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EXP: MacOS compatibility #214

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EXP: MacOS compatibility #214

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085eda4
Add macos-latest to test matrix
camillescott Jan 29, 2021
4b22e76
Attempt making paths portable
camillescott Jan 29, 2021
2ff908e
Use env context
camillescott Jan 29, 2021
9fe86f7
Try using runner.temp for dammit data
camillescott Jan 29, 2021
10126ed
dammit how does this work
camillescott Jan 29, 2021
596f730
Merge cross-platform actions paths commits
camillescott Jan 29, 2021
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20 changes: 10 additions & 10 deletions .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,15 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-18.04]
os: [ubuntu-18.04, macos-latest]
py: [3.7, 3.8]
defaults:
run:
shell: bash -l {0}
env:
DAMMIT_DB_DIR: /home/runner/databases
DAMMIT_CONDA_DIR: /home/runner/snakemake-envs-${{ matrix.os }}
DAMMIT_TESTING_TEMP_BASE_DIR: /home/runner/snakemake-envs-${{ matrix.os }}
DAMMIT_DB_DIR: ${{ github.workspace }}/data/databases
DAMMIT_CONDA_DIR: ${{ github.workspace }}/data/snakemake-envs-${{ matrix.os }}
DAMMIT_TESTING_TEMP_BASE_DIR: ${{ github.workspace }}/data/snakemake-envs-${{ matrix.os }}
steps:
- uses: actions/checkout@v2
with:
Expand Down Expand Up @@ -53,11 +53,11 @@ jobs:
uses: actions/cache@v2
with:
path: |
/home/runner/databases/Pfam-A.hmm
/home/runner/databases/Pfam-A.hmm.h3f
/home/runner/databases/Pfam-A.hmm.h3i
/home/runner/databases/Pfam-A.hmm.h3m
/home/runner/databases/Pfam-A.hmm.h3p
${{ env.DAMMIT_DB_DIR }}/Pfam-A.hmm
${{ env.DAMMIT_DB_DIR }}/Pfam-A.hmm.h3f
${{ env.DAMMIT_DB_DIR }}/Pfam-A.hmm.h3i
${{ env.DAMMIT_DB_DIR }}/Pfam-A.hmm.h3m
${{ env.DAMMIT_DB_DIR }}/Pfam-A.hmm.h3p
key: databases-${{ hashFiles('dammit/databases.yml') }}

- name: setup databases
Expand All @@ -68,7 +68,7 @@ jobs:
uses: actions/cache@v2
with:
path: |
/home/runner/snakemake-envs-${{ matrix.os }}
${{ env.DAMMIT_CONDA_DIR }}
key: ${{ matrix.os }}-snakemake-envs

- name: run pytest
Expand Down
9 changes: 7 additions & 2 deletions dammit/wrappers/download/wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@
__email__ = "cswel@ucdavis.edu"
__license__ = "MIT"

import sys

from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)

Expand Down Expand Up @@ -34,8 +36,11 @@
raise ValueError('Valid filetypes are "gz", "tar.gz", and "uncompressed"')

if snakemake.params.get('md5'):
cmd.append('&& python -c "assert \'`md5sum {output} | '
'awk \'{{print $1}}\'`\' == \'{snakemake.params.md5}\', '
if sys.platform == 'darwin':
md5cmd = "md5 {output} | awk '{{print $4}}'"
else:
md5cmd = "md5sum {output} | awk '{{print $1}}'"
cmd.append('&& python -c "assert \'`' + md5cmd + '`\' == \'{snakemake.params.md5}\', '
'\'MD5sum does not match\'"')

cmd.append("{log}")
Expand Down