From 8063f0cb038db80a3dd05dd70e5a50acfe9e5296 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 9 Sep 2024 08:27:48 -0400 Subject: [PATCH 01/17] Move tests folder to top --- {src/diffpy/snmf/tests => tests}/__init__.py | 0 {src/diffpy/snmf/tests => tests}/conftest.py | 0 {src/diffpy/snmf/tests => tests}/debug.py | 0 {src/diffpy/snmf/tests => tests}/test_containers.py | 0 {src/diffpy/snmf/tests => tests}/test_factorizers.py | 0 {src/diffpy/snmf/tests => tests}/test_optimizers.py | 0 {src/diffpy/snmf/tests => tests}/test_polynomials.py | 0 {src/diffpy/snmf/tests => tests}/test_subroutines.py | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename {src/diffpy/snmf/tests => tests}/__init__.py (100%) rename {src/diffpy/snmf/tests => tests}/conftest.py (100%) rename {src/diffpy/snmf/tests => tests}/debug.py (100%) rename {src/diffpy/snmf/tests => tests}/test_containers.py (100%) rename {src/diffpy/snmf/tests => tests}/test_factorizers.py (100%) rename {src/diffpy/snmf/tests => tests}/test_optimizers.py (100%) rename {src/diffpy/snmf/tests => tests}/test_polynomials.py (100%) rename {src/diffpy/snmf/tests => tests}/test_subroutines.py (100%) diff --git a/src/diffpy/snmf/tests/__init__.py b/tests/__init__.py similarity index 100% rename from src/diffpy/snmf/tests/__init__.py rename to tests/__init__.py diff --git a/src/diffpy/snmf/tests/conftest.py b/tests/conftest.py similarity index 100% rename from src/diffpy/snmf/tests/conftest.py rename to tests/conftest.py diff --git a/src/diffpy/snmf/tests/debug.py b/tests/debug.py similarity index 100% rename from src/diffpy/snmf/tests/debug.py rename to tests/debug.py diff --git a/src/diffpy/snmf/tests/test_containers.py b/tests/test_containers.py similarity index 100% rename from src/diffpy/snmf/tests/test_containers.py rename to tests/test_containers.py diff --git a/src/diffpy/snmf/tests/test_factorizers.py b/tests/test_factorizers.py similarity index 100% rename from src/diffpy/snmf/tests/test_factorizers.py rename to tests/test_factorizers.py diff --git a/src/diffpy/snmf/tests/test_optimizers.py b/tests/test_optimizers.py similarity index 100% rename from src/diffpy/snmf/tests/test_optimizers.py rename to tests/test_optimizers.py diff --git a/src/diffpy/snmf/tests/test_polynomials.py b/tests/test_polynomials.py similarity index 100% rename from src/diffpy/snmf/tests/test_polynomials.py rename to tests/test_polynomials.py diff --git a/src/diffpy/snmf/tests/test_subroutines.py b/tests/test_subroutines.py similarity index 100% rename from src/diffpy/snmf/tests/test_subroutines.py rename to tests/test_subroutines.py From b643887c99a0ef3f79457d6ec3fd0e8cf6b14855 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 9 Sep 2024 08:38:20 -0400 Subject: [PATCH 02/17] Revert commit --- {tests => src/diffpy/snmf/tests}/__init__.py | 0 {tests => src/diffpy/snmf/tests}/conftest.py | 0 {tests => src/diffpy/snmf/tests}/debug.py | 0 {tests => src/diffpy/snmf/tests}/test_containers.py | 0 {tests => src/diffpy/snmf/tests}/test_factorizers.py | 0 {tests => src/diffpy/snmf/tests}/test_optimizers.py | 0 {tests => src/diffpy/snmf/tests}/test_polynomials.py | 0 {tests => src/diffpy/snmf/tests}/test_subroutines.py | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename {tests => src/diffpy/snmf/tests}/__init__.py (100%) rename {tests => src/diffpy/snmf/tests}/conftest.py (100%) rename {tests => src/diffpy/snmf/tests}/debug.py (100%) rename {tests => src/diffpy/snmf/tests}/test_containers.py (100%) rename {tests => src/diffpy/snmf/tests}/test_factorizers.py (100%) rename {tests => src/diffpy/snmf/tests}/test_optimizers.py (100%) rename {tests => src/diffpy/snmf/tests}/test_polynomials.py (100%) rename {tests => src/diffpy/snmf/tests}/test_subroutines.py (100%) diff --git a/tests/__init__.py b/src/diffpy/snmf/tests/__init__.py similarity index 100% rename from tests/__init__.py rename to src/diffpy/snmf/tests/__init__.py diff --git a/tests/conftest.py b/src/diffpy/snmf/tests/conftest.py similarity index 100% rename from tests/conftest.py rename to src/diffpy/snmf/tests/conftest.py diff --git a/tests/debug.py b/src/diffpy/snmf/tests/debug.py similarity index 100% rename from tests/debug.py rename to src/diffpy/snmf/tests/debug.py diff --git a/tests/test_containers.py b/src/diffpy/snmf/tests/test_containers.py similarity index 100% rename from tests/test_containers.py rename to src/diffpy/snmf/tests/test_containers.py diff --git a/tests/test_factorizers.py b/src/diffpy/snmf/tests/test_factorizers.py similarity index 100% rename from tests/test_factorizers.py rename to src/diffpy/snmf/tests/test_factorizers.py diff --git a/tests/test_optimizers.py b/src/diffpy/snmf/tests/test_optimizers.py similarity index 100% rename from tests/test_optimizers.py rename to src/diffpy/snmf/tests/test_optimizers.py diff --git a/tests/test_polynomials.py b/src/diffpy/snmf/tests/test_polynomials.py similarity index 100% rename from tests/test_polynomials.py rename to src/diffpy/snmf/tests/test_polynomials.py diff --git a/tests/test_subroutines.py b/src/diffpy/snmf/tests/test_subroutines.py similarity index 100% rename from tests/test_subroutines.py rename to src/diffpy/snmf/tests/test_subroutines.py From af43e58b78b72e0b4112cb2d9981a67e254282f4 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:21:53 -0400 Subject: [PATCH 03/17] Add codecov, remove gitattributes --- .codecov.yml | 2 +- .coveragerc | 4 ++-- .gitattributes | 1 - .github/workflows/check-news-item.yml | 2 +- .github/workflows/matrix-and-codecov-on-merge-to-main.yml | 2 +- .github/workflows/publish-docs-on-release.yml | 2 +- .github/workflows/tests-on-pr.yml | 2 +- 7 files changed, 7 insertions(+), 8 deletions(-) delete mode 100644 .gitattributes diff --git a/.codecov.yml b/.codecov.yml index 03afe9c..04dd651 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -20,7 +20,7 @@ coverage: target: auto if_no_uploads: error if_not_found: success - if_ci_failed: failure + if_ci_failed: error paths: '!*/tests/.*' tests: diff --git a/.coveragerc b/.coveragerc index fa3fa52..67cad8f 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,12 +1,12 @@ [run] source = - src + diffpy.snmf [report] omit = */python?.?/* */site-packages/nose/* # ignore _version.py and versioneer.py - *version.* + .*version.* *_version.py exclude_lines = diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 42fce5f..0000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -diffpy.snmf/_version.py export-subst diff --git a/.github/workflows/check-news-item.yml b/.github/workflows/check-news-item.yml index 3513cb3..2f95151 100644 --- a/.github/workflows/check-news-item.yml +++ b/.github/workflows/check-news-item.yml @@ -6,7 +6,7 @@ on: - main jobs: - check-news-item: + build: uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0 with: project: diffpy.snmf diff --git a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml index e9e742d..4f8649e 100644 --- a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml +++ b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml @@ -11,7 +11,7 @@ on: workflow_dispatch: jobs: - CI: + coverage: uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0 with: project: diffpy.snmf diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml index 098a344..3a4e7db 100644 --- a/.github/workflows/publish-docs-on-release.yml +++ b/.github/workflows/publish-docs-on-release.yml @@ -7,7 +7,7 @@ on: workflow_dispatch: jobs: - publish-docs-on-release: + docs: uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0 with: project: diffpy.snmf diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml index 988d86b..1e147a1 100644 --- a/.github/workflows/tests-on-pr.yml +++ b/.github/workflows/tests-on-pr.yml @@ -8,7 +8,7 @@ on: workflow_dispatch: jobs: - tests-on-pr: + validate: uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0 with: project: diffpy.snmf From befe7f1d2b3c79f97a4463261a54905cae350fa7 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:22:48 -0400 Subject: [PATCH 04/17] Add test tests --- 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..eccc3cf --- /dev/null +++ b/tests/test_version.py @@ -0,0 +1,10 @@ +"""Unit tests for __version__.py +""" + +import diffpy.snmf + + +def test_package_version(): + """Ensure the package version is defined and not set to the initial placeholder.""" + assert hasattr(diffpy.snmf, "__version__") + assert diffpy.snmf.__version__ != "0.0.0" From f1ce5831b9faed6679b6f2748640b7063b2a098e Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:23:06 -0400 Subject: [PATCH 05/17] Add .gitignore and precommit --- .gitignore | 61 +++++++++++++++++++++-------------------- .pre-commit-config.yaml | 5 +++- 2 files changed, 36 insertions(+), 30 deletions(-) diff --git a/.gitignore b/.gitignore index 36ed155..a25212e 100644 --- a/.gitignore +++ b/.gitignore @@ -20,9 +20,14 @@ lib64/ parts/ sdist/ var/ +venv/ *.egg-info/ .installed.cfg *.egg +bin/ +temp/ +tags/ +errors.err # PyInstaller # Usually these files are written by a python script from a template @@ -33,6 +38,7 @@ var/ # Installer logs pip-log.txt pip-delete-this-directory.txt +MANIFEST # Unit test / coverage reports htmlcov/ @@ -49,48 +55,45 @@ coverage.xml *.mo *.pot +# Mr Developer +.mr.developer.cfg +.project +.pydevproject + # Django stuff: *.log -local_settings.py - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy # Sphinx documentation -docs/_build/ +docs/build/ +docs/source/generated/ + +# pytest +.pytest_cache/ # PyBuilder target/ -# IPython Notebook -.ipynb_checkpoints - -# pyenv -.python-version +# Editor files +# mac +.DS_Store +*~ -# celery beat schedule file -celerybeat-schedule +# vim +*.swp +*.swo -# dotenv -.env +# pycharm +.idea/ -# virtualenv -venv/ -ENV/ +# VSCode +.vscode/ -# Spyder project settings -.spyderproject +# Ipython Notebook +.ipynb_checkpoints -# Rope project settings -.ropeproject +# version information +setup.cfg +/src/diffpy/*/version.cfg -# pycharm -.idea/ -# Mac -.DS_Store # Rever rever/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c458806..3070e19 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,7 +16,10 @@ repos: - id: check-yaml - id: end-of-file-fixer - id: trailing-whitespace - exclude: '\.(rst|txt)$' + - 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: From 598941642f28bc794500c50b8a4bed49f0dda287 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:23:47 -0400 Subject: [PATCH 06/17] Add MANIFEST --- MANIFEST.in | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/MANIFEST.in b/MANIFEST.in index 7371063..f1a78ee 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,14 +1,12 @@ -include AUTHORS.rst -include LICENSE -include README.rst -include requirements.txt - -recursive-exclude * __pycache__ -recursive-exclude * *.py[co] - -recursive-include docs *.rst conf.py Makefile make.bat - -include diffpy.snmf/version.py - -# If including data files in the package, add them like: -# include path/to/data_file +graft src +graft tests +graft requirements + +include AUTHORS.rst LICENSE*.rst README.rst + +# Exclude all bytecode files and __pycache__ directories +global-exclude *.py[cod] # Exclude all .pyc, .pyo, and .pyd files. +global-exclude .DS_Store # Exclude Mac filesystem artifacts. +global-exclude __pycache__ # Exclude Python cache directories. +global-exclude .git* # Exclude git files and directories. +global-exclude .idea # Exclude PyCharm project settings. From ea44a82b093bacb1655bd724e9da6cfa4e599d19 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:24:26 -0400 Subject: [PATCH 07/17] Add pyproject.toml --- pyproject.toml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1250363..f12b200 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,10 @@ [build-system] -requires = ["setuptools>=62.0", "setuptools-git-versioning<2"] +requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"] build-backend = "setuptools.build_meta" [project] name = "diffpy.snmf" -dynamic=['version'] +dynamic=['version', 'dependencies'] authors = [ { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" }, ] @@ -45,9 +45,12 @@ dirty_template = "{tag}" [tool.setuptools.packages.find] where = ["src"] # list of folders that contain the packages (["."] by default) include = ["*"] # package names should match these glob patterns (["*"] by default) -exclude = ["diffpy.snmf.tests*"] # exclude packages matching these glob patterns (empty 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/run.txt"]} + [tool.black] line-length = 115 include = '\.pyi?$' From 45c4bfb7e19a92548a462543cf1ef439c9a3e750 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:24:42 -0400 Subject: [PATCH 08/17] Add authors --- AUTHORS.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AUTHORS.rst b/AUTHORS.rst index 6736f65..4546e68 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -1,7 +1,7 @@ Authors ======= -Billinge Group and community contibutors. +Billinge Group and community contributors. Contributors ------------ From 8d34cb9ed5e679d60cf8cd929b5e2ae3f5067c65 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:26:03 -0400 Subject: [PATCH 09/17] Add requirements --- requirements/build.txt | 2 -- requirements/test.txt | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/requirements/build.txt b/requirements/build.txt index f72d870..e69de29 100644 --- a/requirements/build.txt +++ b/requirements/build.txt @@ -1,2 +0,0 @@ -python -setuptools diff --git a/requirements/test.txt b/requirements/test.txt index f33bd0e..a727786 100644 --- a/requirements/test.txt +++ b/requirements/test.txt @@ -2,5 +2,5 @@ flake8 pytest codecov coverage -pytest-env pytest-cov +pytest-env From 9caa2fdc086f0bdee14bbc782d711702bdede897 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:27:43 -0400 Subject: [PATCH 10/17] Add readme --- README.rst | 10 +++------- src/diffpy/__init__.py | 1 + 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/README.rst b/README.rst index 83998e5..d857c56 100644 --- a/README.rst +++ b/README.rst @@ -15,8 +15,8 @@ .. |Black| image:: https://img.shields.io/badge/code_style-black-black :target: https://github.com/psf/black -.. |CI| image:: https://github.com/diffpy/diffpy.snmf/actions/workflows/main.yml/badge.svg - :target: https://github.com/diffpy/diffpy.snmf/actions/workflows/main.yml +.. |CI| image:: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg + :target: https://github.com/diffpy/diffpy.snmf/actions/workflows/matrix-and-codecov-on-merge-to-main.yml .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.snmf/branch/main/graph/badge.svg :target: https://codecov.io/gh/diffpy/diffpy.snmf @@ -83,11 +83,7 @@ Then, to fully install ``diffpy.snmf`` in our active environment, run :: Another option is to use ``pip`` to download and install the latest release from `Python Package Index `_. -To install using ``pip`` into your ``diffpy.snmf_env`` environment, we will also have to install dependencies :: - - pip install -r https://raw.githubusercontent.com/diffpy/diffpy.snmf/main/requirements/run.txt - -and then install the package :: +To install using ``pip`` into your ``diffpy.snmf_env`` environment, type :: pip install diffpy.snmf diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py index 2baa1ea..8fdf7af 100644 --- a/src/diffpy/__init__.py +++ b/src/diffpy/__init__.py @@ -21,3 +21,4 @@ __path__ = extend_path(__path__, __name__) # End of file + From 4837baa6d26c6d0913801ed846ff94f92a911458 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:34:08 -0400 Subject: [PATCH 11/17] Add doc --- doc/make.bat | 72 +++++++++++++++++----------------- doc/source/api/diffpy.snmf.rst | 1 + doc/source/conf.py | 2 +- doc/source/license.rst | 2 +- doc/source/release.rst | 4 +- 5 files changed, 42 insertions(+), 39 deletions(-) diff --git a/doc/make.bat b/doc/make.bat index 2be8306..ac53d5b 100644 --- a/doc/make.bat +++ b/doc/make.bat @@ -1,36 +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 +@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/doc/source/api/diffpy.snmf.rst b/doc/source/api/diffpy.snmf.rst index 9a808f6..7ece036 100644 --- a/doc/source/api/diffpy.snmf.rst +++ b/doc/source/api/diffpy.snmf.rst @@ -66,3 +66,4 @@ diffpy.snmf.stretchednmfapp module :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/conf.py b/doc/source/conf.py index 195ee2f..eea3def 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -62,7 +62,7 @@ # General information about the project. project = "diffpy.snmf" -copyright = "2023-%Y, The Trustees of Columbia University in the City of New York" +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 diff --git a/doc/source/license.rst b/doc/source/license.rst index 2dd9469..cfab61c 100644 --- a/doc/source/license.rst +++ b/doc/source/license.rst @@ -9,7 +9,7 @@ OPEN SOURCE LICENSE AGREEMENT ============================= BSD 3-Clause License -Copyright (c) 2023-2024, The Trustees of Columbia University in +Copyright (c) 2024, The Trustees of Columbia University in the City of New York. All Rights Reserved. diff --git a/doc/source/release.rst b/doc/source/release.rst index 8956c78..27cd0cc 100644 --- a/doc/source/release.rst +++ b/doc/source/release.rst @@ -1,3 +1,5 @@ +:tocdepth: -1 + .. index:: release notes -.. include:: /../../CHANGELOG.rst +.. include:: ../../CHANGELOG.rst From 52eee4f6d2ab7eba32ed84c24c9ee8ba79bc72a4 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:36:58 -0400 Subject: [PATCH 12/17] Add 2023 to copyright in doc --- doc/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index eea3def..195ee2f 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -62,7 +62,7 @@ # General information about the project. project = "diffpy.snmf" -copyright = "%Y, The Trustees of Columbia University in the City of New York" +copyright = "2023-%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 From 65b27049f3a5ac382d82944672da010a1cfdf57b Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:37:31 -0400 Subject: [PATCH 13/17] Add 2023 to license.rst --- doc/source/license.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/license.rst b/doc/source/license.rst index cfab61c..2dd9469 100644 --- a/doc/source/license.rst +++ b/doc/source/license.rst @@ -9,7 +9,7 @@ OPEN SOURCE LICENSE AGREEMENT ============================= BSD 3-Clause License -Copyright (c) 2024, The Trustees of Columbia University in +Copyright (c) 2023-2024, The Trustees of Columbia University in the City of New York. All Rights Reserved. From 0563da235d114d25139275e407d6b0d26a7a7419 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 26 Sep 2024 01:41:59 +0000 Subject: [PATCH 14/17] [pre-commit.ci] auto fixes from pre-commit hooks --- README.rst | 2 +- doc/source/api/diffpy.snmf.rst | 1 - doc/source/index.rst | 4 ++-- doc/source/license.rst | 4 ++-- src/diffpy/__init__.py | 1 - 5 files changed, 5 insertions(+), 7 deletions(-) diff --git a/README.rst b/README.rst index d857c56..c30f8cf 100644 --- a/README.rst +++ b/README.rst @@ -98,7 +98,7 @@ Support and Contribute `Diffpy user group `_ is the discussion forum for general questions and discussions about the use of diffpy.snmf. Please join the diffpy.snmf users community by joining the Google group. The diffpy.snmf project welcomes your expertise and enthusiasm! -If you see a bug or want to request a feature, please `report it as an issue `_ and/or `submit a fix as a PR `_. You can also post it to the `Diffpy user group `_. +If you see a bug or want to request a feature, please `report it as an issue `_ and/or `submit a fix as a PR `_. You can also post it to the `Diffpy user group `_. Feel free to fork the project and contribute. To install diffpy.snmf in a development mode, with its sources being directly used by Python diff --git a/doc/source/api/diffpy.snmf.rst b/doc/source/api/diffpy.snmf.rst index 7ece036..9a808f6 100644 --- a/doc/source/api/diffpy.snmf.rst +++ b/doc/source/api/diffpy.snmf.rst @@ -66,4 +66,3 @@ diffpy.snmf.stretchednmfapp module :members: :undoc-members: :show-inheritance: - diff --git a/doc/source/index.rst b/doc/source/index.rst index 39fa0d3..b7755b0 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -2,7 +2,7 @@ Welcome to SNMF's Documentation! ==================================== ``SNMF``: This library implements the stretched non negative matrix factorization (sNMF) and sparse stretched NMF -(ssNMF) algorithms described in the paper "Stretched Non-negative Matrix Factorization" by Ran Gu et al. (2023), +(ssNMF) algorithms described in the paper "Stretched Non-negative Matrix Factorization" by Ran Gu et al. (2023), which is referenced under the Citation section below. This algorithm is designed to do an NMF factorization on a set of signals ignoring any uniform stretching of the signal @@ -63,7 +63,7 @@ Jame R. Neilson, Karena W. Chapman, Qiang Du, and Simon J. L. Billinge. This software implementation was developed by members of the Billinge Group at Columbia University and Brookhaven National Laboratory including Ran Gu, Adeolu Ajayi, Qiang Du, and Simon J. L. Billinge. -For a detailed list of contributors, check `here +For a detailed list of contributors, check `here `_. To get started, please go to :ref:`quick_start` diff --git a/doc/source/license.rst b/doc/source/license.rst index 2dd9469..573ccaf 100644 --- a/doc/source/license.rst +++ b/doc/source/license.rst @@ -9,9 +9,9 @@ OPEN SOURCE LICENSE AGREEMENT ============================= BSD 3-Clause License -Copyright (c) 2023-2024, The Trustees of Columbia University in +Copyright (c) 2023-2024, The Trustees of Columbia University in the City of New York. -All Rights Reserved. +All Rights Reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py index 8fdf7af..2baa1ea 100644 --- a/src/diffpy/__init__.py +++ b/src/diffpy/__init__.py @@ -21,4 +21,3 @@ __path__ = extend_path(__path__, __name__) # End of file - From 45c799cce3baf53dbf8b6131079b92d4fdefc72e Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:42:36 -0400 Subject: [PATCH 15/17] Add newds --- news/recut.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/recut.rst diff --git a/news/recut.rst b/news/recut.rst new file mode 100644 index 0000000..25a14db --- /dev/null +++ b/news/recut.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* re-cookiecuter repo to groupd's package standard + +**Security:** + +* From a5d2374a62e8661aa0642b0c78da9fe526cdaa90 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:47:20 -0400 Subject: [PATCH 16/17] Remove null in matrix codecov --- .github/workflows/matrix-and-codecov-on-merge-to-main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml index 4f8649e..670c2e9 100644 --- a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml +++ b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml @@ -8,7 +8,7 @@ on: types: - prereleased - published - workflow_dispatch: + workflow_dispatch: null jobs: coverage: From e964752eddca5b973b6200f5b74a6bdba2a9026e Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Wed, 25 Sep 2024 21:48:29 -0400 Subject: [PATCH 17/17] Remove null in matrix --- .github/workflows/matrix-and-codecov-on-merge-to-main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml index 670c2e9..4f8649e 100644 --- a/.github/workflows/matrix-and-codecov-on-merge-to-main.yml +++ b/.github/workflows/matrix-and-codecov-on-merge-to-main.yml @@ -8,7 +8,7 @@ on: types: - prereleased - published - workflow_dispatch: null + workflow_dispatch: jobs: coverage: