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Code Issues Releases Packages Activity

Proper user tests now :-)

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Alexander Peltzer 2019-11-26 13:57:32 +01:00
parent 7e3efcac5c
commit cb876594a3
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3 changed files with 79 additions and 2 deletions
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3
.github/workflows/main.yml vendored
View file

@ -19,5 +19,8 @@ jobs:
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Check whether profiles are all tested appropriately
run: |
python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
- name: "Check profile"
run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}

71
bin/cchecker.py Normal file
View file

@ -0,0 +1,71 @@
#!/usr/bin/env python
#######################################################################
#######################################################################
## Created on November 26 to check pipeline configs for nf-core/configs
#######################################################################
#######################################################################
import os
import sys
import argparse
import re
############################################
############################################
## PARSE ARGUMENTS
############################################
############################################
Description = 'Double check custom config file and github actions file to test all cases'
Epilog = """Example usage: python cchecker.py <nfcore_custom.config> <github_actions_file>"""
argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)
## REQUIRED PARAMETERS
argParser.add_argument('CUSTOM_CONFIG', help="Input nfcore_custom.config.")
argParser.add_argument('GITHUB_CONFIG', help="Input Github Actions YAML")
args = argParser.parse_args()
############################################
############################################
## MAIN FUNCTION
############################################
############################################
def check_config(Config, Github):
regex = 'includeConfig*'
ERROR_STR = 'ERROR: Please check config file! Did you really update the profiles?'
## CHECK Config First
config_profiles = set()
with open(Config, 'r') as cfg:
for line in cfg:
if re.search(regex, line):
hit = line.split('/')[2].split('.')[0]
config_profiles.add(hit)
###Check Github Config now
tests = set()
with open(Github, 'r') as ghfile:
for line in ghfile:
if re.search('profile: ', line):
line = line.replace('\'','').replace('[','').replace(']','')
profiles = line.split(':')[1].split(',')
for p in profiles:
tests.add(p)
print(len(tests))
print(len(config_profiles))
###Check if sets are equal
if tests == config_profiles:
sys.exit(0)
else:
#Maybe report what is missing here too
#print("Tests don't seem to test these profiles properly!\n")
# print(config_profiles.difference(tests))
sys.exit(1)
check_config(Config=args.CUSTOM_CONFIG,Github=args.GITHUB_CONFIG)

7
nfcore_custom.config
View file

@ -11,6 +11,7 @@
params.custom_config_version = 'master'
params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
//Please use a new line per includeConfig section to allow easier linting/parsing. Thank you.
profiles {
awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
@ -21,7 +22,8 @@ profiles {
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" }
gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
@ -34,7 +36,8 @@ profiles {
shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax_devel.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config";
includeConfig "${params.custom_config_base}/conf/uppmax_devel.config" }
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
}