From f2e0f8e539f90a51bbbc21f06a601181d1c3223f Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 18:24:28 +0200 Subject: [PATCH 01/12] start using reuse --- .github/workflows/ci.yml | 4 ++++ .github/workflows/publish.yml | 4 ++++ Makefile | 4 ++++ REUSE.toml | 16 ++++++++++++++++ setup.cfg | 4 ++++ tutorial/source/sir_hmc.rst | 4 ++++ 6 files changed, 36 insertions(+) create mode 100644 REUSE.toml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 04ec6f2a8b..d1e0edadb5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + name: CI on: diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index c2e8117c33..01914837ff 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + # This workflow uses actions that are not certified by GitHub. # They are provided by a third-party and are governed by # separate terms of service, privacy policy, and support diff --git a/Makefile b/Makefile index 04c6112d47..cfa73f177c 100644 --- a/Makefile +++ b/Makefile @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + .PHONY: all install docs lint format test integration-test clean FORCE all: docs test diff --git a/REUSE.toml b/REUSE.toml new file mode 100644 index 0000000000..1063404b06 --- /dev/null +++ b/REUSE.toml @@ -0,0 +1,16 @@ +version = 1 +SPDX-PackageName = "pyro" +SPDX-PackageSupplier = "TODO add" +SPDX-PackageDownloadLocation = "pyro.ai" + +[[annotations]] +path = "tutorial/source/**ipynb" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "tutorial/source/**rst" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" diff --git a/setup.cfg b/setup.cfg index 1da059e331..a92c6f00d7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + [tool:pytest] filterwarnings = error ignore:numpy.ufunc size changed:RuntimeWarning diff --git a/tutorial/source/sir_hmc.rst b/tutorial/source/sir_hmc.rst index ccc26a33e3..8a196d90f1 100644 --- a/tutorial/source/sir_hmc.rst +++ b/tutorial/source/sir_hmc.rst @@ -1,3 +1,7 @@ +.. Copyright Contributors to the Pyro project. +.. +.. SPDX-License-Identifier: Apache-2.0 + Example: Epidemiological inference via HMC ========================================== From 7fa2c106d1f755c79ef94d957c3664a0900b0ef6 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 18:47:11 +0200 Subject: [PATCH 02/12] introduce reuse --- .github/issue_template.md | 6 ++++ CONTRIBUTING.md | 6 ++++ LICENSES/Apache-2.0.txt | 73 ++++++++++++++++++++++++++++++++++++++ LICENSES/BSD-3-Clause.txt | 11 ++++++ LICENSES/MIT.txt | 9 +++++ README.md | 6 ++++ RELEASE-MANAGEMENT.md | 6 ++++ REUSE.toml | 18 ++++++++++ pyproject.toml | 4 +++ scripts/install_pytorch.sh | 4 +++ scripts/profile_model.sh | 4 +++ 11 files changed, 147 insertions(+) create mode 100644 LICENSES/Apache-2.0.txt create mode 100644 LICENSES/BSD-3-Clause.txt create mode 100644 LICENSES/MIT.txt diff --git a/.github/issue_template.md b/.github/issue_template.md index 4549578b82..e3eb03eb16 100644 --- a/.github/issue_template.md +++ b/.github/issue_template.md @@ -1,3 +1,9 @@ + + ### Guidelines **NOTE:** Issues are for bugs and feature requests only. If you have a question about using Pyro or general modeling questions, please post it on the [forum](https://forum.pyro.ai/). diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 981a2b715c..d4ffc33d26 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,3 +1,9 @@ + + # Development Please follow our established coding style including variable names, module imports, and function definitions. diff --git a/LICENSES/Apache-2.0.txt b/LICENSES/Apache-2.0.txt new file mode 100644 index 0000000000..137069b823 --- /dev/null +++ b/LICENSES/Apache-2.0.txt @@ -0,0 +1,73 @@ +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 [yyyy] [name of copyright owner] + +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. diff --git a/LICENSES/BSD-3-Clause.txt b/LICENSES/BSD-3-Clause.txt new file mode 100644 index 0000000000..ea890afbc7 --- /dev/null +++ b/LICENSES/BSD-3-Clause.txt @@ -0,0 +1,11 @@ +Copyright (c) . + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/LICENSES/MIT.txt b/LICENSES/MIT.txt new file mode 100644 index 0000000000..2071b23b0e --- /dev/null +++ b/LICENSES/MIT.txt @@ -0,0 +1,9 @@ +MIT License + +Copyright (c) + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/README.md b/README.md index 027a1b4e21..66b7407e42 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,9 @@ + + diff --git a/RELEASE-MANAGEMENT.md b/RELEASE-MANAGEMENT.md index 87944fb532..762d85e7cc 100644 --- a/RELEASE-MANAGEMENT.md +++ b/RELEASE-MANAGEMENT.md @@ -1,3 +1,9 @@ + + # Pyro release management This describes the process by which versions of Pyro are officially released to the public. diff --git a/REUSE.toml b/REUSE.toml index 1063404b06..3c3196295c 100644 --- a/REUSE.toml +++ b/REUSE.toml @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + version = 1 SPDX-PackageName = "pyro" SPDX-PackageSupplier = "TODO add" @@ -14,3 +18,17 @@ path = "tutorial/source/**rst" precedence = "aggregate" SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "tutorial/source/**jpg" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + + +[[annotations]] +path = "tutorial/source/**png" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + diff --git a/pyproject.toml b/pyproject.toml index fac4c43928..4ae021c471 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + [tool.ruff] line-length = 120 diff --git a/scripts/install_pytorch.sh b/scripts/install_pytorch.sh index 73447e5cfa..c7d5910f4d 100644 --- a/scripts/install_pytorch.sh +++ b/scripts/install_pytorch.sh @@ -1,5 +1,9 @@ #!/usr/bin/env bash +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + set -xe diff --git a/scripts/profile_model.sh b/scripts/profile_model.sh index 5304196be5..b2a1005e4d 100644 --- a/scripts/profile_model.sh +++ b/scripts/profile_model.sh @@ -1,5 +1,9 @@ #!/usr/bin/env bash +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + set -xe function _cleanup() { From 5c5453f1bddb07c4bc2af66130e0e16ab76e6a82 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 18:58:58 +0200 Subject: [PATCH 03/12] update --- .github/workflows/reuse.yml | 18 ++++++++++++++++++ .readthedocs.yml | 4 ++++ REUSE.toml | 11 +++++++++++ docker/Dockerfile | 4 ++++ docker/README.md | 6 ++++++ docker/install.sh | 5 +++++ scripts/perf_test.sh | 4 ++++ 7 files changed, 52 insertions(+) create mode 100644 .github/workflows/reuse.yml diff --git a/.github/workflows/reuse.yml b/.github/workflows/reuse.yml new file mode 100644 index 0000000000..0fd7431622 --- /dev/null +++ b/.github/workflows/reuse.yml @@ -0,0 +1,18 @@ +# SPDX-FileCopyrightText: 2022 Free Software Foundation Europe e.V. +# +# SPDX-License-Identifier: CC0-1.0 + +name: REUSE Compliance Check + +on: [push, pull_request] + +permissions: # set top-level default permissions as security best practice + contents: read + +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1 + - name: REUSE Compliance Check + uses: fsfe/reuse-action@a46482ca367aef4454a87620aa37c2be4b2f8106 # v3.0.0 \ No newline at end of file diff --git a/.readthedocs.yml b/.readthedocs.yml index ca4e808c59..d27cb95338 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + # Required version: 2 diff --git a/REUSE.toml b/REUSE.toml index 3c3196295c..9a7ae7c972 100644 --- a/REUSE.toml +++ b/REUSE.toml @@ -32,3 +32,14 @@ precedence = "aggregate" SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." SPDX-License-Identifier = "Apache-2.0" +[[annotations]] +path = "docs/source/**png" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "docs/source/**rst" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" \ No newline at end of file diff --git a/docker/Dockerfile b/docker/Dockerfile index f8c67fb178..730256fccb 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + ARG base_img=ubuntu:18.04 FROM ${base_img} diff --git a/docker/README.md b/docker/README.md index fd80be555a..92e5d1e627 100644 --- a/docker/README.md +++ b/docker/README.md @@ -1,3 +1,9 @@ + + ## Using Pyro Docker Some utilities for building docker images and running Pyro inside a Docker container are diff --git a/docker/install.sh b/docker/install.sh index 705533bbaa..1f1f53323f 100755 --- a/docker/install.sh +++ b/docker/install.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + set -xe pip install --upgrade pip diff --git a/scripts/perf_test.sh b/scripts/perf_test.sh index ed911d8cff..86186ad218 100644 --- a/scripts/perf_test.sh +++ b/scripts/perf_test.sh @@ -1,5 +1,9 @@ #!/usr/bin/env bash +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + set -xe function _cleanup() { From b9b5f88eb11130b644d1d38cccf4bfcf9c3372e4 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 19:00:47 +0200 Subject: [PATCH 04/12] update --- scripts/update_headers.py | 77 --------------------------------------- 1 file changed, 77 deletions(-) delete mode 100644 scripts/update_headers.py diff --git a/scripts/update_headers.py b/scripts/update_headers.py deleted file mode 100644 index 48ccf2dfb8..0000000000 --- a/scripts/update_headers.py +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright Contributors to the Pyro project. -# SPDX-License-Identifier: Apache-2.0 - -import argparse -import glob -import os -import sys - -root = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) -blacklist = ["/build/", "/dist/", "/pyro/_version.py"] -file_types = [ - ("*.py", "# {}"), - ("*.cpp", "// {}"), -] - -parser = argparse.ArgumentParser() -parser.add_argument("--check", action="store_true") -args = parser.parse_args() -dirty = [] - -for basename, comment in file_types: - copyright_line = comment.format("Copyright Contributors to the Pyro project.\n") - # See https://spdx.org/ids-how - spdx_line = comment.format("SPDX-License-Identifier: Apache-2.0\n") - - filenames = glob.glob(os.path.join(root, "**", basename), recursive=True) - filenames.sort() - filenames = [ - filename - for filename in filenames - if not any(word in filename for word in blacklist) - ] - for filename in filenames: - with open(filename) as f: - lines = f.readlines() - - # Ignore empty files like __init__.py - if all(line.isspace() for line in lines): - continue - - # Ensure first few line are copyright notices. - changed = False - lineno = 0 - if not lines[lineno].startswith(comment.format("Copyright")): - lines.insert(lineno, copyright_line) - changed = True - lineno += 1 - while lines[lineno].startswith(comment.format("Copyright")): - lineno += 1 - - # Ensure next line is an SPDX short identifier. - if not lines[lineno].startswith(comment.format("SPDX-License-Identifier")): - lines.insert(lineno, spdx_line) - changed = True - lineno += 1 - - # Ensure next line is blank. - if not lines[lineno].isspace(): - lines.insert(lineno, "\n") - changed = True - - if not changed: - continue - - if args.check: - dirty.append(filename) - continue - - with open(filename, "w") as f: - f.write("".join(lines)) - - print("updated {}".format(filename[len(root) + 1 :])) - -if dirty: - print("The following files need license headers:\n{}".format("\n".join(dirty))) - print("Please run 'make license'") - sys.exit(1) From 1ec67ba8c745c807aa685a4edcd056e1eda6d244 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 19:41:52 +0200 Subject: [PATCH 05/12] update --- .github/workflows/reuse.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/reuse.yml b/.github/workflows/reuse.yml index 0fd7431622..d3cb4df968 100644 --- a/.github/workflows/reuse.yml +++ b/.github/workflows/reuse.yml @@ -15,4 +15,5 @@ jobs: steps: - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1 - name: REUSE Compliance Check - uses: fsfe/reuse-action@a46482ca367aef4454a87620aa37c2be4b2f8106 # v3.0.0 \ No newline at end of file + uses: fsfe/reuse-action@3ae3c6bdf1257ab19397fab11fd3312144692083 + From dec146f4a80e361bbf3ef35e4744eee195523456 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 20:13:31 +0200 Subject: [PATCH 06/12] update --- .codecov.yml | 4 + .coveragerc | 4 + .gitattributes | 4 + .github/FUNDING.yml | 4 + .gitignore | 4 + CODE_OF_CONDUCT.md | 7 ++ LICENSES/CC0-1.0.txt | 121 +++++++++++++++++++++++++++ REUSE.toml | 44 +++++++++- docker/Makefile | 4 + docs/Makefile | 4 + docs/README.md | 6 ++ docs/requirements.txt | 4 + examples/eight_schools/README.md | 6 ++ examples/rsa/README.md | 6 ++ pyro/contrib/README.md | 6 ++ tests/README.md | 6 ++ tutorial/Makefile | 4 + tutorial/README.md | 6 ++ tutorial/source/_static/css/pyro.css | 6 ++ 19 files changed, 249 insertions(+), 1 deletion(-) create mode 100644 LICENSES/CC0-1.0.txt diff --git a/.codecov.yml b/.codecov.yml index 0f1430acfa..d74c7ec781 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + ignore: - "pyro/docutil.py" - "pyro/logger.py" diff --git a/.coveragerc b/.coveragerc index 45b8e8e715..30f3c0dd8f 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + [report] omit = pyro/docutil.py diff --git a/.gitattributes b/.gitattributes index 2f77e919cd..38a7c00c06 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,5 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + *.ipynb linguist-documentation diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml index 325287e1a3..a84d4dfdc0 100644 --- a/.github/FUNDING.yml +++ b/.github/FUNDING.yml @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + # These are supported funding model platforms github: [fritzo] # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2] diff --git a/.gitignore b/.gitignore index b35b756605..4e682ce1f7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + run_outputs* .DS_Store .benchmarks diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 8ef523520a..2cc63025aa 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,3 +1,10 @@ + + + # Contributor Covenant Code of Conduct ## Our Pledge diff --git a/LICENSES/CC0-1.0.txt b/LICENSES/CC0-1.0.txt new file mode 100644 index 0000000000..0e259d42c9 --- /dev/null +++ b/LICENSES/CC0-1.0.txt @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. 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Should any part of the License for any +reason be judged legally invalid or ineffective under applicable law, such +partial invalidity or ineffectiveness shall not invalidate the remainder +of the License, and in such case Affirmer hereby affirms that he or she +will not (i) exercise any of his or her remaining Copyright and Related +Rights in the Work or (ii) assert any associated claims and causes of +action with respect to the Work, in either case contrary to Affirmer's +express Statement of Purpose. + +4. Limitations and Disclaimers. + + a. No trademark or patent rights held by Affirmer are waived, abandoned, + surrendered, licensed or otherwise affected by this document. + b. Affirmer offers the Work as-is and makes no representations or + warranties of any kind concerning the Work, express, implied, + statutory or otherwise, including without limitation warranties of + title, merchantability, fitness for a particular purpose, non + infringement, or the absence of latent or other defects, accuracy, or + the present or absence of errors, whether or not discoverable, all to + the greatest extent permissible under applicable law. + c. Affirmer disclaims responsibility for clearing rights of other persons + that may apply to the Work or any use thereof, including without + limitation any person's Copyright and Related Rights in the Work. + Further, Affirmer disclaims responsibility for obtaining any necessary + consents, permissions or other rights required for any use of the + Work. + d. Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work. diff --git a/REUSE.toml b/REUSE.toml index 9a7ae7c972..7922552c3b 100644 --- a/REUSE.toml +++ b/REUSE.toml @@ -42,4 +42,46 @@ SPDX-License-Identifier = "Apache-2.0" path = "docs/source/**rst" precedence = "aggregate" SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." -SPDX-License-Identifier = "Apache-2.0" \ No newline at end of file +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "docs/source/**gif" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "docs/source/**ico" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "docs/source/**csv" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "docs/source/**txt" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "tutorial/source/**gif" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "tutorial/source/**ico" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "exampeles/capture_recapture/**csv" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright (c) 2017-2019 Uber Technologies, Inc." +SPDX-License-Identifier = "Apache-2.0" diff --git a/docker/Makefile b/docker/Makefile index d13ff2f351..0f9abdc53b 100644 --- a/docker/Makefile +++ b/docker/Makefile @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + .PHONY: help create-host-workspace build build-gpu run run-gpu notebook notebook-gpu DOCKER_FILE=Dockerfile diff --git a/docs/Makefile b/docs/Makefile index 06bbf77d2f..3dca05ce3a 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + # Minimal makefile for Sphinx documentation # diff --git a/docs/README.md b/docs/README.md index 38e2a34673..c724cb1246 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,3 +1,9 @@ + + # Documentation # Pyro Documentation is supported by [Sphinx](http://www.sphinx-doc.org/en/stable/). To build the docs, run from the toplevel directory: diff --git a/docs/requirements.txt b/docs/requirements.txt index b14a67b6c4..3bae619297 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + sphinx==4.2.0 sphinx-rtd-theme==1.0.0 graphviz>=0.8 diff --git a/examples/eight_schools/README.md b/examples/eight_schools/README.md index 2b934eb145..c7066b90c1 100644 --- a/examples/eight_schools/README.md +++ b/examples/eight_schools/README.md @@ -1,3 +1,9 @@ + + Analysis of the eight schools data (chapter 5 of [Gelman et al 2013]) using MCMC (NUTS) and SVI. The starting model is the Stan model: diff --git a/examples/rsa/README.md b/examples/rsa/README.md index 270dce7aae..2ca69a16f4 100644 --- a/examples/rsa/README.md +++ b/examples/rsa/README.md @@ -1,3 +1,9 @@ + + ## Rational Speech Acts (RSA) examples This folder contains examples of reasoning about reasoning with nested inference diff --git a/pyro/contrib/README.md b/pyro/contrib/README.md index b6195f026f..bbb71554ad 100644 --- a/pyro/contrib/README.md +++ b/pyro/contrib/README.md @@ -1,3 +1,9 @@ + + # Contributed Code Code in `pyro.contrib` is under various stages of development. diff --git a/tests/README.md b/tests/README.md index 54111e3266..a6fc03918e 100644 --- a/tests/README.md +++ b/tests/README.md @@ -1,3 +1,9 @@ + + # Testing ### Building PyTorch binaries for Travis CI diff --git a/tutorial/Makefile b/tutorial/Makefile index ee10d1f4ed..a1410d5f0e 100644 --- a/tutorial/Makefile +++ b/tutorial/Makefile @@ -1,3 +1,7 @@ +# Copyright Contributors to the Pyro project. +# +# SPDX-License-Identifier: Apache-2.0 + # Minimal makefile for Sphinx documentation # diff --git a/tutorial/README.md b/tutorial/README.md index 9e498f8a04..190fbe2beb 100644 --- a/tutorial/README.md +++ b/tutorial/README.md @@ -1 +1,7 @@ + + [http://pyro.ai/examples](http://pyro.ai/examples) diff --git a/tutorial/source/_static/css/pyro.css b/tutorial/source/_static/css/pyro.css index 335d437a81..0561ba35e6 100644 --- a/tutorial/source/_static/css/pyro.css +++ b/tutorial/source/_static/css/pyro.css @@ -1,3 +1,9 @@ +/* + * Copyright Contributors to the Pyro project. + * + * SPDX-License-Identifier: Apache-2.0 + */ + @import url("theme.css"); .wy-side-nav-search { From ff99154c717d91f741e014d5f4efb5fc106f33a6 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 20:15:48 +0200 Subject: [PATCH 07/12] update --- REUSE.toml | 2 +- docs/source/_static/css/pyro.css | 6 ++++++ docs/source/_static/img/favicon/browserconfig.xml | 7 +++++++ examples/mixed_hmm/README.md | 6 ++++++ tutorial/source/_static/img/dmm.tex | 4 ++++ 5 files changed, 24 insertions(+), 1 deletion(-) diff --git a/REUSE.toml b/REUSE.toml index 7922552c3b..d35fee0da7 100644 --- a/REUSE.toml +++ b/REUSE.toml @@ -81,7 +81,7 @@ SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." SPDX-License-Identifier = "Apache-2.0" [[annotations]] -path = "exampeles/capture_recapture/**csv" +path = "examples/capture_recapture/**csv" precedence = "aggregate" SPDX-FileCopyrightText = "Copyright (c) 2017-2019 Uber Technologies, Inc." SPDX-License-Identifier = "Apache-2.0" diff --git a/docs/source/_static/css/pyro.css b/docs/source/_static/css/pyro.css index 335d437a81..0561ba35e6 100644 --- a/docs/source/_static/css/pyro.css +++ b/docs/source/_static/css/pyro.css @@ -1,3 +1,9 @@ +/* + * Copyright Contributors to the Pyro project. + * + * SPDX-License-Identifier: Apache-2.0 + */ + @import url("theme.css"); .wy-side-nav-search { diff --git a/docs/source/_static/img/favicon/browserconfig.xml b/docs/source/_static/img/favicon/browserconfig.xml index c554148223..6430a6715b 100644 --- a/docs/source/_static/img/favicon/browserconfig.xml +++ b/docs/source/_static/img/favicon/browserconfig.xml @@ -1,2 +1,9 @@ + + + #ffffff \ No newline at end of file diff --git a/examples/mixed_hmm/README.md b/examples/mixed_hmm/README.md index 649c8253ab..380d9d641b 100644 --- a/examples/mixed_hmm/README.md +++ b/examples/mixed_hmm/README.md @@ -1,3 +1,9 @@ + + # Hierarchical mixed-effect hidden Markov models Note: This is a cleaned-up version of the seal experiments in [Bingham et al 2019] that is a simplified variant of some of the analysis in the [momentuHMM harbour seal example](https://github.com/bmcclintock/momentuHMM/blob/master/vignettes/harbourSealExample.R) [McClintock et al 2018]. diff --git a/tutorial/source/_static/img/dmm.tex b/tutorial/source/_static/img/dmm.tex index 4b8b4e6ac0..1d2053b2b2 100644 --- a/tutorial/source/_static/img/dmm.tex +++ b/tutorial/source/_static/img/dmm.tex @@ -1,3 +1,7 @@ +% Copyright Contributors to the Pyro project. +% +% SPDX-License-Identifier: Apache-2.0 + \documentclass[12pt]{article} \usepackage{amsmath,amscd,amssymb} \usepackage[pdftex]{graphicx} From 602ce1e40c57e43cd6d27aa18386a2f07af36aaf Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 20:26:50 +0200 Subject: [PATCH 08/12] update --- Makefile | 1 - REUSE.toml | 12 ++++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index cfa73f177c..7f3fd69c24 100644 --- a/Makefile +++ b/Makefile @@ -24,7 +24,6 @@ tutorial: FORCE lint: FORCE ruff check . black --check *.py pyro examples tests scripts profiler - python scripts/update_headers.py --check mypy --install-types --non-interactive pyro scripts tests license: FORCE diff --git a/REUSE.toml b/REUSE.toml index d35fee0da7..866cadae3e 100644 --- a/REUSE.toml +++ b/REUSE.toml @@ -85,3 +85,15 @@ path = "examples/capture_recapture/**csv" precedence = "aggregate" SPDX-FileCopyrightText = "Copyright (c) 2017-2019 Uber Technologies, Inc." SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "MANIFEST.in" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "docs/source/_static/img/favicon/manifest.json" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" From ef1787127858992825260434f3b2aa01f4735953 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 20:33:26 +0200 Subject: [PATCH 09/12] remove header --- Makefile | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/Makefile b/Makefile index 7f3fd69c24..bb38de5a54 100644 --- a/Makefile +++ b/Makefile @@ -26,10 +26,7 @@ lint: FORCE black --check *.py pyro examples tests scripts profiler mypy --install-types --non-interactive pyro scripts tests -license: FORCE - python scripts/update_headers.py - -format: license FORCE +format: FORCE ruff check --fix . black *.py pyro examples tests scripts profiler From 0962aee6b91bad8e812cc0b3d3d1931f38ce62a7 Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 20:37:03 +0200 Subject: [PATCH 10/12] update --- REUSE.toml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/REUSE.toml b/REUSE.toml index 866cadae3e..e722173689 100644 --- a/REUSE.toml +++ b/REUSE.toml @@ -97,3 +97,11 @@ path = "docs/source/_static/img/favicon/manifest.json" precedence = "aggregate" SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." SPDX-License-Identifier = "Apache-2.0" + +[[annotations]] +path = "tests/infer/enum_growth.ipynb" +precedence = "aggregate" +SPDX-FileCopyrightText = "Copyright Contributors to the Pyro project." +SPDX-License-Identifier = "Apache-2.0" + + From 5533ddd0706e905e3103ff2af7f6e1f65b3cb5bb Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 20:49:13 +0200 Subject: [PATCH 11/12] update workflows --- .github/workflows/ci.yml | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d1e0edadb5..ac43c53ece 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,9 +26,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -45,9 +45,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -73,9 +73,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -107,9 +107,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -139,9 +139,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Setup Graphviz @@ -175,9 +175,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -207,9 +207,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -239,9 +239,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install dependencies @@ -273,9 +273,9 @@ jobs: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Coveralls Finished From eaf4b8cfced9c4b3c7c127d359bfd52b08a1574c Mon Sep 17 00:00:00 2001 From: Andreas Fehlner Date: Sun, 7 Jul 2024 21:31:22 +0200 Subject: [PATCH 12/12] upgrade action --- .github/workflows/ci.yml | 2 +- .github/workflows/publish.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ac43c53ece..84ad85bc3f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -145,7 +145,7 @@ jobs: with: python-version: ${{ matrix.python-version }} - name: Setup Graphviz - uses: ts-graphviz/setup-graphviz@v1 + uses: ts-graphviz/setup-graphviz@v2 - name: Install dependencies run: | sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 01914837ff..7f8de80350 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -23,7 +23,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.x' - name: Install dependencies