From 2b334e0e10dd3e9deb653c57baa409ac57e91e38 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 10 Oct 2025 10:58:31 -0700 Subject: [PATCH 1/6] add more checks --- .pre-commit-config.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 11445c4c6..564f082ab 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,14 +9,18 @@ ci: autoupdate_schedule: quarterly skip: [] submodules: false + repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: - id: check-added-large-files + - id: check-toml + - id: debug-statements + - id: end-of-file-fixer - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.7.0" + rev: "v2.8.0" hooks: - id: pyproject-fmt From afbbb18cef08f1cdce3dedf59bd2261cc0d172aa Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 10 Oct 2025 11:00:13 -0700 Subject: [PATCH 2/6] make precommit manual --- .pre-commit-config.yaml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 564f082ab..f0626ab15 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,12 +1,7 @@ ci: - autofix_commit_msg: | - [pre-commit.ci] auto fixes from pre-commit.com hooks - - for more information, see https://pre-commit.ci - autofix_prs: true - autoupdate_branch: '' - autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate' autoupdate_schedule: quarterly + # comment / label "pre-commit.ci autofix" to a pull request to manually trigger auto-fixing + autofix_prs: false skip: [] submodules: false From b28712b41e4006855315915de5ec45c578ac3eec Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 10 Oct 2025 11:02:22 -0700 Subject: [PATCH 3/6] apply formatting to pyproject.toml --- .pre-commit-config.yaml | 2 +- pyproject.toml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f0626ab15..a6061d982 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,7 +12,7 @@ repos: - id: check-added-large-files - id: check-toml - id: debug-statements - - id: end-of-file-fixer + # - id: end-of-file-fixer - repo: https://github.com/tox-dev/pyproject-fmt rev: "v2.8.0" diff --git a/pyproject.toml b/pyproject.toml index db376a71e..0c82af6bd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,6 +24,7 @@ classifiers = [ "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry", ] From 89f07c57c689ae879b0d785fa1fda495f31f5d6d Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 10 Oct 2025 11:04:26 -0700 Subject: [PATCH 4/6] add TODO --- .pre-commit-config.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a6061d982..834ce0738 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,10 +12,9 @@ repos: - id: check-added-large-files - id: check-toml - id: debug-statements - # - id: end-of-file-fixer + # - id: end-of-file-fixer # TODO: add this back in when we're ready to touch many files - repo: https://github.com/tox-dev/pyproject-fmt rev: "v2.8.0" hooks: - id: pyproject-fmt - From bd1ccdb2e69708c6f47988dfd1eee352245e76c4 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 10 Oct 2025 11:08:16 -0700 Subject: [PATCH 5/6] remove unneeded, add a few more --- .pre-commit-config.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 834ce0738..9665ded87 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,9 +10,12 @@ repos: rev: v6.0.0 hooks: - id: check-added-large-files + - id: check-case-conflict + - id: check-executables-have-shebangs + - id: check-symlinks - id: check-toml + # - id: check-yaml # TODO: resolve violation in devtools/installer/construct.yaml - id: debug-statements - # - id: end-of-file-fixer # TODO: add this back in when we're ready to touch many files - repo: https://github.com/tox-dev/pyproject-fmt rev: "v2.8.0" From 3a4bb732ae5babc86a8657c27015ec9e2bd6468b Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 27 Oct 2025 10:22:02 -0700 Subject: [PATCH 6/6] exclude contruct.yaml from precommit check --- .pre-commit-config.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a06805559..a18de9747 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,7 +14,8 @@ repos: - id: check-executables-have-shebangs - id: check-symlinks - id: check-toml - # - id: check-yaml # TODO: resolve violation in devtools/installer/construct.yaml + - id: check-yaml + exclude: devtools/installer/construct.yaml # not a true YAML file - id: debug-statements - repo: https://github.com/tox-dev/pyproject-fmt