ggd cli update

[mikecormier]

Add prefix flag to

• install
• list-files
• utils (Helper function to ensure correct prefix entry)

Unit test for prefix flag

Update post-link scripts to work with prefix flag

• Results in ggd only data package install (conda install <data-package> will not work anymore)

Refactor code for: (not just for prefix flag)

• install
• list-files
• uninstall
• make-recipe
• check-recipe
• pkg-info
• utils
• All unit tests

Update to species, genome build, and ggd channel metadata files.

• No longer use local clones of ggd repos
• Create new species, genome build, and ggd channel metadata files during ggd-recipe nightly testing in ggd-metadata
• Update each script from old system to new system

Update conda version

• Update conda sovler bypass

New internet free capability for info scripts. Functions that can work without internet now include:

• make-recipe
• list-files
• pkg-info
• show-env
• uninstall

Functions still requiring internet include:

• install
• search
• check-recipe

Update yaml.load to yaml.safe_load

Speed up solver bypass

New unit tests for internet free contexts

New conda list function to get ggd specific install data packages as a dictionary using conda module

Rename ggd list-files command to ggd get-files

New ggd list command (List installed data packages files for a specific conda environment)

• list

New function for updating local metadata file containing installed data packages

• utils (function)
• install (Update metadata file)
• uninstall (Update metadata file)
• test_info_scripts (Unit tests for ggd list)
• test_internet_free (Unit test for ggd list)
• test_utils (Unit test for new metadata file function)
• test_install (Unit test for metadata file update)
• test_unisntall (Unit test for metadata file update)

Prefix name can now be used for the prefix argument and not just the prefix flag

• Changes to utils.prefix_in_conda, utils.conda_rootm and utils.get_conda_env to allow for prefix handling using the conda prefix module
• New functions utils.get_conda_prefix_path to help get the prefix path from a prefix path or prefix name
• Updates in ggd.install, ggd.get-files, ggd.list to use prefix name and prefix path
• Additional updates for prefix processing
• New unit test for utils, install, and info scripts created

Update package removal during uninstall within a specific prefix

• Uninstalling a package, including when a package fails to install, now works for a specific prefix
• Only package within that prefix is removed. Package in above or bellow nested prefixes are preserved
• Environment variables in a specific prefix are now removed
• New unit test for uninstall process for a specific prefix and environment variable removal for a specific prefix

Add checksum for data file contents

• running check-recipe will add md5sum for each data file created by the recipe to the recipe dir
• new final-files and file-type keys added to yaml from check-recipe

New make-recipes flag requirement for coordinate base

New predict-path method

• predict the installed file path of a data file that has not been installed yet.
• Support for Snakemake and other workflows that need to know the location of the file before running the workflow

Update gsort version to 0.1.2

Install refactor

• Install now takes multiple packages names (instead of just one).
• Install can now take install a list of packages in a file (--file argument)
  • 1 package per line
• update solver bypass to include multiple packages
• update package error handling for multiple packages
• refactor install code (speed up)
• update unit tests
• New checksum check during installation
• update output report
• remove -v for version checking.
  • This is inherent in the package name now

Search refactor

• Main search include package names and keywords
• search will try to filter based on a given genome build or species even if the -g or -s argument are not given
• Remove -t as an argument. (Now a positional argument)
• speed up search
• update output report

Update pkg-info

• update output
• remove -av argument

New stdout

• stdout will include :ggd:<function>:

Refactor imports to speed up ggd startup

Optimize some tests

Split macos python2 unit tests into two parts

• Changes to conda-build cause an extended time for building a package. Without splitting the unit test, the tests will time out

Code reformated