--git-range fails on GitHub CI

[grst]

Hi @mbargull,

maybe you can help.
Your suggestion in actions/checkout#160 indeed works for git diff, but unfortunately not for the bioconda-utils --git-range parameter.

I tried

modules/.github/workflows/build.yml

Lines 29 to 30 in e43419a

	run: |
	bioconda-utils lint tools config.yml --exclude missing_hash missing_tests --git-range origin/master HEAD

but it still fails with

AttributeError: 'NoneType' object has no attribute 'diff'

Any idea what could be the problem?

Thanks,
Gregor

Full log

Run bioconda-utils lint tools config.yml --exclude missing_hash missing_tests --git-range origin/master HEAD
2020-02-20T17:50:42.0574914Z �[36;1mbioconda-utils lint tools config.yml --exclude missing_hash missing_tests --git-range origin/master HEAD�[0m
2020-02-20T17:50:42.0611050Z shell: /bin/bash -l {0}
2020-02-20T17:50:42.0611146Z ##[endgroup]
2020-02-20T17:50:43.4015794Z 17:50:43 �[32mBIOCONDA INFO�[0m Considering total of 4 recipes (bwa-index, gatk-dict, fastqc, trim_galore).�[0m
2020-02-20T17:50:43.4016638Z 17:50:43 �[31mBIOCONDA ERROR�[0m No merge base found for HEAD and master�[0m
2020-02-20T17:50:43.4017425Z 17:50:43 �[31mBIOCONDA ERROR�[0m Dropping into debugger
2020-02-20T17:50:43.4017594Z Traceback (most recent call last):
2020-02-20T17:50:43.4017958Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 71, in wrapper
2020-02-20T17:50:43.4018075Z     func(*args, **kwargs)
2020-02-20T17:50:43.4018594Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 345, in do_lint
2020-02-20T17:50:43.4018701Z     recipes = get_recipes(config, recipe_folder, packages, git_range)
2020-02-20T17:50:43.4019089Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 168, in get_recipes
2020-02-20T17:50:43.4019201Z     changed_recipes = get_recipes_to_build(git_range, recipe_folder)
2020-02-20T17:50:43.4019567Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 152, in get_recipes_to_build
2020-02-20T17:50:43.4019682Z     return repo.get_recipes_to_build(ref, other)
2020-02-20T17:50:43.4020037Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/githandler.py", line 491, in get_recipes_to_build
2020-02-20T17:50:43.4020150Z     tobuild = set(self.get_changed_recipes(ref, other))
2020-02-20T17:50:43.4020621Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/githandler.py", line 433, in get_changed_recipes
2020-02-20T17:50:43.4020727Z     for path in self.list_changed_files(ref, other):
2020-02-20T17:50:43.4021053Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/githandler.py", line 329, in list_changed_files
2020-02-20T17:50:43.4021159Z     for diffobj in merge_base.diff(ref):
2020-02-20T17:50:43.4021430Z AttributeError: 'NoneType' object has no attribute 'diff'�[0m
2020-02-20T17:50:43.4043548Z Traceback (most recent call last):
2020-02-20T17:50:43.4044081Z   File "/usr/share/miniconda/envs/test/bin/bioconda-utils", line 8, in <module>
2020-02-20T17:50:43.4044185Z     sys.exit(main())
2020-02-20T17:50:43.4044562Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 947, in main
2020-02-20T17:50:43.4044683Z     bioconductor_skeleton, clean_cran_skeleton, autobump, bot
2020-02-20T17:50:43.4045114Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/argh/dispatching.py", line 328, in dispatch_commands
2020-02-20T17:50:43.4045223Z     dispatch(parser, *args, **kwargs)
2020-02-20T17:50:43.4045590Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/argh/dispatching.py", line 174, in dispatch
2020-02-20T17:50:43.4045709Z     for line in lines:
2020-02-20T17:50:43.4046078Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/argh/dispatching.py", line 277, in _execute_command
2020-02-20T17:50:43.4046191Z     for line in result:
2020-02-20T17:50:43.4046646Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/argh/dispatching.py", line 260, in _call
2020-02-20T17:50:43.4046755Z     result = function(*positional, **keywords)
2020-02-20T17:50:43.4047050Z   File "<boltons.funcutils.FunctionBuilder-3>", line 8, in do_lint
2020-02-20T17:50:43.4047495Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 130, in wrapper
2020-02-20T17:50:43.4047580Z     func(*args, **kwargs)
2020-02-20T17:50:43.4048090Z   File "<boltons.funcutils.FunctionBuilder-2>", line 8, in do_lint
2020-02-20T17:50:43.4048468Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 59, in wrapper
2020-02-20T17:50:43.4048687Z     func(*args, **kwargs)
2020-02-20T17:50:43.4048971Z   File "<boltons.funcutils.FunctionBuilder-1>", line 8, in do_lint
2020-02-20T17:50:43.4049295Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 71, in wrapper
2020-02-20T17:50:43.4049394Z     func(*args, **kwargs)
2020-02-20T17:50:43.4049708Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 345, in do_lint
2020-02-20T17:50:43.4049795Z     recipes = get_recipes(config, recipe_folder, packages, git_range)
2020-02-20T17:50:43.4050124Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 168, in get_recipes
2020-02-20T17:50:43.4050231Z     changed_recipes = get_recipes_to_build(git_range, recipe_folder)
2020-02-20T17:50:43.4050574Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/cli.py", line 152, in get_recipes_to_build
2020-02-20T17:50:43.4050684Z     return repo.get_recipes_to_build(ref, other)
2020-02-20T17:50:43.4051013Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/githandler.py", line 491, in get_recipes_to_build
2020-02-20T17:50:43.4051118Z     tobuild = set(self.get_changed_recipes(ref, other))
2020-02-20T17:50:43.4051458Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/githandler.py", line 433, in get_changed_recipes
2020-02-20T17:50:43.4051564Z     for path in self.list_changed_files(ref, other):
2020-02-20T17:50:43.4051885Z   File "/usr/share/miniconda/envs/test/lib/python3.7/site-packages/bioconda_utils/githandler.py", line 329, in list_changed_files
2020-02-20T17:50:43.4051990Z     for diffobj in merge_base.diff(ref):
2020-02-20T17:50:43.4052260Z AttributeError: 'NoneType' object has no attribute 'diff'
2020-02-20T17:50:43.5213914Z ##[error]Process completed with exit code 1.

[mbargull]

Ah, I vaguely remember something like this. Maybe try to git fetch origin master and use FETCH_HEAD instead of origin/master? Or, if that does not work, git fetch origin master:some_random_name and use some_random_name then.

[grst]

Hmm, neither of the following seems to work :/
Same error message as before.

git fetch origin master:latest_master && bioconda-utils lint tools config.yml --exclude missing_hash missing_tests --git-range latest_master HEAD

git fetch origin master && bioconda-utils lint tools config.yml --exclude missing_hash missing_tests --git-range FETCH_HEAD HEAD

[mbargull]

Oh, sorry, I didn't look at the context of what you were doing overall.
You are using actions/checkout@v2 which does a shallow checkout by default. Because of that, the history to determine the merge base is not there.
You'd want to set the fetch-depth parameter to some reasonable value (0 fetches everything).

[mbargull]

Maybe origin/master will work directly then, too.

[grst]

This did indeed do the trick :)
Thanks a lot for your help!