[Debian-med-packaging] Bug#1020106: macsyfinder: FTBFS: AssertionError: "Models Parsing\nunable to parse model def[104 chars]del." != "unable to parse model definition 'foo/mod[88 chars]del."

Sun Sep 18 07:30:59 BST 2022

Source: macsyfinder
Version: 2.0~rc7-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220917 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
>  debian/rules binary
> dh binary --with python3,sphinxdoc --buildsystem=pybuild
>    dh_update_autotools_config -O--buildsystem=pybuild
>    dh_autoreconf -O--buildsystem=pybuild
>    dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:240: python3.10 setup.py config 
> running config
>    dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:240: /usr/bin/python3 setup.py build 
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/package.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/solution.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/definition_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/report.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/model_conf_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/hit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/profile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/registries.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/gene.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/system.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/serialization.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/search_genes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/database.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/error.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> copying macsypy/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
> copying macsypy/scripts/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
> copying macsypy/scripts/macsydata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
> copying macsypy/scripts/macsyfinder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
> copying macsypy/scripts/macsyprofile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
> copying macsypy/scripts/macsy_gembase_split.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
> copying macsypy/scripts/macsy_merge_results.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
> copying macsypy/scripts/macsyconfig.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/macsypy/scripts
>    dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:240: python3.10 setup.py test 
> running test
> WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
> running egg_info
> creating MacSyFinder.egg-info
> writing MacSyFinder.egg-info/PKG-INFO
> writing dependency_links to MacSyFinder.egg-info/dependency_links.txt
> writing entry points to MacSyFinder.egg-info/entry_points.txt
> writing requirements to MacSyFinder.egg-info/requires.txt
> writing top-level names to MacSyFinder.egg-info/top_level.txt
> writing manifest file 'MacSyFinder.egg-info/SOURCES.txt'
> reading manifest file 'MacSyFinder.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no previously-included files matching '*' found under directory 'data'
> warning: no files found matching '*' under directory 'doc/build/html'
> warning: no files found matching 'doc/build/latex/macsyfinder.pdf'
> warning: no files found matching 'etc/macsyfinder.conf'
> warning: no previously-included files matching '*' found under directory 'tests/__pycache__/'
> warning: no previously-included files found matching 'tests/__init__.pyc'
> warning: no previously-included files found matching '.coverage'
> warning: no previously-included files found matching 'coverage_html/'
> warning: no previously-included files found matching '.gitignore'
> warning: no previously-included files found matching '.travis.yml'
> warning: no files found matching 'CONTRIBUTORS'
> warning: no files found matching 'NEWS'
> adding license file 'COPYING'
> writing manifest file 'MacSyFinder.egg-info/SOURCES.txt'
> running build_ext
> test_Config (test_Config.TestConfig) ... ok
> test_Config_args (test_Config.TestConfig) ... ok
> test_Config_conf_file_virtualenv (test_Config.TestConfig) ... ok
> test_Config_default_conf_file (test_Config.TestConfig) ... ok
> test_Config_file_bad_values (test_Config.TestConfig) ... ok
> test_Config_file_n_args (test_Config.TestConfig) ... ok
> test_bad_db_type (test_Config.TestConfig) ... ok
> test_bad_models_dir (test_Config.TestConfig) ... ok
> test_bad_sequence_db (test_Config.TestConfig) ... ok
> test_bad_topology (test_Config.TestConfig) ... ok
> test_bad_topology_file (test_Config.TestConfig) ... ok
> test_bad_values (test_Config.TestConfig) ... ok
> test_cmd_config_file (test_Config.TestConfig) ... ok
> test_config_file_2_dict (test_Config.TestConfig) ... ok
> test_e_value_search (test_Config.TestConfig) ... ok
> test_hit_weights (test_Config.TestConfig) ... ok
> test_model_conf (test_Config.TestConfig) ... ok
> test_models_dir (test_Config.TestConfig) ... ok
> test_no_cut_ga (test_Config.TestConfig) ... ok
> test_out_dir (test_Config.TestConfig) ... ok
> test_previous_n_sequence_db (test_Config.TestConfig) ... ignore sequence_db '/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta' use sequence_db from previous_run '/<<PKGBUILDDIR>>/tests/data/data_set/results_1'.
> ok
> test_previous_wo_cfg (test_Config.TestConfig) ... ok
> test_project_config_file (test_Config.TestConfig) ... ok
> test_save (test_Config.TestConfig) ... ok
> test_set_log_level (test_Config.TestConfig) ... ok
> test_set_option (test_Config.TestConfig) ... ok
> test_str_2_tuple (test_Config.TestConfig) ... ok
> test_working_dir (test_Config.TestConfig) ... ok
> test_NoneConfig (test_Config.TestNoneConfig) ... ok
> test_bad_exchangeable_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition 'bad_exchangeable_inter_gene_max_space': inter_gene_max_space must be an integer: 1.5
> ok
> test_bad_gene_inter_gene_max_space_2 (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition 'bad_inter_gene_max_space_2': inter_gene_max_space must be an integer: 2.5
> ok
> test_bad_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_inter_gene_max_space.xml): inter_gene_max_space must be an integer: 12.5
> ok
> test_bad_max_nb_genes (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_max_nb_genes.xml): max_nb_genes must be an integer: HOHOHO
> ok
> test_bad_min_genes_required (test_DefinitionParser.TestModelParser) ... Models Parsing
> model 'bad_min_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6
> ok
> test_bad_min_genes_required_2 (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_min_genes_required_2.xml): min_genes_required must be an integer: 16.5
> ok
> test_bad_min_mandatory_genes_required (test_DefinitionParser.TestModelParser) ... Models Parsing
> model 'bad_min_mandatory_genes_required' is not consistent: min_genes_required 16 must be lesser or equal than the number of "accessory" and "mandatory" components in the model: 6
> ok
> test_bad_min_mandatory_genes_required_2 (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_bad_min_mandatory_genes_required_4 (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_min_mandatory_genes_required_4.xml): min_mandatory_genes_required must be an integer: 12.5
> ok
> test_exchangeable_inheritance (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_gene_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_gene_no_name (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition 'foo/gene_no_name': gene without name
> ok
> test_gene_w_unkown_attr (test_DefinitionParser.TestModelParser) ... Models Parsing
> unable to parse model definition 'foo/gene_w_unknown_attribute' : The model definition gene_w_unknown_attribute.xml has an unknown attribute 'multi-system' for a gene. Please fix the definition.
> ok
> test_inter_gene_max_space_cfg (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_invalid_homolog (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_invalid_homolog_2 (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition 'foo/invalid_homolog_2': gene without name
> ok
> test_invalid_presence (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model 'fail_invalid_presence' definition: presence value must be either: 'mandatory', 'accessory', 'neutral', 'forbidden' not foo_bar
> ok
> test_loner (test_DefinitionParser.TestModelParser) ... Models Parsing
> Models Parsing
> ok
> test_max_nb_genes_cfg (test_DefinitionParser.TestModelParser) ... Models Parsing
> Models Parsing
> ok
> test_min_genes_required_cfg (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_min_mandatory_genes_required_cfg (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_min_mandatory_genes_required_lesser_than_mandatory_genes (test_DefinitionParser.TestModelParser) ... Models Parsing
> model 'bad_min_mandatory_genes_required_3' is not consistent: 'min_mandatory_genes_required': 6 must be lesser or equal than the number of 'mandatory' components in the model: 5
> ok
> test_model_w_unkown_attr (test_DefinitionParser.TestModelParser) ... Models Parsing
> unable to parse model definition 'foo/model_w_unknown_attribute' : The model definition model_w_unknown_attribute.xml has an unknow attribute 'multi-loci'. Please fix the definition.
> ok
> test_multi_loci_cfg (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_multi_model (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_multi_system (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_no_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/no_inter_gene_max_space.xml): inter_gene_max_space must be defined
> ok
> test_only_one_accessory (test_DefinitionParser.TestModelParser) ... Models Parsing
> model 'only_one_accessory' is not consistent: there is only one gene in your model. So its status should be 'mandatory'.
> ok
> test_parse_model_old_syntax (test_DefinitionParser.TestModelParser) ... Models Parsing
> unable to parse model definition 'foo/model_old_1' : The model definition model_old_1.xml is not versioned. Please update your model.
> FAIL
> test_parse_with_exchangeable (test_DefinitionParser.TestModelParser) ... Models Parsing
> ok
> test_wo_presence (test_DefinitionParser.TestModelParser) ... Models Parsing
> Invalid model definition 'foo/fail_wo_presence': gene 'sctN_FLG' without presence
> ok
> test_add_exchangeable (test_Exchangeable.TestExchangeable) ... ok
> test_alternate_of (test_Exchangeable.TestExchangeable) ... ok
> test_is_exchangeable (test_Exchangeable.TestExchangeable) ... ok
> test_loner (test_Exchangeable.TestExchangeable) ... ok
> test_model (test_Exchangeable.TestExchangeable) ... ok
> test_multi_system (test_Exchangeable.TestExchangeable) ... ok
> test_add_get_gene (test_GeneBank.Test) ... ok
> test_contains (test_GeneBank.Test) ... ok
> test_genes_fqn (test_GeneBank.Test) ... ok
> test_get_uniq_object (test_GeneBank.Test) ... ok
> test_iter (test_GeneBank.Test) ... ok
> test_build_force (test_Indexes.TestIndex) ... ok
> test_build_my_indexes (test_Indexes.TestIndex) ... unable to index the sequence dataset: /tmp/test_macsyfinder_indexes/test_base_with_errors.fa : list index out of range
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/macsypy/database.py", line 192, in _build_my_indexes
>     for seq_id, comment, length in f_iter:
>   File "/<<PKGBUILDDIR>>/macsypy/database.py", line 53, in fasta_iter
>     _id = header[0]
> IndexError: list index out of range
> ok
> test_build_no_idx (test_Indexes.TestIndex) ... ok
> test_build_not_writable (test_Indexes.TestIndex) ... The '/tmp/test_macsyfinder_indexes' dir is not writable.
> ok
> test_build_with_idx (test_Indexes.TestIndex) ... The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building.
> The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. Force index building.
> ok
> test_find_my_indexes (test_Indexes.TestIndex) ... ok
> test_index_dir (test_Indexes.TestIndex) ... ok
> test_iter (test_Indexes.TestIndex) ... ok
> test_allowed_hits (test_LikelySystem.LikelySystemTest) ... ok
> test_forbidden_hits (test_LikelySystem.LikelySystemTest) ... ok
> test_hits (test_LikelySystem.LikelySystemTest) ... ok
> test_init (test_LikelySystem.LikelySystemTest) ... ok
> test_str (test_LikelySystem.LikelySystemTest) ... ok
> test_hits (test_LikelySystem.UnlikelySystemTest) ... ok
> test_init (test_LikelySystem.UnlikelySystemTest) ... ok
> test_reason (test_LikelySystem.UnlikelySystemTest) ... ok
> test_str (test_LikelySystem.UnlikelySystemTest) ... ok
> test_MacsyDefaults_no_virtual_env (test_MacsyDefaults.TestMacsyDefaults) ... ok
> test_MacsyDefaults_virtual_env (test_MacsyDefaults.TestMacsyDefaults) ... ok
> test_ordered_match (test_MatchMaker.MatchMakerTest) ... ok
> test_sort_hits_by_status (test_MatchMaker.MatchMakerTest) ... Gene 'fliE' not found in model 'foo/model_B'
> ok
> test_unordered_match (test_MatchMaker.MatchMakerTest) ... ok
> test_accessor_mutator (test_Model.TestModel) ... ok
> test_eq (test_Model.TestModel) ... ok
> test_filter (test_Model.TestModel) ... ok
> test_fqn (test_Model.TestModel) ... ok
> test_get_gene (test_Model.TestModel) ... ok
> test_gt (test_Model.TestModel) ... ok
> test_hash (test_Model.TestModel) ... ok
> test_inter_gene_max_space (test_Model.TestModel) ... ok
> test_lt (test_Model.TestModel) ... ok
> test_max_nb_genes (test_Model.TestModel) ... ok
> test_min_genes_required (test_Model.TestModel) ... ok
> test_min_mandatory_genes_required (test_Model.TestModel) ... ok
> test_multi_loci (test_Model.TestModel) ... ok
> test_str (test_Model.TestModel) ... ok
> test_add_get_model (test_ModelBank.Test) ... ok
> test_contains (test_ModelBank.Test) ... ok
> test_get_uniq_object (test_ModelBank.Test) ... ok
> test_iter (test_ModelBank.Test) ... ok
> test_execute_hmm_protected_path (test_Profile.TestProfile) ... ok
> test_execute_hmm_w_GA_n_nocutga (test_Profile.TestProfile) ... ok
> test_execute_hmm_with_GA (test_Profile.TestProfile) ... skipped 'For some reason this fails to find hmmer_results - skipping'
> test_execute_hmm_wo_GA (test_Profile.TestProfile) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000)
> ok
> test_execute_hmmer_failed (test_Profile.TestProfile) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000)
> an error occurred during Hmmer execution: command = /tmp/hmmer_failed --cpu 0 -o '/tmp/macsyfinder-20220917_19-55-27/hmmer_results/abc.search_hmm.out' -E 0.100000 '/<<PKGBUILDDIR>>/tests/data/models/foo/profiles/abc.hmm' '/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta'  : return code = 127 check /tmp/macsyfinder-20220917_19-55-27/hmmer_results/abc.search_hmm.err
> ok
> test_execute_unknown_binary (test_Profile.TestProfile) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000)
> an error occurred during Hmmer execution: command = Nimportnaoik --cpu 0 -o '/tmp/macsyfinder-20220917_19-55-27/hmmer_results/abc.search_hmm.out' -E 0.100000 '/<<PKGBUILDDIR>>/tests/data/models/foo/profiles/abc.hmm' '/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta'  : return code = 127 check /tmp/macsyfinder-20220917_19-55-27/hmmer_results/abc.search_hmm.err
> ok
> test_ga_threshold (test_Profile.TestProfile) ... bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''.
> GA score will not used for gene 'bad_GA'.
> bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''.
> GA score will not used for gene 'bad_GA'.
> bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA    22.00'.
> GA score will not used for gene 'bad_GA_2'.
> bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA    22.00'.
> GA score will not used for gene 'bad_GA_2'.
> ok
> test_len (test_Profile.TestProfile) ... ok
> test_str (test_Profile.TestProfile) ... ok
> test_get_profile (test_ProfileFactory.TestProfileFactory) ... ok
> test_get_uniq_object (test_ProfileFactory.TestProfileFactory) ... ok
> test_unknow_profile (test_ProfileFactory.TestProfileFactory) ... ok
> test_hits (test_RejectedClusters.TestRejectedCluster) ... ok
> test_init (test_RejectedClusters.TestRejectedCluster) ... ok
> test_str (test_RejectedClusters.TestRejectedCluster) ... ok
> test_fill_gembase_min_max_default_topology (test_RepliconDB.Test) ... ok
> test_fill_gembase_min_max_oredered_replicon (test_RepliconDB.Test) ... Error during sequence-db '/tmp/test_macsyfinder_repliconDB/ordered_replicon_base.fasta' parsing. Are you sure db-type is 'gembase'?
> ok
> test_fill_gembase_min_max_with_topology (test_RepliconDB.Test) ... ok
> test_fill_ordered_replicon_min_max (test_RepliconDB.Test) ... ok
> test_fill_topology (test_RepliconDB.Test) ... ok
> test_get (test_RepliconDB.Test) ... ok
> test_getitem (test_RepliconDB.Test) ... ok
> test_in (test_RepliconDB.Test) ... ok
> test_items (test_RepliconDB.Test) ... ok
> test_iteritems (test_RepliconDB.Test) ... ok
> test_names (test_RepliconDB.Test) ... ok
> test_replicon_infos (test_RepliconDB.Test) ... ok
> test_extract (test_Report.TestGembaseHMMReport) ... ok
> test_extract_concurent (test_Report.TestGembaseHMMReport) ... /<<PKGBUILDDIR>>/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead
>   main_thread = threading.currentThread()
> ok
> test_extract (test_Report.TestGeneralHMMReport) ... ok
> test_extract_concurent (test_Report.TestGeneralHMMReport) ... /<<PKGBUILDDIR>>/tests/test_Report.py:539: DeprecationWarning: currentThread() is deprecated, use current_thread() instead
>   main_thread = threading.currentThread()
> ok
> test_HMMReport (test_Report.TestHMMReport) ... ok
> test_best_hit (test_Report.TestHMMReport) ... ok
> test_build_my_db (test_Report.TestHMMReport) ... ok
> test_fill_my_db (test_Report.TestHMMReport) ... ok
> test_hit_start (test_Report.TestHMMReport) ... ok
> test_parse_hmm_body (test_Report.TestHMMReport) ... ok
> test_parse_hmm_header (test_Report.TestHMMReport) ... ok
> test_save_extract (test_Report.TestHMMReport) ... ok
> test_str (test_Report.TestHMMReport) ... ok
> test_extract (test_Report.TestOrderedHMMReport) ... hit id 'NC_xxxxx_xx_056141' was not indexed, rebuild sequence 'test_base.fa' index
> ok
> test_extract_concurent (test_Report.TestOrderedHMMReport) ... /<<PKGBUILDDIR>>/tests/test_Report.py:460: DeprecationWarning: currentThread() is deprecated, use current_thread() instead
>   main_thread = threading.currentThread()
> ok
> test_HitSystemTracker (test_System.SystemTest) ... ok
> test_count (test_System.SystemTest) ... ok
> test_fulfilled_function (test_System.SystemTest) ... ok
> test_get_hits_encoding_multisystem (test_System.SystemTest) ... ok
> test_get_loners (test_System.SystemTest) ... ok
> test_get_multisystems (test_System.SystemTest) ... ok
> test_hits (test_System.SystemTest) ... ok
> test_init (test_System.SystemTest) ... ok
> test_is_compatible (test_System.SystemTest) ... ok
> test_loci_nb (test_System.SystemTest) ... ok
> test_loci_num (test_System.SystemTest) ... ok
> test_multi_loci (test_System.SystemTest) ... ok
> test_occurrence (test_System.SystemTest) ... ok
> test_position (test_System.SystemTest) ... ok
> test_score (test_System.SystemTest) ... ok
> test_wholeness (test_System.SystemTest) ... ok
> test_build_clusters (test_cluster.TestBuildCluster) ... ok
> test_clusterize (test_cluster.TestBuildCluster) ... ok
> test_colocates (test_cluster.TestBuildCluster) ... ok
> test_get_true_loners (test_cluster.TestBuildCluster) ... ok
> test_contains (test_cluster.TestCluster) ... ok
> test_fulfilled_function (test_cluster.TestCluster) ... ok
> test_init (test_cluster.TestCluster) ... Cannot build a cluster from hits coming from different replicons
> ok
> test_len (test_cluster.TestCluster) ... ok
> test_loner (test_cluster.TestCluster) ... ok
> test_merge (test_cluster.TestCluster) ... ok
> test_multi_system (test_cluster.TestCluster) ... ok
> test_replace (test_cluster.TestCluster) ... ok
> test_replicon_name (test_cluster.TestCluster) ... ok
> test_score (test_cluster.TestCluster) ... ok
> test_str (test_cluster.TestCluster) ... ok
> test_2_systems_not_compatible (test_functional_test.Test) ... ok
> test_cfg_n_previous_run (test_functional_test.Test) ... ok
> test_degenerated_systems (test_functional_test.Test) ... ok
> test_gembase (test_functional_test.Test) ... ok
> test_index_dir (test_functional_test.Test) ... ok
> test_model_unknown (test_functional_test.Test) ... ok
> test_no_db_type (test_functional_test.Test) ... ok
> test_no_models (test_functional_test.Test) ... ok
> test_no_seq_db (test_functional_test.Test) ... ok
> test_only_loners (test_functional_test.Test) ... ok
> test_ordered_1_cluster_3_loners (test_functional_test.Test) ... ok
> test_ordered_1_clusters_3_loners_w_exchangeable (test_functional_test.Test) ... ok
> test_ordered_1_loner_exch_in_clust (test_functional_test.Test) ... ok
> test_ordered_1_loner_in_clust (test_functional_test.Test) ... ok
> test_ordered_2_clusters_1_loner (test_functional_test.Test) ... ok
> test_ordered_2_clusters_3_loners (test_functional_test.Test) ... ok
> test_ordered_circular (test_functional_test.Test) ... ok
> test_ordered_linear (test_functional_test.Test) ... ok
> test_ordered_multi_loci (test_functional_test.Test) ... ok
> test_ordered_multi_model (test_functional_test.Test) ... ok
> test_ordered_multi_system (test_functional_test.Test) ... ok
> test_ordered_multi_system_out_system (test_functional_test.Test) ... ok
> test_ordered_single_loci (test_functional_test.Test) ... ok
> test_uncomplete_degenerated_systems (test_functional_test.Test) ... ok
> test_unordered (test_functional_test.Test) ... ok
> test_unordered_no_hits (test_functional_test.Test) ... ok
> test_unordered_only_forbidden (test_functional_test.Test) ... ok
> test_working_dir_exists (test_functional_test.Test) ... ok
> test_working_dir_exists_and_not_dir (test_functional_test.Test) ... ok
> test_core_gene (test_gene.TestCoreGene) ... ok
> test_str (test_gene.TestGeneStatus) ... ok
> test_add_exchangeable (test_gene.TestModelGene) ... ok
> test_alternate_of (test_gene.TestModelGene) ... ok
> test_exhangeables (test_gene.TestModelGene) ... ok
> test_hash (test_gene.TestModelGene) ... ok
> test_init (test_gene.TestModelGene) ... ok
> test_inter_gene_max_space (test_gene.TestModelGene)
> test getter for inter_gene_max_space property ... ok
> test_is_Forbidden (test_gene.TestModelGene)
> test if gene belong to model mandatory genes ... ok
> test_is_accessory (test_gene.TestModelGene)
> test if gene belong to model mandatory genes ... ok
> test_is_exchangeable (test_gene.TestModelGene) ... ok
> test_is_mandatory (test_gene.TestModelGene)
> test if gene belong to model mandatory genes ... ok
> test_loner (test_gene.TestModelGene)
> test getter for loner property ... ok
> test_model (test_gene.TestModelGene)
> test getter/setter for model property ... ok
> test_multi_model (test_gene.TestModelGene)
> test getter for multi_modelproperty ... ok
> test_multi_system (test_gene.TestModelGene)
> test getter for multi_system property ... ok
> test_str (test_gene.TestModelGene) ... ok
> test_unknown_attribute (test_gene.TestModelGene) ... ok
> test_cmp (test_hit.CoreHitTest) ... ok
> test_eq (test_hit.CoreHitTest) ... ok
> test_get_position (test_hit.CoreHitTest) ... ok
> test_hash (test_hit.CoreHitTest) ... ok
> test_str (test_hit.CoreHitTest) ... ok
> test_compute_best_MSHit (test_hit.GetBestHitTest) ... ok
> test_get_best_hits (test_hit.GetBestHitTest) ... ok
> test_get_best_hits_4_func (test_hit.GetBestHitTest) ... ok
> test_sort_multisystem_hits (test_hit.GetBestHitTest) ... ok
> test_hit_weight_default (test_hit.HitWeightTest) ... ok
> test_hit_weight_not_default (test_hit.HitWeightTest) ... ok
> test_counterpart (test_hit.LonerMultiSystemTest) ... Try to set counterpart for hit 'gspD' with non compatible hits: ['gspD', 'sctJ']
> ok
> test_init (test_hit.LonerMultiSystemTest) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system
> ok
> test_loner (test_hit.LonerMultiSystemTest) ... ok
> test_multi_system (test_hit.LonerMultiSystemTest) ... ok
> test_str (test_hit.LonerMultiSystemTest) ... ok
> test_counterpart (test_hit.LonerTest) ... ok
> test_init (test_hit.LonerTest) ... hit_2 cannot be a loner gene_ref 'sctJ' not tag as loner
> ok
> test_len (test_hit.LonerTest) ... ok
> test_loner (test_hit.LonerTest) ... ok
> test_multi_system (test_hit.LonerTest) ... ok
> test_str (test_hit.LonerTest) ... ok
> test_delegation (test_hit.ModelHitTest) ... ok
> test_eq (test_hit.ModelHitTest) ... ok
> test_hash (test_hit.ModelHitTest) ... ok
> test_init (test_hit.ModelHitTest) ... ok
> test_loner (test_hit.ModelHitTest) ... ok
> test_multi_model (test_hit.ModelHitTest) ... ok
> test_multi_system (test_hit.ModelHitTest) ... ok
> test_counterpart (test_hit.MultiSystemTest) ... ok
> test_init (test_hit.MultiSystemTest) ... hit_2 cannot be a multi systems, gene_ref 'sctJ' not tag as multi_system
> ok
> test_len (test_hit.MultiSystemTest) ... ok
> test_loner (test_hit.MultiSystemTest) ... ok
> test_multi_system (test_hit.MultiSystemTest) ... ok
> test_str (test_hit.MultiSystemTest) ... ok
> test_functional_split (test_macsy_gembase_split.TestSplit) ... /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='UTF-8'>
>   for h in logger.handlers[:]:
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /usr/lib/python3.10/unittest/case.py:552: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpi90w89vb/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='UTF-8'>
>   self.tearDown()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_functional_split_out_error (test_macsy_gembase_split.TestSplit) ... /tmp/tmpow3hk3a3/macsyfinder_test_split/base is not a directory
> ok
> test_functional_split_out_not_writable (test_macsy_gembase_split.TestSplit) ... /tmp/tmpy4eh0p1q/macsyfinder_test_split/base is not writable
> Cannot create /tmp/tmpy4eh0p1q/macsyfinder_test_split/base : [Errno 13] Permission denied: '/tmp/tmpy4eh0p1q/macsyfinder_test_split/base'
> ok
> test_functional_merge (test_macsy_merge_results.TestMerge) ... Merging 'all_best_solutions.tsv' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv'
> Merging 'best_solution.tsv' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_best_solution.tsv'
> Merging 'all_systems.tsv' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_all_systems.tsv'
> Merging 'best_solution_multisystems.tsv' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv'
> Merging 'best_solution_loners.tsv' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv'
> Merging 'all_systems.txt' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_all_systems.txt'
> Merging 'rejected_clusters.txt' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_rejected_clusters.txt'
> Merging 'best_solution_summary' in to '/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/merged_best_solution_summary.tsv'
> /usr/lib/python3.10/unittest/case.py:552: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpeja1c1tc/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'>
>   self.tearDown()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_functional_merge_one_results_empty (test_macsy_merge_results.TestMerge) ... /usr/lib/python3.10/unittest/case.py:552: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpwx71u6b3/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'>
>   self.tearDown()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_functional_merge_out_error (test_macsy_merge_results.TestMerge) ... /tmp/tmpra4jmnbf/macsyfinder_test_merge/merged_results is not a directory
> ok
> test_functional_merge_out_not_writable (test_macsy_merge_results.TestMerge) ... /tmp/tmpy6v4qub2/macsyfinder_test_merge/merged_results is not writable
> Cannot create /tmp/tmpy6v4qub2/macsyfinder_test_merge/merged_results : [Errno 13] Permission denied: '/tmp/tmpy6v4qub2/macsyfinder_test_merge/merged_results'
> ok
> test_functional_merge_results_empty (test_macsy_merge_results.TestMerge) ... /usr/lib/python3.10/unittest/case.py:552: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp06hi9rfc/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='UTF-8'>
>   self.tearDown()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_merge_and_reindex_invalid_solid (test_macsy_merge_results.TestMerge) ... Cannot reindex int(GCF_000006845) + 1: invalid literal for int() with base 10: 'GCF_000006845'
> ok
> test_add_comment (test_macsyconfig.TestConfigParserWithComment) ... ok
> test_write (test_macsyconfig.TestConfigParserWithComment) ... ok
> test_ask (test_macsyconfig.TestMacsyconfig) ... ok
> test_ask_bad_value (test_macsyconfig.TestMacsyconfig) ... ok
> test_ask_default_is_sequence (test_macsyconfig.TestMacsyconfig) ... ok
> test_ask_use_default (test_macsyconfig.TestMacsyconfig) ... ok
> test_ask_value_is_sequence (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_bool (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_choice (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_dir (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_exe (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_file (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_float (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_positive_int (test_macsyconfig.TestMacsyconfig) ... ok
> test_check_str (test_macsyconfig.TestMacsyconfig) ... ok
> test_functional_dark_theme (test_macsyconfig.TestMacsyconfig) ... ok
> test_functional_file_already_exists (test_macsyconfig.TestMacsyconfig) ... ok
> test_parse_args (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_base_options (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_general_options (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_hmmer_options (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_path_options (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_path_options_with_system_models_dir (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_score_options (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_section (test_macsyconfig.TestMacsyconfig) ... ok
> test_set_section_use_defaults (test_macsyconfig.TestMacsyconfig) ... ok
> test_available (test_macsydata.TestMacsydata) ... ok
> test_build_argparser (test_macsydata.TestMacsydata) ... ok
> test_check (test_macsydata.TestMacsydata) ... If everyone were like you, I'd be out of business
> To push the models in organization:
> 	cd /tmp/tmpvsur3n3z/fake_1
> Transform the models into a git repository
> 	git init .
> 	git add .
> 	git commit -m 'initial commit'
> add a remote repository to host the models
> for instance if you want to add the models to 'macsy-models'
> 	git remote add origin https://github.com/macsy-models/
> 	git tag 0.0b2
> 	git push --tags
> ok
> test_check_with_errors (test_macsydata.TestMacsydata) ... The package 'fake_1' have no 'definitions' directory.
> The package 'fake_1' have no 'profiles' directory.
> Please fix issues above, before publishing these models.
> ok
> test_check_with_warnings (test_macsydata.TestMacsydata) ... The package 'fake_1' have not any LICENSE file. May be you have not right to use it.
> The package 'fake_1' have not any README file.
> 
> macsydata says: You're only giving me a partial QA payment?
> I'll take it this time, but I'm not happy.
> I'll be really happy, if you fix warnings above, before to publish these models.
> ok
> test_cite (test_macsydata.TestMacsydata) ... Models 'nimportnaoik' not found locally.
> ok
> test_cmd_name (test_macsydata.TestMacsydata) ... ok
> test_definition_all_def (test_macsydata.TestMacsydata) ... /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:606: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp3m0pqkmd/fake_1/definitions/model_1.xml' mode='r' encoding='UTF-8'>
>   return open(path, 'r').read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:606: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp3m0pqkmd/fake_1/definitions/model_2.xml' mode='r' encoding='UTF-8'>
>   return open(path, 'r').read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_definition_bad_def (test_macsydata.TestMacsydata) ... Model 'fake_1/niportnaoik' not found.
> ok
> test_definition_bad_pack (test_macsydata.TestMacsydata) ... Package 'nimportnaoik' not found.
> ok
> test_definition_bad_subfamily (test_macsydata.TestMacsydata) ... 'niportnaoik' not found in package 'fake_1'.
> ok
> test_definition_models_dir (test_macsydata.TestMacsydata) ... /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:606: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp1qcx7ev9/model_dir/fake_1/definitions/model_1.xml' mode='r' encoding='UTF-8'>
>   return open(path, 'r').read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:606: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp1qcx7ev9/model_dir/fake_1/definitions/model_2.xml' mode='r' encoding='UTF-8'>
>   return open(path, 'r').read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_definition_one_def (test_macsydata.TestMacsydata) ... /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:606: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpvvca4sok/fake_1/definitions/model_1.xml' mode='r' encoding='UTF-8'>
>   return open(path, 'r').read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:606: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpvvca4sok/fake_1/definitions/model_2.xml' mode='r' encoding='UTF-8'>
>   return open(path, 'r').read()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_download (test_macsydata.TestMacsydata) ... Downloading fake_1 1.0
> Successfully downloaded packaging fake_1 in /tmp/tmpu_b9vvw2/fake_1-1.0.tar.gz
> No version that satisfy requirements '>2.0' for 'fake_1'.
> Available versions: 1.0
> Downloading fake_1 1.0
> github limit error
> ok
> test_freeze (test_macsydata.TestMacsydata) ... ok
> test_help (test_macsydata.TestMacsydata) ... Models 'nimportnaoik' not found locally.
> ok
> test_info (test_macsydata.TestMacsydata) ... Models 'nimportnaoik' not found locally.
> ok
> test_install_bad_target (test_macsydata.TestMacsydata) ... ok
> test_install_installed_package_corrupted (test_macsydata.TestMacsydata) ... Extracting fake_pack (0.0b2).
> Installing fake_pack (0.0b2) in /tmp/tmpnh1t1595/models
> Cleaning.
> The models fake_pack (0.0b2) have been installed successfully.
> fake_pack locally installed is corrupted.
> You can fix it by removing '/tmp/tmpnh1t1595/models/fake_pack'.
> ok
> test_install_local (test_macsydata.TestMacsydata) ... Extracting fake_pack (3.0).
> Installing fake_pack (3.0) in /tmp/tmpoqhebvo4/models
> Cleaning.
> The models fake_pack (3.0) have been installed successfully.
> ok
> test_install_local_already_installed (test_macsydata.TestMacsydata) ... Extracting fake_pack (0.0b2).
> Installing fake_pack (0.0b2) in /tmp/tmpsfbc79_h/models
> Cleaning.
> The models fake_pack (0.0b2) have been installed successfully.
> Requirement already satisfied: fake_pack==0.0b2 in /tmp/tmpsfbc79_h/models/fake_pack.
> To force installation use option -f --force-reinstall.
> ok
> test_install_local_already_installed_force (test_macsydata.TestMacsydata) ... Extracting fake_pack (0.0b2).
> Installing fake_pack (0.0b2) in /tmp/tmp95r7fair/models
> Cleaning.
> The models fake_pack (0.0b2) have been installed successfully.
> Extracting fake_pack (0.0b2).
> Installing fake_pack (0.0b2) in /tmp/tmp95r7fair/models
> Cleaning.
> The models fake_pack (0.0b2) have been installed successfully.
> ok
> test_install_remote (test_macsydata.TestMacsydata) ... Downloading fake_pack (0.0b2).
> Extracting fake_pack (0.0b2).
> Installing fake_pack (0.0b2) in /tmp/tmp_cjghuww/models
> Cleaning.
> The models fake_pack (0.0b2) have been installed successfully.
> ok
> test_install_remote_already_in_local (test_macsydata.TestMacsydata) ... Requirement already satisfied: fake_pack>0.0b2 in /tmp/tmpsvm4u71_/models/fake_pack.
> To force installation use option -f --force-reinstall.
> ok
> test_install_remote_already_in_local_force (test_macsydata.TestMacsydata) ... Downloading fake_pack (0.0b2).
> Extracting fake_pack (0.0b2).
> Installing fake_pack (0.0b2) in /tmp/tmp3pzxf4d8/models
> Cleaning.
> The models fake_pack (0.0b2) have been installed successfully.
> ok
> test_install_remote_lower_in_local (test_macsydata.TestMacsydata) ... fake_pack (0.0b2) is already installed but 1.0 version is available.
> To install it please run 'macsydata install --upgrade fake_pack'
> ok
> test_install_remote_permision_error (test_macsydata.TestMacsydata) ... /tmp/tmpviaq3sso/models is not readable: [Errno 13] Permission denied: '/tmp/tmpviaq3sso/models' : skip it.
> Downloading fake_pack (0.0b2).
> Extracting fake_pack (0.0b2).
> Installing fake_pack (0.0b2) in /tmp/tmpviaq3sso/models
> /tmp/tmpviaq3sso/models is not writable: [Errno 13] Permission denied: '/tmp/tmpviaq3sso/models/fake_pack'
> Maybe you can use --user option to install in your HOME.
> ok
> test_install_remote_spec_not_found (test_macsydata.TestMacsydata) ... Could not find version that satisfied 'fake_pack>0.0b2'
> ok
> test_install_remote_upper_in_local (test_macsydata.TestMacsydata) ... fake_pack (0.0b2) is already installed.
> To downgrade to 0.0b1 use option -f --force-reinstall.
> ok
> test_install_target (test_macsydata.TestMacsydata) ... Extracting fake_pack (3.0).
> Installing fake_pack (3.0) in /tmp/tmp6pj2kpl7/target
> Cleaning.
> The models fake_pack (3.0) have been installed successfully.
> ok
> test_list (test_macsydata.TestMacsydata) ... ok
> test_list_outdated (test_macsydata.TestMacsydata) ... ok
> test_list_uptodate (test_macsydata.TestMacsydata) ... ok
> test_list_verbose (test_macsydata.TestMacsydata) ... [Errno 2] No such file or directory: '/tmp/tmpzcgufiwg/models/fake_1/metadata.yml'
> ok
> test_no_subcommand (test_macsydata.TestMacsydata) ... ok
> test_search_in_pack_desc (test_macsydata.TestMacsydata) ... ok
> test_search_in_pack_desc_match_case (test_macsydata.TestMacsydata) ... ok
> test_search_in_pack_name (test_macsydata.TestMacsydata) ... ok
> test_search_in_pack_name_match_case (test_macsydata.TestMacsydata) ... ok
> test_search_reach_limit (test_macsydata.TestMacsydata) ... bla
> ok
> test_uninstall (test_macsydata.TestMacsydata) ... models 'fake_1' in /tmp/tmprz78thc2/models/fake_1 uninstalled.
> Models 'foo' not found locally.
> ok
> test_verbosity_to_log_level (test_macsydata.TestMacsydata) ... ok
> test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok
> test_likely_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok
> test_list_models (test_macsyfinder.TestMacsyfinder) ... ok
> test_loners_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok
> test_multisystem_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok
> test_parse_args (test_macsyfinder.TestMacsyfinder) ... ok
> test_rejected_clst_to_txt (test_macsyfinder.TestMacsyfinder) ... ok
> test_search_systems (test_macsyfinder.TestMacsyfinder) ... ok
> test_search_systems_unordered (test_macsyfinder.TestMacsyfinder) ... ok
> test_solutions_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok
> test_summary_best_solution (test_macsyfinder.TestMacsyfinder) ... ok
> test_summary_best_solution_empty (test_macsyfinder.TestMacsyfinder) ... ok
> test_summary_best_solution_lack_models (test_macsyfinder.TestMacsyfinder) ... ok
> test_summary_best_solution_lack_models_replicons (test_macsyfinder.TestMacsyfinder) ... ok
> test_summary_best_solution_lack_replicon (test_macsyfinder.TestMacsyfinder) ... ok
> test_systems_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok
> test_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok
> test_unnlikely_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok
> test_LightHit (test_macsyprofile.TestMacsyprofile) ... ok
> test_build_my_db (test_macsyprofile.TestMacsyprofile) ... ok
> test_fill_my_db (test_macsyprofile.TestMacsyprofile) ... ok
> test_functional (test_macsyprofile.TestMacsyprofile) ... ok
> test_functional_best_score (test_macsyprofile.TestMacsyprofile) ... ok
> test_functional_coverage (test_macsyprofile.TestMacsyprofile) ... ok
> test_functional_evalue (test_macsyprofile.TestMacsyprofile) ... ok
> test_functional_no_hits (test_macsyprofile.TestMacsyprofile) ... ok
> test_functional_no_previous_run (test_macsyprofile.TestMacsyprofile) ... nimportnaoik: No such directory.
> ok
> test_functional_out_exists (test_macsyprofile.TestMacsyprofile) ... The file /tmp/tmp5cgfvh1v already exists. Remove it or specify a new output name --out or use --force option
> ok
> test_functional_pattern (test_macsyprofile.TestMacsyprofile) ... ok
> test_getProfile_len (test_macsyprofile.TestMacsyprofile) ... ok
> test_get_gene_name (test_macsyprofile.TestMacsyprofile) ... ok
> test_header (test_macsyprofile.TestMacsyprofile) ... ok
> test_hit_start (test_macsyprofile.TestMacsyprofile) ... ok
> test_parse (test_macsyprofile.TestMacsyprofile) ... ok
> test_parse_hmm_body (test_macsyprofile.TestMacsyprofile) ... ok
> test_parse_hmm_header (test_macsyprofile.TestMacsyprofile) ... ok
> test_pasre_args (test_macsyprofile.TestMacsyprofile) ... ok
> test_verbosity_to_log_level (test_macsyprofile.TestMacsyprofile) ... ok
> test_init_logger_default (test_macsypy.Test) ... ok
> test_init_logger_logfile (test_macsypy.Test) ... /usr/lib/python3.10/unittest/case.py:552: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp23e3gdm9' mode='a' encoding='UTF-8'>
>   self.tearDown()
> ResourceWarning: Enable tracemalloc to get the object allocation traceback
> ok
> test_init_logger_no_out (test_macsypy.Test) ... ok
> test_logger_set_level_bad_level (test_macsypy.Test) ... ok
> test_logger_set_level_default (test_macsypy.Test) ... ok
> test_logger_set_level_error (test_macsypy.Test) ... ok
> test_logger_set_level_handlers (test_macsypy.Test) ... ok
> test_parse (test_model_conf_parser.TestModelConfParser) ... ok
> test_parse_bad_file (test_model_conf_parser.TestModelConfParser) ... unable to parse model configuration '/<<PKGBUILDDIR>>/tests/data/conf_files/project.conf' : syntax error: line 2, column 0
> ok
> test_parse_filtering (test_model_conf_parser.TestModelConfParser) ... cannot parse 'cut_ga' element in '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' expect True, 1, False, 0 got : 'FOO'
> ok
> test_parse_w_bad_value (test_model_conf_parser.TestModelConfParser) ... The model configuration file '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO'
> ok
> test_parse_w_unkown_tag (test_model_conf_parser.TestModelConfParser) ... unknown element 'nimportnaoik' in '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' ignore it.
> ok
> test_parse_weights (test_model_conf_parser.TestModelConfParser) ... ok
> test_parse_wo_filtering (test_model_conf_parser.TestModelConfParser) ... ok
> test_parse_wo_weights (test_model_conf_parser.TestModelConfParser) ... ok
> test_init (test_package.TestLocalModelIndex) ... ok
> test_init (test_package.TestModelIndex) ... ok
> test_check (test_package.TestPackage) ... ok
> test_check_metadata (test_package.TestPackage) ... ok
> test_check_model_conf (test_package.TestPackage) ... ok
> test_check_model_conf_bad_conf (test_package.TestPackage) ... The model configuration file '/tmp/macsy_test_package/fake_model/model_conf.xml' cannot be parsed: could not convert string to float: 'FOO'
> ok
> test_check_model_conf_no_conf (test_package.TestPackage) ... ok
> test_check_model_consistency (test_package.TestPackage) ... ok
> test_check_model_consistency_bad_definitions (test_package.TestPackage) ... ok
> test_check_model_consistency_extra_profile (test_package.TestPackage) ... ok
> test_check_model_consistency_lack_one_profile (test_package.TestPackage) ... ok
> test_check_no_readme_n_no_license (test_package.TestPackage) ... ok
> test_check_structure (test_package.TestPackage) ... ok
> test_check_structure_bad_path (test_package.TestPackage) ... ok
> test_check_structure_no_def (test_package.TestPackage) ... ok
> test_check_structure_no_license (test_package.TestPackage) ... ok
> test_check_structure_no_metadata (test_package.TestPackage) ... ok
> test_check_structure_no_profiles (test_package.TestPackage) ... ok
> test_check_structure_no_readme (test_package.TestPackage) ... ok
> test_find_readme (test_package.TestPackage) ... ok
> test_help (test_package.TestPackage) ... ok
> test_info (test_package.TestPackage) ... ok
> test_init (test_package.TestPackage) ... ok
> test_metadata (test_package.TestPackage) ... ok
> test_parse_arch_path (test_package.TestPackageFunc) ... ok
> test_download (test_package.TestRemoteModelIndex) ... ok
> test_get_metadata (test_package.TestRemoteModelIndex) ... ok
> test_init (test_package.TestRemoteModelIndex) ... ok
> test_list_package_vers (test_package.TestRemoteModelIndex) ... ok
> test_list_packages (test_package.TestRemoteModelIndex) ... ok
> test_remote_exists (test_package.TestRemoteModelIndex) ... ok
> test_unarchive (test_package.TestRemoteModelIndex) ... ok
> test_url_json (test_package.TestRemoteModelIndex) ... ok
> test_url_json_reach_limit (test_package.TestRemoteModelIndex) ... ok
> test_DefinitionLocationn (test_registries.DefinitionLocationTest) ... ok
> test_add_submodel (test_registries.DefinitionLocationTest) ... ok
> test_all (test_registries.DefinitionLocationTest) ... ok
> test_eq (test_registries.DefinitionLocationTest) ... ok
> test_family_name (test_registries.DefinitionLocationTest) ... ok
> test_greater (test_registries.DefinitionLocationTest) ... ok
> test_hash (test_registries.DefinitionLocationTest) ... ok
> test_lesser (test_registries.DefinitionLocationTest) ... ok
> test_root_name (test_registries.DefinitionLocationTest) ... ok
> test_separator (test_registries.DefinitionLocationTest) ... ok
> test_split_fqn (test_registries.DefinitionLocationTest) ... ok
> test_str (test_registries.DefinitionLocationTest) ... ok
> test_ModelLocation (test_registries.ModelLocationTest) ... ok
> test_get_all_definitions (test_registries.ModelLocationTest) ... ok
> test_get_definition (test_registries.ModelLocationTest) ... ok
> test_get_definitions (test_registries.ModelLocationTest) ... ok
> test_get_profile (test_registries.ModelLocationTest) ... ok
> test_get_profiles_names (test_registries.ModelLocationTest) ... ok
> test_str (test_registries.ModelLocationTest) ... ok
> test_add_get (test_registries.ModelRegistryTest) ... ok
> test_models (test_registries.ModelRegistryTest) ... ok
> test_scan_models_dir (test_registries.ModelRegistryTest) ... ok
> test_str (test_registries.ModelRegistryTest) ... ok
> test_join_def_path (test_registries.RegitriesUtilsTest) ... ok
> test_split_def_name (test_registries.RegitriesUtilsTest) ... ok
> test_search (test_search_genes.TestSearchGenes) ... ok
> test_search_recover (test_search_genes.TestSearchGenes) ... ok
> test_LikelySystemSerializer_txt (test_serialization.SerializationTest) ... ok
> test_SolutionSerializer_tsv (test_serialization.SerializationTest) ... ok
> test_SpecialHitSerializer_tsv (test_serialization.SerializationTest) ... ok
> test_SystemSerializer_str (test_serialization.SerializationTest) ... ok
> test_SystemSerializer_tsv (test_serialization.SerializationTest) ... ok
> test_UnlikelySystemSerializer_txt (test_serialization.SerializationTest) ... ok
> test_combine_clusters (test_solution.SolutionExplorerTest) ... ok
> test_combine_multisystems (test_solution.SolutionExplorerTest) ... ok
> test_find_best_solution (test_solution.SolutionExplorerTest) ... ok
> test_average_wholeness (test_solution.SolutionTest) ... ok
> test_gt (test_solution.SolutionTest) ... ok
> test_hits_number (test_solution.SolutionTest) ... ok
> test_hits_positions (test_solution.SolutionTest) ... ok
> test_iteration (test_solution.SolutionTest) ... ok
> test_lt (test_solution.SolutionTest) ... ok
> test_score (test_solution.SolutionTest) ... ok
> test_sorting (test_solution.SolutionTest) ... ok
> test_systems (test_solution.SolutionTest) ... ok
> test_get_def_to_detect (test_utils.TestUtils) ... ok
> test_get_replicon_names (test_utils.TestUtils) ... ok
> test_threads_available (test_utils.TestUtils) ... ok
> 
> ======================================================================
> FAIL: test_parse_model_old_syntax (test_DefinitionParser.TestModelParser)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/tests/test_DefinitionParser.py", line 550, in test_parse_model_old_syntax
>     self.assertEqual(log_msg,
> AssertionError: "Models Parsing\nunable to parse model def[104 chars]del." != "unable to parse model definition 'foo/mod[88 chars]del."
> - Models Parsing
>   unable to parse model definition 'foo/model_old_1' : The model definition model_old_1.xml is not versioned. Please update your model.
> 
> ----------------------------------------------------------------------
> Ran 478 tests in 14.209s
> 
> FAILED (failures=1, skipped=1)
> Test failed: <unittest.runner.TextTestResult run=478 errors=0 failures=1>
> error: Test failed: <unittest.runner.TextTestResult run=478 errors=0 failures=1>
> E: pybuild pybuild:379: test: plugin distutils failed with: exit code=1: python3.10 setup.py test 
> dh_auto_test: error: pybuild --test -i python{version} -p 3.10 returned exit code 13

The full build log is available from:
http://qa-logs.debian.net/2022/09/17/macsyfinder_2.0~rc7-1_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220917;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220917&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.