From c1c0e04f7f25ce1a068f4d793cd29b6a19a7323f Mon Sep 17 00:00:00 2001 From: Eleanor Lewis Date: Tue, 18 Jun 2024 17:21:48 -0700 Subject: [PATCH 1/2] fix version --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 558062d..84016b4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -18,7 +18,7 @@ known_standard_library = requests [metadata] name = pori_python -version = 0.1.0 +version = 0.0.0 url = https://github.com/bcgsc/pori_python author_email = dat@bcgsc.ca maintainer_email = dat@bcgsc.ca From af7d939b54f4f22e985773a8daabbf49b1ef8768 Mon Sep 17 00:00:00 2001 From: Dustin Bleile Date: Wed, 10 Jul 2024 14:40:04 -0700 Subject: [PATCH 2/2] SDEV-4409 - bugfix - replace progressbar2 with tqdm to display progress in long matching. --- pori_python/ipr/annotate.py | 8 ++++---- setup.cfg | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pori_python/ipr/annotate.py b/pori_python/ipr/annotate.py index 9a85d3e..a7f20d3 100644 --- a/pori_python/ipr/annotate.py +++ b/pori_python/ipr/annotate.py @@ -11,7 +11,7 @@ from pori_python.graphkb.types import Variant from pori_python.graphkb.util import FeatureNotFoundError from pandas import isnull -from progressbar import progressbar +from tqdm import tqdm from typing import Dict, List, Sequence from .constants import TMB_HIGH_CATEGORY @@ -102,7 +102,7 @@ def annotate_expression_variants( problem_genes = set() logger.info(f"Starting annotation of {len(variants)} expression category_variants") - iterfunc = progressbar if show_progress else iter + iterfunc = tqdm if show_progress else iter for row in iterfunc(variants): gene = row['gene'] variant = row['variant'] @@ -155,7 +155,7 @@ def annotate_copy_variants( problem_genes = set() logger.info(f"Starting annotation of {len(variants)} copy category_variants") - iterfunc = progressbar if show_progress else iter + iterfunc = tqdm if show_progress else iter for row in iterfunc(variants): gene = row['gene'] variant = row['variant'] @@ -213,7 +213,7 @@ def annotate_positional_variants( alterations = [] problem_genes = set() - iterfunc = progressbar if show_progress else iter + iterfunc = tqdm if show_progress else iter for row in iterfunc(variants): if not row.get('gene') and (not row.get('gene1') or not row.get('gene2')): # https://www.bcgsc.ca/jira/browse/GERO-56?focusedCommentId=1234791&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-1234791 diff --git a/setup.cfg b/setup.cfg index c69b087..b26b858 100644 --- a/setup.cfg +++ b/setup.cfg @@ -32,10 +32,10 @@ dependency_links = [] include_package_data = True install_requires = biopython - progressbar2 - pandas>=1.1.0 jsonschema + pandas>=1.1.0 requests + tqdm typing_extensions>=3.7.4.2,<5 [options.extras_require]