From fe68cb0c18233826942bee0b08957dee229880cb Mon Sep 17 00:00:00 2001 From: Alex Rubinsteyn Date: Tue, 29 Sep 2026 11:26:02 -0400 Subject: [PATCH 1/2] Support pandas 3 with Sercol 1.0.3 (10.9.1) --- requirements.txt | 4 ++-- varcode/version.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index c0eef087..09ec848a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ numpy>=2.0.0,<3.0.0 -pandas>=2.0.0,<3.0.0 +pandas>=2.0.0,<4.0.0 pyensembl>=2.6.4 memoized_property>=1.0.2 serializable>=1.1.0 -sercol>=0.1.4 +sercol>=1.0.3 diff --git a/varcode/version.py b/varcode/version.py index e6f90235..71004d19 100644 --- a/varcode/version.py +++ b/varcode/version.py @@ -1 +1 @@ -__version__ = "10.10.0" +__version__ = "10.10.1" From fa232e1708314997f8fa4e6dd26c5da93e0b42dc Mon Sep 17 00:00:00 2001 From: Alex Rubinsteyn Date: Tue, 29 Sep 2026 11:45:17 -0400 Subject: [PATCH 2/2] Align explicit genome URLs with CI and avoid duplicate matrices --- .github/workflows/tests.yml | 5 ++++- tests/test_mouse.py | 6 +++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ec6d3c6b..f9d497ba 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -6,7 +6,10 @@ # - get a badge for tests passing # - download binary dependencies from conda name: Tests -on: [push, pull_request] +on: + push: + branches: [main] + pull_request: jobs: build: diff --git a/tests/test_mouse.py b/tests/test_mouse.py index 319e916a..97e585a1 100644 --- a/tests/test_mouse.py +++ b/tests/test_mouse.py @@ -18,12 +18,12 @@ from .data import data_path MOUSE_ENSEMBL_RELEASE = 95 -SERVER = "ftp://ftp.ensembl.org" +SERVER = "https://ftp.ensembl.org" MOUSE_GTF_PATH = \ - SERVER + "/pub/release-%d/gtf/mus_musculus/Mus_musculus.GRCm38.%d.gtf.gz" % ( + SERVER + "/pub/release-%d/gtf/mus_musculus/Mus_musculus.GRCm38.%d.chr_patch_hapl_scaff.gtf.gz" % ( MOUSE_ENSEMBL_RELEASE, MOUSE_ENSEMBL_RELEASE) MOUSE_TRANSCRIPT_FASTA_PATH = \ - SERVER + "/pub/release-%d/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz" + SERVER + "/pub/release-%d/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz" % MOUSE_ENSEMBL_RELEASE MOUSE_PROTEIN_FASTA_PATH = \ SERVER + "/pub/release-%d/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz" % ( MOUSE_ENSEMBL_RELEASE)