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CHANGELOG.rst

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Changelog

Version 1.8.7: Wrapped gradients and tsconcat commands & explicit Apptainer support

  • Wrap ghcr.io/childmindresearch/ba-timeseries-gradients:main as gradients command
  • Wrap ba-tsconcat as tsconcat command
  • Require Python ≥ 3.10
  • Fix a bug in which an argument with the same string as a command would supercede the given command if the same-string argument is listed first in argument parser and the usage string (e.g., cpac gradients ${BIDS_DIR} ${OUTPUT_DIR} group would run cpac group gradients ${BIDS_DIR} ${OUTPUT_DIR} instead of cpac gradients ${BIDS_DIR} ${OUTPUT_DIR} group)
  • Adds explicit support for Apptainer
  • Replaces disabled Singularity tests with enabled Apptainer tests in GitHub Actions

Version 1.8.6.post1: Broader Singularity & Apptainer support

  • Fixes a bug when trying to run in some versions of Singularity

Version 1.8.6: Support for C-PAC v1.8.6

  • Fixes a bug in checking for C-PAC version
  • Updates dependabot configuration

Version 1.8.5: Support for C-PAC v1.8.5

  • Changes versioning scheme to match supported C-PAC version
  • Handles relocation of default pipeline in C-PAC 1.8.5
  • Fixes a bug preventing default bindings in Mac OS ≥ 10.15
  • Replaces setup.cfg with pyproject.toml
  • Replaces setuptools with poetry
  • Adds pre-commit hooks for linting and formatting
  • Require Python ≥ 3.8

Version 0.5.0: Parse Resources

  • 🧮 Evaluates memory usage for specific nodes from callback.log files
  • ✨ Adds enter command to enter a container's BASH
  • ✨ Adds version command to give version of in-container C-PAC
  • ✨ Adds parse-resources command to parse resources from callback.log
  • 🐛 Fixes issue where --version command was not working
  • 🐛 Fixes issue where custom pipeline configurations were not binding to temporary container prior to checking for bind paths
  • ✅ Updates for tests that were failing
  • 📝 Add known issues to usage string
  • ⬆ Require Python ≥ 3.7 (for typing annotations)
  • 📝 Documents support for Singularity 3

Version 0.4.0: Goodbye Singularity Hub

  • 👽 Drop call to now-deprecated Singularity Hub
  • 🐛 Resolves issue where minimal configs would cause wrapper to crash

Version 0.3.2: Pull / Upgrade

  • ➖ Remove dependecy on Nipype
  • 🐛 Pass commandline arguments through to cpac crash
  • 🚸 Add pull / upgrade command
  • ⚡️🐳 Stop Docker containers when finished
  • 👽 Handle changes from C-PAC 1.7 to 1.8
  • 👷 Move tests from Travis to GitHub Actions
  • 📝 Note needlessness of crash command for C-PAC ≥ 1.8.0
  • 🚸 Use repeated flags in place of multi-value tags

Version 0.3.1

  • 🚸 Print without emoji if terminal can't handle extended Unicode set
  • 📚 Add PyPI badge to README

Version 0.3.0

Version 0.2.5

  • 📚 Update the main usage string to better articulate functionality
  • 📢🐳 Provide a clearer error message if package cannot connect to Docker.
  • 🐳 Fix a bug introduced in v0.2.4 <https://github.com/shnizzedy/cpac/releases/tag/v0.2.4> where some crashfiles would print for cpac --platform singularity crash but not for cpac --platform docker crash
  • 🚑 Fix some installation issues:
    • All required packages are now installed with pip install cpac
    • Version is now set correctly
  • 🐳 Fix a bug introduced in v0.2.4 where some crashfiles would print for cpac --platform singularity crash but not for cpac --platform docker crash
  • 🔬 Set coverage reports to report local paths

Version 0.2.4

  • 💪 Make crash command automatically touch (within a container) all missing files a crashfile requires to exist and print the underlying output
  • 🐳 Make Docker commands (especially pull and crash) more robust
  • ⬆️ Require Python ≥3.6 (for fstrings)

Version 0.2.3: Crashfile

  • ✨ Added group and crash commands
  • 🚑 Fixed a bug where pass-through flags were being mangled
  • 🖇️ Binds any directories necessary to access any paths found in pass-through CLI arguments

Version 0.2.2: Autobind

Version 0.2.2.post1

  • 🖉 Pass run -h through like run --help

Version 0.2.2

  • ✨ Automatic binding of necessary local directories to Docker or Singularity
  • 📚 Pass run --help through to container without positional arguments to get full current helpstring

Version 0.2.1

  • Ⓢ Enabled specifying Singularity image file or Docker tag for Singularity

Version 0.2.0

  • ✨Ⓢ Added Singularity support

Version 0.1.5

  • ⬆ Added installation depenencies

Version 0.1.4

  • 🚑 Removed erroneous import statement

Version 0.1.3

  • ➕ Require docker-pycreds, websocket-client

Version 0.1.2

  • 🚑 Fixed bug preventing binding the same local directory to multiple Docker directories

Version 0.1.1

  • ✨ Added support for pip install
  • ✨ Added support for cpac run
  • ✨ Added support for cpac utils
  • 🔊🐳 Routed live Docker logging to stdout
  • 🔬 Added tests for cpac run and cpac utils

Version 0.1.0

  • ✨🐳 Ported Docker support from Theodore