From f439ecc998093931d1688f0e719e4a0bbce5daaf Mon Sep 17 00:00:00 2001 From: Erik Serrano Date: Mon, 11 May 2026 11:59:02 -0600 Subject: [PATCH 1/4] add cff file --- CITATION.cff | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..5e1d828 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,21 @@ +cff-version: 1.2.0 +message: If you use Buscar, please cite it using the metadata from this file. +title: >- + Buscar: Bioactive Unbiased Single-cell Compound Assessment and Ranking +version: 0.1.0 +date-released: 2026-05-09 +authors: + - family-names: Serrano + given-names: Erik + - family-names: Wei-shan + given-names: Li + - family-names: Bunten + given-names: Dave + - family-names: Way + given-names: Greg + email: erik.serrano@cuanschutz.com +title: Single-cell hit calling in high-content imaging screens with Buscar +license: BSD-3-Clause +doi: 10.64898/2026.04.15.718737 +repository-code: https://github.com/WayScience/buscar +abstract: Buscar is a Python framework for prioritizing compounds in high-content imaging drug screening using single-cell profiles. From 219bb590f965361a573b605b3e372be04d3de13b Mon Sep 17 00:00:00 2001 From: Erik Serrano <31600622+axiomcura@users.noreply.github.com> Date: Mon, 11 May 2026 15:10:20 -0600 Subject: [PATCH 2/4] Update CITATION.cff Co-authored-by: Dave Bunten --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 5e1d828..58a56ed 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ cff-version: 1.2.0 -message: If you use Buscar, please cite it using the metadata from this file. +message: If you use Buscar, please cite it using the metadata from the CITATION.cff file. title: >- Buscar: Bioactive Unbiased Single-cell Compound Assessment and Ranking version: 0.1.0 From 99733623c179d86544ad3b08ceea0ec2e59ed17e Mon Sep 17 00:00:00 2001 From: Erik Serrano Date: Mon, 11 May 2026 15:54:37 -0600 Subject: [PATCH 3/4] updates cff and pre commit --- .pre-commit-config.yaml | 26 ++++++++++++++++---------- CITATION.cff | 19 +++++++++++-------- 2 files changed, 27 insertions(+), 18 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index dccadb0..767c6ad 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # Documentation: https://pre-commit.com/ repos: - # Basic file checks first (fast and foundational) + # Basic file checks first (fast and foundational) - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -12,36 +12,36 @@ repos: - id: check-added-large-files args: ["--maxkb=102400"] - # Format TOML files early (before other tools might read config) + # Format TOML files early (before other tools might read config) - repo: https://github.com/pappasam/toml-sort rev: v0.24.4 hooks: - id: toml-sort args: ["--in-place"] - # Python syntax upgrades (should run before linting/formatting) + # Python syntax upgrades (should run before linting/formatting) - repo: https://github.com/asottile/pyupgrade rev: v3.21.2 hooks: - id: pyupgrade args: ["--py311-plus"] - # Import sorting (should run before Ruff to avoid conflicts) + # Import sorting (should run before Ruff to avoid conflicts) - repo: https://github.com/pre-commit/mirrors-isort rev: v5.10.1 hooks: - id: isort args: ["--profile", "black"] - # Ruff for linting and formatting Python files + # Ruff for linting and formatting Python files - repo: https://github.com/astral-sh/ruff-pre-commit rev: v0.15.12 hooks: - id: ruff-check args: ["--fix"] - - id: ruff-format # Add Ruff formatter + - id: ruff-format # Add Ruff formatter - # nbQA to run Ruff on Jupyter Notebooks (after Python tools) + # nbQA to run Ruff on Jupyter Notebooks (after Python tools) - repo: https://github.com/nbQA-dev/nbQA rev: 1.9.1 hooks: @@ -50,14 +50,20 @@ repos: args: ["--fix"] additional_dependencies: ["ruff"] - # Final cleanup (whitespace and newlines) + # validates CITATION.cff file formatting expectations +- repo: https://github.com/citation-file-format/cffconvert + rev: b6045d78aac9e02b039703b030588d54d53262ac + hooks: + - id: validate-cff + + # Final cleanup (whitespace and newlines) - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: - id: end-of-file-fixer - id: trailing-whitespace - # Keep pre-commit itself up to date (run last) + # Keep pre-commit itself up to date (run last) - repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update rev: v0.9.0 hooks: @@ -70,7 +76,7 @@ repos: name: ShellCheck description: Test shell scripts with ShellCheck entry: shellcheck - language: python + language: system types: [shell] args: ["--exclude=SC1091"] require_serial: true diff --git a/CITATION.cff b/CITATION.cff index 58a56ed..a102884 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,21 +1,24 @@ cff-version: 1.2.0 message: If you use Buscar, please cite it using the metadata from the CITATION.cff file. -title: >- - Buscar: Bioactive Unbiased Single-cell Compound Assessment and Ranking -version: 0.1.0 +title: Single-cell hit calling in high-content imaging screens with Buscar date-released: 2026-05-09 authors: - family-names: Serrano given-names: Erik - - family-names: Wei-shan + orcid: https://orcid.org/0000-0003-4188-9080 + email: erik.serrano@cuanschutz.com + - family-names: Weishan given-names: Li + orcid: https://orcid.org/0009-0001-4643-9372 - family-names: Bunten given-names: Dave + orcid: https://orcid.org/0000-0001-6041-3665 - family-names: Way - given-names: Greg - email: erik.serrano@cuanschutz.com -title: Single-cell hit calling in high-content imaging screens with Buscar + given-names: Gregory + orcid: https://orcid.org/0000-0002-0503-9348 license: BSD-3-Clause -doi: 10.64898/2026.04.15.718737 +identifiers: + - type: doi + value: 10.64898/2026.04.15.718737 repository-code: https://github.com/WayScience/buscar abstract: Buscar is a Python framework for prioritizing compounds in high-content imaging drug screening using single-cell profiles. From 9531ac335ac4dbe3bead66dde8c8d8cd379fc209 Mon Sep 17 00:00:00 2001 From: Erik Serrano Date: Tue, 12 May 2026 12:00:50 -0600 Subject: [PATCH 4/4] updated pre-commit cff --- .pre-commit-config.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e5ed35a..79a6517 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -52,10 +52,10 @@ repos: additional_dependencies: ["ruff"] # validates CITATION.cff file formatting expectations -# - repo: https://github.com/citation-file-format/cffconvert -# rev: 45126d07c5866674d438c0c905dc2c76fb0a15af -# hooks: -# - id: validate-cff +- repo: https://github.com/citation-file-format/cffconvert + rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c + hooks: + - id: validate-cff # Final cleanup (whitespace and newlines) - repo: https://github.com/pre-commit/pre-commit-hooks @@ -69,7 +69,7 @@ repos: rev: v0.9.0 hooks: - id: pre-commit-update - args: ["--verbose"] + args: ["--verbose", "--exclude", "cffconvert"] - repo: local hooks: