From bbed7fe33ebc0c2a44e680254a8de1ecf03d226c Mon Sep 17 00:00:00 2001 From: Anthony Simard Date: Thu, 15 Feb 2024 10:04:03 -0700 Subject: [PATCH 1/3] No more types genomics (#176) --- ci/recipe/meta.yaml | 1 - rescript/ncbi_datasets.py | 2 +- rescript/plugin_setup.py | 2 +- rescript/tests/test_ncbi_datasets.py | 2 +- 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml index 6f817fcb..ea8d7f30 100644 --- a/ci/recipe/meta.yaml +++ b/ci/recipe/meta.yaml @@ -26,7 +26,6 @@ requirements: - scikit-learn {{ scikit_learn }} - scikit-bio {{ scikit_bio }} - q2-types {{ qiime2_epoch }}.* - - q2-types-genomics >2023.2 - q2-feature-classifier {{ qiime2_epoch }}.* - qiime2 {{ qiime2_epoch }}.* diff --git a/rescript/ncbi_datasets.py b/rescript/ncbi_datasets.py index 94c77044..d7ef1379 100644 --- a/rescript/ncbi_datasets.py +++ b/rescript/ncbi_datasets.py @@ -21,7 +21,7 @@ from multiprocessing import Manager from ncbi.datasets import ApiException from q2_types.feature_data import DNAFASTAFormat -from q2_types_genomics.genome_data import (LociDirectoryFormat, +from q2_types.genome_data import (LociDirectoryFormat, ProteinsDirectoryFormat) from rescript.ncbi import get_taxonomies, _default_ranks diff --git a/rescript/plugin_setup.py b/rescript/plugin_setup.py index 4ade7cd9..469cd351 100644 --- a/rescript/plugin_setup.py +++ b/rescript/plugin_setup.py @@ -8,7 +8,7 @@ import importlib -from q2_types_genomics.genome_data import GenomeData, Loci, Proteins +from q2_types.genome_data import GenomeData, Loci, Proteins from qiime2.core.type import TypeMatch from qiime2.plugin import (Str, Plugin, Choices, List, Citations, Range, Int, Float, Visualization, Bool, TypeMap, Metadata, diff --git a/rescript/tests/test_ncbi_datasets.py b/rescript/tests/test_ncbi_datasets.py index 4e6d43ce..35e20138 100644 --- a/rescript/tests/test_ncbi_datasets.py +++ b/rescript/tests/test_ncbi_datasets.py @@ -13,7 +13,7 @@ import pandas as pd from ncbi.datasets import GenomeApi, ApiClient, ApiException from q2_types.feature_data import DNAFASTAFormat -from q2_types_genomics.genome_data import (LociDirectoryFormat, +from q2_types.genome_data import (LociDirectoryFormat, ProteinsDirectoryFormat) from qiime2.plugin.testing import TestPluginBase from rescript.ncbi import _default_ranks From ba1e29cda62a93088dce8d531539d6dabe900510 Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Thu, 15 Feb 2024 15:13:25 -0700 Subject: [PATCH 2/3] LINT: fixing a couple of flake8 errors --- rescript/ncbi_datasets.py | 2 +- rescript/tests/test_ncbi_datasets.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/rescript/ncbi_datasets.py b/rescript/ncbi_datasets.py index d7ef1379..e08e89e5 100644 --- a/rescript/ncbi_datasets.py +++ b/rescript/ncbi_datasets.py @@ -22,7 +22,7 @@ from ncbi.datasets import ApiException from q2_types.feature_data import DNAFASTAFormat from q2_types.genome_data import (LociDirectoryFormat, - ProteinsDirectoryFormat) + ProteinsDirectoryFormat) from rescript.ncbi import get_taxonomies, _default_ranks diff --git a/rescript/tests/test_ncbi_datasets.py b/rescript/tests/test_ncbi_datasets.py index 35e20138..d758b8b5 100644 --- a/rescript/tests/test_ncbi_datasets.py +++ b/rescript/tests/test_ncbi_datasets.py @@ -14,7 +14,7 @@ from ncbi.datasets import GenomeApi, ApiClient, ApiException from q2_types.feature_data import DNAFASTAFormat from q2_types.genome_data import (LociDirectoryFormat, - ProteinsDirectoryFormat) + ProteinsDirectoryFormat) from qiime2.plugin.testing import TestPluginBase from rescript.ncbi import _default_ranks from rescript.ncbi_datasets import (_get_assembly_descriptors, From 6c92af9a7497032a3b1a221bd2a0d0dc318ddcf6 Mon Sep 17 00:00:00 2001 From: q2d2 Date: Fri, 16 Feb 2024 22:02:35 +0000 Subject: [PATCH 3/3] DEV: 2024.5