Merge remote-tracking branch 'origin/main' into replace_pval_extensio…

…n_with_scipyl

.github/workflows/build_wheels.yml

@@ -19,7 +19,7 @@ on:
       - '.github/workflows/documentation.yaml'
       - '.github/workflows/buildjet_arm64.yml'
       - '.github/workflows/release-drafter.yml'
-      - '.github/workflows/codeql.yml'      
+      - '.github/workflows/codeql.yml'
       - '.gitattributes'
   push:
     paths-ignore:
@@ -34,7 +34,7 @@ on:
       - '.github/workflows/documentation.yaml'
       - '.github/workflows/buildjet_arm64.yml'      
       - '.github/workflows/release-drafter.yml'
-      - '.github/workflows/codeql.yml'      
+      - '.github/workflows/codeql.yml'
       - '.gitattributes'
   release:
     types:
@@ -178,12 +178,45 @@ jobs:
         if: runner.os == 'Linux'
         uses: docker/setup-qemu-action@v3
         with:
-          platforms: all          
+          platforms: all
+      - name: Install a recent stable Python to handle Python deps
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+      - name: Query version with setuptools_scm
+        id: version
+        shell: bash
+        run: |
+          python -m pip install setuptools_scm
+          VERSION=$(python -c "from src.PyPop import __version_scheme__; import setuptools_scm; print(setuptools_scm.get_version(version_scheme=__version_scheme__))")
+          echo "VERSION=${VERSION}"
+          echo "VERSION=${VERSION}" >> $GITHUB_ENV
+      - name: Install toml and remove cffconvert from pyproject.toml
+        run: |
+          python -m pip install toml
+          python -c "
+          import toml
+          with open('pyproject.toml', 'r') as f:
+             config = toml.load(f)
+          if 'build-system' in config and 'requires' in config['build-system']:
+             config['build-system']['requires'] = [
+                 dep for dep in config['build-system']['requires'] if 'cffconvert' not in dep.lower()
+             ]
+          with open('pyproject.toml', 'w') as f:
+             toml.dump(config, f)
+          "
+      - name: Generate citation formats
+        run: |
+          python --version
+          python -m pip install git+https://github.com/alexlancaster/cffconvert.git@combine_features#egg=cffconvert
+          python src/PyPop/citation.py
       - name: Build and test wheels
         uses: pypa/[email protected]
         env:
           # FIXME: only run the slow tests when doing regular pushes, or manual - not for PRs
           CIBW_TEST_COMMAND: "pytest -v {package}/tests ${{ (github.event_name == 'push' || github.event_name == 'workflow_dispatch') && '--runslow' || '' }}"
+          SETUPTOOLS_SCM_PRETEND_VERSION: ${{ env.VERSION }}
+          CIBW_ENVIRONMENT_PASS_LINUX: SETUPTOOLS_SCM_PRETEND_VERSION
         with:
           only: ${{ matrix.only }}
           package-dir: .

CITATION.cff

@@ -73,6 +73,9 @@ url: http://pypop.org/
 repository-artifact: https://pypi.org/project/pypop-genomics/
 repository-code: https://github.com/alexlancaster/pypop
 type: software
+license: GPL-2.0-or-later
+version: v1.1.1
+doi: 10.5281/zenodo.13742984
 keywords:
   - population genetics
   - population genomics
@@ -83,6 +86,3 @@ keywords:
   - Major histocompatibility complex
   - HLA
   - MHC
-license: GPL-2.0-or-later
-version: v1.1.1
-doi: 10.5281/zenodo.13742984

MANIFEST.in

@@ -3,6 +3,7 @@ include DEV_NOTES.md
 include LICENSE
 include NEWS.rst
 include MANIFEST.in
+include CITATION.cff
 prune .github
 prune website 
 prune data/*

README.rst

@@ -27,31 +27,55 @@ If you write a paper that uses PyPop in your analysis, please cite
       `10.3389/fimmu.2024.1378512
       <https://doi.org/10.3389/fimmu.2024.1378512>`__
 
-* **and** the `Zenodo record <https://zenodo.org/records/10080667>`__
-  for the software. To cite the correct version, follow these steps:
-
-  1) First visit the DOI for the overall Zenodo record:
-     `10.5281/zenodo.10080667
-     <https://zenodo.org/doi/10.5281/zenodo.10080667>`__. This DOI
-     represents **all versions**, and will always resolve to the
-     latest one.
-
-  2) When you are viewing the record, look for the **Versions** box
-     in the right-sidebar. Here are listed all versions (including
-     older versions).
-
-  3) Select and click the version-specific DOI that matches the
-     specific version of PyPop that you used for your analysis.
-
-  4) Once you are visiting the Zenodo record for the specific version,
-     under the **Citation** box in the right-sidebar, select the
-     citation format you wish to use and click to copy the citation.
-     It will contain link to the version-specific DOI, and be of the
-     form:
-
-       Lancaster, AK et al. (YYYY) "PyPop: Python for Population
-       Genomics" (Version X.Y.Z) [Computer
-       software]. Zenodo. https://doi.org/10.5281/zenodo.XXXXX
+* **and** a citation to the `Zenodo record
+  <https://zenodo.org/records/10080667>`__ which includes a DOI for
+  the version of the software you used in your analyses. Citing this
+  record and DOI supports reproducibility by allowing researchers to
+  to determine the exact version of PyPop used in any particular
+  analysis. In addition, it allows retrieval of long-term software
+  source-code archives, independent of the original developers.
+
+  Here's how to cite the correct version:
+
+  * If you have PyPop version 1.1.2 or later, currently installed, you
+    can run:
+
+    .. code-block:: shell
+
+       pypop --citation
+
+    which outputs the Zenodo record citation in the simple "APA"
+    format (you can also choose from BibTeX, EndNote, RIS and other
+    formats, see the section on `command-line interfaces
+    <http://pypop.org/docs/guide-chapter-usage.html#command-line-interfaces>`_
+    in the *User Guide* for more details).
+
+  * If you do not have PyPop installed, have a release of PyPop
+    earlier than 1.1.2, or otherwise want to obtain the DOI and
+    citation for specific versions, follow these steps:
+
+    1) First visit the DOI for the overall Zenodo record:
+       `10.5281/zenodo.10080667
+       <https://zenodo.org/doi/10.5281/zenodo.10080667>`__. This DOI
+       represents **all versions**, and will always resolve to the
+       latest one.
+
+    2) When you are viewing the record, look for the **Versions** box
+       in the right-sidebar. Here are listed all versions (including
+       older versions).
+
+    3) Select and click the version-specific DOI that matches the
+       specific version of PyPop that you used for your analysis.
+
+    4) Once you are visiting the Zenodo record for the specific version,
+       under the **Citation** box in the right-sidebar, select the
+       citation format you wish to use and click to copy the citation.
+       It will contain link to the version-specific DOI, and be of the
+       form:
+
+         Lancaster, AK et al. (YYYY) "PyPop: Python for Population
+         Genomics" (Version X.Y.Z) [Computer
+         software]. Zenodo. https://doi.org/10.5281/zenodo.XXXXX
 
   Note that citation metadata for the current Zenodo record is also
   stored in `CITATION.cff

pyproject.toml

@@ -18,16 +18,18 @@ skip = ["*-win32", "*_i686",  # skip 32-bit builds
         "cp313-musllinux_x86_64", # problem with this version
         "cp36-musllinux_*", "cp37-musllinux_*", "cp38-musllinux_*"] # older musllinux missing numpy wheels
 test-extras = ["test"]
-test-command = "pytest -v {package}/tests"
-# FIXME: add below test-command unit tests need to be saved
-# "&& echo {package} && ls && tar zcvf unit_tests_output.tar.gz run_test_* && cp unit_tests_output.tar.gz {package}/wheelhouse/"
-
-# Skip trying to test arm64 builds on Intel Macs as per
-# https://cibuildwheel.readthedocs.io/en/stable/faq/#apple-silicon
-# test-skip = "*-macosx_arm64 *-macosx_universal2:arm64"
-# don't try and install pypi packages and build from source
+
+# FIXME: can add "test-command" that would allow unit test output to be saved
+# "pytest -v {package}/tests && echo {package} && ls && tar zcvf unit_tests_output.tar.gz run_test_* && cp unit_tests_output.tar.gz {package}/wheelhouse/"
+
+# don't try and install pypi packages that need build from source
+# this is mainly import during the testing phase
 environment = { PIP_ONLY_BINARY=":all:" }
 
+# use pip and override the PIP_ONLY_BINARY=:all: during wheel generation
+# so that certain source-only build deps (like cffconvert) install
+build-frontend = { name = "pip", args = ["--only-binary=:none:"] }
+
 [[tool.cibuildwheel.overrides]]
 # for latest CPython use newer manylinux image
 select = "cp312-*linux*"
@@ -94,10 +96,15 @@ select ="*-win_*"
 inherit.environment="append"
 environment = { CPATH="gsl-msvc14-x64.2.3.0.2779\\\\build\\\\native", LIBRARY_PATH="gsl-msvc14-x64.2.3.0.2779\\\\build\\\\native\\\\static" }
 
+[tool.setuptools_scm]
+write_to = "src/PyPop/_version.py"  # matches the path where version will be written
+
 [build-system]
 build-backend = "setuptools.build_meta:__legacy__"
 requires = ["setuptools>=42",
 	    "setuptools_scm[toml]>=6.2",
+	    "cffconvert @ git+https://github.com/alexlancaster/cffconvert.git@combine_features#egg=cffconvert",
 	    "importlib-metadata; python_version <= '3.8'"
 	    ]
 
+

setup.py

@@ -38,6 +38,8 @@
 from glob import glob
 from setuptools import setup
 from setuptools.extension import Extension
+from setuptools.command.build_py import build_py as _build_py
+from setuptools.command.install import install as _install
 from distutils.command import clean
 from sysconfig import _PREFIX, get_config_vars, get_config_var
 from src.PyPop import __pkgname__, __version_scheme__
@@ -186,10 +188,36 @@ def path_to_src(source_path_list):
 # don't include HWEEnum 
 # extensions.append(ext_HweEnum)
 
-data_file_paths = []
+xslt_data_file_paths = []
 # xslt files are in a subdirectory
 xslt_files = [f + '.xsl' for f in ['text', 'html', 'lib', 'common', 'filter', 'hardyweinberg', 'homozygosity', 'emhaplofreq', 'meta-to-tsv', 'sort-by-locus', 'haplolist-by-group', 'phylip-allele', 'phylip-haplo']]
-data_file_paths.extend(xslt_files)
+xslt_data_file_paths.extend(xslt_files)
+
+citation_data_file_paths = []
+# citation files are in a subdirectory of PyPop, but not a separate module
+from src.PyPop.citation import citation_output_formats, convert_citation_formats
+citation_files = [os.path.join("citation", 'CITATION.' + suffix) for suffix in citation_output_formats]
+citation_data_file_paths.extend(citation_files)
+
+# currently disabled (these are built in a github action)
+class CustomBuildPy(_build_py):
+    def run(self):
+
+        # do standard build process
+        super().run()
+
+        # if not running from a CIBUILDWHEEL environment variable
+        # we need to create the citations
+        if os.environ.get('CIBUILDWHEEL') != '1':
+
+            # source citation path (single-source of truth)
+            citation_path = "CITATION.cff"
+
+            # then copy CITATION.cff to temp build directory
+            # use setuptools' temp build directory
+            build_lib = self.get_finalized_command('build').build_lib
+
+            convert_citation_formats(build_lib, citation_path)
 
 # read the contents of your README file
 from pathlib import Path
@@ -226,7 +254,8 @@ def path_to_src(source_path_list):
                       ],
        package_dir = {"": src_dir},
        packages = ["PyPop", "PyPop.xslt"],
-       package_data={"PyPop.xslt": data_file_paths},
+       package_data = {"PyPop.xslt": xslt_data_file_paths,
+                       "PyPop": citation_data_file_paths},
        install_requires = ["numpy <= 2.1.3",
                            "SciPy <= 1.14.1",                           
                            "lxml <= 5.3.0",
@@ -242,6 +271,8 @@ def path_to_src(source_path_list):
                                'pypop-interactive=PyPop.pypop:main_interactive']
        },
        ext_modules=extensions,
-       cmdclass={'clean': CleanCommand,},
+       cmdclass={'clean': CleanCommand,
+                 # enable the custom build
+                 'build_py': CustomBuildPy,
+                 },
        )
-

src/PyPop/CommandLineInterface.py

@@ -34,9 +34,10 @@
 # UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
 
 import os, sys
-from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, RawDescriptionHelpFormatter, FileType
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, RawDescriptionHelpFormatter, FileType, Action
 from pathlib import Path
-from PyPop import platform_info  # global info
+from PyPop import platform_info            # global info
+from PyPop.citation import citation_output_formats  # and citation formats
 
 """Command-line interface for PyPop scripts
 """
@@ -45,13 +46,46 @@
 class PyPopFormatter(ArgumentDefaultsHelpFormatter, RawDescriptionHelpFormatter):
     pass
 
+class CitationAction(Action):
+
+    def __call__(self, parser, namespace, values, option_string=None):
+
+        citation_format = values or 'apalike'
+        citation_file_name = f'citation/CITATION.{citation_format}'
+
+        try:  # looking in installed package
+            from importlib.resources import files
+            citation_file = files('PyPop').joinpath(citation_file_name)
+            citation_text = citation_file.read_text()
+        except (ModuleNotFoundError, ImportError, FileNotFoundError):  # fallback to using backport if not found
+            try:
+                from importlib_resources import files
+                citation_file = files('PyPop').joinpath(citation_file_name)
+                citation_text = citation_file.read_text()
+            except (ModuleNotFoundError, ImportError, FileNotFoundError):  # fallback to looking in top-level directory if running from repo
+                top_level_dir = Path(__file__).resolve().parent.parent.parent
+                citation_file = top_level_dir / 'CITATION.cff'  # only output CFF 
+
+                if citation_file.exists():
+                    print("only CITATION.cff is available")
+                    print()
+                    citation_text = citation_file.read_text()
+                else:
+                    print("could not locate the specified citation format.")
+                    parser.exit()
+
+        print(citation_text)
+        parser.exit()  # exit after printing the file
+
 def get_parent_cli(version="", copyright_message=""):
     # options common to both scripts
     parent_parser = ArgumentParser(add_help=False)
 
     # define function arguments as signatures - need to be added in child parser as part of the selection logic
     common_args = [
         (["-h", "--help"], {'action': "help", 'help': "show this help message and exit"}),
+        (["--citation"], {'help': "generate citation to PyPop for this version of PyPop",
+                          'action': CitationAction, 'nargs':'?', 'choices': citation_output_formats, 'default':'apalike'}),
         (["-o", "--outputdir"], {'help':"put output in directory OUTPUTDIR",
                                  'required':False, 'type':Path, 'default':None}),
         (["-V", "--version"], {'action':'version',