From dc9a57d5466404d8bf128902e4c5afbd484aac8e Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Sat, 19 Jul 2025 14:03:37 -0400 Subject: [PATCH 1/5] fix: license designation in pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3bdcbb03..fbbe0c3e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ classifiers = [ 'Environment :: Console', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', + 'License :: Free To Use But Restricted', 'Operating System :: MacOS :: MacOS X', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', From 6828d6c7117aecba0220f0561face4fed3237d9b Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Sat, 19 Jul 2025 14:07:51 -0400 Subject: [PATCH 2/5] fix: doc -> docs per latest group standards --- .flake8 | 2 +- .readthedocs.yaml | 2 +- {doc => docs}/Makefile | 0 {doc => docs}/examples/README | 2 +- {doc => docs}/examples/coreshellnp.py | 0 {doc => docs}/examples/crystalpdf.py | 0 {doc => docs}/examples/crystalpdfall.py | 0 {doc => docs}/examples/crystalpdfobjcryst.py | 0 {doc => docs}/examples/crystalpdftwodata.py | 0 {doc => docs}/examples/crystalpdftwophase.py | 0 {doc => docs}/examples/data/C60.gr | 0 {doc => docs}/examples/data/C60.stru | 0 {doc => docs}/examples/data/CdS.cif | 0 {doc => docs}/examples/data/CdS_ZnS_nano.gr | 0 {doc => docs}/examples/data/ZnS.cif | 0 {doc => docs}/examples/data/gaussian.dat | 0 {doc => docs}/examples/data/lorentzian.dat | 0 {doc => docs}/examples/data/ni-q27r100-neutron.gr | 0 {doc => docs}/examples/data/ni-q27r60-xray.gr | 0 {doc => docs}/examples/data/ni-q27r60nodg-xray.gr | 0 {doc => docs}/examples/data/ni.cif | 0 {doc => docs}/examples/data/ni.iq | 0 {doc => docs}/examples/data/pb.cif | 0 {doc => docs}/examples/data/pb_100.xyz | 0 {doc => docs}/examples/data/pb_100_qmax1.iq | 0 {doc => 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docs}/source/_static/.placeholder | 0 {doc => docs}/source/api/.placeholder | 0 .../source/api/diffpy.srfit.equation.literals.rst | 0 {doc => docs}/source/api/diffpy.srfit.equation.rst | 0 .../source/api/diffpy.srfit.equation.visitors.rst | 0 .../source/api/diffpy.srfit.example_package.rst | 0 {doc => docs}/source/api/diffpy.srfit.fitbase.rst | 0 {doc => docs}/source/api/diffpy.srfit.interface.rst | 0 {doc => docs}/source/api/diffpy.srfit.pdf.rst | 0 {doc => docs}/source/api/diffpy.srfit.rst | 0 {doc => docs}/source/api/diffpy.srfit.sas.rst | 0 {doc => docs}/source/api/diffpy.srfit.structure.rst | 0 {doc => docs}/source/api/diffpy.srfit.util.rst | 0 {doc => docs}/source/conf.py | 2 +- {doc => docs}/source/examples.rst | 0 {doc => docs}/source/examples/coreshellnp.rst | 0 {doc => docs}/source/examples/crystalpdf.rst | 0 {doc => docs}/source/examples/crystalpdfall.rst | 0 .../source/examples/crystalpdfobjcryst.rst | 0 {doc => docs}/source/examples/crystalpdftwodata.rst | 0 .../source/examples/crystalpdftwophase.rst | 0 {doc => docs}/source/examples/debyemodel.rst | 0 {doc => docs}/source/examples/debyemodelII.rst | 0 {doc => docs}/source/examples/ellipsoidsas.rst | 0 {doc => docs}/source/examples/gaussiangenerator.rst | 0 {doc => docs}/source/examples/gaussianrecipe.rst | 0 {doc => docs}/source/examples/interface.rst | 0 {doc => docs}/source/examples/npintensity.rst | 0 {doc => docs}/source/examples/npintensityII.rst | 0 {doc => docs}/source/examples/nppdfcrystal.rst | 0 {doc => docs}/source/examples/nppdfobjcryst.rst | 0 {doc => docs}/source/examples/nppdfsas.rst | 0 {doc => docs}/source/examples/simplepdf.rst | 0 {doc => docs}/source/examples/simplepdftwophase.rst | 0 {doc => docs}/source/examples/simplerecipe.rst | 0 {doc => docs}/source/extending.rst | 0 {doc => docs}/source/img/.placeholder | 0 {doc => docs}/source/img/fitting_architecture.dia | Bin {doc => docs}/source/img/fitting_architecture.png | Bin {doc => docs}/source/img/overview.odg | Bin {doc => docs}/source/img/partition_equation.dia | Bin {doc => docs}/source/img/partition_equation.png | Bin {doc => docs}/source/img/simple_equation.dia | Bin {doc => docs}/source/img/simple_equation.png | Bin {doc => docs}/source/img/visitor_interaction.dia | Bin {doc => docs}/source/img/visitor_interaction.png | Bin {doc => docs}/source/index.rst | 0 {doc => docs}/source/license.rst | 0 {doc => docs}/source/release.rst | 0 {doc => docs}/source/snippets/.placeholder | 0 97 files changed, 4 insertions(+), 4 deletions(-) rename {doc => docs}/Makefile (100%) rename {doc => docs}/examples/README (98%) rename {doc => docs}/examples/coreshellnp.py (100%) rename {doc => docs}/examples/crystalpdf.py (100%) rename {doc => docs}/examples/crystalpdfall.py (100%) rename {doc => docs}/examples/crystalpdfobjcryst.py (100%) rename {doc => docs}/examples/crystalpdftwodata.py (100%) rename {doc => docs}/examples/crystalpdftwophase.py (100%) rename {doc => docs}/examples/data/C60.gr (100%) rename {doc 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docs}/source/snippets/.placeholder (100%) diff --git a/.flake8 b/.flake8 index 7b2865c1..88077af0 100644 --- a/.flake8 +++ b/.flake8 @@ -6,7 +6,7 @@ exclude = __pycache__, build, dist, - doc/source/conf.py + 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 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 47f7a017..aaa88895 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,4 +10,4 @@ python: - requirements: requirements/docs.txt sphinx: - configuration: doc/source/conf.py + configuration: docs/source/conf.py diff --git a/doc/Makefile b/docs/Makefile similarity index 100% rename from doc/Makefile rename to docs/Makefile diff --git a/doc/examples/README b/docs/examples/README similarity index 98% rename from doc/examples/README rename to docs/examples/README index 92b43cb0..a48a5705 100644 --- a/doc/examples/README +++ b/docs/examples/README @@ -48,7 +48,7 @@ The examples described below will go into detail about each of these points. ## Examples -The following examples are contained in the _doc/examples/_ directory of the +The following examples are contained in the _docs/examples/_ directory of the SrFit source distribution. They can be downloaded from http://dev.danse.us/packages/srfit_examples-alpha9.zip diff --git a/doc/examples/coreshellnp.py b/docs/examples/coreshellnp.py similarity index 100% rename from doc/examples/coreshellnp.py rename to docs/examples/coreshellnp.py diff --git a/doc/examples/crystalpdf.py b/docs/examples/crystalpdf.py similarity index 100% rename from doc/examples/crystalpdf.py rename to docs/examples/crystalpdf.py diff --git a/doc/examples/crystalpdfall.py b/docs/examples/crystalpdfall.py similarity index 100% rename from doc/examples/crystalpdfall.py rename to docs/examples/crystalpdfall.py diff --git a/doc/examples/crystalpdfobjcryst.py b/docs/examples/crystalpdfobjcryst.py similarity index 100% rename from doc/examples/crystalpdfobjcryst.py rename to docs/examples/crystalpdfobjcryst.py diff --git a/doc/examples/crystalpdftwodata.py b/docs/examples/crystalpdftwodata.py similarity index 100% rename from doc/examples/crystalpdftwodata.py rename to docs/examples/crystalpdftwodata.py diff --git a/doc/examples/crystalpdftwophase.py b/docs/examples/crystalpdftwophase.py similarity index 100% rename from doc/examples/crystalpdftwophase.py rename to docs/examples/crystalpdftwophase.py diff --git a/doc/examples/data/C60.gr b/docs/examples/data/C60.gr similarity index 100% rename from doc/examples/data/C60.gr rename to docs/examples/data/C60.gr diff --git a/doc/examples/data/C60.stru b/docs/examples/data/C60.stru similarity index 100% rename from doc/examples/data/C60.stru rename to docs/examples/data/C60.stru diff --git a/doc/examples/data/CdS.cif b/docs/examples/data/CdS.cif similarity index 100% rename from doc/examples/data/CdS.cif rename to docs/examples/data/CdS.cif diff --git a/doc/examples/data/CdS_ZnS_nano.gr b/docs/examples/data/CdS_ZnS_nano.gr similarity index 100% rename from doc/examples/data/CdS_ZnS_nano.gr rename to docs/examples/data/CdS_ZnS_nano.gr diff --git a/doc/examples/data/ZnS.cif b/docs/examples/data/ZnS.cif similarity index 100% rename from doc/examples/data/ZnS.cif rename to docs/examples/data/ZnS.cif diff --git a/doc/examples/data/gaussian.dat b/docs/examples/data/gaussian.dat similarity index 100% rename from doc/examples/data/gaussian.dat rename to docs/examples/data/gaussian.dat diff --git a/doc/examples/data/lorentzian.dat b/docs/examples/data/lorentzian.dat similarity index 100% rename from doc/examples/data/lorentzian.dat rename to docs/examples/data/lorentzian.dat diff --git a/doc/examples/data/ni-q27r100-neutron.gr b/docs/examples/data/ni-q27r100-neutron.gr similarity index 100% rename from doc/examples/data/ni-q27r100-neutron.gr rename to docs/examples/data/ni-q27r100-neutron.gr diff --git a/doc/examples/data/ni-q27r60-xray.gr b/docs/examples/data/ni-q27r60-xray.gr similarity index 100% rename from doc/examples/data/ni-q27r60-xray.gr rename to docs/examples/data/ni-q27r60-xray.gr diff --git a/doc/examples/data/ni-q27r60nodg-xray.gr b/docs/examples/data/ni-q27r60nodg-xray.gr similarity index 100% rename from doc/examples/data/ni-q27r60nodg-xray.gr rename to docs/examples/data/ni-q27r60nodg-xray.gr diff --git a/doc/examples/data/ni.cif b/docs/examples/data/ni.cif similarity index 100% rename from doc/examples/data/ni.cif rename to docs/examples/data/ni.cif diff --git a/doc/examples/data/ni.iq b/docs/examples/data/ni.iq similarity index 100% rename from doc/examples/data/ni.iq rename to docs/examples/data/ni.iq diff --git a/doc/examples/data/pb.cif b/docs/examples/data/pb.cif similarity index 100% rename from doc/examples/data/pb.cif rename to docs/examples/data/pb.cif diff --git a/doc/examples/data/pb_100.xyz b/docs/examples/data/pb_100.xyz similarity index 100% rename from doc/examples/data/pb_100.xyz rename to docs/examples/data/pb_100.xyz diff --git a/doc/examples/data/pb_100_qmax1.iq b/docs/examples/data/pb_100_qmax1.iq similarity index 100% rename from doc/examples/data/pb_100_qmax1.iq rename to docs/examples/data/pb_100_qmax1.iq diff --git a/doc/examples/data/pb_100_qmin1.gr b/docs/examples/data/pb_100_qmin1.gr similarity index 100% rename from doc/examples/data/pb_100_qmin1.gr rename to docs/examples/data/pb_100_qmin1.gr diff --git a/doc/examples/data/sas_ellipsoid_testdata.txt b/docs/examples/data/sas_ellipsoid_testdata.txt similarity index 100% rename from doc/examples/data/sas_ellipsoid_testdata.txt rename to docs/examples/data/sas_ellipsoid_testdata.txt diff --git a/doc/examples/data/si-q27r60-xray.gr b/docs/examples/data/si-q27r60-xray.gr similarity index 100% rename from doc/examples/data/si-q27r60-xray.gr rename to docs/examples/data/si-q27r60-xray.gr diff --git a/doc/examples/data/si.cif b/docs/examples/data/si.cif similarity index 100% rename from doc/examples/data/si.cif rename to docs/examples/data/si.cif diff --git a/doc/examples/data/si90ni10-q27r60-xray.gr b/docs/examples/data/si90ni10-q27r60-xray.gr similarity index 100% rename from doc/examples/data/si90ni10-q27r60-xray.gr rename to 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a/doc/examples/gaussianrecipe.py b/docs/examples/gaussianrecipe.py similarity index 100% rename from doc/examples/gaussianrecipe.py rename to docs/examples/gaussianrecipe.py diff --git a/doc/examples/interface.py b/docs/examples/interface.py similarity index 100% rename from doc/examples/interface.py rename to docs/examples/interface.py diff --git a/doc/examples/npintensity.py b/docs/examples/npintensity.py similarity index 100% rename from doc/examples/npintensity.py rename to docs/examples/npintensity.py diff --git a/doc/examples/npintensityII.py b/docs/examples/npintensityII.py similarity index 100% rename from doc/examples/npintensityII.py rename to docs/examples/npintensityII.py diff --git a/doc/examples/nppdfcrystal.py b/docs/examples/nppdfcrystal.py similarity index 100% rename from doc/examples/nppdfcrystal.py rename to docs/examples/nppdfcrystal.py diff --git a/doc/examples/nppdfobjcryst.py b/docs/examples/nppdfobjcryst.py similarity index 100% rename from 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similarity index 99% rename from doc/source/conf.py rename to docs/source/conf.py index 8d285db5..453d9b6a 100644 --- a/doc/source/conf.py +++ b/docs/source/conf.py @@ -141,7 +141,7 @@ "github_user": "diffpy", "github_repo": "diffpy.srfit", "github_version": "main", - "conf_py_path": "/doc/source/", + "conf_py_path": "/docs/source/", } # Theme options are theme-specific and customize the look and feel of a theme diff --git a/doc/source/examples.rst b/docs/source/examples.rst similarity index 100% rename from doc/source/examples.rst rename to docs/source/examples.rst diff --git a/doc/source/examples/coreshellnp.rst b/docs/source/examples/coreshellnp.rst similarity index 100% rename from doc/source/examples/coreshellnp.rst rename to docs/source/examples/coreshellnp.rst diff --git a/doc/source/examples/crystalpdf.rst b/docs/source/examples/crystalpdf.rst similarity index 100% rename from doc/source/examples/crystalpdf.rst rename to docs/source/examples/crystalpdf.rst diff --git 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to docs/source/extending.rst diff --git a/doc/source/img/.placeholder b/docs/source/img/.placeholder similarity index 100% rename from doc/source/img/.placeholder rename to docs/source/img/.placeholder diff --git a/doc/source/img/fitting_architecture.dia b/docs/source/img/fitting_architecture.dia similarity index 100% rename from doc/source/img/fitting_architecture.dia rename to docs/source/img/fitting_architecture.dia diff --git a/doc/source/img/fitting_architecture.png b/docs/source/img/fitting_architecture.png similarity index 100% rename from doc/source/img/fitting_architecture.png rename to docs/source/img/fitting_architecture.png diff --git a/doc/source/img/overview.odg b/docs/source/img/overview.odg similarity index 100% rename from doc/source/img/overview.odg rename to docs/source/img/overview.odg diff --git a/doc/source/img/partition_equation.dia b/docs/source/img/partition_equation.dia similarity index 100% rename from doc/source/img/partition_equation.dia rename to 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doc/source/img/visitor_interaction.png rename to docs/source/img/visitor_interaction.png diff --git a/doc/source/index.rst b/docs/source/index.rst similarity index 100% rename from doc/source/index.rst rename to docs/source/index.rst diff --git a/doc/source/license.rst b/docs/source/license.rst similarity index 100% rename from doc/source/license.rst rename to docs/source/license.rst diff --git a/doc/source/release.rst b/docs/source/release.rst similarity index 100% rename from doc/source/release.rst rename to docs/source/release.rst diff --git a/doc/source/snippets/.placeholder b/docs/source/snippets/.placeholder similarity index 100% rename from doc/source/snippets/.placeholder rename to docs/source/snippets/.placeholder From 2de9ea65ffdc252ba352208a7bb3bb8579caeb7c Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Sat, 19 Jul 2025 14:12:20 -0400 Subject: [PATCH 3/5] fix: requirements/test.txt -> requirements/tests.txt --- requirements/{test.txt => tests.txt} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename requirements/{test.txt => tests.txt} (100%) diff --git a/requirements/test.txt b/requirements/tests.txt similarity index 100% rename from requirements/test.txt rename to requirements/tests.txt From 129e188fede1f466a6febf4932c5560625dff667 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Sat, 19 Jul 2025 14:23:33 -0400 Subject: [PATCH 4/5] fix: some formatting issues in the license.rst --- LICENSE.rst | 22 +++++++++------------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/LICENSE.rst b/LICENSE.rst index 7342dda5..acbe6078 100644 --- a/LICENSE.rst +++ b/LICENSE.rst @@ -1,18 +1,14 @@ OPEN SOURCE LICENSE AGREEMENT ============================= -Copyright (c) 2009-2011, University of Tennessee -Copyright (c) 1989, 1991 Free Software Foundation, Inc. -Copyright (c) 2006, The Regents of the University of California through - Lawrence Berkeley National Laboratory -Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP") -Copyright (c) 2006-2007, Board of Trustees of Michigan State University -Copyright (c) 2008-2012, The Trustees of Columbia University in the City - of New York -Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National - Laboratory -Copyright (c) 2020-2025, The Trustees of Columbia University in the City - of New York +- Copyright (c) 2009-2011, University of Tennessee +- Copyright (c) 1989, 1991 Free Software Foundation, Inc. +- Copyright (c) 2006, The Regents of the University of California through Lawrence Berkeley National Laboratory +- Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP") +- Copyright (c) 2006-2007, Board of Trustees of Michigan State University +- Copyright (c) 2008-2012, The Trustees of Columbia University in the City of New York +- Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory +- Copyright (c) 2020-2025, The Trustees of Columbia University in the City of New York The "DiffPy-CMI" is distributed subject to the following license conditions: @@ -20,7 +16,7 @@ The "DiffPy-CMI" is distributed subject to the following license conditions: SOFTWARE LICENSE AGREEMENT - Software: DiffPy-CMI +**Software:** DiffPy-CMI (1) The "Software", below, refers to the aforementioned DiffPy-CMI (in either From 42daa6a5c1b19b35ea2b856f8d570eb76a56e9b3 Mon Sep 17 00:00:00 2001 From: Simon Billinge Date: Sat, 19 Jul 2025 14:28:35 -0400 Subject: [PATCH 5/5] news --- news/license.rst | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 news/license.rst diff --git a/news/license.rst b/news/license.rst new file mode 100644 index 00000000..afd4d06e --- /dev/null +++ b/news/license.rst @@ -0,0 +1,24 @@ +**Added:** + +* + +**Changed:** + +* doc/ -> docs/ +* requirements/test.txt -> requirements/tests.txt + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* Better license designation in `pyproject.toml` + +**Security:** + +*