1.1.3

Release for paper publication

1.1.2

Update ggd search

• keyword substrings (Like 'clinvar' for grch37-clinically-associated-variants-ensembl-v1)

• Increase match score cutoff to 90. (Require more strict match scores by default)

1.1.1

Add minor features for meta-recipes

CLI Update

• Update to version 1.1.1
• Update predict-path to predict the directory path of a meta-recipe. (Provides at least some "prediction" of the directory path of installed files for a meta-recipe based on an ID.)
• Update search to reflect the --id parameter when installing a meta-recipe

Test Update

• Add unit test to predict-path for directory path and meta-recipes
• Add unit tests to search for meta-recipes

1.1.0

Update to GGD CLI for minor bug fixes and the addition of meta-recipes

CLI Update

• Update to version 1.1.0
• Add make-meta-recipe script for making meta-recipes. (Major update to post-link for meta-recipe installation)
• Update check-recipe to support meta-recipe checking. (NOTE: checksum and final files are not checked for meta-recipes)
• Update to pkg-info for updated ID specific meta-recipes
• Update to pkg-info to support --prefix. (Get pkg-info in a different conda environment)
• Update to utils for meta-recipe support:
  • get_base_env
  • get_repodata (Method to get the ggd specific conda channel repo data from the Anaconda Cloud)
  • check_for_meta_recipes (Check if the a recipe is a meta-recipe)
  • get_meta_recipe_pkg (Download the meta-recipe pkg tar file from the Anaconda Cloud) (Check md5sum)
  • create_tmp_meta_recipe_env_file (Temp dir and files for ID specific meta-recipe environment variables used to update meta-recipe info)
  • extract_metarecipe_recipe_from_bz2 (Update tar.bz2 meta-recipe pkg to a ID specific meta-recipe)
  • update_metarecipe_metadata (Method to update the ID specific meta-recipe metadata using environment variables set during pkg installation. Environment Variables include:
    • GGD_METARECIPE_SUMMARY
    • GGD_METARECIPE_SPECIES
    • GGD_METARECIPE_GENOME_BUILD
    • GGD_METARECIPE_VERSION
    • GGD_METARECIPE_KEYWORDS
    • GGD_METARECIPE_DATA_PROVIDER
    • GGD_METARECIPE_GENOMIC_COORDINATE_BASE
  • get_meta_recipe_checksum (If precomputed checksum available for a ID specific meta-recipe, get it)
• Update install to be able to install a meta-recipe
• Update uninstall to uninstall a meta-recipe
• Update list to list installed meta-recipes. (Meta-recipes are installed locally. Previously, locally installed files were not included in the list of installed files)
• Update get-files to get the files of installed meta-recipes. (Previously, get-files could not access locally installed files.)
• NO Update for predict-path. (Currently, predicting an arbitrary path to a nonexistent file for an ID specific meta-recipe is not implemented.)
• Depreciate Python 2 (No longer testing Python 2, as well as no longer supporting/maintaining python2 within the CLI)
• Update stdout for meta-recipes

Test Update

• Update all unit tests to comply with updated CLI
• Add new unit tests for new methods/functions added
• Add/update unit tests for existing methods with support for meta-recipe

1.0.2

Update to conda 4.9.0

Other Minor Fixes

1.0.1

Update prefix handling

1.0.0

New major version of GGD

CLI Update

• Update file size info
• Update get-file size and file size check
• Add kilobyte size buffer
• Require Samtools >= 1.10
• Warning when check-recipes is checking .bcf file (check-sort-order is unable to check this type of file)
• Update command options and help messages
• Update command stdout and stderr.
• Add --prefix check to search and install. Set warnings/errors if recipe is unable to install with --prefix when --prefix is set
• Update search workflow
• Add search-type to search. (Filter search based on how the search terms are combined)
• Replace conda uninstall with conda remove
• Remove duplicate output in uninstall
• Update code formatting
• Update README
• Other minor fixes and update

Test Update

• Test associated with the updates, additions, and fixes from the CLI update

0.1.3

Major Update to CLI to fix bugs, add functionality, and improved unit tests.

CLI Update

• Update metadata dir permission
• Update uninstall
• Update metadata for each data package removed include run deps
• Uninstall ggd specific run dependencies
• Allow mutliple data packages to be uninstalled at the same time
• Add reset for metadata reset
• Handle metadata channeldata update with ggd specific run dependencies
• Update metadata channeldata handling for local recipes
• Add python 2 warning when using python 2
• Fix error with packages uninstalled by conda but maintained by ggd
• Bug fixes in check-sort-order
• Update search with more stringent package searching and sorting
• Update check-sort-order requirement
• Skip env var activate (BUG)
• Update support for alternative genome files
• Yaml literal block handling
• Add yaml literal block support
• Add alternative genome file check-sort-order
• Add checks for final files in check-recipes
• Update stdout
• Update normal conda install
• Update install debuging
• Update req
• Update conda requirement collection
• Update output to include approximate data file sizes
• Update package handling
• Update error report
• Update conda and conda build requirements
• Add file size as a field in the yaml file
• Add strict channel priority to the .condarc

Test Update

• Update and add test to uninstall
• Add test for metadata reset
• Test metadata channeldata handling for local recipes
• Skip certian checks if python 2
• Update check-recipe tests
• Add test for error with packages uninstalled by conda but maintained by ggd
• Test new check-sort-order
• Require Python 3.7
• Updates search tests for improved searching
• Additional tests for alternative genome files
• Update brew instructions
• New xcode version
• Test Yaml literal block handling
• Add test for yaml literal block support
• Add test for alternative genome file check-sort-order
• Add test for getting approximate file sizes
• Add support and tests for final-file-sizes
• Update test for checking yaml updates
• Update test for final file checks
• update yaml file checks
• Update Install tests
• Test new package handling
• Update checks for yaml tag info
• test file size as a field in the yaml file
• Update miniconda install for testing
• Add strict channel priority to the .condarc

0.1.2

CLI Update

Enhancements:

• Update check-recipe

  • Improve conda list pkg searching
  • Add method to check for header in genomic files
  • Add .csi support

• Update check-recipe test

  • New tests for check-header function
  • Update helper function for header tests
  • New test for add_files to add extra files to the yaml
  • New test for check-files to account for extra files
  • test for .csi files

• Update install test to use better conda info searching

• Update and add new requirements

  • Newest version of conda = 4.8.2
  • Newest version of conda-buld = 3.8.12
  • Add pysam
  • Add cyvcf2

• Update conda version to conda 4.8.2

Bug fixes:

• Update stdout for user

• Update extra file error to a warning and attempt to fix the problem

• Update utils with new methods

  • Method to check that conda pkg dir for installed ggd metadata. If missing will replace

• Update utils tests

  • New test for checking conda pkg dir for ggd installed metadata

• Update Error Handling

Contributors:

• @mikecormier

0.1.1

bump gsort