added scripts

pirl-unc · Feb 9, 2024 · 25ee7d4 · 25ee7d4
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commit 25ee7d4
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diff --git a/develop.sh b/develop.sh
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+set -e
+
+pip install -e .
diff --git a/lint-and-test.sh b/lint-and-test.sh
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+./lint.sh && ./test.sh 
diff --git a/test.sh b/test.sh
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+pytest --cov=mhcgnomes/ --cov-report=term-missing tests
diff --git a/test/IMGT_Allele_status.txt → tests/IMGT_Allele_status.txt b/test/IMGT_Allele_status.txt → tests/IMGT_Allele_status.txt
diff --git a/test/IMGT_DLA.txt → tests/IMGT_DLA.txt b/test/IMGT_DLA.txt → tests/IMGT_DLA.txt
diff --git a/test/IMGT_ELA.txt → tests/IMGT_ELA.txt b/test/IMGT_ELA.txt → tests/IMGT_ELA.txt
diff --git a/test/IMGT_FISH.txt → tests/IMGT_FISH.txt b/test/IMGT_FISH.txt → tests/IMGT_FISH.txt
diff --git a/test/IMGT_NHP.txt → tests/IMGT_NHP.txt b/test/IMGT_NHP.txt → tests/IMGT_NHP.txt
diff --git a/test/IMGT_SLA.txt → tests/IMGT_SLA.txt b/test/IMGT_SLA.txt → tests/IMGT_SLA.txt
diff --git a/test/MHC_prot.fasta → tests/MHC_prot.fasta b/test/MHC_prot.fasta → tests/MHC_prot.fasta
diff --git a/test/generate_iedb_functions.py → tests/generate_iedb_functions.py b/test/generate_iedb_functions.py → tests/generate_iedb_functions.py
diff --git a/test/generate_imgt_hla_function.py → tests/generate_imgt_hla_function.py b/test/generate_imgt_hla_function.py → tests/generate_imgt_hla_function.py
diff --git a/test/generate_ipd_mhc_functions.py → tests/generate_ipd_mhc_functions.py b/test/generate_ipd_mhc_functions.py → tests/generate_ipd_mhc_functions.py
diff --git a/test/generate_netmhciipan_3_1_functions.py → tests/generate_netmhciipan_3_1_functions.py b/test/generate_netmhciipan_3_1_functions.py → tests/generate_netmhciipan_3_1_functions.py
diff --git a/test/generate_netmhcpan_functions.py → tests/generate_netmhcpan_functions.py b/test/generate_netmhcpan_functions.py → tests/generate_netmhcpan_functions.py
diff --git a/test/hla_prot.fasta → tests/hla_prot.fasta b/test/hla_prot.fasta → tests/hla_prot.fasta
diff --git a/test/iedb_allele_counts.csv → tests/iedb_allele_counts.csv b/test/iedb_allele_counts.csv → tests/iedb_allele_counts.csv
diff --git a/test/netmhciipan_3_1_alleles.txt → tests/netmhciipan_3_1_alleles.txt b/test/netmhciipan_3_1_alleles.txt → tests/netmhciipan_3_1_alleles.txt
diff --git a/test/netmhcpan_3_0_alleles.txt → tests/netmhcpan_3_0_alleles.txt b/test/netmhcpan_3_0_alleles.txt → tests/netmhcpan_3_0_alleles.txt
diff --git a/test/netmhcpan_4_0_alleles.txt → tests/netmhcpan_4_0_alleles.txt b/test/netmhcpan_4_0_alleles.txt → tests/netmhcpan_4_0_alleles.txt
diff --git a/test/test_Bofr.py → tests/test_Bofr.py b/test/test_Bofr.py → tests/test_Bofr.py
diff --git a/test/test_allele.py → tests/test_allele.py b/test/test_allele.py → tests/test_allele.py
diff --git a/test/test_allele_aliases.py → tests/test_allele_aliases.py b/test/test_allele_aliases.py → tests/test_allele_aliases.py
diff --git a/test/test_annotations.py → tests/test_annotations.py b/test/test_annotations.py → tests/test_annotations.py
diff --git a/test/test_bad_inputs.py → tests/test_bad_inputs.py b/test/test_bad_inputs.py → tests/test_bad_inputs.py
diff --git a/test/test_cat.py → tests/test_cat.py b/test/test_cat.py → tests/test_cat.py
diff --git a/test/test_cd1.py → tests/test_cd1.py b/test/test_cd1.py → tests/test_cd1.py
diff --git a/test/test_chicken.py → tests/test_chicken.py b/test/test_chicken.py → tests/test_chicken.py
diff --git a/test/test_class2_locus.py → tests/test_class2_locus.py b/test/test_class2_locus.py → tests/test_class2_locus.py
diff --git a/test/test_class2_pair.py → tests/test_class2_pair.py b/test/test_class2_pair.py → tests/test_class2_pair.py
diff --git a/test/test_cow.py → tests/test_cow.py b/test/test_cow.py → tests/test_cow.py
diff --git a/test/test_dog.py → tests/test_dog.py b/test/test_dog.py → tests/test_dog.py
diff --git a/test/test_fish.py → tests/test_fish.py b/test/test_fish.py → tests/test_fish.py
diff --git a/test/test_github_issues.py → tests/test_github_issues.py b/test/test_github_issues.py → tests/test_github_issues.py
diff --git a/test/test_haplotype.py → tests/test_haplotype.py b/test/test_haplotype.py → tests/test_haplotype.py
diff --git a/test/test_horse.py → tests/test_horse.py b/test/test_horse.py → tests/test_horse.py
diff --git a/test/test_human.py → tests/test_human.py b/test/test_human.py → tests/test_human.py
diff --git a/test/test_iedb_names.py → tests/test_iedb_names.py b/test/test_iedb_names.py → tests/test_iedb_names.py
diff --git a/test/test_imgt_hla_names.py → tests/test_imgt_hla_names.py b/test/test_imgt_hla_names.py → tests/test_imgt_hla_names.py
diff --git a/test/test_ipd_mhc_names.py → tests/test_ipd_mhc_names.py b/test/test_ipd_mhc_names.py → tests/test_ipd_mhc_names.py
diff --git a/test/test_mhc_class_parsing.py → tests/test_mhc_class_parsing.py b/test/test_mhc_class_parsing.py → tests/test_mhc_class_parsing.py
diff --git a/test/test_mouse.py → tests/test_mouse.py b/test/test_mouse.py → tests/test_mouse.py
diff --git a/test/test_netmhciipan_3_1_alleles.py → tests/test_netmhciipan_3_1_alleles.py b/test/test_netmhciipan_3_1_alleles.py → tests/test_netmhciipan_3_1_alleles.py
diff --git a/test/test_netmhcpan_3_0_alleles.py → tests/test_netmhcpan_3_0_alleles.py b/test/test_netmhcpan_3_0_alleles.py → tests/test_netmhcpan_3_0_alleles.py
diff --git a/test/test_netmhcpan_4_0_alleles.py → tests/test_netmhcpan_4_0_alleles.py b/test/test_netmhcpan_4_0_alleles.py → tests/test_netmhcpan_4_0_alleles.py
diff --git a/test/test_nhp.py → tests/test_nhp.py b/test/test_nhp.py → tests/test_nhp.py
diff --git a/test/test_normalizing_dictionary.py → tests/test_normalizing_dictionary.py b/test/test_normalizing_dictionary.py → tests/test_normalizing_dictionary.py
diff --git a/test/test_normalizing_set.py → tests/test_normalizing_set.py b/test/test_normalizing_set.py → tests/test_normalizing_set.py
diff --git a/test/test_parser.py → tests/test_parser.py b/test/test_parser.py → tests/test_parser.py
diff --git a/test/test_rat.py → tests/test_rat.py b/test/test_rat.py → tests/test_rat.py
diff --git a/test/test_serotype.py → tests/test_serotype.py b/test/test_serotype.py → tests/test_serotype.py
diff --git a/test/test_sheep.py → tests/test_sheep.py b/test/test_sheep.py → tests/test_sheep.py
diff --git a/test/test_species.py → tests/test_species.py b/test/test_species.py → tests/test_species.py
diff --git a/test/test_standard_format.py → tests/test_standard_format.py b/test/test_standard_format.py → tests/test_standard_format.py
diff --git a/test/test_swine.py → tests/test_swine.py b/test/test_swine.py → tests/test_swine.py
diff --git a/test/test_tokenize.py → tests/test_tokenize.py b/test/test_tokenize.py → tests/test_tokenize.py
diff --git a/test/test_uniprot_descriptions.py → tests/test_uniprot_descriptions.py b/test/test_uniprot_descriptions.py → tests/test_uniprot_descriptions.py
diff --git a/test/test_workshop_alleles.py → tests/test_workshop_alleles.py b/test/test_workshop_alleles.py → tests/test_workshop_alleles.py
diff --git a/test/timing.py → tests/timing.py b/test/timing.py → tests/timing.py
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		pytest --cov=mhcgnomes/ --cov-report=term-missing tests