Fix diamond tests failing with each new version

[AroneyS]

Compare diamond eval and bitscore with assertAlmostEqual using assertEquivalent function

[AroneyS]

The external GraftM command is also erroring. I guess PATH=bin:$PATH nosetests -v from the workflow isn't working as intended?

[wwood]

Yeh that PATH issue I'm not sure about. I'm not actually sure that bin is the right thing to add to the PATH since not 100% sure on what the CWD is. Maybe print it and result of ls to be sure.

[AroneyS]

Yeh that PATH issue I'm not sure about. I'm not actually sure that bin is the right thing to add to the PATH since not 100% sure on what the CWD is. Maybe print it and result of ls to be sure.

One of the failing commands says it is running root: DEBUG: Running extern cmd: /home/runner/work/graftM/graftM/test/../bin/graftM update --graftm_package /home/runner/work/graftM/graftM/test/data/mcrA.10seqs.gpkg --sequences /tmp/tmpojkmn3mr --taxonomy /tmp/tmpa3ku0fgt --output updated.gpkg, which should find it?

[AroneyS]

Yeh that PATH issue I'm not sure about. I'm not actually sure that bin is the right thing to add to the PATH since not 100% sure on what the CWD is. Maybe print it and result of ls to be sure.

One of the failing commands says it is running root: DEBUG: Running extern cmd: /home/runner/work/graftM/graftM/test/../bin/graftM update --graftm_package /home/runner/work/graftM/graftM/test/data/mcrA.10seqs.gpkg --sequences /tmp/tmpojkmn3mr --taxonomy /tmp/tmpa3ku0fgt --output updated.gpkg, which should find it?

Its the self._test_package which actually fails. It is an internal GraftM function and so doesn't add the script path.

[AroneyS]

echo $PATH
/usr/share/miniconda/envs/test/bin:/usr/share/miniconda/condabin:/usr/share/miniconda/condabin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/runner/.dotnet/tools

echo $GITHUB_PATH
/home/runner/work/_temp/_runner_file_commands/add_path_f29c64b8-b57a-4b49-b765-90f34c91bc78

echo bin >> $GITHUB_PATH
echo $GITHUB_PATH
/home/runner/work/_temp/_runner_file_commands/add_path_f29c64b8-b57a-4b49-b765-90f34c91bc78

ls
LICENCE.txt
MANIFEST.in
README.md
SILVA.LICENCE.txt
bin
check-for-untracked-files.sh
example_data
graftm
graftm.yml
setup.py
share
test

graftM -h
/home/runner/work/_temp/3734861c-7714-48e4-9ec3-b16ec4923234.sh: line 6: graftM: command not found

[AroneyS]

One of the previous guesses turned out to be correct.