
+  "version": "v1.3.0"
 }

PyPop/citation/CITATION.zenodo

@@ -173,12 +173,12 @@
       "scheme": "url"
     },
     {
-      "identifier": "https://github.com/alexlancaster/pypop/tree/v1.2.2",
+      "identifier": "https://github.com/alexlancaster/pypop/tree/v1.3.0",
       "relation": "isSupplementTo",
       "scheme": "url"
     },
     {
-      "identifier": "https://pypi.org/project/pypop-genomics/1.2.2",
+      "identifier": "https://pypi.org/project/pypop-genomics/1.3.0",
       "relation": "isSourceOf",
       "scheme": "url"
     },
@@ -188,7 +188,7 @@
       "scheme": "doi"
     },
     {
-      "identifier": "10.5281/zenodo.16555858",
+      "identifier": "10.5281/zenodo.17081295",
       "relation": "isSupplementedBy",
       "scheme": "doi"
     },
@@ -205,5 +205,5 @@
   ],
   "title": "PyPop: Python for Population Genomics",
   "upload_type": "software",
-  "version": "v1.2.2"
+  "version": "v1.3.0"
 }

PyPop/pypop.py

@@ -241,14 +241,24 @@ return for each prompt.""")
         print(f"PyPop is processing {fileNames[0]} ...")
 
     else:
-        # non-interactive mode: run in 'batch' mode
+        # non-interactive mode: run in 'batch'xb mode
 
         if fileList:
             # if we are providing the filelist
             # use list from file as list to check
-            # li = [f.strip('\n') for f in open(fileList).readlines()]
-            li = [f.strip("\n") for f in fileList.readlines()]
-            fileList.close()  # make sure we close it
+
+            with open(fileList) as fileListHandle:
+                base_dir = (
+                    Path(fileListHandle.name).resolve().parent
+                )  # interpret paths relative to the fileListHandle location
+                li = []
+                for line in fileListHandle:
+                    entry = line.strip()
+                    if not entry:
+                        continue
+                    p = Path(entry)
+                    li.append(p if p.is_absolute() else (base_dir / p).resolve())
+
         elif popFilenames:
             # check number of arguments, must be at least one, but can be more
             # use args as list to check
@@ -264,7 +274,7 @@ return for each prompt.""")
         # arguments
         for fileName in li:
             # globbedFiles = glob_with_pathlib(fileName)
-            globbedFiles = glob(fileName)  # noqa: PTH207
+            globbedFiles = glob(str(fileName))  # noqa: PTH207
             if len(globbedFiles) == 0:
                 # if no files were found for that glob, please exit and warn
                 # the user

{pypop_genomics-1.2.2.dist-info → pypop_genomics-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pypop-genomics
-Version: 1.2.2
+Version: 1.3.0
 Summary: PyPop: Python for Population Genomics
 Author: Alex Lancaster
 Maintainer: PyPop team
@@ -20,8 +20,8 @@ Classifier: Operating System :: POSIX :: Linux
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.rst
-Requires-Dist: numpy<=2.3.1
-Requires-Dist: lxml<=6.0.0
+Requires-Dist: numpy<=2.3.2
+Requires-Dist: lxml<=6.0.1
 Requires-Dist: pooch<=v1.8.2
 Requires-Dist: importlib-resources; python_version <= "3.8"
 Requires-Dist: importlib-metadata; python_version <= "3.8"

{pypop_genomics-1.2.2.dist-info → pypop_genomics-1.3.0.dist-info}/RECORD

@@ -1,19 +1,19 @@
-PyPop/_Gthwe.cpython-310-darwin.so,sha256=R4VTa_DRoR_cl9hK1AuGEB8GL7mLSEZ65_HpijyRAOI,100576
+PyPop/_Gthwe.cpython-310-darwin.so,sha256=m1nxKteyPvgBDBXXBKOXXVB9Uqu3kr1tQe7eja00D6c,100576
 PyPop/_metadata.py,sha256=klJm9CiOzcoi5lD8TksmMF_uy_VSn8ONj0dbpxonDcQ,84
 PyPop/citation.py,sha256=0Cz7N9SjAM5PIPbAxzN87R4xwRnNLMsAo5HCkwV1LfE,2909
-PyPop/_Haplostats.cpython-310-darwin.so,sha256=NPLWpA1MTLok2WMTlwGm9WH2Qn4s-x2M-adzoTEvOjY,77248
-PyPop/pypop.py,sha256=Rl5OBaRlEafCoukagBeo6xk-GH2L0kNhuszghDDClRQ,13057
+PyPop/_Haplostats.cpython-310-darwin.so,sha256=Ikk3zl34qWD3WTbburHFVFv-HivFVhNGx7mYdGrh85I,77248
+PyPop/pypop.py,sha256=RiFy2fpXQv8oBxYXSHOkY8fnohf-VuGdb9Nx3A3AZlg,13392
 PyPop/HardyWeinberg.py,sha256=kFQBNPeeodORdeAuAbZgINVUYkw-21gFciMfX21aulI,45496
 PyPop/Arlequin.py,sha256=lYkGQDvmX6b9aZ1lt4QWQOhkmL-DlFHSsr5NIJ5xXbI,26264
-PyPop/CommandLineInterface.py,sha256=ChfyDs5wCmrciOJWn5Uqdb6m-OHrYLxxKS-xmyJ-PfU,10512
-PyPop/_version.py,sha256=o0zEAUXpMoJZCULVYplCdjcZuIQ-3sIIZKyfNu_loQE,511
-PyPop/_Emhaplofreq.cpython-310-darwin.so,sha256=EHl7GtWyywM-Ntn2IvjCvyKikXerMrHTx338t7divmM,93784
+PyPop/CommandLineInterface.py,sha256=EDG8XjzaKRB5kiWTmYeQYFMLuh2sUplg9milUAotXlM,10527
+PyPop/_version.py,sha256=0Oc4EBzGTJOvXX0Vym4evglW1NQPpe8RLn8TdxsKzfs,704
+PyPop/_Emhaplofreq.cpython-310-darwin.so,sha256=0KH2-7R5g00S4pWuHXFGw-sc8ph2HqMVKaN_cxiCK_4,93784
 PyPop/GUIApp.py,sha256=-Hk7UpEperP4_aaZOydR95ZIlWJm_Hx7d_gXZ0HCP_c,8326
-PyPop/_Pvalue.cpython-310-darwin.so,sha256=vl0sDOXJZV6mX4At7S3fKxm8KkUs5OtKG7Dr_mWYIFM,80080
+PyPop/_Pvalue.cpython-310-darwin.so,sha256=CG7sNURXegCn9rk1Sh8sR7WGC1SgGebH7-ftX3GTxLI,80080
 PyPop/ParseFile.py,sha256=GEXwFyYnebt80ozbWYaGlw7RgfYiTj3PjvWtt3nSFOY,25137
 PyPop/Homozygosity.py,sha256=mWWrdVYOmRH96qvU5RShWZpWbKFhKzn1ummSLTAlw_A,17640
 PyPop/__init__.py,sha256=HAkR6vghF3uKG_L0OSWhHOF8EEHu9rZivA2OLkZs3Vs,3523
-PyPop/_EWSlatkinExact.cpython-310-darwin.so,sha256=tS_jovkUBIKVR_gITJdmIgnaZBeL8rpIrjRAKrr1olw,77520
+PyPop/_EWSlatkinExact.cpython-310-darwin.so,sha256=wcEJl1nbStIwzY5-vzo864-3dcPzaZvG5mR7ed9aCE4,77520
 PyPop/Haplo.py,sha256=Gn9-lulpGIF6Wao1I_2jCrTCjUKG29vMybQo9eoV9BU,43611
 PyPop/DataTypes.py,sha256=VMbq4tJDcS9ZFqFJ40tFHCBPc5v0XC6LqqpdsxwV-Po,17828
 PyPop/Utils.py,sha256=_5F3ebv6v5yz3J715G39DisYrvwJ3cIZFgFr0VoA6Fk,27878
@@ -22,14 +22,14 @@ PyPop/RandomBinning.py,sha256=dY10mmoMfHvq85D6DSucgeP_p05itlZ2Cd-37_sNuLU,11794
 PyPop/popmeta.py,sha256=00aPgpMu3emjGGZhfHf4PO97uPjqr02zgV4jBe6VlOg,3097
 PyPop/Main.py,sha256=ebO3EG2kEE_nP9a-KjwjN739yLlkTMxMykSUpikOVKk,58916
 PyPop/Meta.py,sha256=JA0AS2Nb8zogzkcVq--K4ZS549NyhB6XsZxeyoUB4tY,16421
-PyPop/citation/CITATION.schema.org,sha256=IfsvlxklmZXAngHFp_LHSKvSJBOZW9q7BT45IZslegk,6103
-PyPop/citation/CITATION.cff,sha256=6dMU_VQMH6kXveyE91dp-GMr3ke-awLocK4yI6uv4fE,5203
-PyPop/citation/CITATION.codemeta,sha256=SKX1PCi1c5ZYgYeYTUarn1AMVIqOZxEeXArKo5MLOMI,6128
-PyPop/citation/CITATION.ris,sha256=lFsg_nF2Z7o94Usj2jlM8vfodLh85MZy_fZhcjvc4QI,1473
-PyPop/citation/CITATION.endnote,sha256=VkaY-JfDCYcB-PjgboY9Xw_hRCz_Df7Jsvm3r1QqG4Q,542
-PyPop/citation/CITATION.zenodo,sha256=ihvpZZEDAvr3wa1YjvGYZ6QtrSfle4jtIIJb_K6WLCw,5813
-PyPop/citation/CITATION.apalike,sha256=ZYM1iE2gse7AE_PDSGm4ZbUbcufJekYBHfYashJDlcQ,266
-PyPop/citation/CITATION.bibtex,sha256=TZk8QoxP3YNEdzTDU_aaqHIzImfp-68xpK9md32Oirw,734
+PyPop/citation/CITATION.schema.org,sha256=jyLWVl3BEkxk4fp3q0FR-NRjQ57hKzRVyMlgdqJcC0Y,6103
+PyPop/citation/CITATION.cff,sha256=YMy1x5I1KX9ia-iBeJoOygNkE8XS0Hkt6ydqo-9KnqE,5203
+PyPop/citation/CITATION.codemeta,sha256=MiA6kNsNJAhzTF38s71MlCmMCV0At-pIr_hqUVzjJQI,6128
+PyPop/citation/CITATION.ris,sha256=D4mo4-25txU12VsEa0qZkAevjTSWXWy_lMfqqzTzBRY,1473
+PyPop/citation/CITATION.endnote,sha256=0GQp6QiZH_NB1otIrl0Tb9PuAHFTbVSpeGzW0gvYGBc,542
+PyPop/citation/CITATION.zenodo,sha256=PBPNiFigw0wPU-0z4m1FMDchKOJOWfhOrCM7JqgHREc,5813
+PyPop/citation/CITATION.apalike,sha256=NBRvEAr-DIyVldf0e1zsL1YaW3grcUQ1da3OdruarMY,266
+PyPop/citation/CITATION.bibtex,sha256=N0WZCylgHpqWzC73PwcW8h7gd8yZtW3i2v79BzgoqTY,734
 PyPop/.dylibs/libgsl.27.dylib,sha256=juXh8NCR9B9AjcJcjikljdHEkoKq0Td67jRmyA9Gqkk,2267952
 PyPop/.dylibs/libgslcblas.0.dylib,sha256=KnGI2qPoh50puWytYITePeL3XcbsGQOHjC7awSK2ey0,272784
 PyPop/xslt/html.xsl,sha256=gnGcMZWd_TxwdYAET3FymQaaV9w_X7yOEJ7ZSyNszLg,4003
@@ -48,10 +48,10 @@ PyPop/xslt/emhaplofreq.xsl,sha256=9dnAB-NZoDm82qkvbt211g86rLqORlkGJhjqE6FE_9w,20
 PyPop/xslt/summary.xsl,sha256=65ELgLKiACtDzg513zPeeRJgh2D2JiJodVmIYkrFt4o,8104
 PyPop/xslt/sort-by-locus.xsl,sha256=Hho3vRPmh4MwA78N6IOGnHSbw1eFuTPvDJYMoh09jPg,3557
 PyPop/xslt/homozygosity.xsl,sha256=t8kzz2jI1D12cuO4pvdNIp9FlCvgJ2JREBplkFyDQWY,8635
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