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GGitHubModernize build system, release process and pin Cython version (#155)

7bab71a2创建于 2025年5月19日历史提交

文件	最后提交记录	最后更新时间
api	p3helpers.pyx houses new sequence and design helper functions Sequence sanitization of IUPAC non-{A,C,G,T,a,c,g,t} bases become {N, n} and also reverse complement added. Separate methods exist for byte strings and unicode strings with error handling documentation update for p3helpers.pyx	3 年前
Makefile	big build-out of documentation; moved cython files from src to primer3 module directory; remove coveralls.io support (does not support cython, so is of limited usefulness)	11 年前
changes_link.md	update pass for `README`, `CHANGES`, `quickstart`, `miscellany` and `index` documentation for 1.0.0 staging updates to `howtobuild.md` and `cython_help.md` for better Markdown formatting Migrated docs to MyST for sphinx Markdown. `CHANGES` and `changes.md` are now pre-prended. Sphinx Docs support type hinting via sphinx-autodoc-typehints Made it consistent that primer3-py supports Python 3.8+ and not 3.7 or Python 2 Added a ReST `include` link to top level `CHANGES` file to get rid of duplicate file for maintenance that is, `changes.rst` is now `changes_link.md` .gitignore update `__version__` string in `__init__.py` file is the unified source of version truth now until a possible SCM versioning update added `.github/workflows/update-docs.yml` to build docs when a new version tag is pushed line length style updates for `thermoanalysis.pyx`	3 年前
conf.py	update pass for `README`, `CHANGES`, `quickstart`, `miscellany` and `index` documentation for 1.0.0 staging updates to `howtobuild.md` and `cython_help.md` for better Markdown formatting Migrated docs to MyST for sphinx Markdown. `CHANGES` and `changes.md` are now pre-prended. Sphinx Docs support type hinting via sphinx-autodoc-typehints Made it consistent that primer3-py supports Python 3.8+ and not 3.7 or Python 2 Added a ReST `include` link to top level `CHANGES` file to get rid of duplicate file for maintenance that is, `changes.rst` is now `changes_link.md` .gitignore update `__version__` string in `__init__.py` file is the unified source of version truth now until a possible SCM versioning update added `.github/workflows/update-docs.yml` to build docs when a new version tag is pushed line length style updates for `thermoanalysis.pyx`	3 年前
cython_help.md	2.0.0 release (#113) * migrated primer3 header file Cython extern imports to `thermoanalysis.pxi` (#100) Optional C structure string argument `c_ascii_structure` added to `_ThermoAnalysis` methods to enable 3rd party use for structures version bump to 2.0.0a1 due to breaking change * fix for issue 108 whereby no_structure is not correctly 1 set to 1 when no secondary structure in found (#109) * Issue 50 update to add list version of (#110) PRIMER_{PAIR, LEFT, RIGHT, INTERNAL} output dictionary keys. Retaining original keys as well for compatibility version bump to 2.0.0 updated CHANGES and cython_help.md for a note about the `c_ascii_structure` argument Consistent free of `c_ascii_structure` in thermoanalysis.pyx methods * fixes missing `thal_result.sec_struct` and `dpal_results.sec_struct` (#112) initialization to `NULL` in `recalc_primer_sec_struct` in `libprimer3.c` and `libprimer3flex.c`. `CHANGES` updated * doc string update for _ThermoAnalysis.run_design for new list based keys	3 年前
development.md	Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in	1 年前
index.md	Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in	1 年前
make.bat	big build-out of documentation; moved cython files from src to primer3 module directory; remove coveralls.io support (does not support cython, so is of limited usefulness)	11 年前
miscellany.md	Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in	1 年前
quickstart.md	Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in	1 年前