From 248111d51fb75154a3196ccc1d26d04ad273f00e Mon Sep 17 00:00:00 2001 From: Shlok Natarajan Date: Wed, 26 Mar 2025 11:35:13 -0700 Subject: [PATCH 1/6] feat: pixi init + gitignore --- .gitattributes | 2 ++ .gitignore | 15 +++++++++++++++ pixi.toml | 13 +++++++++++++ 3 files changed, 30 insertions(+) create mode 100644 .gitattributes create mode 100644 pixi.toml diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..887a2c1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore index 722d5e7..27fa708 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,16 @@ .vscode + +# pixi environments +.pixi +*.egg-info + +# python +__pycache__ +*.pyc +*.pyo +*.pyd +*.pyw + +# environments +.pyenv +.env \ No newline at end of file diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 0000000..fda41e5 --- /dev/null +++ b/pixi.toml @@ -0,0 +1,13 @@ +[project] +authors = [ + "Aaron Fanous ", + "Shlok Natarajan " +] +channels = ["conda-forge"] +name = "AutoGKB" +platforms = ["osx-arm64"] +version = "0.1.0" + +[tasks] + +[dependencies] From 48289321d2fca80dfbbcc847005e57ed0cf0ad5a Mon Sep 17 00:00:00 2001 From: gtcha2 Date: Wed, 26 Mar 2025 23:24:18 -0700 Subject: [PATCH 2/6] Create .yamllint Adding the yamllint... feel free to change --- .yamllint | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 .yamllint diff --git a/.yamllint b/.yamllint new file mode 100644 index 0000000..7c5e7b3 --- /dev/null +++ b/.yamllint @@ -0,0 +1,14 @@ +--- +extends: default + +rules: + truthy: + level: warning + allowed-values: ["false", "true", "on", "off"] + document-start: + level: warning + line-length: + max: 180 + level: warning + document-start: + present: false From 207519bea40217799f8cf3b1ce506b3d3d5372ca Mon Sep 17 00:00:00 2001 From: gtcha2 Date: Wed, 26 Mar 2025 23:34:26 -0700 Subject: [PATCH 3/6] added licensing --- .gitattributes | 2 ++ .gitignore | 3 +++ .yamllint | 2 ++ pixi.toml | 3 +++ 4 files changed, 10 insertions(+) diff --git a/.gitattributes b/.gitattributes index 887a2c1..13a7fd8 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,2 +1,4 @@ +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) +# SPDX-License-Identifier: Apache-2.0 # SCM syntax highlighting & preventing 3-way merges pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore index 27fa708..b1317f0 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) +# SPDX-License-Identifier: Apache-2.0 + .vscode # pixi environments diff --git a/.yamllint b/.yamllint index 7c5e7b3..0096d43 100644 --- a/.yamllint +++ b/.yamllint @@ -1,3 +1,5 @@ +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) +# SPDX-License-Identifier: Apache-2.0 --- extends: default diff --git a/pixi.toml b/pixi.toml index fda41e5..11d286a 100644 --- a/pixi.toml +++ b/pixi.toml @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) +# SPDX-License-Identifier: Apache-2.0 + [project] authors = [ "Aaron Fanous ", From c6b99ccdb024a25d292e36b7731f28a3753cf82c Mon Sep 17 00:00:00 2001 From: gtcha2 Date: Wed, 26 Mar 2025 23:46:30 -0700 Subject: [PATCH 4/6] more license changes --- .github/workflows/build-and-test.yml | 3 +-- .github/workflows/pull_request.yml | 3 +-- .reuse/dep5.txt | 4 ++-- README.MD | 3 +++ requirements.txt | 2 ++ src/__init__.py | 3 +++ 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index f01b800..9ddd61b 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -1,9 +1,8 @@ -# # This source file is part of the Daneshjou Lab projects # # SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) # -# SPDX-License-Identifier: Apache +# SPDX-License-Identifier: Apache-2.0 # name: Build and Test diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 613fb36..c5fb06a 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -1,9 +1,8 @@ -# # This source file is part of the Daneshjou Lab projects # # SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) # -# SPDX-License-Identifier: Apache +# SPDX-License-Identifier: Apache-2.0 # name: Pull Request diff --git a/.reuse/dep5.txt b/.reuse/dep5.txt index 756bb8c..c188f2d 100644 --- a/.reuse/dep5.txt +++ b/.reuse/dep5.txt @@ -2,10 +2,10 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Files: DataSet/** Copyright: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) -License: Apache +License: Apache-2.0 Comment: All files are part of the Daneshjou Lab projects. Files: Config/** Copyright: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) -License: Apache +License: Apache-2.0 Comment: All files are part of the Daneshjou Lab projects. \ No newline at end of file diff --git a/README.MD b/README.MD index 7096ce6..1787f4d 100644 --- a/README.MD +++ b/README.MD @@ -1,3 +1,6 @@ + + + ![Build and Test](https://github.com/DaneshjouLab/AutoGKB/actions/workflows/build-and-test.yml/badge.svg) diff --git a/requirements.txt b/requirements.txt index e69de29..96fa6de 100644 --- a/requirements.txt +++ b/requirements.txt @@ -0,0 +1,2 @@ +# SPDX-FileCopyrightText: 22025 Stanford University and the project authors (see CONTRIBUTORS.md) +# SPDX-License-Identifier: Apache-2.0 diff --git a/src/__init__.py b/src/__init__.py index e69de29..2f8dae7 100644 --- a/src/__init__.py +++ b/src/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) +# +# SPDX-License-Identifier: Apache-2.0 \ No newline at end of file From eaa08b2c3f9f951b1a420cf369685fda73619adc Mon Sep 17 00:00:00 2001 From: gtcha2 Date: Wed, 26 Mar 2025 23:50:36 -0700 Subject: [PATCH 5/6] changed name --- LICENSE => LICENSES/Apache-2.0.txt | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename LICENSE => LICENSES/Apache-2.0.txt (100%) diff --git a/LICENSE b/LICENSES/Apache-2.0.txt similarity index 100% rename from LICENSE rename to LICENSES/Apache-2.0.txt From 2f3d7e77448f5a9d1a68659c17733603f59eef2c Mon Sep 17 00:00:00 2001 From: gtcha2 Date: Wed, 26 Mar 2025 23:51:06 -0700 Subject: [PATCH 6/6] fixed pylint annoying extra line --- src/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/__init__.py b/src/__init__.py index 2f8dae7..60e6ed9 100644 --- a/src/__init__.py +++ b/src/__init__.py @@ -1,3 +1,3 @@ # SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) # -# SPDX-License-Identifier: Apache-2.0 \ No newline at end of file +# SPDX-License-Identifier: Apache-2.0