From c919ec1a3633bf46607591ea2c9451e47af10bb7 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 20 Jul 2025 00:18:47 -0400 Subject: [PATCH 01/33] py3: update distanceprinter module to python 3.13 Signed-off-by: Dasun Abeykoon --- DistancePrinter/distanceprinter.py | 28 +++++++++++++++++----------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/DistancePrinter/distanceprinter.py b/DistancePrinter/distanceprinter.py index 3a16d94..a0999b9 100644 --- a/DistancePrinter/distanceprinter.py +++ b/DistancePrinter/distanceprinter.py @@ -12,13 +12,11 @@ # ############################################################################## -import os import sys -import itertools import numpy as np from diffpy.pdffit2 import PdfFit -from diffpy.Structure import PDFFitStructure +from diffpy.structure import PDFFitStructure def calDistance(strufile, atomi, atomj, lb, ub, complete): @@ -38,14 +36,14 @@ def calDistance(strufile, atomi, atomj, lb, ub, complete): distlist = np.zeros(len(dij), dtype=dtypec) if not complete: - for i, dist, dd, ij in itertools.izip(range(len(dij)), dij, ddij, ij0): + for i, dist, dd, ij in zip(list(range(len(dij)), dij, ddij, ij0)): if ij[0] > ij[1]: distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]]) else: distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]]) distlist = np.unique(distlist) else: - for i, dist, dd, ij in itertools.izip(range(len(dij)), dij, ddij, ij0): + for i, dist, dd, ij in zip(list(range(len(dij)), dij, ddij, ij0)): distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1])) distlist.sort(order='distance') @@ -78,18 +76,26 @@ def formatResults(stru, distlist, complete, all0ddij, **kw): if complete: for dist in distlist: - lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0])) + try: + lines.append('%s-%s:\t%2.6f' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0])) + except AttributeError: + lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0])) else: for dist in distlist: - lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1])) + try: + lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0], dist[1])) + except AttributeError: + lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1])) rv = '\n'.join(lines) return rv def writeToFile(filename, rv): - f = file(filename, 'w') - f.write(rv) - f.close() - return + f = open(filename, 'w', encoding="utf-8") + try: + rv = rv.decode('utf-8') + except AttributeError: + # No need to decode in python 3 + pass def main(): sysargv = sys.argv[1:] From 9d236316b468a3ca81283d357a5f7af69caa10bf Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 20 Jul 2025 22:52:58 -0400 Subject: [PATCH 02/33] py3: update setup.py to python 3.13 Signed-off-by: Dasun Abeykoon --- setup.py | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/setup.py b/setup.py index a564855..a8556cc 100755 --- a/setup.py +++ b/setup.py @@ -6,11 +6,7 @@ """ import os -import glob -from setuptools import setup, find_packages - - -import os +import glob from setuptools import setup, find_packages # Use this version when git data are not available, like in git zip archive. @@ -32,13 +28,13 @@ def gitinfo(): glog = proc.stdout.read() rv = dict(version=FALLBACK_VERSION) if desc != '': - rv['version'] = '-'.join(desc.strip().split('-')[:2]).lstrip('v') + rv['version'] = b'-'.join(desc.strip().split(b'-')[:2]).lstrip(b'v') rv['commit'], rv['timestamp'], rv['date'] = glog.strip().split(None, 2) return rv def getversioncfg(): - from ConfigParser import RawConfigParser + from configparser import RawConfigParser vd0 = dict(version=FALLBACK_VERSION, commit='', date='', timestamp=0) # first fetch data from gitarchivecfgfile, ignore if it is unexpanded g = vd0.copy() @@ -102,8 +98,7 @@ def getversioncfg(): 'Operating System :: MacOS', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', - 'Programming Language :: Python :: 2.6', - 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.13', 'Topic :: Scientific/Engineering :: Physics', ], ) From c3e9ecc0397d45598f9c5d692ad85d971fc0defc Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Mon, 21 Jul 2025 00:12:45 -0400 Subject: [PATCH 03/33] fix: make sure writeToFile function actually writes to file Signed-off-by: Dasun Abeykoon --- DistancePrinter/distanceprinter.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/DistancePrinter/distanceprinter.py b/DistancePrinter/distanceprinter.py index a0999b9..7a653ca 100644 --- a/DistancePrinter/distanceprinter.py +++ b/DistancePrinter/distanceprinter.py @@ -36,14 +36,14 @@ def calDistance(strufile, atomi, atomj, lb, ub, complete): distlist = np.zeros(len(dij), dtype=dtypec) if not complete: - for i, dist, dd, ij in zip(list(range(len(dij)), dij, ddij, ij0)): + for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): if ij[0] > ij[1]: distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]]) else: distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]]) distlist = np.unique(distlist) else: - for i, dist, dd, ij in zip(list(range(len(dij)), dij, ddij, ij0)): + for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1])) distlist.sort(order='distance') @@ -93,8 +93,12 @@ def writeToFile(filename, rv): f = open(filename, 'w', encoding="utf-8") try: rv = rv.decode('utf-8') + f.write(rv) + f.close() except AttributeError: # No need to decode in python 3 + f.write(rv) + f.close() pass def main(): From 9095fdbed3525f3cb6848275e9605645a2e2f90b Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Mon, 21 Jul 2025 00:13:22 -0400 Subject: [PATCH 04/33] chore: upload fixed tests Signed-off-by: Dasun Abeykoon --- .gitignore | 3 + tests/data/Ni-9008476.cif | 250 ++++++ tests/outputs/expected.res | 1530 +++++++++++++++++++++++++++++++++ tests/test_distanceprinter.py | 38 + 4 files changed, 1821 insertions(+) create mode 100644 tests/data/Ni-9008476.cif create mode 100644 tests/outputs/expected.res create mode 100644 tests/test_distanceprinter.py diff --git a/.gitignore b/.gitignore index a122710..bcd8ba5 100644 --- a/.gitignore +++ b/.gitignore @@ -43,3 +43,6 @@ nosetests.xml setup.cfg /DistancePrinter/version.cfg /DistancePrinter/gitarchive.cfg + +# test output +actual.res \ No newline at end of file diff --git a/tests/data/Ni-9008476.cif b/tests/data/Ni-9008476.cif new file mode 100644 index 0000000..12aeff6 --- /dev/null +++ b/tests/data/Ni-9008476.cif @@ -0,0 +1,250 @@ +#------------------------------------------------------------------------------ +#$Date: 2017-10-15 03:23:08 +0300 (Sun, 15 Oct 2017) $ +#$Revision: 202022 $ +#$URL: file:///home/coder/svn-repositories/cod/cif/9/00/84/9008476.cif $ +#------------------------------------------------------------------------------ +# +# This file is available in the Crystallography Open Database (COD), +# http://www.crystallography.net/. The original data for this entry +# were provided the American Mineralogist Crystal Structure Database, +# http://rruff.geo.arizona.edu/AMS/amcsd.php +# +# The file may be used within the scientific community so long as +# proper attribution is given to the journal article from which the +# data were obtained. +# +data_9008476 +loop_ +_publ_author_name +'Wyckoff, R. W. G.' +_publ_section_title +; + Second edition. Interscience Publishers, New York, New York + Cubic closest packed, ccp, structure +; +_journal_name_full 'Crystal Structures' +_journal_page_first 7 +_journal_page_last 83 +_journal_volume 1 +_journal_year 1963 +_chemical_formula_sum Ni +_chemical_name_mineral Nickel +_space_group_IT_number 225 +_symmetry_space_group_name_Hall '-F 4 2 3' +_symmetry_space_group_name_H-M 'F m -3 m' +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 +_cell_length_a 3.52387 +_cell_length_b 3.52387 +_cell_length_c 3.52387 +_cell_volume 43.758 +_exptl_crystal_density_diffrn 8.909 +_cod_original_sg_symbol_H-M 'F m 3 m' +_cod_database_code 9008476 +loop_ +_symmetry_equiv_pos_as_xyz +x,y,z +x,1/2+y,1/2+z +1/2+x,y,1/2+z +1/2+x,1/2+y,z +z,-x,y +z,1/2-x,1/2+y +1/2+z,-x,1/2+y +1/2+z,1/2-x,y +-y,z,-x +-y,1/2+z,1/2-x +1/2-y,z,1/2-x +1/2-y,1/2+z,-x +x,-y,z +x,1/2-y,1/2+z +1/2+x,-y,1/2+z +1/2+x,1/2-y,z +-z,x,-y +-z,1/2+x,1/2-y +1/2-z,x,1/2-y +1/2-z,1/2+x,-y +y,-z,x +y,1/2-z,1/2+x +1/2+y,-z,1/2+x 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0.500000 0.500000 1.0000 +# 2 Ni 0.500000 0.000000 0.500000 1.0000 +# 3 Ni 0.500000 0.500000 0.000000 1.0000 +# +# Inter-atomic distance of (all, all) in (1.00, 10.00) A + +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.3-Ni.0: 2.491752 +Ni.3-Ni.0: 2.491752 +Ni.3-Ni.0: 2.491752 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9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 \ No newline at end of file diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py new file mode 100644 index 0000000..565a03e --- /dev/null +++ b/tests/test_distanceprinter.py @@ -0,0 +1,38 @@ +import os +from io import open + +from DistancePrinter.distanceprinter import main + + +def test_distanceprinter(monkeypatch): + current_module_dir = os.path.dirname(__file__) + example_file_dir = os.path.join(current_module_dir, "data") + # must be cif, stru, or xyz file + strufile = os.path.join(example_file_dir, "Ni-9008476.cif") + # atoms typically pull from list of elements in stru output of PDFFitStructure. 'all' is always first option + atomi = 'all' + atomj = 'all' + # lb and ub are lower an upper bound of distance to list in angstroms + lb = 1 + ub = 10 + # 1 means keep duplicate atom pairs with same inter-atomic distance, 0 means not to + comp = '1' + monkeypatch.setattr("sys.argv", ['distanceprinter', strufile, atomi, atomj, lb, ub, comp, 'tests\\outputs\\actual.res']) + cwd = os.getcwd() + main() + generated_file_path = os.path.join(cwd, 'tests\\outputs\\actual.res') + f = open(generated_file_path, 'r', encoding="utf-8") + rv0 = f.readlines() + rv0 = ''.join(rv0) + resultstr = rv0 + output_file_dir = os.path.join(current_module_dir, "outputs") + example_output = os.path.join(output_file_dir, "expected.res") + f = open(example_output, 'r', encoding="utf-8") + rv1 = f.readlines() + rv1 = ''.join(rv1) + teststr = rv1 + + # Remove structure file path when comparing as it may differ between machines + resultstr = resultstr.split("\n", 2)[2] + teststr = teststr.split("\n", 2)[2] + assert resultstr == teststr From 9f0505d616b8238121282ce65bd495b60de028d7 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Tue, 12 Aug 2025 23:07:07 -0400 Subject: [PATCH 05/33] pyproject.toml --- DistancePrinter/distanceprinter.py | 2 +- DistancePrinter/requirements/pip.txt | 3 + pyproject.toml | 88 +++++++++++++++++++++ setup.py | 114 --------------------------- 4 files changed, 92 insertions(+), 115 deletions(-) create mode 100644 DistancePrinter/requirements/pip.txt create mode 100644 pyproject.toml delete mode 100755 setup.py diff --git a/DistancePrinter/distanceprinter.py b/DistancePrinter/distanceprinter.py index 3a16d94..27e659c 100644 --- a/DistancePrinter/distanceprinter.py +++ b/DistancePrinter/distanceprinter.py @@ -18,7 +18,7 @@ import numpy as np from diffpy.pdffit2 import PdfFit -from diffpy.Structure import PDFFitStructure +from diffpy.structure import PDFFitStructure def calDistance(strufile, atomi, atomj, lb, ub, complete): diff --git a/DistancePrinter/requirements/pip.txt b/DistancePrinter/requirements/pip.txt new file mode 100644 index 0000000..92111f9 --- /dev/null +++ b/DistancePrinter/requirements/pip.txt @@ -0,0 +1,3 @@ +numpy +diffpy.pdffit2 +diffpy.structure diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..65c5c37 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,88 @@ +[build-system] +requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "diffpy.distanceprinter" +dynamic=['version', 'dependencies'] +authors = [ + { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" }, +] +maintainers = [ + { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" }, +] +description = "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite" +keywords = ['diffpy', 'pdf', 'data interpretation'] +readme = "README.rst" +requires-python = ">=3.11, <3.14" +classifiers = [ + 'Development Status :: 5 - Production/Stable', + 'Environment :: Console', + 'Intended Audience :: Developers', + 'Intended Audience :: Science/Research', + 'License :: OSI Approved :: BSD License', + 'Operating System :: MacOS :: MacOS X', + 'Operating System :: Microsoft :: Windows', + 'Operating System :: POSIX', + 'Operating System :: Unix', + 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', + 'Programming Language :: Python :: 3.13', + 'Topic :: Scientific/Engineering :: Physics', + 'Topic :: Scientific/Engineering :: Chemistry', +] + +[project.entrypoints] +distanceprinter = 'DistancePrinter.distanceprinter:main' + +[project.urls] +Homepage = "https://github.com/diffpy/diffpy.distanceprinter/" +Issues = "https://github.com/diffpy/diffpy.distanceprinter/issues/" + +[tool.setuptools-git-versioning] +enabled = true +template = "{tag}" +dev_template = "{tag}" +dirty_template = "{tag}" + +[tool.setuptools.packages.find] +where = ["DistancePrinter"] # list of folders that contain the packages (["."] by default) +include = ["*"] # package names should match these glob patterns (["*"] by default) +exclude = [] # exclude packages matching these glob patterns (empty by default) +namespaces = false # to disable scanning PEP 420 namespaces (true by default) + +[tool.setuptools.dynamic] +dependencies = {file = ["requirements/pip.txt"]} + +[tool.codespell] +exclude-file = ".codespell/ignore_lines.txt" +ignore-words = ".codespell/ignore_words.txt" +skip = "*.cif,*.dat,*agr" + +[tool.docformatter] +recursive = true +wrap-summaries = 72 +wrap-descriptions = 72 + +[tool.black] +line-length = 79 +include = '\.pyi?$' +exclude = ''' +/( + \.git + | \.hg + | \.mypy_cache + | \.tox + | \.venv + | \.rst + | \.txt + | _build + | buck-out + | build + | dist + + # The following are specific to Black, you probably don't want those. + | blib2to3 + | tests/data +)/ +''' diff --git a/setup.py b/setup.py deleted file mode 100755 index a564855..0000000 --- a/setup.py +++ /dev/null @@ -1,114 +0,0 @@ -#!/usr/bin/env python - -# Installation script for dpx.pdfgetegui - -"""Distance Printer -""" - -import os -import glob -from setuptools import setup, find_packages - - -import os -from setuptools import setup, find_packages - -# Use this version when git data are not available, like in git zip archive. -# Update when tagging a new release. -FALLBACK_VERSION = '1.0-x' - -# versioncfgfile holds version data for git commit hash and date. -# It must reside in the same directory as version.py. -MYDIR = os.path.dirname(os.path.abspath(__file__)) -versioncfgfile = os.path.join(MYDIR, 'DistancePrinter', 'version.cfg') -gitarchivecfgfile = versioncfgfile.replace('version.cfg', 'gitarchive.cfg') - -def gitinfo(): - from subprocess import Popen, PIPE - kw = dict(stdout=PIPE, cwd=MYDIR) - proc = Popen(['git', 'describe', '--match=v[[:digit:]]*'], **kw) - desc = proc.stdout.read() - proc = Popen(['git', 'log', '-1', '--format=%H %at %ai'], **kw) - glog = proc.stdout.read() - rv = dict(version=FALLBACK_VERSION) - if desc != '': - rv['version'] = '-'.join(desc.strip().split('-')[:2]).lstrip('v') - rv['commit'], rv['timestamp'], rv['date'] = glog.strip().split(None, 2) - return rv - - -def getversioncfg(): - from ConfigParser import RawConfigParser - vd0 = dict(version=FALLBACK_VERSION, commit='', date='', timestamp=0) - # first fetch data from gitarchivecfgfile, ignore if it is unexpanded - g = vd0.copy() - cp0 = RawConfigParser(vd0) - cp0.read(gitarchivecfgfile) - if '$Format:' not in cp0.get('DEFAULT', 'commit'): - g = cp0.defaults() - # then try to obtain version data from git. - gitdir = os.path.join(MYDIR, '.git') - if os.path.isdir(gitdir) or 'GIT_DIR' in os.environ: - try: - g = gitinfo() - except OSError: - pass - # finally, check and update the active version file - cp = RawConfigParser() - cp.read(versioncfgfile) - d = cp.defaults() - rewrite = not d or (g['commit'] and ( - g['version'] != d.get('version') or g['commit'] != d.get('commit'))) - if rewrite: - cp.set('DEFAULT', 'version', g['version']) - cp.set('DEFAULT', 'commit', g['commit']) - cp.set('DEFAULT', 'date', g['date']) - cp.set('DEFAULT', 'timestamp', g['timestamp']) - cp.write(open(versioncfgfile, 'w')) - return cp - -versiondata = getversioncfg() - -# define distribution -setup_args = dict( - name='DistancePrinter', - version='1.0', - namespace_packages=['DistancePrinter'], - packages=find_packages(), - include_package_data=True, - zip_safe=False, - entry_points={ - # define console_scripts here, see setuptools docs for details. - 'console_scripts' : ['distanceprinter = DistancePrinter.distanceprinter:main' - ], - }, - - author='Simon J.L. Billinge', - author_email='sb2896@columbia.edu', - description='Distance Printer, calculate the inter atomic distance', - maintainer='Xiaohao Yang', - maintainer_email='xiaohao.yang@outlook.com', - license='see LICENSENOTICE.txt', - url='', - keywords='atomic structure', - classifiers=[ - # List of possible values at - # http://pypi.python.org/pypi?:action=list_classifiers - 'Development Status :: 5 - Production/Stable', - 'Environment :: MacOS X', - 'Environment :: Win32 (MS Windows)', - 'Environment :: X11 Applications', - 'Intended Audience :: Science/Research', - 'Operating System :: MacOS', - 'Operating System :: Microsoft :: Windows', - 'Operating System :: POSIX', - 'Programming Language :: Python :: 2.6', - 'Programming Language :: Python :: 2.7', - 'Topic :: Scientific/Engineering :: Physics', - ], -) - -if __name__ == '__main__': - setup(**setup_args) - -# End of file \ No newline at end of file From 06b82eda5425574877beea447fea040ec47b8c9f Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Tue, 12 Aug 2025 23:14:39 -0400 Subject: [PATCH 06/33] successfully installed, didn't successfully run the app --- pyproject.toml | 2 +- {DistancePrinter/requirements => requirements}/pip.txt | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename {DistancePrinter/requirements => requirements}/pip.txt (100%) diff --git a/pyproject.toml b/pyproject.toml index 65c5c37..ecaf836 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ classifiers = [ 'Topic :: Scientific/Engineering :: Chemistry', ] -[project.entrypoints] +[project.scripts] distanceprinter = 'DistancePrinter.distanceprinter:main' [project.urls] diff --git a/DistancePrinter/requirements/pip.txt b/requirements/pip.txt similarity index 100% rename from DistancePrinter/requirements/pip.txt rename to requirements/pip.txt From 9509a0753b8ec62a67c346c9133f6a0f0a6dae89 Mon Sep 17 00:00:00 2001 From: Zhi Ming Xu Date: Sat, 16 Aug 2025 02:23:52 -0400 Subject: [PATCH 07/33] chore: embed DistancePrinter under src/diffpy --- src/diffpy/__init__.py | 15 +++ src/diffpy/distanceprinter/__init__.py | 22 ++++ src/diffpy/distanceprinter/distanceprinter.py | 116 ++++++++++++++++++ src/diffpy/distanceprinter/version.py | 35 ++++++ 4 files changed, 188 insertions(+) create mode 100644 src/diffpy/__init__.py create mode 100644 src/diffpy/distanceprinter/__init__.py create mode 100644 src/diffpy/distanceprinter/distanceprinter.py create mode 100644 src/diffpy/distanceprinter/version.py diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py new file mode 100644 index 0000000..5138d34 --- /dev/null +++ b/src/diffpy/__init__.py @@ -0,0 +1,15 @@ +#!/usr/bin/env python +############################################################################## +# +# DistancePrinter by Simon J. L. Billinge group +# (c) 2013 Trustees of the Columbia University +# in the City of New York. All rights reserved. +# +# File coded by: Xiaohao Yang +# +# See AUTHORS.txt for a list of people who contributed. +# See LICENSENOTICE.txt for license information. +# +############################################################################## + +# Placeholder until this gets scikit-packaged later \ No newline at end of file diff --git a/src/diffpy/distanceprinter/__init__.py b/src/diffpy/distanceprinter/__init__.py new file mode 100644 index 0000000..5dc714a --- /dev/null +++ b/src/diffpy/distanceprinter/__init__.py @@ -0,0 +1,22 @@ +#!/usr/bin/env python +############################################################################## +# +# DistancePrinter by Simon J. L. Billinge group +# (c) 2013 Trustees of the Columbia University +# in the City of New York. All rights reserved. +# +# File coded by: Xiaohao Yang +# +# See AUTHORS.txt for a list of people who contributed. +# See LICENSENOTICE.txt for license information. +# +############################################################################## + +""" +Blank namespace package. +""" + +__import__('pkg_resources').declare_namespace(__name__) + + +# End of file diff --git a/src/diffpy/distanceprinter/distanceprinter.py b/src/diffpy/distanceprinter/distanceprinter.py new file mode 100644 index 0000000..7a653ca --- /dev/null +++ b/src/diffpy/distanceprinter/distanceprinter.py @@ -0,0 +1,116 @@ +#!/usr/bin/env python +############################################################################## +# +# DistancePrinter by Simon J. L. Billinge group +# (c) 2013 Trustees of the Columbia University +# in the City of New York. All rights reserved. +# +# File coded by: Xiaohao Yang +# +# See AUTHORS.txt for a list of people who contributed. +# See LICENSENOTICE.txt for license information. +# +############################################################################## + +import sys +import numpy as np + +from diffpy.pdffit2 import PdfFit +from diffpy.structure import PDFFitStructure + +def calDistance(strufile, atomi, atomj, lb, ub, complete): + + stru = PDFFitStructure(filename=strufile) + pdffit = PdfFit() + pdffit.add_structure(stru) + ele = stru.element + + rv = pdffit.bond_length_types(atomi, atomj, lb, ub) + dij = np.around(rv['dij'], 6) + ddij = np.around(rv['ddij'], 10) + rv['all0ddij'] = np.all(ddij == 0) + ij0 = rv['ij0'] + + chardtype = 'S8' if complete else 'S4' + dtypec = [('distance', float), ('dd', float), ('i', chardtype), ('j', chardtype)] + distlist = np.zeros(len(dij), dtype=dtypec) + + if not complete: + for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): + if ij[0] > ij[1]: + distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]]) + else: + distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]]) + distlist = np.unique(distlist) + else: + for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): + distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1])) + + distlist.sort(order='distance') + rv['distlist'] = distlist + rv['atomi'] = atomi + rv['atomj'] = atomj + rv['lb'] = lb + rv['ub'] = ub + rv['complete'] = complete + rv['stru'] = stru + rv['strufile'] = strufile + return rv + +def formatResults(stru, distlist, complete, all0ddij, **kw): + ''' + format the distlist to string + ''' + lines = [] + # header + lines.append("# Structure file: %s" % kw['strufile']) + lines.append('# ') + strustr = stru.__str__().splitlines() + lines.append('# ' + strustr[0]) + for i in range(1, len(strustr)): + lines.append('# %2i ' % (i - 1) + strustr[i]) + lines.append('# ') + lines.append('# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A' + % (kw['atomi'], kw['atomj'], kw['lb'], kw['ub'])) + lines.append('') + + if complete: + for dist in distlist: + try: + lines.append('%s-%s:\t%2.6f' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0])) + except AttributeError: + lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0])) + else: + for dist in distlist: + try: + lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0], dist[1])) + except AttributeError: + lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1])) + rv = '\n'.join(lines) + return rv + +def writeToFile(filename, rv): + f = open(filename, 'w', encoding="utf-8") + try: + rv = rv.decode('utf-8') + f.write(rv) + f.close() + except AttributeError: + # No need to decode in python 3 + f.write(rv) + f.close() + pass + +def main(): + sysargv = sys.argv[1:] + strufile, atomi, atomj, lb, ub, complete, filename = sysargv + lb = float(lb) + ub = float(ub) + complete = ('1' == complete) + rv = calDistance(strufile, atomi, atomj, lb, ub, complete) + strv = formatResults(**rv) + writeToFile(filename, strv) + return + +if __name__ == '__main__': + main() diff --git a/src/diffpy/distanceprinter/version.py b/src/diffpy/distanceprinter/version.py new file mode 100644 index 0000000..486d6b7 --- /dev/null +++ b/src/diffpy/distanceprinter/version.py @@ -0,0 +1,35 @@ +#!/usr/bin/env python +############################################################################## +# +# DistancePrinter by Simon J. L. Billinge group +# (c) 2013 Trustees of the Columbia University +# in the City of New York. All rights reserved. +# +# File coded by: Xiaohao Yang +# +# See AUTHORS.txt for a list of people who contributed. +# See LICENSENOTICE.txt for license information. +# +############################################################################## + + +"""Definition of __version__, __date__, __gitsha__. +""" + +from pkg_resources import resource_filename +from ConfigParser import RawConfigParser + +# obtain version information from the version.cfg file +cp = RawConfigParser(dict(version='', date='', commit='', timestamp=0)) +if not cp.read(resource_filename(__name__, 'version.cfg')): + from warnings import warn + warn('Package metadata not found, execute "./setup.py egg_info".') + +__version__ = cp.get('DEFAULT', 'version') +__date__ = cp.get('DEFAULT', 'date') +__gitsha__ = cp.get('DEFAULT', 'commit') +__timestamp__ = cp.getint('DEFAULT', 'timestamp') + +del cp + +# End of file From ea265682cc591a1843691af3dddf629dc81503d5 Mon Sep 17 00:00:00 2001 From: Zhi Ming Xu Date: Sat, 16 Aug 2025 02:24:02 -0400 Subject: [PATCH 08/33] chore: change distanceprinter imports --- tests/test_distanceprinter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py index 565a03e..9d1d618 100644 --- a/tests/test_distanceprinter.py +++ b/tests/test_distanceprinter.py @@ -1,7 +1,7 @@ import os from io import open -from DistancePrinter.distanceprinter import main +from diffpy.distanceprinter.distanceprinter import main def test_distanceprinter(monkeypatch): From e62950562cd010b2521f3c3fb50900d250fbeea7 Mon Sep 17 00:00:00 2001 From: Zhi Ming Xu Date: Sat, 16 Aug 2025 02:24:22 -0400 Subject: [PATCH 09/33] chore: change distanceprinter references in pyproject.toml --- DistancePrinter/__init__.py | 22 ------ DistancePrinter/distanceprinter.py | 116 ----------------------------- DistancePrinter/version.py | 35 --------- pyproject.toml | 4 +- 4 files changed, 2 insertions(+), 175 deletions(-) delete mode 100644 DistancePrinter/__init__.py delete mode 100644 DistancePrinter/distanceprinter.py delete mode 100644 DistancePrinter/version.py diff --git a/DistancePrinter/__init__.py b/DistancePrinter/__init__.py deleted file mode 100644 index 5dc714a..0000000 --- a/DistancePrinter/__init__.py +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. -# -# File coded by: Xiaohao Yang -# -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. -# -############################################################################## - -""" -Blank namespace package. -""" - -__import__('pkg_resources').declare_namespace(__name__) - - -# End of file diff --git a/DistancePrinter/distanceprinter.py b/DistancePrinter/distanceprinter.py deleted file mode 100644 index 7a653ca..0000000 --- a/DistancePrinter/distanceprinter.py +++ /dev/null @@ -1,116 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. -# -# File coded by: Xiaohao Yang -# -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. -# -############################################################################## - -import sys -import numpy as np - -from diffpy.pdffit2 import PdfFit -from diffpy.structure import PDFFitStructure - -def calDistance(strufile, atomi, atomj, lb, ub, complete): - - stru = PDFFitStructure(filename=strufile) - pdffit = PdfFit() - pdffit.add_structure(stru) - ele = stru.element - - rv = pdffit.bond_length_types(atomi, atomj, lb, ub) - dij = np.around(rv['dij'], 6) - ddij = np.around(rv['ddij'], 10) - rv['all0ddij'] = np.all(ddij == 0) - ij0 = rv['ij0'] - - chardtype = 'S8' if complete else 'S4' - dtypec = [('distance', float), ('dd', float), ('i', chardtype), ('j', chardtype)] - distlist = np.zeros(len(dij), dtype=dtypec) - - if not complete: - for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): - if ij[0] > ij[1]: - distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]]) - else: - distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]]) - distlist = np.unique(distlist) - else: - for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): - distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1])) - - distlist.sort(order='distance') - rv['distlist'] = distlist - rv['atomi'] = atomi - rv['atomj'] = atomj - rv['lb'] = lb - rv['ub'] = ub - rv['complete'] = complete - rv['stru'] = stru - rv['strufile'] = strufile - return rv - -def formatResults(stru, distlist, complete, all0ddij, **kw): - ''' - format the distlist to string - ''' - lines = [] - # header - lines.append("# Structure file: %s" % kw['strufile']) - lines.append('# ') - strustr = stru.__str__().splitlines() - lines.append('# ' + strustr[0]) - for i in range(1, len(strustr)): - lines.append('# %2i ' % (i - 1) + strustr[i]) - lines.append('# ') - lines.append('# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A' - % (kw['atomi'], kw['atomj'], kw['lb'], kw['ub'])) - lines.append('') - - if complete: - for dist in distlist: - try: - lines.append('%s-%s:\t%2.6f' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0])) - except AttributeError: - lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0])) - else: - for dist in distlist: - try: - lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0], dist[1])) - except AttributeError: - lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1])) - rv = '\n'.join(lines) - return rv - -def writeToFile(filename, rv): - f = open(filename, 'w', encoding="utf-8") - try: - rv = rv.decode('utf-8') - f.write(rv) - f.close() - except AttributeError: - # No need to decode in python 3 - f.write(rv) - f.close() - pass - -def main(): - sysargv = sys.argv[1:] - strufile, atomi, atomj, lb, ub, complete, filename = sysargv - lb = float(lb) - ub = float(ub) - complete = ('1' == complete) - rv = calDistance(strufile, atomi, atomj, lb, ub, complete) - strv = formatResults(**rv) - writeToFile(filename, strv) - return - -if __name__ == '__main__': - main() diff --git a/DistancePrinter/version.py b/DistancePrinter/version.py deleted file mode 100644 index 486d6b7..0000000 --- a/DistancePrinter/version.py +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. -# -# File coded by: Xiaohao Yang -# -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. -# -############################################################################## - - -"""Definition of __version__, __date__, __gitsha__. -""" - -from pkg_resources import resource_filename -from ConfigParser import RawConfigParser - -# obtain version information from the version.cfg file -cp = RawConfigParser(dict(version='', date='', commit='', timestamp=0)) -if not cp.read(resource_filename(__name__, 'version.cfg')): - from warnings import warn - warn('Package metadata not found, execute "./setup.py egg_info".') - -__version__ = cp.get('DEFAULT', 'version') -__date__ = cp.get('DEFAULT', 'date') -__gitsha__ = cp.get('DEFAULT', 'commit') -__timestamp__ = cp.getint('DEFAULT', 'timestamp') - -del cp - -# End of file diff --git a/pyproject.toml b/pyproject.toml index ecaf836..45c8729 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ classifiers = [ ] [project.scripts] -distanceprinter = 'DistancePrinter.distanceprinter:main' +distanceprinter = 'diffpy.distanceprinter.distanceprinter:main' [project.urls] Homepage = "https://github.com/diffpy/diffpy.distanceprinter/" @@ -46,7 +46,7 @@ dev_template = "{tag}" dirty_template = "{tag}" [tool.setuptools.packages.find] -where = ["DistancePrinter"] # list of folders that contain the packages (["."] by default) +where = ["src"] # list of folders that contain the packages (["."] by default) include = ["*"] # package names should match these glob patterns (["*"] by default) exclude = [] # exclude packages matching these glob patterns (empty by default) namespaces = false # to disable scanning PEP 420 namespaces (true by default) From 8ba53b3832b8b0e1f05b7589ed501ec8014f3e62 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 21 Sep 2025 15:17:01 -0500 Subject: [PATCH 10/33] skpkg: apply black to all files in the project directory Signed-off-by: Dasun Abeykoon --- src/diffpy/__init__.py | 2 +- src/diffpy/distanceprinter/__init__.py | 2 +- src/diffpy/distanceprinter/distanceprinter.py | 119 +++++++++++------- src/diffpy/distanceprinter/version.py | 16 +-- tests/test_distanceprinter.py | 30 +++-- 5 files changed, 108 insertions(+), 61 deletions(-) diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py index 5138d34..3df6e4e 100644 --- a/src/diffpy/__init__.py +++ b/src/diffpy/__init__.py @@ -12,4 +12,4 @@ # ############################################################################## -# Placeholder until this gets scikit-packaged later \ No newline at end of file +# Placeholder until this gets scikit-packaged later diff --git a/src/diffpy/distanceprinter/__init__.py b/src/diffpy/distanceprinter/__init__.py index 5dc714a..72d8855 100644 --- a/src/diffpy/distanceprinter/__init__.py +++ b/src/diffpy/distanceprinter/__init__.py @@ -16,7 +16,7 @@ Blank namespace package. """ -__import__('pkg_resources').declare_namespace(__name__) +__import__("pkg_resources").declare_namespace(__name__) # End of file diff --git a/src/diffpy/distanceprinter/distanceprinter.py b/src/diffpy/distanceprinter/distanceprinter.py index 7a653ca..daeaaf1 100644 --- a/src/diffpy/distanceprinter/distanceprinter.py +++ b/src/diffpy/distanceprinter/distanceprinter.py @@ -18,23 +18,29 @@ from diffpy.pdffit2 import PdfFit from diffpy.structure import PDFFitStructure + def calDistance(strufile, atomi, atomj, lb, ub, complete): - + stru = PDFFitStructure(filename=strufile) pdffit = PdfFit() pdffit.add_structure(stru) ele = stru.element - + rv = pdffit.bond_length_types(atomi, atomj, lb, ub) - dij = np.around(rv['dij'], 6) - ddij = np.around(rv['ddij'], 10) - rv['all0ddij'] = np.all(ddij == 0) - ij0 = rv['ij0'] - - chardtype = 'S8' if complete else 'S4' - dtypec = [('distance', float), ('dd', float), ('i', chardtype), ('j', chardtype)] + dij = np.around(rv["dij"], 6) + ddij = np.around(rv["ddij"], 10) + rv["all0ddij"] = np.all(ddij == 0) + ij0 = rv["ij0"] + + chardtype = "S8" if complete else "S4" + dtypec = [ + ("distance", float), + ("dd", float), + ("i", chardtype), + ("j", chardtype), + ] distlist = np.zeros(len(dij), dtype=dtypec) - + if not complete: for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): if ij[0] > ij[1]: @@ -44,55 +50,82 @@ def calDistance(strufile, atomi, atomj, lb, ub, complete): distlist = np.unique(distlist) else: for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): - distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1])) - - distlist.sort(order='distance') - rv['distlist'] = distlist - rv['atomi'] = atomi - rv['atomj'] = atomj - rv['lb'] = lb - rv['ub'] = ub - rv['complete'] = complete - rv['stru'] = stru - rv['strufile'] = strufile + distlist[i] = ( + dist, + dd, + "%s.%i" % (ele[ij[0]], ij[0]), + "%s.%i" % (ele[ij[1]], ij[1]), + ) + + distlist.sort(order="distance") + rv["distlist"] = distlist + rv["atomi"] = atomi + rv["atomj"] = atomj + rv["lb"] = lb + rv["ub"] = ub + rv["complete"] = complete + rv["stru"] = stru + rv["strufile"] = strufile return rv - + + def formatResults(stru, distlist, complete, all0ddij, **kw): - ''' + """ format the distlist to string - ''' + """ lines = [] # header - lines.append("# Structure file: %s" % kw['strufile']) - lines.append('# ') + lines.append("# Structure file: %s" % kw["strufile"]) + lines.append("# ") strustr = stru.__str__().splitlines() - lines.append('# ' + strustr[0]) + lines.append("# " + strustr[0]) for i in range(1, len(strustr)): - lines.append('# %2i ' % (i - 1) + strustr[i]) - lines.append('# ') - lines.append('# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A' - % (kw['atomi'], kw['atomj'], kw['lb'], kw['ub'])) - lines.append('') - + lines.append("# %2i " % (i - 1) + strustr[i]) + lines.append("# ") + lines.append( + "# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A" + % (kw["atomi"], kw["atomj"], kw["lb"], kw["ub"]) + ) + lines.append("") + if complete: for dist in distlist: try: - lines.append('%s-%s:\t%2.6f' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0])) + lines.append( + "%s-%s:\t%2.6f" + % ( + dist[2].decode("utf-8"), + dist[3].decode("utf-8"), + dist[0], + ) + ) except AttributeError: - lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0])) + lines.append("%s-%s:\t%2.6f" % (dist[2], dist[3], dist[0])) else: for dist in distlist: try: - lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0], dist[1])) + lines.append( + "%s-%s:\t%2.6f (%1.1e)" + % ( + dist[2].decode("utf-8"), + dist[3].decode("utf-8"), + dist[0], + dist[1], + ) + ) except AttributeError: - lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1])) - rv = '\n'.join(lines) + lines.append( + "%s-%s:\t%2.6f (%1.1e)" + % (dist[2], dist[3], dist[0], dist[1]) + ) + rv = "\n".join(lines) return rv + def writeToFile(filename, rv): - f = open(filename, 'w', encoding="utf-8") + f = open(filename, "w", encoding="utf-8") try: - rv = rv.decode('utf-8') + rv = rv.decode("utf-8") f.write(rv) f.close() except AttributeError: @@ -101,16 +134,18 @@ def writeToFile(filename, rv): f.close() pass + def main(): sysargv = sys.argv[1:] strufile, atomi, atomj, lb, ub, complete, filename = sysargv lb = float(lb) ub = float(ub) - complete = ('1' == complete) + complete = "1" == complete rv = calDistance(strufile, atomi, atomj, lb, ub, complete) strv = formatResults(**rv) writeToFile(filename, strv) return -if __name__ == '__main__': + +if __name__ == "__main__": main() diff --git a/src/diffpy/distanceprinter/version.py b/src/diffpy/distanceprinter/version.py index 486d6b7..ec518ce 100644 --- a/src/diffpy/distanceprinter/version.py +++ b/src/diffpy/distanceprinter/version.py @@ -13,22 +13,22 @@ ############################################################################## -"""Definition of __version__, __date__, __gitsha__. -""" +"""Definition of __version__, __date__, __gitsha__.""" from pkg_resources import resource_filename from ConfigParser import RawConfigParser # obtain version information from the version.cfg file -cp = RawConfigParser(dict(version='', date='', commit='', timestamp=0)) -if not cp.read(resource_filename(__name__, 'version.cfg')): +cp = RawConfigParser(dict(version="", date="", commit="", timestamp=0)) +if not cp.read(resource_filename(__name__, "version.cfg")): from warnings import warn + warn('Package metadata not found, execute "./setup.py egg_info".') -__version__ = cp.get('DEFAULT', 'version') -__date__ = cp.get('DEFAULT', 'date') -__gitsha__ = cp.get('DEFAULT', 'commit') -__timestamp__ = cp.getint('DEFAULT', 'timestamp') +__version__ = cp.get("DEFAULT", "version") +__date__ = cp.get("DEFAULT", "date") +__gitsha__ = cp.get("DEFAULT", "commit") +__timestamp__ = cp.getint("DEFAULT", "timestamp") del cp diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py index 9d1d618..652e601 100644 --- a/tests/test_distanceprinter.py +++ b/tests/test_distanceprinter.py @@ -10,26 +10,38 @@ def test_distanceprinter(monkeypatch): # must be cif, stru, or xyz file strufile = os.path.join(example_file_dir, "Ni-9008476.cif") # atoms typically pull from list of elements in stru output of PDFFitStructure. 'all' is always first option - atomi = 'all' - atomj = 'all' + atomi = "all" + atomj = "all" # lb and ub are lower an upper bound of distance to list in angstroms lb = 1 ub = 10 # 1 means keep duplicate atom pairs with same inter-atomic distance, 0 means not to - comp = '1' - monkeypatch.setattr("sys.argv", ['distanceprinter', strufile, atomi, atomj, lb, ub, comp, 'tests\\outputs\\actual.res']) + comp = "1" + monkeypatch.setattr( + "sys.argv", + [ + "distanceprinter", + strufile, + atomi, + atomj, + lb, + ub, + comp, + "tests\\outputs\\actual.res", + ], + ) cwd = os.getcwd() main() - generated_file_path = os.path.join(cwd, 'tests\\outputs\\actual.res') - f = open(generated_file_path, 'r', encoding="utf-8") + generated_file_path = os.path.join(cwd, "tests\\outputs\\actual.res") + f = open(generated_file_path, "r", encoding="utf-8") rv0 = f.readlines() - rv0 = ''.join(rv0) + rv0 = "".join(rv0) resultstr = rv0 output_file_dir = os.path.join(current_module_dir, "outputs") example_output = os.path.join(output_file_dir, "expected.res") - f = open(example_output, 'r', encoding="utf-8") + f = open(example_output, "r", encoding="utf-8") rv1 = f.readlines() - rv1 = ''.join(rv1) + rv1 = "".join(rv1) teststr = rv1 # Remove structure file path when comparing as it may differ between machines From d6b688d1e8cf2daec1f44cfea76977fe8a54bd47 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 23 Sep 2025 22:55:23 -0500 Subject: [PATCH 11/33] style: apply pre-commit hooks with no manual edits Signed-off-by: Dasun Abeykoon --- .flake8 | 13 ++++ .gitignore | 2 +- .isort.cfg | 5 ++ .pre-commit-config.yaml | 66 +++++++++++++++++++ AUTHORS.txt | 2 +- MANIFEST.in | 2 +- README.rst | 8 +-- src/diffpy/distanceprinter/__init__.py | 4 +- src/diffpy/distanceprinter/distanceprinter.py | 5 +- src/diffpy/distanceprinter/version.py | 2 +- tests/outputs/expected.res | 6 +- 11 files changed, 98 insertions(+), 17 deletions(-) create mode 100644 .flake8 create mode 100644 .isort.cfg create mode 100644 .pre-commit-config.yaml diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..88077af --- /dev/null +++ b/.flake8 @@ -0,0 +1,13 @@ +# As of now, flake8 does not natively support configuration via pyproject.toml +# https://github.com/microsoft/vscode-flake8/issues/135 +[flake8] +exclude = + .git, + __pycache__, + build, + dist, + docs/source/conf.py +max-line-length = 79 +# Ignore some style 'errors' produced while formatting by 'black' +# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings +extend-ignore = E203 diff --git a/.gitignore b/.gitignore index bcd8ba5..1be1fdf 100644 --- a/.gitignore +++ b/.gitignore @@ -45,4 +45,4 @@ setup.cfg /DistancePrinter/gitarchive.cfg # test output -actual.res \ No newline at end of file +actual.res diff --git a/.isort.cfg b/.isort.cfg new file mode 100644 index 0000000..86f162b --- /dev/null +++ b/.isort.cfg @@ -0,0 +1,5 @@ +[settings] +# Keep import statement below line_length character limit +line_length = 79 +multi_line_output = 3 +include_trailing_comma = True diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..0e4a84d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,66 @@ +default_language_version: + python: python3 +ci: + autofix_commit_msg: | + [pre-commit.ci] auto fixes from pre-commit hooks + autofix_prs: true + autoupdate_branch: "pre-commit-autoupdate" + autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate" + autoupdate_schedule: monthly + skip: [no-commit-to-branch] + submodules: false +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: check-yaml + - id: end-of-file-fixer + - id: trailing-whitespace + - id: check-case-conflict + - id: check-merge-conflict + - id: check-toml + - id: check-added-large-files + - repo: https://github.com/psf/black + rev: 24.4.2 + hooks: + - id: black + - repo: https://github.com/pycqa/flake8 + rev: 7.0.0 + hooks: + - id: flake8 + - repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + args: ["--profile", "black"] + - repo: https://github.com/kynan/nbstripout + rev: 0.7.1 + hooks: + - id: nbstripout + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: no-commit-to-branch + name: Prevent Commit to Main Branch + args: ["--branch", "main"] + stages: [pre-commit] + - repo: https://github.com/codespell-project/codespell + rev: v2.3.0 + hooks: + - id: codespell + additional_dependencies: + - tomli + # prettier - multi formatter for .json, .yml, and .md files + - repo: https://github.com/pre-commit/mirrors-prettier + rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8 + hooks: + - id: prettier + additional_dependencies: + - "prettier@^3.2.4" + # docformatter - PEP 257 compliant docstring formatter + - repo: https://github.com/s-weigand/docformatter + rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c + hooks: + - id: docformatter + additional_dependencies: [tomli] + args: [--in-place, --config, ./pyproject.toml] diff --git a/AUTHORS.txt b/AUTHORS.txt index f0671d8..e36df7d 100644 --- a/AUTHORS.txt +++ b/AUTHORS.txt @@ -1 +1 @@ -Xiaohao Yang \ No newline at end of file +Xiaohao Yang diff --git a/MANIFEST.in b/MANIFEST.in index 35a5d8c..0ecc683 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,3 +1,3 @@ recursive-include DistancePrinter * prune doc -exclude MANIFEST.in \ No newline at end of file +exclude MANIFEST.in diff --git a/README.rst b/README.rst index 0e636ba..15b7d2a 100644 --- a/README.rst +++ b/README.rst @@ -18,10 +18,10 @@ To install the DistancePrinter package: python setup.py install -By default the files are installed in the system directories, which are -usually only writeable by the root. See the usage info "./setup.py install ---help" for options to install as a normal user under a different location. -Note that installation to non-standard directories you may require adjustments +By default the files are installed in the system directories, which are +usually only writeable by the root. See the usage info "./setup.py install +--help" for options to install as a normal user under a different location. +Note that installation to non-standard directories you may require adjustments to the PATH and PYTHONPATH environment variables. CONTACTS diff --git a/src/diffpy/distanceprinter/__init__.py b/src/diffpy/distanceprinter/__init__.py index 72d8855..57b5f4d 100644 --- a/src/diffpy/distanceprinter/__init__.py +++ b/src/diffpy/distanceprinter/__init__.py @@ -12,9 +12,7 @@ # ############################################################################## -""" -Blank namespace package. -""" +"""Blank namespace package.""" __import__("pkg_resources").declare_namespace(__name__) diff --git a/src/diffpy/distanceprinter/distanceprinter.py b/src/diffpy/distanceprinter/distanceprinter.py index daeaaf1..5dcd81f 100644 --- a/src/diffpy/distanceprinter/distanceprinter.py +++ b/src/diffpy/distanceprinter/distanceprinter.py @@ -13,6 +13,7 @@ ############################################################################## import sys + import numpy as np from diffpy.pdffit2 import PdfFit @@ -70,9 +71,7 @@ def calDistance(strufile, atomi, atomj, lb, ub, complete): def formatResults(stru, distlist, complete, all0ddij, **kw): - """ - format the distlist to string - """ + """Format the distlist to string.""" lines = [] # header lines.append("# Structure file: %s" % kw["strufile"]) diff --git a/src/diffpy/distanceprinter/version.py b/src/diffpy/distanceprinter/version.py index ec518ce..5664eb5 100644 --- a/src/diffpy/distanceprinter/version.py +++ b/src/diffpy/distanceprinter/version.py @@ -15,8 +15,8 @@ """Definition of __version__, __date__, __gitsha__.""" -from pkg_resources import resource_filename from ConfigParser import RawConfigParser +from pkg_resources import resource_filename # obtain version information from the version.cfg file cp = RawConfigParser(dict(version="", date="", commit="", timestamp=0)) diff --git a/tests/outputs/expected.res b/tests/outputs/expected.res index a9dcd12..845f832 100644 --- a/tests/outputs/expected.res +++ b/tests/outputs/expected.res @@ -1,11 +1,11 @@ # Structure file: /home/zthatcher/GitLab/dev/dpx.distanceprinter/tests/test_files/Ni-9008476.cif -# +# # lattice=Lattice(a=3.52387, b=3.52387, c=3.52387, alpha=90, beta=90, gamma=90) # 0 Ni 0.000000 0.000000 0.000000 1.0000 # 1 Ni 0.000000 0.500000 0.500000 1.0000 # 2 Ni 0.500000 0.000000 0.500000 1.0000 # 3 Ni 0.500000 0.500000 0.000000 1.0000 -# +# # Inter-atomic distance of (all, all) in (1.00, 10.00) A Ni.0-Ni.1: 2.491752 @@ -1527,4 +1527,4 @@ Ni.3-Ni.3: 9.967009 Ni.3-Ni.3: 9.967009 Ni.3-Ni.3: 9.967009 Ni.3-Ni.3: 9.967009 -Ni.3-Ni.3: 9.967009 \ No newline at end of file +Ni.3-Ni.3: 9.967009 From c1433c8daae14975fc94533655c0fbb2e6dc618e Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 24 Sep 2025 10:49:31 -0500 Subject: [PATCH 12/33] pre-commit: create codespell ignore files Signed-off-by: Dasun Abeykoon --- .codespell/ignore_lines.txt | 2 ++ .codespell/ignore_words.txt | 8 ++++++++ 2 files changed, 10 insertions(+) create mode 100644 .codespell/ignore_lines.txt create mode 100644 .codespell/ignore_words.txt diff --git a/.codespell/ignore_lines.txt b/.codespell/ignore_lines.txt new file mode 100644 index 0000000..07fa7c8 --- /dev/null +++ b/.codespell/ignore_lines.txt @@ -0,0 +1,2 @@ +;; Please include filenames and explanations for each ignored line. +;; See https://docs.openverse.org/meta/codespell.html for docs. diff --git a/.codespell/ignore_words.txt b/.codespell/ignore_words.txt new file mode 100644 index 0000000..04b4fcf --- /dev/null +++ b/.codespell/ignore_words.txt @@ -0,0 +1,8 @@ +;; Please include explanations for each ignored word (lowercase). +;; See https://docs.openverse.org/meta/codespell.html for docs. + +;; abbreviation for "materials" often used in a journal title +mater + +;; Frobenius norm used in np.linalg.norm +fro From 27c46c6e42c2491c77efad4877926aa7ad1a0d60 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Fri, 3 Oct 2025 06:53:01 -0500 Subject: [PATCH 13/33] flake8: shorten test_distanceprinter comments to <79 length Signed-off-by: Dasun Abeykoon --- tests/test_distanceprinter.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py index 652e601..c58d41b 100644 --- a/tests/test_distanceprinter.py +++ b/tests/test_distanceprinter.py @@ -9,13 +9,15 @@ def test_distanceprinter(monkeypatch): example_file_dir = os.path.join(current_module_dir, "data") # must be cif, stru, or xyz file strufile = os.path.join(example_file_dir, "Ni-9008476.cif") - # atoms typically pull from list of elements in stru output of PDFFitStructure. 'all' is always first option + # atoms typically pull from list of elements in output of PDFFitStructure. + # 'all' is always first option atomi = "all" atomj = "all" # lb and ub are lower an upper bound of distance to list in angstroms lb = 1 ub = 10 - # 1 means keep duplicate atom pairs with same inter-atomic distance, 0 means not to + # 1 means keep duplicate atom pairs with same inter-atomic distance + # 0 means not to comp = "1" monkeypatch.setattr( "sys.argv", @@ -44,7 +46,7 @@ def test_distanceprinter(monkeypatch): rv1 = "".join(rv1) teststr = rv1 - # Remove structure file path when comparing as it may differ between machines + # Remove stru file path when comparing as it may differ between machines resultstr = resultstr.split("\n", 2)[2] teststr = teststr.split("\n", 2)[2] assert resultstr == teststr From 8458ace2da550c94c57f277eca936d756a13f151 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 7 Oct 2025 08:24:43 -0500 Subject: [PATCH 14/33] skpkg: migrate src directory Signed-off-by: Dasun Abeykoon --- src/diffpy/__init__.py | 16 +++---- src/diffpy/distanceprinter/__init__.py | 23 ++++++---- src/diffpy/distanceprinter/distanceprinter.py | 14 ++++--- src/diffpy/distanceprinter/version.py | 42 ++++++++----------- 4 files changed, 48 insertions(+), 47 deletions(-) diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py index 3df6e4e..c8b38e3 100644 --- a/src/diffpy/__init__.py +++ b/src/diffpy/__init__.py @@ -1,15 +1,15 @@ #!/usr/bin/env python ############################################################################## # -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. +# (c) 2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. # -# File coded by: Xiaohao Yang +# File coded by: Xiaohao Yang and Billinge Group members # -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. # ############################################################################## - -# Placeholder until this gets scikit-packaged later diff --git a/src/diffpy/distanceprinter/__init__.py b/src/diffpy/distanceprinter/__init__.py index 57b5f4d..703fa12 100644 --- a/src/diffpy/distanceprinter/__init__.py +++ b/src/diffpy/distanceprinter/__init__.py @@ -1,20 +1,27 @@ #!/usr/bin/env python ############################################################################## # -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. +# (c) 2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. # -# File coded by: Xiaohao Yang +# File coded by: Xiaohao Yang and Billinge Group members # -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. # ############################################################################## +"""Distance Printer, calculate the inter atomic distances. -"""Blank namespace package.""" +Part of xPDFsuite +""" -__import__("pkg_resources").declare_namespace(__name__) +# package version +from diffpy.distanceprinter.version import __version__ # noqa +# silence the pyflakes syntax checker +assert __version__ or True # End of file diff --git a/src/diffpy/distanceprinter/distanceprinter.py b/src/diffpy/distanceprinter/distanceprinter.py index 5dcd81f..dea848a 100644 --- a/src/diffpy/distanceprinter/distanceprinter.py +++ b/src/diffpy/distanceprinter/distanceprinter.py @@ -1,14 +1,16 @@ #!/usr/bin/env python ############################################################################## # -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. +# (c) 2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. # -# File coded by: Xiaohao Yang +# File coded by: Xiaohao Yang and Billinge Group members # -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. # ############################################################################## diff --git a/src/diffpy/distanceprinter/version.py b/src/diffpy/distanceprinter/version.py index 5664eb5..9b68c6f 100644 --- a/src/diffpy/distanceprinter/version.py +++ b/src/diffpy/distanceprinter/version.py @@ -1,35 +1,27 @@ #!/usr/bin/env python ############################################################################## # -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. +# (c) 2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. # -# File coded by: Xiaohao Yang +# File coded by: Xiaohao Yang and Billinge Group members # -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. # ############################################################################## +"""Definition of __version__.""" +# We do not use the other three variables, but can be added back if needed. +# __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"] -"""Definition of __version__, __date__, __gitsha__.""" - -from ConfigParser import RawConfigParser -from pkg_resources import resource_filename - -# obtain version information from the version.cfg file -cp = RawConfigParser(dict(version="", date="", commit="", timestamp=0)) -if not cp.read(resource_filename(__name__, "version.cfg")): - from warnings import warn - - warn('Package metadata not found, execute "./setup.py egg_info".') - -__version__ = cp.get("DEFAULT", "version") -__date__ = cp.get("DEFAULT", "date") -__gitsha__ = cp.get("DEFAULT", "commit") -__timestamp__ = cp.getint("DEFAULT", "timestamp") - -del cp +# obtain version information +from importlib.metadata import PackageNotFoundError, version -# End of file +try: + __version__ = version("diffpy.distanceprinter") +except PackageNotFoundError: + __version__ = "unknown" From af75df83c81f9aeeb5aee5c273e5c7630225914c Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 7 Oct 2025 08:25:00 -0500 Subject: [PATCH 15/33] skpkg: migrate test directory Signed-off-by: Dasun Abeykoon --- tests/test_version.py | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 tests/test_version.py diff --git a/tests/test_version.py b/tests/test_version.py new file mode 100644 index 0000000..b8b38df --- /dev/null +++ b/tests/test_version.py @@ -0,0 +1,10 @@ +"""Unit tests for __version__.py.""" + +import diffpy.distanceprinter # noqa + + +def test_package_version(): + """Ensure the package version is defined and not set to the initial + placeholder.""" + assert hasattr(diffpy.distanceprinter, "__version__") + assert diffpy.distanceprinter.__version__ != "0.0.0" From 152bb9cbe8d2e0469c4bfe14dd956ef92a0fcbf5 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Tue, 7 Oct 2025 08:25:59 -0500 Subject: [PATCH 16/33] skpkg: list dependancies in requirements directory Signed-off-by: Dasun Abeykoon --- requirements/build.txt | 0 requirements/{pip.txt => conda.txt} | 0 requirements/docs.txt | 5 +++++ requirements/tests.txt | 6 ++++++ 4 files changed, 11 insertions(+) create mode 100644 requirements/build.txt rename requirements/{pip.txt => conda.txt} (100%) create mode 100644 requirements/docs.txt create mode 100644 requirements/tests.txt diff --git a/requirements/build.txt b/requirements/build.txt new file mode 100644 index 0000000..e69de29 diff --git a/requirements/pip.txt b/requirements/conda.txt similarity index 100% rename from requirements/pip.txt rename to requirements/conda.txt diff --git a/requirements/docs.txt b/requirements/docs.txt new file mode 100644 index 0000000..5f34c6e --- /dev/null +++ b/requirements/docs.txt @@ -0,0 +1,5 @@ +sphinx +sphinx_rtd_theme +sphinx-copybutton +doctr +m2r diff --git a/requirements/tests.txt b/requirements/tests.txt new file mode 100644 index 0000000..a727786 --- /dev/null +++ b/requirements/tests.txt @@ -0,0 +1,6 @@ +flake8 +pytest +codecov +coverage +pytest-cov +pytest-env From d38db29be801b01c0ee65b0c3082c631c329956c Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 08:34:52 -0500 Subject: [PATCH 17/33] skpkg: add CI and issue/PR templates Signed-off-by: Dasun Abeykoon --- .github/ISSUE_TEMPLATE/bug_feature.md | 16 ++++ .github/ISSUE_TEMPLATE/release_checklist.md | 46 ++++++++++ .../pull_request_template.md | 15 +++ .../workflows/build-wheel-release-upload.yml | 18 ++++ .github/workflows/check-news-item.yml | 12 +++ .../matrix-and-codecov-on-merge-to-main.yml | 21 +++++ .github/workflows/publish-docs-on-release.yml | 12 +++ .github/workflows/tests-on-pr.yml | 15 +++ .gitignore | 91 ++++++++++++++----- 9 files changed, 223 insertions(+), 23 deletions(-) create mode 100644 .github/ISSUE_TEMPLATE/bug_feature.md create mode 100644 .github/ISSUE_TEMPLATE/release_checklist.md create mode 100644 .github/PULL_REQUEST_TEMPLATE/pull_request_template.md create mode 100644 .github/workflows/build-wheel-release-upload.yml create mode 100644 .github/workflows/check-news-item.yml create mode 100644 .github/workflows/matrix-and-codecov-on-merge-to-main.yml create mode 100644 .github/workflows/publish-docs-on-release.yml create mode 100644 .github/workflows/tests-on-pr.yml diff --git a/.github/ISSUE_TEMPLATE/bug_feature.md b/.github/ISSUE_TEMPLATE/bug_feature.md new file mode 100644 index 0000000..b3454de --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_feature.md @@ -0,0 +1,16 @@ +--- +name: Bug Report or Feature Request +about: Report a bug or suggest a new feature! +title: "" +labels: "" +assignees: "" +--- + +### Problem + + + +### Proposed solution diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md new file mode 100644 index 0000000..56bcd01 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/release_checklist.md @@ -0,0 +1,46 @@ +--- +name: Release +about: Checklist and communication channel for PyPI and GitHub release +title: "Ready for PyPI/GitHub release" +labels: "release" +assignees: "" +--- + +### PyPI/GitHub rc-release preparation checklist: + +- [ ] All PRs/issues attached to the release are merged. +- [ ] All the badges on the README are passing. +- [ ] License information is verified as correct. If you are unsure, please comment below. +- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are + missing), tutorials, and other human-written text is up-to-date with any changes in the code. +- [ ] Installation instructions in the README, documentation, and the website are updated. +- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version. +- [ ] Grammar and writing quality are checked (no typos). +- [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release. + +Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here: + +### PyPI/GitHub full-release preparation checklist: + +- [ ] Create a new conda environment and install the rc from PyPI (`pip install ==??`) +- [ ] License information on PyPI is correct. +- [ ] Docs are deployed successfully to `https:///`. +- [ ] Successfully run all tests, tutorial examples or do functional testing. + +Please let the maintainer know that all checks are done and the package is ready for full release. + +### conda-forge release preparation checklist: + + + +- [ ] Ensure that the full release has appeared on PyPI successfully. +- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock. +- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions. +- [ ] Tag the maintainer for conda-forge release. + +### Post-release checklist + + + +- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments. +- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures. diff --git a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md new file mode 100644 index 0000000..1099d86 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md @@ -0,0 +1,15 @@ +### What problem does this PR address? + + + +### What should the reviewer(s) do? + + + + diff --git a/.github/workflows/build-wheel-release-upload.yml b/.github/workflows/build-wheel-release-upload.yml new file mode 100644 index 0000000..4d246d8 --- /dev/null +++ b/.github/workflows/build-wheel-release-upload.yml @@ -0,0 +1,18 @@ +name: Release (GitHub/PyPI) and Deploy Docs + +on: + workflow_dispatch: + push: + tags: + - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml + +jobs: + build-release: + uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0 + with: + project: diffpy.distanceprinter + c_extension: false + maintainer_GITHUB_username: sbillinge + secrets: + PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} diff --git a/.github/workflows/check-news-item.yml b/.github/workflows/check-news-item.yml new file mode 100644 index 0000000..31a88bf --- /dev/null +++ b/.github/workflows/check-news-item.yml @@ -0,0 +1,12 @@ +name: Check for News + +on: + pull_request_target: + branches: + - main + +jobs: + check-news-item: + uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0 + with: + project: diffpy.distanceprinter diff --git a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml new file mode 100644 index 0000000..ca02afa --- /dev/null +++ b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml @@ -0,0 +1,21 @@ +name: CI + +on: + push: + branches: + - main + release: + types: + - prereleased + - published + workflow_dispatch: + +jobs: + matrix-coverage: + uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0 + with: + project: diffpy.distanceprinter + c_extension: false + headless: false + secrets: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml new file mode 100644 index 0000000..6803e26 --- /dev/null +++ b/.github/workflows/publish-docs-on-release.yml @@ -0,0 +1,12 @@ +name: Deploy Documentation on Release + +on: + workflow_dispatch: + +jobs: + docs: + uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0 + with: + project: diffpy.distanceprinter + c_extension: false + headless: false diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml new file mode 100644 index 0000000..4f1528b --- /dev/null +++ b/.github/workflows/tests-on-pr.yml @@ -0,0 +1,15 @@ +name: Tests on PR + +on: + pull_request: + workflow_dispatch: + +jobs: + tests-on-pr: + uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0 + with: + project: diffpy.distanceprinter + c_extension: false + headless: false + secrets: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore index 1be1fdf..099e294 100644 --- a/.gitignore +++ b/.gitignore @@ -1,48 +1,93 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ *.py[cod] +*$py.class # C extensions *.so -# Packages -*.egg -*.egg-info -dist -build -eggs -parts -bin -var -sdist -temp -develop-eggs +# Distribution / packaging +.Python +env/ +build/ +_build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +venv/ +*.egg-info/ .installed.cfg -lib -lib64 -tags +*.egg +bin/ +temp/ +tags/ errors.err +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + # Installer logs pip-log.txt +pip-delete-this-directory.txt MANIFEST # Unit test / coverage reports +htmlcov/ +.tox/ .coverage -.tox +.coverage.* +.cache nosetests.xml +coverage.xml +*,cover +.hypothesis/ # Translations *.mo +*.pot # Mr Developer .mr.developer.cfg .project .pydevproject -.settings -# version information -setup.cfg -/DistancePrinter/version.cfg -/DistancePrinter/gitarchive.cfg +# Django stuff: +*.log + +# Sphinx documentation +docs/build/ +docs/source/generated/ + +# pytest +.pytest_cache/ + +# PyBuilder +target/ + +# Editor files +# mac +.DS_Store +*~ + +# vim +*.swp +*.swo + +# pycharm +.idea/ + +# VSCode +.vscode/ -# test output -actual.res +# Ipython Notebook +.ipynb_checkpoints From 82cfc67894c05931854fcd3bb0f4d4b0e676eede Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 08:38:05 -0500 Subject: [PATCH 18/33] skpkg: add pyproject.toml Signed-off-by: Dasun Abeykoon --- pyproject.toml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 45c8729..4ee6df6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,13 +6,13 @@ build-backend = "setuptools.build_meta" name = "diffpy.distanceprinter" dynamic=['version', 'dependencies'] authors = [ - { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" }, + { name="Simon J.L. Billinge Group", email="sb2896@columbia.edu" }, ] maintainers = [ - { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" }, + { name="Simon J.L. Billinge Group", email="sb2896@columbia.edu" }, ] description = "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite" -keywords = ['diffpy', 'pdf', 'data interpretation'] +keywords = ['diffpy', 'pdf', 'data-interpretation'] readme = "README.rst" requires-python = ">=3.11, <3.14" classifiers = [ @@ -32,9 +32,6 @@ classifiers = [ 'Topic :: Scientific/Engineering :: Chemistry', ] -[project.scripts] -distanceprinter = 'diffpy.distanceprinter.distanceprinter:main' - [project.urls] Homepage = "https://github.com/diffpy/diffpy.distanceprinter/" Issues = "https://github.com/diffpy/diffpy.distanceprinter/issues/" @@ -51,13 +48,16 @@ include = ["*"] # package names should match these glob patterns (["*"] by defa exclude = [] # exclude packages matching these glob patterns (empty by default) namespaces = false # to disable scanning PEP 420 namespaces (true by default) +[project.scripts] +diffpy-distanceprinter = "diffpy.distanceprinter.app:main" + [tool.setuptools.dynamic] dependencies = {file = ["requirements/pip.txt"]} [tool.codespell] exclude-file = ".codespell/ignore_lines.txt" ignore-words = ".codespell/ignore_words.txt" -skip = "*.cif,*.dat,*agr" +skip = "*.cif,*.dat" [tool.docformatter] recursive = true From ef5fe65b0c844f6c74b3e9e82f417ef14c9cddd9 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Wed, 8 Oct 2025 08:48:49 -0500 Subject: [PATCH 19/33] skpkg: add config files for readthedocs and codecov Signed-off-by: Dasun Abeykoon --- .codecov.yml | 14 ++++++++++++++ .readthedocs.yaml | 13 +++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 .codecov.yml create mode 100644 .readthedocs.yaml diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 0000000..4af5eb2 --- /dev/null +++ b/.codecov.yml @@ -0,0 +1,14 @@ +coverage: + status: + project: # more options at https://docs.codecov.com/docs/commit-status + default: + target: auto # use the coverage from the base commit, fail if coverage is lower + threshold: 0% # allow the coverage to drop by + +comment: + layout: " diff, flags, files" + behavior: default + require_changes: false + require_base: false # [true :: must have a base report to post] + require_head: false # [true :: must have a head report to post] + hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage] diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..aaa8889 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: 2 + +build: + os: "ubuntu-22.04" + tools: + python: "latest" + +python: + install: + - requirements: requirements/docs.txt + +sphinx: + configuration: docs/source/conf.py From 949f045a3268a18b20862676d059ff950f3b36f1 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Thu, 9 Oct 2025 19:04:09 -0500 Subject: [PATCH 20/33] fix: change main project script to diffpy.distanceprinter:main Signed-off-by: Dasun Abeykoon --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4ee6df6..836946d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ exclude = [] # exclude packages matching these glob patterns (empty by default) namespaces = false # to disable scanning PEP 420 namespaces (true by default) [project.scripts] -diffpy-distanceprinter = "diffpy.distanceprinter.app:main" +diffpy-distanceprinter = "diffpy.distanceprinter:main" [tool.setuptools.dynamic] dependencies = {file = ["requirements/pip.txt"]} From ebc4b25869dee15eda93aa8f63c724fe328182d7 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Thu, 9 Oct 2025 19:05:29 -0500 Subject: [PATCH 21/33] doc: update copyright range to 2013-2025 Signed-off-by: Dasun Abeykoon --- src/diffpy/__init__.py | 2 +- src/diffpy/distanceprinter/__init__.py | 2 +- src/diffpy/distanceprinter/distanceprinter.py | 2 +- src/diffpy/distanceprinter/version.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py index c8b38e3..c82d1a5 100644 --- a/src/diffpy/__init__.py +++ b/src/diffpy/__init__.py @@ -1,7 +1,7 @@ #!/usr/bin/env python ############################################################################## # -# (c) 2025 The Trustees of Columbia University in the City of New York. +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. # All rights reserved. # # File coded by: Xiaohao Yang and Billinge Group members diff --git a/src/diffpy/distanceprinter/__init__.py b/src/diffpy/distanceprinter/__init__.py index 703fa12..24623df 100644 --- a/src/diffpy/distanceprinter/__init__.py +++ b/src/diffpy/distanceprinter/__init__.py @@ -1,7 +1,7 @@ #!/usr/bin/env python ############################################################################## # -# (c) 2025 The Trustees of Columbia University in the City of New York. +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. # All rights reserved. # # File coded by: Xiaohao Yang and Billinge Group members diff --git a/src/diffpy/distanceprinter/distanceprinter.py b/src/diffpy/distanceprinter/distanceprinter.py index dea848a..23acd5e 100644 --- a/src/diffpy/distanceprinter/distanceprinter.py +++ b/src/diffpy/distanceprinter/distanceprinter.py @@ -1,7 +1,7 @@ #!/usr/bin/env python ############################################################################## # -# (c) 2025 The Trustees of Columbia University in the City of New York. +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. # All rights reserved. # # File coded by: Xiaohao Yang and Billinge Group members diff --git a/src/diffpy/distanceprinter/version.py b/src/diffpy/distanceprinter/version.py index 9b68c6f..e05d9ea 100644 --- a/src/diffpy/distanceprinter/version.py +++ b/src/diffpy/distanceprinter/version.py @@ -1,7 +1,7 @@ #!/usr/bin/env python ############################################################################## # -# (c) 2025 The Trustees of Columbia University in the City of New York. +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. # All rights reserved. # # File coded by: Xiaohao Yang and Billinge Group members From df9f78deb6b1c6613e3cfb07182928a517f738ba Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Thu, 9 Oct 2025 19:07:20 -0500 Subject: [PATCH 22/33] skpkg: replace build-wheel-release-upload.yml workflow with build-wheel-release.yml workflow Signed-off-by: Dasun Abeykoon --- .../workflows/build-wheel-release-upload.yml | 18 -- .github/workflows/build-wheel-release.yml | 230 ++++++++++++++++++ 2 files changed, 230 insertions(+), 18 deletions(-) delete mode 100644 .github/workflows/build-wheel-release-upload.yml create mode 100644 .github/workflows/build-wheel-release.yml diff --git a/.github/workflows/build-wheel-release-upload.yml b/.github/workflows/build-wheel-release-upload.yml deleted file mode 100644 index 4d246d8..0000000 --- a/.github/workflows/build-wheel-release-upload.yml +++ /dev/null @@ -1,18 +0,0 @@ -name: Release (GitHub/PyPI) and Deploy Docs - -on: - workflow_dispatch: - push: - tags: - - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml - -jobs: - build-release: - uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0 - with: - project: diffpy.distanceprinter - c_extension: false - maintainer_GITHUB_username: sbillinge - secrets: - PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} - PAT_TOKEN: ${{ secrets.PAT_TOKEN }} diff --git a/.github/workflows/build-wheel-release.yml b/.github/workflows/build-wheel-release.yml new file mode 100644 index 0000000..7691787 --- /dev/null +++ b/.github/workflows/build-wheel-release.yml @@ -0,0 +1,230 @@ +name: Build Wheels and Release + +on: + workflow_dispatch: + push: + tags: + - "*" + +env: + PYTHON_VERSIONS: '["3.11","3.12","3.13"]' + +permissions: + contents: write + actions: read + packages: write + +concurrency: + group: build-wheels-${{ github.ref }} + cancel-in-progress: true + +defaults: + run: + shell: bash {0} + +jobs: + get-python-versions: + runs-on: ubuntu-latest + outputs: + py_ver: ${{ steps.set.outputs.py_ver }} + py_last: ${{ steps.set.outputs.py_last }} + steps: + - id: set + run: | + echo py_ver=$PYTHON_VERSIONS >> $GITHUB_OUTPUT + echo "py_last=${{ fromJson(env.PYTHON_VERSIONS)[0] }}" >> $GITHUB_OUTPUT + + check-tag-on-main: + runs-on: ubuntu-latest + steps: + - name: Checkout repository with full history + uses: actions/checkout@v4 + with: + token: ${{ secrets.PAT_TOKEN }} + fetch-depth: 0 + + - name: Verify tag + run: | + git fetch origin main + TAG_COMMIT=$(git rev-parse ${{ github.ref_name }}) + if git merge-base --is-ancestor "$TAG_COMMIT" origin/main; then + echo "Tag ${{ github.ref_name }} ($TAG_COMMIT) is contained in main" + else + echo "::error::Tag ${{ github.ref_name }} ($TAG_COMMIT) is not found in main. Please release from the main branch." + exit 1 + fi + + check-tag-privilege: + # No third party actions used + uses: scikit-package/release-scripts/.github/workflows/_check-tag-privilege.yml@v0 + with: + maintainer_github_username: sbillinge + + build-sdist: + needs: [check-tag-privilege, get-python-versions, check-tag-on-main] + runs-on: ubuntu-latest + + steps: + - name: Checkout + # GitHub officially-maintained actions + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Set up Python + # GitHub officially-maintained actions + uses: actions/setup-python@v5 + with: + python-version: ${{ needs.get-python-versions.outputs.py_last }} + + - name: Build docs and remove fonts that blow up the wheel size + run: | + python -m pip install Sphinx sphinx-rtd-theme sphinx-copybutton m2r + cd docs + make html + cd build/html/_static/css/fonts + find . -type f ! -name '*.ttf' -delete + cd ../.. + rm -rf fonts + cd .. + rm -rf _sources + cd .. + rm -rf doctrees + cd ../.. + + - name: Make sdist + run: | + python -m pip install --upgrade pip build cython setuptools setuptools-git-versioning + python -m build --sdist --no-isolation + + - name: Strip source codes + run: | + set -euo pipefail + tar xf dist/diffpy_distanceprinter-*.tar.gz + SRC_DIR=$(find . -maxdepth 1 -type d -name 'diffpy_distanceprinter-*' | head -n1) + find "$SRC_DIR" -type f -name '*.c' -print0 \ + | xargs -0 perl -i.bak -0777 -pe 's{/\*.*?\*/}{}gs' + find "$SRC_DIR" -type f -name '*.c.bak' -delete + tar czf dist/"${SRC_DIR#./}".tar.gz "$SRC_DIR" + rm -rf "$SRC_DIR" + + - name: Upload sdist + # GitHub officially-maintained actions + uses: actions/upload-artifact@v4 + with: + name: sdist + path: dist/ + retention-days: 1 + + - name: Upload INSTRUCTIONS.txt + uses: actions/upload-artifact@v4 + with: + name: instructions + path: INSTRUCTIONS.txt + + build-wheels: + needs: [build-sdist, get-python-versions] + + name: Build wheels ${{ matrix.python }}-${{ matrix.buildplat }} + runs-on: ${{ matrix.buildplat }} + strategy: + fail-fast: false + matrix: + buildplat: + - ubuntu-latest + - macos-14 + - windows-latest + python: ${{ fromJSON(needs.get-python-versions.outputs.py_ver) }} + steps: + - name: Download sdist + # GitHub officially-maintained actions + uses: actions/download-artifact@v4 + with: + name: sdist + path: dist/ + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python }} + + - name: Build wheels + run: | + # setuptools-git-versioning only look into .git and PKG-INFO in the top directory + which python; python --version + which pip; pip --version + python -m pip install --upgrade pip build cython setuptools setuptools-git-versioning + tar xf dist/diffpy_distanceprinter-*.tar.gz + cd diffpy_distanceprinter-* + python -m pip wheel . --no-deps --no-build-isolation --wheel-dir ./../dist + + - name: Upload wheels + uses: actions/upload-artifact@v4 + with: + name: wheels-${{ matrix.python }}-${{ matrix.buildplat }} + path: dist/*.whl + + test-wheels: + needs: [build-wheels, get-python-versions] + + name: Test wheels ${{ matrix.python }}-${{ matrix.buildplat }} + runs-on: ${{ matrix.buildplat }} + strategy: + fail-fast: false + matrix: + buildplat: + - ubuntu-latest + - macos-14 + - windows-latest + python: ${{ fromJson(needs.get-python-versions.outputs.py_ver) }} + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Download wheels + uses: actions/download-artifact@v4 + with: + name: wheels-${{ matrix.python }}-${{ matrix.buildplat }} + path: dist/ + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python }} + + - name: Install wheels + run: | + python -m pip install --upgrade pip pytest setuptools-git-versioning + python -m pip install dist/*.whl + + - name: Assert no source files in installed package + run: | + # For debugging + # touch $(python -c "import sysconfig, os; print(os.path.join(sysconfig.get_paths()['purelib'], 'diffpy/distanceprinter', 'fake.py'))") + python - << 'EOF' + import os, glob, sys, sysconfig + sp = sysconfig.get_paths()['purelib'] + pkg = os.path.join(sp, 'diffpy', 'distanceprinter') + patterns = [os.path.join(pkg, '*.py'), + os.path.join(pkg, '*.c')] + bad = [] + for p in patterns: + bad.extend(glob.glob(p)) + + if bad: + print("Found leftover source files in installed package:") + for f in bad: + print(" -", f) + sys.exit(1) + + print("No .py or .c files present in diffpy/distanceprinter/") + EOF + + - name: Run tests + run: python -m pytest + + release: + needs: [test-wheels] + uses: ./.github/workflows/release-github.yml + secrets: + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} \ No newline at end of file From 581faa97823e129c01722989a734df0fac1668fe Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Thu, 9 Oct 2025 19:10:55 -0500 Subject: [PATCH 23/33] skpkg: remove codecov uses in workflows Signed-off-by: Dasun Abeykoon --- ...-to-main.yml => matrix-no-codecov-on-merge-to-main.yml} | 4 +--- .github/workflows/tests-on-pr.yml | 7 ++++--- 2 files changed, 5 insertions(+), 6 deletions(-) rename .github/workflows/{matrix-and-codecov-on-merge-to-main.yml => matrix-no-codecov-on-merge-to-main.yml} (75%) diff --git a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml b/.github/workflows/matrix-no-codecov-on-merge-to-main.yml similarity index 75% rename from .github/workflows/matrix-and-codecov-on-merge-to-main.yml rename to .github/workflows/matrix-no-codecov-on-merge-to-main.yml index ca02afa..48385d1 100644 --- a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml +++ b/.github/workflows/matrix-no-codecov-on-merge-to-main.yml @@ -12,10 +12,8 @@ on: jobs: matrix-coverage: - uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0 + uses: scikit-package/release-scripts/.github/workflows/_matrix-no-codecov-on-merge-to-main.yml@v0 with: project: diffpy.distanceprinter c_extension: false headless: false - secrets: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml index 4f1528b..7b4b312 100644 --- a/.github/workflows/tests-on-pr.yml +++ b/.github/workflows/tests-on-pr.yml @@ -6,10 +6,11 @@ on: jobs: tests-on-pr: - uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0 + uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr-no-codecov.yml@v0 with: project: diffpy.distanceprinter c_extension: false headless: false - secrets: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + run: | + conda install pre-commit + pre-commit run --all-files From 9e394cec6e89518e1aa04e9ce773fb3a16c35a46 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Thu, 9 Oct 2025 19:11:21 -0500 Subject: [PATCH 24/33] skpkg: add release-github.yml workflow Signed-off-by: Dasun Abeykoon --- .github/workflows/publish-docs-on-release.yml | 12 -- .github/workflows/release-github.yml | 163 ++++++++++++++++++ 2 files changed, 163 insertions(+), 12 deletions(-) delete mode 100644 .github/workflows/publish-docs-on-release.yml create mode 100644 .github/workflows/release-github.yml diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml deleted file mode 100644 index 6803e26..0000000 --- a/.github/workflows/publish-docs-on-release.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: Deploy Documentation on Release - -on: - workflow_dispatch: - -jobs: - docs: - uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0 - with: - project: diffpy.distanceprinter - c_extension: false - headless: false diff --git a/.github/workflows/release-github.yml b/.github/workflows/release-github.yml new file mode 100644 index 0000000..204d34c --- /dev/null +++ b/.github/workflows/release-github.yml @@ -0,0 +1,163 @@ +name: Release on GitHub + +on: + workflow_call: + secrets: + PAT_TOKEN: + description: "GitHub Personal Access Token" + required: true + +env: + TAG: ${{ github.ref_name }} + +defaults: + run: + shell: bash {0} + +jobs: + prepare-release: + if: ${{ ! contains(github.ref, 'rc') }} + runs-on: ubuntu-latest + steps: + - name: Checkout the repository + uses: actions/checkout@v4 + with: + token: ${{ secrets.GITHUB_TOKEN }} + fetch-depth: 0 + ref: main + + - name: Update CHANGELOG + run: | + wget https://raw.githubusercontent.com/scikit-package/release-scripts/v0/.github/workflows/update-changelog.py + python update-changelog.py "$TAG" + rm update-changelog.py + + - name: Commit updated CHANGELOG.rst + run: | + git config user.name "github-actions[bot]" + git config user.email "github-actions[bot]@users.noreply.github.com" + git add . + if ! git diff --cached --quiet; then + git commit -m "update changelog for $TAG" + git push origin main + else + echo "No CHANGELOG.rst changes" + fi + + - name: New tag + run: | + git fetch --tags + git tag -d "$TAG" 2>/dev/null || true + git push origin ":$TAG" 2>/dev/null || true + git tag "$TAG" + git push origin "$TAG" + + - name: Get CHANGELOG.txt + run: | + wget https://raw.githubusercontent.com/scikit-package/release-scripts/v0/.github/workflows/get-latest-changelog.py + python get-latest-changelog.py "$TAG" + rm get-latest-changelog.py + + - name: Upload changelog.txt + uses: actions/upload-artifact@v4 + with: + name: changelog + path: CHANGELOG.txt + + release: + needs: [prepare-release] + if: always() + runs-on: ubuntu-latest + env: + REPO_FULL: ${{ github.repository }} + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} + steps: + - name: Check prepare release + run: | + if [[ ${{ needs.prepare-release.result }} != 'success' && "$TAG" != *rc* ]]; then + echo "::error::Skipping release job because prepare-release failed" + exit 78 + fi + echo "Continuing with release job" + + - name: Download built wheels + uses: actions/download-artifact@v4 + with: + path: dist/ + + - name: Download changelog + if: ${{ needs.prepare-release.result == 'success' }} + uses: actions/download-artifact@v4 + with: + name: changelog + path: . + + - name: Download instructions + uses: actions/download-artifact@v4 + with: + name: instructions + path: . + + - name: Zip wheels and instructions into dist/distanceprinter-$TAG-wheels.zip + run: | + mkdir -p dist + find dist -type f -name '*.whl' | zip -j dist/distanceprinter-"$TAG"-wheels.zip -@ + zip -j dist/distanceprinter-"$TAG"-wheels.zip INSTRUCTIONS.txt + + - name: Prepare release metadata + id: meta + run: | + if [[ "$TAG" == *rc* ]]; then + PRERELEASE=true + TITLE="Pre-release $TAG" + BODY_RAW="Changelog: https://github.com/$REPO_FULL/commits/$TAG" + else + PRERELEASE=false + TITLE="Release $TAG" + BODY_RAW=$( payload.json + + echo "Release metadata:" + cat payload.json + + - name: Create GitHub Release + id: create_release + run: | + set -euo pipefail + + HTTP_STATUS=$( + curl --silent --output resp.json --write-out "%{http_code}" \ + -X POST "https://api.github.com/repos/$REPO_FULL/releases" \ + -H "Accept: application/vnd.github+json" \ + -H "Content-Type: application/json" \ + -H "Authorization: Bearer $PAT_TOKEN" \ + --data @payload.json + ) + if [[ "$HTTP_STATUS" -ne 201 ]]; then + echo "::error::Failed to create release (status $HTTP_STATUS)" + exit 1 + fi + + UPLOAD_URL=$(jq -r .upload_url resp.json | sed 's/{.*}//') + echo "upload_url=$UPLOAD_URL" >> $GITHUB_OUTPUT + + - name: Upload distanceprinter-$TAG-wheels.zip + if: steps.create_release.outputs.upload_url != '' + run: | + FILE=dist/distanceprinter-$TAG-wheels.zip + echo "Uploading asset: $FILE" + curl --silent --fail --data-binary @"$FILE" \ + -H "Content-Type: application/zip" \ + -H "Authorization: Bearer $PAT_TOKEN" \ + "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")" \ No newline at end of file From 635d035c72f94a395fecd32143e485b045b07b4c Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:50:53 -0500 Subject: [PATCH 25/33] skpkg: create temp doc directory Signed-off-by: Dasun Abeykoon --- docs/Makefile | 194 ++++++++++++ docs/make.bat | 36 +++ docs/source/_static/.placeholder | 0 docs/source/api/diffpy.distanceprinter.rst | 30 ++ docs/source/conf.py | 324 +++++++++++++++++++++ docs/source/release.rst | 5 + 6 files changed, 589 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/_static/.placeholder create mode 100644 docs/source/api/diffpy.distanceprinter.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/release.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..9d60f49 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,194 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build +BASENAME = $(subst .,,$(subst $() $(),,diffpy.distanceprinter)) + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(BASENAME).qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +# Manual publishing to the gh-pages branch + +GITREPOPATH = $(shell cd $(CURDIR) && git rev-parse --git-dir) +GITREMOTE = origin +GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url) +GITLASTCOMMIT = $(shell git rev-parse --short HEAD) + +publish: + @test -d build/html || \ + ( echo >&2 "Run 'make html' first!"; false ) + git show-ref --verify --quiet refs/heads/gh-pages || \ + git branch --track gh-pages $(GITREMOTE)/gh-pages + test -d build/gh-pages || \ + git clone -s -b gh-pages $(GITREPOPATH) build/gh-pages + cd build/gh-pages && \ + git pull $(GITREMOTEURL) gh-pages + rsync -acv --delete --exclude=.git --exclude=.rsync-exclude \ + --exclude-from=build/gh-pages/.rsync-exclude \ + --link-dest=$(CURDIR)/build/html build/html/ build/gh-pages/ + cd build/gh-pages && \ + git add --all . && \ + git diff --cached --quiet || \ + git commit -m "Sync with the source at $(GITLASTCOMMIT)." + cd build/gh-pages && \ + git push origin gh-pages diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..2be8306 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,36 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build +set SPHINXPROJ=PackagingScientificPython + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% + +:end +popd diff --git a/docs/source/_static/.placeholder b/docs/source/_static/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/docs/source/api/diffpy.distanceprinter.rst b/docs/source/api/diffpy.distanceprinter.rst new file mode 100644 index 0000000..ae0bb79 --- /dev/null +++ b/docs/source/api/diffpy.distanceprinter.rst @@ -0,0 +1,30 @@ +:tocdepth: -1 + +|title| +======= + +.. |title| replace:: diffpy.distanceprinter package + +.. automodule:: diffpy.distanceprinter + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + diffpy.distanceprinter.example_package + +Submodules +---------- + +|module| +-------- + +.. |module| replace:: diffpy.distanceprinter.example_submodule module + +.. automodule:: diffpy.distanceprinter.example_submodule + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..e797146 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,324 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# diffpy.distanceprinter documentation build configuration file, created by # noqa: E501 +# sphinx-quickstart on Thu Jan 30 15:49:41 2014. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import time +from importlib.metadata import version +from pathlib import Path + +# Attempt to import the version dynamically from GitHub tag. +try: + fullversion = version("diffpy.distanceprinter") +except Exception: + fullversion = "No version found. The correct version will appear in the released version." # noqa: E501 + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use Path().resolve() to make it absolute, like shown here. # noqa: E501 +# sys.path.insert(0, str(Path(".").resolve())) +sys.path.insert(0, str(Path("../..").resolve())) +sys.path.insert(0, str(Path("../../src").resolve())) + +# abbreviations +ab_authors = ( + "Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members" +) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinx_rtd_theme", + "sphinx_copybutton", + "m2r", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = [".rst", ".md"] + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "diffpy.distanceprinter" +copyright = "%Y, The Trustees of Columbia University in the City of New York" + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. + +# The short X.Y version. +version = "".join(fullversion.split(".post")[:1]) +# The full version, including alpha/beta/rc tags. +release = fullversion + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +today = time.strftime("%B %d, %Y", time.localtime()) +year = today.split()[-1] +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' +# substitute YEAR in the copyright string +copyright = copyright.replace("%Y", year) + +# For sphinx_copybutton extension. +# Do not copy "$" for shell commands in code-blocks. +copybutton_prompt_text = r"^\$ " +copybutton_prompt_is_regexp = True + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ["build"] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# A list of ignored prefixes for module index sorting. +modindex_common_prefix = ["diffpy.distanceprinter"] + +# Display all warnings for missing links. +nitpicky = True + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_rtd_theme" + +html_context = { + "display_github": True, + "github_user": "diffpy", + "github_repo": "diffpy.distanceprinter", + "github_version": "main", + "conf_py_path": "/docs/source/", +} + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# +html_theme_options = { + "navigation_with_keys": "true", +} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +# html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +basename = "diffpy.distanceprinter".replace(" ", "").replace(".", "") +htmlhelp_basename = basename + "doc" + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # 'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + # 'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + # 'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ( + "index", + "diffpy.distanceprinter.tex", + "diffpy.distanceprinter Documentation", + ab_authors, + "manual", + ), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ( + "index", + "diffpy.distanceprinter", + "diffpy.distanceprinter Documentation", + ab_authors, + 1, + ) +] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ( + "index", + "diffpy.distanceprinter", + "diffpy.distanceprinter Documentation", + ab_authors, + "diffpy.distanceprinter", + "One line description of project.", + "Miscellaneous", + ), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + + +# Example configuration for intersphinx: refer to the Python standard library. +# intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/docs/source/release.rst b/docs/source/release.rst new file mode 100644 index 0000000..27cd0cc --- /dev/null +++ b/docs/source/release.rst @@ -0,0 +1,5 @@ +:tocdepth: -1 + +.. index:: release notes + +.. include:: ../../CHANGELOG.rst From f561d7218159052014ecc0d17605afcb94bd68ac Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:51:40 -0500 Subject: [PATCH 26/33] skpkg: replace AUTHORS.txt with AUTHORS.rst Signed-off-by: Dasun Abeykoon --- AUTHORS.rst | 10 ++++++++++ AUTHORS.txt | 1 - 2 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 AUTHORS.rst delete mode 100644 AUTHORS.txt diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 0000000..68e8471 --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,10 @@ +Authors +======= + +Xiaohao Yang and Billinge Group members + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors diff --git a/AUTHORS.txt b/AUTHORS.txt deleted file mode 100644 index e36df7d..0000000 --- a/AUTHORS.txt +++ /dev/null @@ -1 +0,0 @@ -Xiaohao Yang From 4c43dee8825b834c4f38f2617e944e4eedadcd2c Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:52:47 -0500 Subject: [PATCH 27/33] skpkg: add CHANGELOG.rst and CODE-OF-CONDUCT.rst Signed-off-by: Dasun Abeykoon --- CHANGELOG.rst | 5 ++ CODE-OF-CONDUCT.rst | 133 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 138 insertions(+) create mode 100644 CHANGELOG.rst create mode 100644 CODE-OF-CONDUCT.rst diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 0000000..f29d3b5 --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,5 @@ +============= +Release notes +============= + +.. current developments diff --git a/CODE-OF-CONDUCT.rst b/CODE-OF-CONDUCT.rst new file mode 100644 index 0000000..e8199ca --- /dev/null +++ b/CODE-OF-CONDUCT.rst @@ -0,0 +1,133 @@ +===================================== + Contributor Covenant Code of Conduct +===================================== + +Our Pledge +---------- + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socioeconomic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +Our Standards +------------- + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +Enforcement Responsibilities +---------------------------- + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +Scope +----- + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +Enforcement +----------- + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +Enforcement Guidelines +---------------------- + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +1. Correction +**************** + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +2. Warning +************* + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +3. Temporary Ban +****************** + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +4. Permanent Ban +****************** + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +Attribution +----------- + +This Code of Conduct is adapted from the `Contributor Covenant `_. + +Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder `_. + +For answers to common questions about this code of conduct, see the `FAQ `_. `Translations are available `_ From dabccd621052d1ff2668724b2ab630bddcd5f529 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:53:44 -0500 Subject: [PATCH 28/33] doc: update README.rst with updated installation instructions, badges, and citations Signed-off-by: Dasun Abeykoon --- README.rst | 110 +++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 89 insertions(+), 21 deletions(-) diff --git a/README.rst b/README.rst index 15b7d2a..63b9120 100644 --- a/README.rst +++ b/README.rst @@ -1,34 +1,102 @@ -DistancePrinter -======================================================================== +|Icon| |title|_ +=============== -Software for calculating inter-atomic distance for given structure +.. |title| replace:: diffpy.distanceprinter +.. _title: https://diffpy.github.io/diffpy.distanceprinter +.. |Icon| image:: https://avatars.githubusercontent.com/diffpy + :target: https://diffpy.github.io/diffpy.distanceprinter + :height: 100px -REQUIREMENTS ------------------------------------------------------------------------- +|PythonVersion| |PR| -The DistancePrinter requires Python 2.7 and the following software: +|Black| |Tracking| -* ``diffpy.pdffit`` +.. |Black| image:: https://img.shields.io/badge/code_style-black-black + :target: https://github.com/psf/black -INSTALLATION ------------------------------------------------------------------------- +.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff + :target: https://github.com/diffpy/diffpy.distanceprinter/pulls -To install the DistancePrinter package: +.. |PythonVersion| image:: https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue + :target: https://pypi.org/project/diffpy.distanceprinter/ - python setup.py install +.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue + :target: https://github.com/diffpy/diffpy.distanceprinter/issues -By default the files are installed in the system directories, which are -usually only writeable by the root. See the usage info "./setup.py install ---help" for options to install as a normal user under a different location. -Note that installation to non-standard directories you may require adjustments -to the PATH and PYTHONPATH environment variables. +Distance Printer, calculate the inter atomic distances. Part of xPDFsuite -CONTACTS ------------------------------------------------------------------------- +Citation +-------- -For more information on diffpy.Structure please visit the project web-page +If you use diffpy.distanceprinter in a scientific publication, we would like you to cite this package as -http://www.diffpy.org/ + Xiaohao Yang, Pavol Juhas, Christopher L. Farrow and Simon J. L. Billinge, xPDFsuite: an end-to-end + software solution for high throughput pair distribution function transformation, visualization and + analysis, arXiv 1402.3163 (2014) -or email Prof. Simon Billinge at sb2896@columbia.edu. +Installation +------------ +``diffpy.distanceprinter`` is normally installed as part of the ``xpdfsuite`` software, so please refer to the +installation instructions detailed in the ``README.rst`` file of ``xpdfsuite`` `here `_. + +Independent Installation +------------------------ +You can also install ``diffpy.distanceprinter`` independently for yourself. + +Assuming you have a wheel file in the current working directory, in an active conda environment please type + + pip install ./diffpy.distanceprinter-VERSION.whl + +where you replace VERSION with the actual version you have so the command matches the filename of the +wheel file you have. + +The commands to create and activate the conda environment with name "conf-env" is + + conda create -n conf-env python=3.13 + conda activate conf-env + +If you don't have conda installed, we recomment you install `miniconda +`_ +To install this software from a Python wheel distribution format execute + + pip install ./diffpy.distanceprinter-VERSION.whl + +If you are a developer, you can also install this package from sources. First, obtain the source archive +from `GitHub `_. +Install the packages in ``./requirements/conda.txt`` and ``./requirements/tests.txt`` +using the `--file`` command: + + conda activate conf-env + conda install --file ./requirements/conda.txt + conda install --file ./requirements/tests.txt + pip install -e . # assuming you are in the top level directory of the package + +After installing the dependencies, ``cd`` into your ``diffpy.distanceprinter`` directory +and run the following :: + + pip install . + +This package also provides command-line utilities. To check the software has been installed correctly, type :: + + diffpy.distanceprinter --version + +You can also type the following command to verify the installation. :: + + python -c "import diffpy.distanceprinter; print(diffpy.distanceprinter.__version__)" + + +To view the basic usage and available commands, type :: + + diffpy.distanceprinter -h + + +Contact +------- + +For more information on diffpy.distanceprinter please visit the project `web-page `_ or email Simon J.L. Billinge Group at sb2896@columbia.edu. + +Acknowledgements +---------------- + +``diffpy.distanceprinter`` is built and maintained with `scikit-package `_. From ae732560b4fb19fbab9320bb0e896c8047392cbd Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:54:26 -0500 Subject: [PATCH 29/33] skpkg: add news files Signed-off-by: Dasun Abeykoon --- news/TEMPLATE.rst | 23 +++++++++++++++++++++++ news/doc.rst | 24 ++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 news/TEMPLATE.rst create mode 100644 news/doc.rst diff --git a/news/TEMPLATE.rst b/news/TEMPLATE.rst new file mode 100644 index 0000000..790d30b --- /dev/null +++ b/news/TEMPLATE.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/news/doc.rst b/news/doc.rst new file mode 100644 index 0000000..35c29f4 --- /dev/null +++ b/news/doc.rst @@ -0,0 +1,24 @@ +**Added:** + +* + +**Changed:** + +* Updated from Python 2.6-2.7 to Python 3.11-3.13 +* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/). + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From c2caa4eac7acced0563d1cce25869b6ea0395696 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:55:27 -0500 Subject: [PATCH 30/33] pre-commit: format workflow files Signed-off-by: Dasun Abeykoon --- .github/workflows/build-wheel-release.yml | 2 +- .github/workflows/release-github.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-wheel-release.yml b/.github/workflows/build-wheel-release.yml index 7691787..14c1dc3 100644 --- a/.github/workflows/build-wheel-release.yml +++ b/.github/workflows/build-wheel-release.yml @@ -227,4 +227,4 @@ jobs: needs: [test-wheels] uses: ./.github/workflows/release-github.yml secrets: - PAT_TOKEN: ${{ secrets.PAT_TOKEN }} \ No newline at end of file + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} diff --git a/.github/workflows/release-github.yml b/.github/workflows/release-github.yml index 204d34c..be9c891 100644 --- a/.github/workflows/release-github.yml +++ b/.github/workflows/release-github.yml @@ -160,4 +160,4 @@ jobs: curl --silent --fail --data-binary @"$FILE" \ -H "Content-Type: application/zip" \ -H "Authorization: Bearer $PAT_TOKEN" \ - "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")" \ No newline at end of file + "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")" From 225bcef0d40597f9ca9ccc89722c6ab22047c674 Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 17:58:02 -0500 Subject: [PATCH 31/33] doc: replace copyright year ranges to 2009-2025 Signed-off-by: Dasun Abeykoon --- LICENSENOTICE.txt | 2 +- README.rst | 2 +- docs/source/conf.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/LICENSENOTICE.txt b/LICENSENOTICE.txt index 68ada6a..c5cdb02 100644 --- a/LICENSENOTICE.txt +++ b/LICENSENOTICE.txt @@ -5,6 +5,6 @@ prohibited. If you don’t know whether or not your anticipated use is under a license, you must contact Prof. Simon Billinge at sb2896@columbia.edu. Use of this software without a license is prohibited. -Copyright 2009-2014, Trustees of Columbia University in the City of New York. +Copyright 2009-2025, Trustees of Columbia University in the City of New York. For more information please email Prof. Simon Billinge at sb2896@columbia.edu diff --git a/README.rst b/README.rst index 63b9120..bff2696 100644 --- a/README.rst +++ b/README.rst @@ -33,7 +33,7 @@ If you use diffpy.distanceprinter in a scientific publication, we would like you Xiaohao Yang, Pavol Juhas, Christopher L. Farrow and Simon J. L. Billinge, xPDFsuite: an end-to-end software solution for high throughput pair distribution function transformation, visualization and - analysis, arXiv 1402.3163 (2014) + analysis, arXiv 1402.3163 (2025) Installation ------------ diff --git a/docs/source/conf.py b/docs/source/conf.py index e797146..451aec0 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -2,7 +2,7 @@ # -*- coding: utf-8 -*- # # diffpy.distanceprinter documentation build configuration file, created by # noqa: E501 -# sphinx-quickstart on Thu Jan 30 15:49:41 2014. +# sphinx-quickstart on Thu Jan 30 15:49:41 2025. # # This file is execfile()d with the current directory set to its # containing dir. From 65ed969a61c0242b299f42a523c631dc4658a68d Mon Sep 17 00:00:00 2001 From: Dasun Abeykoon Date: Sun, 19 Oct 2025 18:35:30 -0500 Subject: [PATCH 32/33] tests: remove irrelevant whitespace from strings before comparing --- tests/test_distanceprinter.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py index c58d41b..f4c987a 100644 --- a/tests/test_distanceprinter.py +++ b/tests/test_distanceprinter.py @@ -49,4 +49,9 @@ def test_distanceprinter(monkeypatch): # Remove stru file path when comparing as it may differ between machines resultstr = resultstr.split("\n", 2)[2] teststr = teststr.split("\n", 2)[2] + + # Remove irrelevant whitespace when comparing + resultstr = "".join(resultstr.split()) + teststr = "".join(teststr.split()) + assert resultstr == teststr From 7c8e5e9989848e32d936a6c3aeae83eec04c5ca6 Mon Sep 17 00:00:00 2001 From: "Dasun L. Abeykoon" Date: Sun, 19 Oct 2025 19:37:15 -0500 Subject: [PATCH 33/33] doc: rename example conda env name to "distanceprinter-env" in install instructions --- README.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index bff2696..90cf3c6 100644 --- a/README.rst +++ b/README.rst @@ -51,10 +51,10 @@ Assuming you have a wheel file in the current working directory, in an active co where you replace VERSION with the actual version you have so the command matches the filename of the wheel file you have. -The commands to create and activate the conda environment with name "conf-env" is +The commands to create and activate the conda environment with name "distanceprinter-env" is - conda create -n conf-env python=3.13 - conda activate conf-env + conda create -n distanceprinter-env python=3.13 + conda activate distanceprinter-env If you don't have conda installed, we recomment you install `miniconda `_ @@ -67,7 +67,7 @@ from `GitHub `_. Install the packages in ``./requirements/conda.txt`` and ``./requirements/tests.txt`` using the `--file`` command: - conda activate conf-env + conda activate distanceprinter-env conda install --file ./requirements/conda.txt conda install --file ./requirements/tests.txt pip install -e . # assuming you are in the top level directory of the package