Merge remote-tracking branch 'origin/output-citation' into citation-c…

…ff-zenodo

.github/workflows/build_wheels.yml

@@ -20,8 +20,6 @@ on:
       - '.github/workflows/buildjet_arm64.yml'
       - '.github/workflows/release-drafter.yml'
       - '.github/workflows/codeql.yml'
-      - '.github/workflows/run_citations.yml'
-      - '.github/actions/update_citations/action.yml'      
       - '.gitattributes'
   push:
     paths-ignore:
@@ -37,8 +35,6 @@ on:
       - '.github/workflows/buildjet_arm64.yml'      
       - '.github/workflows/release-drafter.yml'
       - '.github/workflows/codeql.yml'
-      - '.github/workflows/run_citations.yml'
-      - '.github/actions/update_citations/action.yml'      
       - '.gitattributes'
   release:
     types:
@@ -215,7 +211,30 @@ jobs:
         if: runner.os == 'Linux'
         uses: docker/setup-qemu-action@v3
         with:
-          platforms: all          
+          platforms: all
+      - 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: Install a recent stable Python to handle cffconvert
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+      - 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/cibuildwheel@v2.21.3
         env:

pyproject.toml

@@ -102,7 +102,7 @@ write_to = "src/PyPop/_version.py"  # matches the path where version will be wri
 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",
+	    "cffconvert @ git+https://github.com/alexlancaster/cffconvert.git@combine_features#egg=cffconvert",
 	    "importlib-metadata; python_version <= '3.8'"
 	    ]
 

setup.py

@@ -35,7 +35,6 @@
 # UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
 
 import sys, os
-import shutil
 from glob import glob
 from setuptools import setup
 from setuptools.extension import Extension
@@ -221,50 +220,29 @@ def path_to_src(source_path_list):
 
 citation_data_file_paths = []
 # citation files are in a subdirectory of PyPop, but not a separate module
-from src.PyPop import citation_output_formats
+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):
 
-        from cffconvert import Citation
-
         # do standard build process
         super().run()
 
-        # 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
-
-        # target directory for the CITATION file within the build directory
-        target_dir = os.path.join(build_lib, "PyPop", "citation")
+        # 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"
 
-        # create the citation directory if it doesn’t exist
-        os.makedirs(target_dir, exist_ok=True)
-        shutil.copy(citation_path, target_dir)
+            # then copy CITATION.cff to temp build directory
+            # use setuptools' temp build directory
+            build_lib = self.get_finalized_command('build').build_lib
 
-        # load the CITATION.cff content
-        cff = Citation(cffstr=open(citation_path).read())
-
-        # remove 'cff' from generated list - since we don't generate that
-        citation_output_formats.remove('cff')
-
-        for fmt in citation_output_formats:
-            # use getattr to get the method based on the format string
-            convert_method = getattr(cff, f"as_{fmt}", None)
-            if callable(convert_method):
-                converted_content = convert_method()
-            else:
-                print(f"Conversion format '{fmt}' not supported.")
-
-            # save the converted output (e.g., as CITATION.json)
-            with open(os.path.join(target_dir, "CITATION." + fmt), "w") as f:
-                f.write(converted_content)
+            convert_citation_formats(build_lib, citation_path)
 
 # read the contents of your README file
 from pathlib import Path
@@ -318,7 +296,8 @@ def run(self):
        },
        ext_modules=extensions,
        cmdclass={'clean': CleanCommand,
-                 # disable the custom build
-                 # 'build_py': CustomBuildPy,
+                 # enable the custom build
+                 'build_py': CustomBuildPy,
                  },
+
        )

src/PyPop/CommandLineInterface.py

@@ -36,7 +36,8 @@
 import os, sys
 from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, RawDescriptionHelpFormatter, FileType, Action
 from pathlib import Path
-from PyPop import platform_info, citation_output_formats  # global info and citation formats
+from PyPop import platform_info            # global info
+from PyPop.citation import citation_output_formats  # and citation formats
 
 """Command-line interface for PyPop scripts
 """
@@ -61,16 +62,18 @@ def __call__(self, parser, namespace, values, option_string=None):
                 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 current directory if running from repo
-                pypop_dir = Path(__file__).resolve().parent
-                citation_file = pypop_dir / citation_file_name
+            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
 

src/PyPop/__init__.py

@@ -1,38 +1,3 @@
-#!/usr/bin/env python
-
-# This file is part of PyPop
-
-# Copyright (C) 2017. 
-# All Rights Reserved.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-# IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT,
-# INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
-# LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS
-# DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY
-# OF SUCH DAMAGE.
-
-# REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
-# FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING
-# DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS
-# IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
-# UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
-
 import platform
 
 __pkgname__ = 'pypop-genomics'
@@ -56,7 +21,6 @@
 
 platform_info="[Python {python_version} | {system} | {arch}]".format(python_version=platform.python_version(), system=platform.platform(), arch=platform.machine())
 
-citation_output_formats = ['apalike', 'bibtex', 'endnote', 'ris', 'codemeta', 'cff']
 
 import locale
 import logging

src/PyPop/citation.py

@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+
+# This file is part of PyPop
+
+# Copyright (C) 2017. 
+# All Rights Reserved.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT,
+# INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
+# LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS
+# DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY
+# OF SUCH DAMAGE.
+
+# REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING
+# DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS
+# IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
+# UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+
+import os
+import shutil
+
+citation_output_formats = ['apalike', 'bibtex', 'endnote', 'ris', 'codemeta', 'cff']
+
+def convert_citation_formats(build_lib, citation_path):
+
+    from cffconvert import Citation
+
+    # target directory for the CITATION file within the build directory
+    target_dir = os.path.join(build_lib, "PyPop", "citation")
+
+    # create the citation directory if it doesn’t exist
+    os.makedirs(target_dir, exist_ok=True)
+    shutil.copy(citation_path, target_dir)
+
+    # load the CITATION.cff content
+    cff = Citation(cffstr=open(citation_path).read())
+
+    # remove 'cff' from generated list - since we don't generate that
+    citation_output_formats.remove('cff')
+
+    for fmt in citation_output_formats:
+        # use getattr to get the method based on the format string
+        convert_method = getattr(cff, f"as_{fmt}", None)
+        if callable(convert_method):
+            converted_content = convert_method()
+        else:
+            print(f"Conversion format '{fmt}' not supported.")
+
+        # save the converted output (e.g., as CITATION.json)
+        with open(os.path.join(target_dir, "CITATION." + fmt), "w") as f:
+            f.write(converted_content)
+
+if __name__ == "__main__":
+
+    convert_citation_formats("src", "CITATION.cff")
+