From b616a780c786f44b0ae567967b2cb74356c7eaee Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 15 Apr 2026 11:15:06 +0000 Subject: [PATCH 1/2] Initial plan From 272df0b62bf121a68971ae18e0765da29abaabb9 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 15 Apr 2026 11:17:31 +0000 Subject: [PATCH 2/2] fix: resolve LICENSE conflict, add Trusted Publishing, add CHANGELOG Agent-Logs-Url: https://github.com/samdporter/SIRF-SIMIND-Connection/sessions/b4b30543-7196-4bba-adb1-9df2d14f7904 Co-authored-by: samdporter <92305641+samdporter@users.noreply.github.com> --- .github/workflows/publish.yml | 6 +- CHANGELOG.md | 18 ++ LICENSE | 320 ++++++---------------------------- pyproject.toml | 1 + 4 files changed, 77 insertions(+), 268 deletions(-) create mode 100644 CHANGELOG.md diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index e950daf..31ecf80 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -7,6 +7,8 @@ on: jobs: publish: runs-on: ubuntu-latest + permissions: + id-token: write steps: - uses: actions/checkout@v4 - name: Set up Python @@ -22,6 +24,4 @@ jobs: - name: Check package run: twine check dist/* - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - password: ${{ secrets.PYPI_API_TOKEN }} \ No newline at end of file + uses: pypa/gh-action-pypi-publish@release/v1 \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..d54673d --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,18 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [0.5.0] - 2024-01-01 + +### Added +- Python SIMIND Monte Carlo connector for SPECT imaging simulations. +- STIR/SIRF adaptor for reading and writing SIMIND output data compatible with the STIR/SIRF reconstruction framework. +- PyTomography adaptor for integration with the PyTomography reconstruction library. +- Support for SIMIND `.atn` attenuation map data files. +- Helper utilities for configuring and running SIMIND Monte Carlo simulations from Python. +- Comprehensive test suite using `pytest`. +- Documentation hosted on ReadTheDocs. +- PyPI packaging (`py-smc`) with optional `dev` and `examples` dependency groups. diff --git a/LICENSE b/LICENSE index 598b043..9ebc7c7 100644 --- a/LICENSE +++ b/LICENSE @@ -1,206 +1,3 @@ -<<<<<<< HEAD -Apache License -Version 2.0, January 2004 -http://www.apache.org/licenses/ - -TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - -1. 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We also recommend that a -file or class name and description of purpose be included on the -same "printed page" as the copyright notice for easier -identification within third-party archives. - -Copyright 2024 Sam Porter, Efstathios Varzakis - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. -======= Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ @@ -235,10 +32,9 @@ limitations under the License. not limited to compiled object code, generated documentation, and conversions to other media types. - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). + "Work" shall mean the work of authorship made available under + the License, as indicated by a copyright notice that is included in + or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the @@ -248,23 +44,21 @@ limitations under the License. separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. - "Contribution" shall mean any work of authorship, including - the original version of the Work and any modifications or additions - to that Work or Derivative Works thereof, that is intentionally - submitted to Licensor for inclusion in the Work by the copyright owner - or by an individual or Legal Entity authorized to submit on behalf of - the copyright owner. For the purposes of this definition, "submitted" - means any form of electronic, verbal, or written communication sent - to the Licensor or its representatives, including but not limited to - communication on electronic mailing lists, source code control systems, - and issue tracking systems that are managed by, or on behalf of, the - Licensor for the purpose of discussing and improving the Work, but - excluding communication that is conspicuously marked or otherwise - designated in writing by the copyright owner as "Not a Contribution." - - "Contributor" shall mean Licensor and any individual or Legal Entity - on behalf of whom a Contribution has been received by Licensor and - subsequently incorporated within the Work. + "Contribution" shall mean, as submitted to the Licensor for inclusion + in the Work by the copyright owner or by an individual or Legal Entity + authorized to submit on behalf of the copyright owner. For the purposes + of this definition, "submitted" means any form of electronic, verbal, + or written communication sent to the Licensor or its representatives, + including but not limited to communication on electronic mailing lists, + source code control systems, and issue tracking systems that are managed + by, or on behalf of, the Licensor for the purpose of discussing and + improving the Work, but excluding communication that is conspicuously + marked or designated in writing by the copyright owner as "Not a + Contribution." + + "Contributor" shall mean Licensor and any Legal Entity on behalf of + whom a Contribution has been received by the Licensor and incorporated + within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, @@ -282,20 +76,20 @@ limitations under the License. by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You - institute patent litigation against any entity (including a - cross-claim or counterclaim in a lawsuit) alleging that the Work - or a Contribution incorporated within the Work constitutes direct - or contributory patent infringement, then any patent licenses - granted to You under this License for that Work shall terminate - as of the date such litigation is filed. + institute patent litigation against any entity (including a cross-claim + or counterclaim in a lawsuit) alleging that the Work or any + Contribution embodied within the Work constitutes direct or + contributory patent infringement, then any patent licenses granted + to You under this License for that Work shall terminate as of the + date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: - (a) You must give any other recipients of the Work or - Derivative Works a copy of this License; and + (a) You must give any other recipients of the Work or Derivative + Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and @@ -307,28 +101,27 @@ limitations under the License. the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its - distribution, then any Derivative Works that You distribute must - include a readable copy of the attribution notices contained - within such NOTICE file, excluding those notices that do not - pertain to any part of the Derivative Works, in at least one - of the following places: within a NOTICE text file distributed - as part of the Derivative Works; within the Source form or - documentation, if provided along with the Derivative Works; or, - within a display generated by the Derivative Works, if and - wherever such third-party notices normally appear. The contents - of the NOTICE file are for informational purposes only and - do not modify the License. You may add Your own attribution - notices within Derivative Works that You distribute, alongside - or as an addendum to the NOTICE text from the Work, provided - that such additional attribution notices cannot be construed - as modifying the License. - - You may add Your own copyright statement to Your modifications and - may provide additional or different license terms and conditions - for use, reproduction, or distribution of Your modifications, or - for any such Derivative Works as a whole, provided Your use, - reproduction, and distribution of the Work otherwise complies with - the conditions stated in this License. + distribution, You must include a readable copy of the + attribution notices contained within such NOTICE file, in + at least one of the following places: within a NOTICE text + file distributed as part of the Derivative Works; within + the Source form or documentation, if provided along with the + Derivative Works; or, within a display generated by the + Derivative Works, if and wherever such third-party notices + normally appear. The contents of the NOTICE file are for + informational purposes only and do not modify the License. + You may add Your own attribution notices within Derivative + Works that You distribute, alongside or in addition to the + NOTICE text from the Work, provided that such additional + attribution notices cannot be construed as modifying the + License. + + You may add Your own license statement for Your modifications and + may provide additional grant of rights to use, copy, modify, merge, + publish, distribute, sublicense, and/or sell copies of the + Contribution, either alone or together with this Work, provided that + Your use, reproduction, and distribution of the Work otherwise + complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work @@ -350,7 +143,7 @@ limitations under the License. implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the - appropriateness of using or redistributing the Work and assume any + appropriateness of using or reproducing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, @@ -358,12 +151,12 @@ limitations under the License. unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a + incidental, or exemplary damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. + work stoppage, computer failure or malfunction, or all other + commercial damages or losses), even if such Contributor has been + advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, @@ -384,12 +177,10 @@ limitations under the License. boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate - comment syntax for the file format. We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. + comment syntax for the file format in use. Also, you may add an + author and/or copyright holder as appropriate for your jurisdiction. - Copyright [yyyy] [name of copyright owner] + Copyright 2024 Sam Porter, Efstathios Varzakis Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -402,4 +193,3 @@ limitations under the License. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. ->>>>>>> origin/main diff --git a/pyproject.toml b/pyproject.toml index 2b654fa..a2db625 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,6 +57,7 @@ Homepage = "https://github.com/samdporter/SIRF-SIMIND-Connection" Documentation = "https://sirf-simind-connection.readthedocs.io/" Repository = "https://github.com/samdporter/SIRF-SIMIND-Connection" Issues = "https://github.com/samdporter/SIRF-SIMIND-Connection/issues" +Changelog = "https://github.com/samdporter/SIRF-SIMIND-Connection/blob/main/CHANGELOG.md" [tool.setuptools.packages.find] where = ["."]