Tests are slow due to too many web queries and limits set by web resources

[fabianegli]

Description of feature

Many tests will pull form the github repo. 55 in total. This means running the tests once already pulls 55 times, running them repeatedly every couple of minutes over the course of a day apparently isn't well appreciated by github. There are other connections, too, that are done by the tests: refgenie 1x, nf-co.re 12x, api.github.com 1x, pypi.org 2x.

The repeated pulls make the tests slow and repeating the pull can probably be avoided for many tests. One pull, should be enough, and the resulting directory used could e.g. just be copied locally. It would even be nice to have the tests be mostly reduced to local folders. Git supports local repos and as such it might be possible to have the complete test suite contained in this project. After all, if we allow arbitrary git repos, it should not be restricted to repos available over http(s).

There might be some parts of the code that might have to be adapted to allow local folders as resources.

E           git.exc.GitCommandError: Cmd('git') failed due to: exit code(1)
E             cmdline: git pull -v --progress origin
E             stderr: 'fatal: unable to access 'https://github.com/nf-core/modules.git/': Could not resolve host: github.com'

[fabianegli]

OH! it's even worse. After deleting the cache and rerunning the tests with no internet connectivity:

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================== short test summary info ==============================================================================
FAILED tests/test_bump_version.py::test_bump_pipeline_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_bump_version.py::test_dev_bump_pipeline_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with...
FAILED tests/test_bump_version.py::test_bump_nextflow_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_create.py::NfcoreCreateTest::test_pipeline_creation_initiation - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_download.py::DownloadTest::test_download_configs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_download.py::DownloadTest::test_download_wf_files - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
FAILED tests/test_download.py::DownloadTest::test_download_workflow_with_success - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_download.py::DownloadTest::test_find_container_images - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_download.py::DownloadTest::test_get_release_hash_branch - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries excee...
FAILED tests/test_download.py::DownloadTest::test_get_release_hash_non_existent_release - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max...
FAILED tests/test_download.py::DownloadTest::test_get_release_hash_release - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_download.py::DownloadTest::test_matching_md5sums - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_download.py::DownloadTest::test_mismatching_md5sums - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_download.py::DownloadTest::test_singularity_pull_image_singularity_installed - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=44...
FAILED tests/test_download.py::DownloadTest::test_wf_use_local_configs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_launch.py::TestLaunch::test_build_command_empty - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with...
FAILED tests/test_launch.py::TestLaunch::test_build_command_nf - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ur...
FAILED tests/test_launch.py::TestLaunch::test_build_command_params - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_launch.py::TestLaunch::test_build_command_params_cl - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_launch.py::TestLaunch::test_get_pipeline_defaults - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
FAILED tests/test_launch.py::TestLaunch::test_get_pipeline_defaults_input_params - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_launch.py::TestLaunch::test_get_pipeline_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with...
FAILED tests/test_launch.py::TestLaunch::test_get_web_launch_response_error - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_launch.py::TestLaunch::test_get_web_launch_response_missing_keys - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retr...
FAILED tests/test_launch.py::TestLaunch::test_get_web_launch_response_unexpected - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_launch.py::TestLaunch::test_get_web_launch_response_valid - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_launch.py::TestLaunch::test_get_web_launch_response_waiting - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries e...
FAILED tests/test_launch.py::TestLaunch::test_launch_file_exists - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ...
FAILED tests/test_launch.py::TestLaunch::test_launch_file_exists_overwrite - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_launch.py::TestLaunch::test_launch_pipeline - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_launch.py::TestLaunch::test_launch_web_gui - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url:...
FAILED tests/test_launch.py::TestLaunch::test_launch_web_gui_missing_keys - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries excee...
FAILED tests/test_launch.py::TestLaunch::test_make_pipeline_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_launch.py::TestLaunch::test_nf_merge_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_launch.py::TestLaunch::test_ob_to_questionary_bool - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_launch.py::TestLaunch::test_ob_to_questionary_enum - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_launch.py::TestLaunch::test_ob_to_questionary_integer - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_launch.py::TestLaunch::test_ob_to_questionary_number - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_launch.py::TestLaunch::test_ob_to_questionary_pattern - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_launch.py::TestLaunch::test_ob_to_questionary_range - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_launch.py::TestLaunch::test_ob_to_questionary_string - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_launch.py::TestLaunch::test_prompt_web_gui_false - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_launch.py::TestLaunch::test_prompt_web_gui_true - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with...
FAILED tests/test_launch.py::TestLaunch::test_sanitise_web_response - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
FAILED tests/test_launch.py::TestLaunch::test_strip_default_params - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_lint.py::TestLint::test_actions_awsfulltest_fail - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_lint.py::TestLint::test_actions_awsfulltest_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_lint.py::TestLint::test_actions_awsfulltest_warn - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_lint.py::TestLint::test_actions_awstest_fail - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ur...
FAILED tests/test_lint.py::TestLint::test_actions_awstest_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ur...
FAILED tests/test_lint.py::TestLint::test_actions_ci_fail_wrong_docker_ver - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_lint.py::TestLint::test_actions_ci_fail_wrong_nf - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_lint.py::TestLint::test_actions_ci_fail_wrong_trigger - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_lint.py::TestLint::test_actions_ci_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /l...
FAILED tests/test_lint.py::TestLint::test_actions_schema_validation_fails_for_additional_property - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port...
FAILED tests/test_lint.py::TestLint::test_actions_schema_validation_missing_jobs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_lint.py::TestLint::test_actions_schema_validation_missing_on - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ...
FAILED tests/test_lint.py::TestLint::test_files_exist_depreciated_file - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_lint.py::TestLint::test_files_exist_missing_config - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_lint.py::TestLint::test_files_exist_missing_main - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_lint.py::TestLint::test_files_exist_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /...
FAILED tests/test_lint.py::TestLint::test_files_unchanged_fail - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ur...
FAILED tests/test_lint.py::TestLint::test_files_unchanged_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ur...
FAILED tests/test_lint.py::TestLint::test_init_PipelineLint - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: ...
FAILED tests/test_lint.py::TestLint::test_json_output - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /logo/...
FAILED tests/test_lint.py::TestLint::test_load_lint_config_ignore_all_tests - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_lint.py::TestLint::test_load_lint_config_not_found - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_lint.py::TestLint::test_merge_markers_found - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_lint.py::TestLint::test_modules_json_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: ...
FAILED tests/test_lint.py::TestLint::test_nextflow_config_bad_name_fail - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_lint.py::TestLint::test_nextflow_config_dev_in_release_mode_failed - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max re...
FAILED tests/test_lint.py::TestLint::test_nextflow_config_example_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_lint.py::TestLint::test_run_linting_function - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ur...
FAILED tests/test_lint.py::TestLint::test_sphinx_md_files - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /l...
FAILED tests/test_lint.py::TestLint::test_strip_ansi_codes - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /...
FAILED tests/test_lint.py::TestLint::test_version_consistency - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_lint.py::TestLint::test_wrap_quotes - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /logo/...
FAILED tests/test_list.py::TestLint::test_working_listcall - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /...
FAILED tests/test_list.py::TestLint::test_working_listcall_archived - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
FAILED tests/test_list.py::TestLint::test_working_listcall_json - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_modules.py::TestModules::test_get_modules_json - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ...
FAILED tests/test_modules.py::TestModules::test_install_and_update - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_modules.py::TestModules::test_install_at_hash_and_update - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_modules.py::TestModules::test_install_at_hash_and_update_and_save_diff_to_file - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=...
FAILED tests/test_modules.py::TestModules::test_mod_json_create - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_modules.py::TestModules::test_mod_json_dump - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_modules.py::TestModules::test_mod_json_get_base_path - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_modules.py::TestModules::test_mod_json_get_git_url - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_modules.py::TestModules::test_mod_json_get_module_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_modules.py::TestModules::test_mod_json_module_present - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_modules.py::TestModules::test_mod_json_repo_present - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_modules.py::TestModules::test_mod_json_up_to_date - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
FAILED tests/test_modules.py::TestModules::test_mod_json_up_to_date_module_removed - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retr...
FAILED tests/test_modules.py::TestModules::test_mod_json_up_to_date_reinstall_fails - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max ret...
FAILED tests/test_modules.py::TestModules::test_mod_json_update - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_modules.py::TestModules::test_modules_bump_versions_all_modules - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retri...
FAILED tests/test_modules.py::TestModules::test_modules_bump_versions_fail - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_modules.py::TestModules::test_modules_bump_versions_fail_unknown_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): ...
FAILED tests/test_modules.py::TestModules::test_modules_bump_versions_single_module - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max ret...
FAILED tests/test_modules.py::TestModules::test_modules_create_fail_exists - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_modules.py::TestModules::test_modules_create_nfcore_modules - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries e...
FAILED tests/test_modules.py::TestModules::test_modules_create_nfcore_modules_subtool - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max r...
FAILED tests/test_modules.py::TestModules::test_modules_create_succeed - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_modules.py::TestModules::test_modules_create_test_yml_check_inputs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max re...
FAILED tests/test_modules.py::TestModules::test_modules_create_test_yml_entry_points - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max re...
FAILED tests/test_modules.py::TestModules::test_modules_create_test_yml_get_md5 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries...
FAILED tests/test_modules.py::TestModules::test_modules_custom_yml_dumper - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries excee...
FAILED tests/test_modules.py::TestModules::test_modules_install_and_list_pipeline - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retri...
FAILED tests/test_modules.py::TestModules::test_modules_install_emptypipeline - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries e...
FAILED tests/test_modules.py::TestModules::test_modules_install_from_gitlab - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_modules.py::TestModules::test_modules_install_gitlab_and_list_pipeline - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Ma...
FAILED tests/test_modules.py::TestModules::test_modules_install_nomodule - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceed...
FAILED tests/test_modules.py::TestModules::test_modules_install_nopipeline - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_modules.py::TestModules::test_modules_install_trimgalore - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_modules.py::TestModules::test_modules_install_trimgalore_twice - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_modules.py::TestModules::test_modules_lint_empty - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_modules.py::TestModules::test_modules_lint_new_modules - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceed...
FAILED tests/test_modules.py::TestModules::test_modules_lint_trimgalore - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_modules.py::TestModules::test_modules_list_pipeline - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_modules.py::TestModules::test_modules_list_remote - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
FAILED tests/test_modules.py::TestModules::test_modules_list_remote_gitlab - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_modules.py::TestModules::test_modules_remove_trimgalore - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries excee...
FAILED tests/test_modules.py::TestModules::test_modules_remove_trimgalore_uninstalled - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max r...
FAILED tests/test_modules.py::TestModules::test_modules_test_check_inputs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries excee...
FAILED tests/test_modules.py::TestModules::test_modules_test_file_dict - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_modules.py::TestModules::test_modules_test_no_installed_modules - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retri...
FAILED tests/test_modules.py::TestModules::test_modules_test_no_name_no_prompts - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries...
FAILED tests/test_modules.py::TestModules::test_modulesrepo_class - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with...
FAILED tests/test_modules.py::TestModules::test_update_all - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /...
FAILED tests/test_modules.py::TestModules::test_update_with_config_dont_update - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ...
FAILED tests/test_modules.py::TestModules::test_update_with_config_fix_all - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_modules.py::TestModules::test_update_with_config_fixed_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_modules.py::TestModules::test_update_with_config_no_updates - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries e...
FAILED tests/test_refgenie.py::TestRefgenie::test_update_refgenie_genomes_config - subprocess.CalledProcessError: Command '['refgenie', 'pull', 't7/fasta', '-c', '/var/folders/lh...
FAILED tests/test_schema.py::TestSchema::test_add_schema_found_configs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_schema.py::TestSchema::test_build_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /...
FAILED tests/test_schema.py::TestSchema::test_build_schema_from_scratch - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_schema.py::TestSchema::test_build_schema_param_bool - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_schema.py::TestSchema::test_build_schema_param_float - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_schema.py::TestSchema::test_build_schema_param_int - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_schema.py::TestSchema::test_build_schema_param_str - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_schema.py::TestSchema::test_get_schema_path_dir - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with...
FAILED tests/test_schema.py::TestSchema::test_get_schema_path_name - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_schema.py::TestSchema::test_get_schema_path_name_notexist - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_schema.py::TestSchema::test_get_schema_path_path - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_schema.py::TestSchema::test_get_schema_path_path_notexist - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_schema.py::TestSchema::test_get_web_builder_response_404 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exce...
FAILED tests/test_schema.py::TestSchema::test_get_web_builder_response_connection_error - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max...
FAILED tests/test_schema.py::TestSchema::test_get_web_builder_response_error - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ex...
FAILED tests/test_schema.py::TestSchema::test_get_web_builder_response_saved - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ex...
FAILED tests/test_schema.py::TestSchema::test_get_web_builder_response_timeout - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ...
FAILED tests/test_schema.py::TestSchema::test_get_web_builder_response_waiting - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ...
FAILED tests/test_schema.py::TestSchema::test_get_wf_params - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: ...
FAILED tests/test_schema.py::TestSchema::test_launch_web_builder_404 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_schema.py::TestSchema::test_launch_web_builder_connection_error - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retri...
FAILED tests/test_schema.py::TestSchema::test_launch_web_builder_invalid_status - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries...
FAILED tests/test_schema.py::TestSchema::test_launch_web_builder_success - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceed...
FAILED tests/test_schema.py::TestSchema::test_launch_web_builder_timeout - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceed...
FAILED tests/test_schema.py::TestSchema::test_load_input_params_invalid - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_schema.py::TestSchema::test_load_input_params_json - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_schema.py::TestSchema::test_load_input_params_yaml - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_schema.py::TestSchema::test_load_lint_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ur...
FAILED tests/test_schema.py::TestSchema::test_load_lint_schema_nofile - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_schema.py::TestSchema::test_load_lint_schema_noparams - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_schema.py::TestSchema::test_load_lint_schema_notjson - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_schema.py::TestSchema::test_load_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /l...
FAILED tests/test_schema.py::TestSchema::test_make_skeleton_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_schema.py::TestSchema::test_prompt_remove_schema_notfound_config_returnfalse - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=44...
FAILED tests/test_schema.py::TestSchema::test_prompt_remove_schema_notfound_config_returntrue - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443...
FAILED tests/test_schema.py::TestSchema::test_remove_schema_notfound_configs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ex...
FAILED tests/test_schema.py::TestSchema::test_remove_schema_notfound_configs_childschema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Ma...
FAILED tests/test_schema.py::TestSchema::test_save_schema - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /l...
FAILED tests/test_schema.py::TestSchema::test_schema_docs - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /l...
FAILED tests/test_schema.py::TestSchema::test_validate_params_fail - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_schema.py::TestSchema::test_validate_params_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_schema.py::TestSchema::test_validate_schema_fail_duplicate_ids - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retrie...
FAILED tests/test_schema.py::TestSchema::test_validate_schema_fail_missing_def - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ...
FAILED tests/test_schema.py::TestSchema::test_validate_schema_fail_noparams - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_schema.py::TestSchema::test_validate_schema_fail_unexpected_allof - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max ret...
FAILED tests/test_schema.py::TestSchema::test_validate_schema_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wit...
FAILED tests/test_sync.py::TestModules::test_checkout_template_branch - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_sync.py::TestModules::test_commit_template_changes_changes - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ex...
FAILED tests/test_sync.py::TestModules::test_commit_template_changes_nochanges - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ...
FAILED tests/test_sync.py::TestModules::test_create_template_pipeline - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_sync.py::TestModules::test_delete_template_branch_files - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries excee...
FAILED tests/test_sync.py::TestModules::test_get_wf_config_missing_required_config - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retr...
FAILED tests/test_sync.py::TestModules::test_get_wf_config_no_branch - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_sync.py::TestModules::test_inspect_sync_dir_dirty - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
FAILED tests/test_sync.py::TestModules::test_inspect_sync_dir_notgit - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_sync.py::TestModules::test_make_pull_request_bad_response - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exc...
FAILED tests/test_sync.py::TestModules::test_make_pull_request_success - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded...
FAILED tests/test_sync.py::TestModules::test_push_template_branch_error - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceede...
FAILED tests/test_utils.py::TestUtils::test_check_if_outdated_1 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_utils.py::TestUtils::test_check_if_outdated_2 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_utils.py::TestUtils::test_check_if_outdated_3 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_utils.py::TestUtils::test_check_if_outdated_4 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_utils.py::TestUtils::test_check_if_outdated_5 - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_utils.py::TestUtils::test_get_repo_releases_branches_nf_core - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries ...
FAILED tests/test_utils.py::TestUtils::test_get_repo_releases_branches_not_exists - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retri...
FAILED tests/test_utils.py::TestUtils::test_get_repo_releases_branches_not_exists_slash - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max...
FAILED tests/test_utils.py::TestUtils::test_get_repo_releases_branches_not_nf_core - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retr...
FAILED tests/test_utils.py::TestUtils::test_list_files_git - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url: /...
FAILED tests/test_utils.py::TestUtils::test_list_files_no_git - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url...
FAILED tests/test_utils.py::TestUtils::test_load_pipeline_config - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with ...
FAILED tests/test_utils.py::TestUtils::test_pip_erroneous_package - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with...
FAILED tests/test_utils.py::TestUtils::test_pip_package_connection_error - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceed...
FAILED tests/test_utils.py::TestUtils::test_pip_package_pass - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with url:...
FAILED tests/test_utils.py::TestUtils::test_pip_package_timeout - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded with u...
FAILED tests/test_utils.py::TestUtils::test_request_cant_create_cache - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded ...
FAILED tests/test_utils.py::TestUtils::test_rich_force_colours_false - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded w...
FAILED tests/test_utils.py::TestUtils::test_rich_force_colours_true - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='nf-co.re', port=443): Max retries exceeded wi...
========================================================== 211 failed, 22 passed, 1 skipped, 1 warning in 84.70s (0:01:24) ==========================================================