.gitignore

# Build artifacts and generated files
*.cached
*.deb
*.pyc
*.swp
# Temporary files generated during the unit tests have $NAME.tmp.$EXTENSION pattern
*.tmp.*
*.tmp

*.user
**/.DS_Store
*.canno

# Cache files created by SwathFile with unique timestamps (YYYYMMDD_HHMMSS_hostname_pid_number.mzML)
[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]_[0-9][0-9][0-9][0-9][0-9][0-9]_*_*_*.mzML

# SwathFile test cache files
openswath_tmpfile_*.mzML
tmp_osw_cached_*.mzML
tmp_osw_cached*.mzML.cached
tmp_osw_cached_ms1.mzML*
_CPack_Packages
_deps
/src/tests/class_tests/bin
/bin
/lib

#These are the typical build directories
/build
/build-debug/*
/build-release/*
/OpenMS-build/*
/openms-build
/openms_build

/contrib-build
/contrib_build
DartConfiguration.tcl
install_manifest.txt
Makefile
moc_*.cxx*

# NB: this is the build dir not src/pyOpenMS which is tracked
/pyOpenMS

qrc_resources.cxx
resources.qrc.depends

# Autogenerated files and directories
/src/openms/OpenMS_autogen
/src/openms_gui/*_autogen
/src/openswathalgo/*_autogen
/src/tests/class_tests/openms_gui/*_autogen

# Various test outputs
/src/tests/topp/tmp_path/
/src/tests/toppas/TOPPAS_out/
/src/tests/class_tests/Testing/
/src/tests/class_tests/openms/Testing/
/src/tests/class_tests/openms/data/Testing/
/Testing/

thirdparty_licenses.txt
vcpkg_installed

# Generated CMake files
cmake-*-build
cmake-build-*
cmake_install.cmake
CMakeCache.txt
CMakeDoxyfile.in
CMakeDoxygenDefaults.cmake
CMakeFiles
CPackConfig.cmake
CPackSourceConfig.cmake
CTestTestfile.cmake
OpenMSConfig.cmake
OpenMSConfigVersion.cmake
OpenMSTargets.cmake
# NOTE: Modules/ is a generated directory, but cmake/modules/ contains tracked files
Modules/

# IDE and editor files
*.code-workspace
.cache/*
.clion.*
.idea
.qt/
.vs
.vscode
OpenMS.config
OpenMS.creator
OpenMS.files
OpenMS.includes

# Documentation build outputs (keep source files)
/doc/html/
/doc/xml/
/doc/latex/
/doc/doxygen/parameters/
/doc/doxygen/html/
/doc/doxygen/xml/
/doc/doxygen/Doxyfile
/doc/doxygen/Doxyfile_*
/doc/doxygen/doxygen-error.log
/doc/code_examples/*.mzML
/doc/code_examples/*.consensusXML
/doc/code_examples/*.featureXML
/doc/code_examples/*.arrow
/doc/code_examples/*.csv
/doc/code_examples/*.parquet
/doc/code_examples/output/
/doc/code_examples/data/

# Generated header files (CMake-configured)
/src/openms/include/OpenMS/config.h
/src/openms/include/OpenMS/OpenMSConfig.h
/src/openms/include/OpenMS/build_config*.h
/src/openms/include/OpenMS/openms_data_path.h
/src/openms/include/OpenMS/openms_package_version.h
/src/openms/extern/**/*Config.cmake
/src/openms/extern/**/*ConfigVersion.cmake
/src/openms/extern/**/*config*.cmake
/src/openms/extern/**/*.pc
/src/openms_gui/include/OpenMS/VISUAL/OpenMS_GUIConfig.h
/src/openms_gui/qrc_resources.cpp
/src/openswathalgo/include/OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h

# Log files
TOPP.log
TOPPAS.log

# Test data and output files
/src/tests/class_tests/*/include/OpenMS/test_config.h
/src/tests/topp/OpenNuXL_1_input.mzML.ambiguous_masses.csv
/src/tests/toppas/*.trf

# Test files in root (should be in proper directories)
/test.mzML
/test.mzData
/test_output.log

# Security - Credentials, tokens, and secrets
.env
.env.*
.env.local
.env.*.local
*.pem
*.key
*.p12
*.pfx
*.crt
*.cer
*.der
!*.crt.example
!*.key.example
credentials.json
credentials.yaml
credentials.yml
secrets.json
secrets.yaml
secrets.yml
secrets.toml
**/secrets/
**/credentials/
.secrets
.credentials
*.secret
*.secrets

# AWS
.aws/
aws_credentials
.boto

# SSH keys
id_rsa
id_rsa.pub
id_dsa
id_dsa.pub
id_ecdsa
id_ecdsa.pub
id_ed25519
id_ed25519.pub
*.ppk

# API tokens and keys
.npmrc
.pypirc
.netrc
.htpasswd
.htaccess
*.token
api_key*
apikey*
auth.json
auth.yaml
auth.yml

# Docker secrets
docker-compose.override.yml
docker-compose.*.yml
!docker-compose.example.yml

# Kubernetes
kubeconfig
*.kubeconfig
kube/config

# OAuth
oauth_token*
oauth-token*
client_secret*
client-secret*

# GPG
*.gpg
secring.*
pubring.*
trustdb.*

# Terraform
*.tfstate
*.tfstate.*
*.tfvars
!*.tfvars.example
.terraform/

# Ansible
*.vault
vault.yml
vault.yaml
group_vars/*/vault*
host_vars/*/vault*

# IDE credential storage
.idea/**/dataSources/
.idea/**/dataSources.ids
.idea/**/dataSources.xml
.idea/**/dataSources.local.xml

# Shell history (may contain credentials)
.bash_history
.zsh_history
.sh_history

# Local configuration that may contain secrets
config.local.*
settings.local.*
*.local.json
*.local.yaml
*.local.yml
*.local.toml

# Jupyter notebooks checkpoints (may contain credentials in outputs)
.ipynb_checkpoints/

# GitHub tokens
.github_token
github_token*

# Claude/AI tokens
.claude_token
.anthropic_key