From 890dbdbda0d2ec6bb972ddb6bc003c3890afbdc5 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 11 Apr 2024 15:32:25 +0200 Subject: [PATCH 1/5] use importlib_metadata with python 3.7 --- .github/workflows/test.yml | 1 + hicmatrix/lib/cool.py | 5 ++++- pyproject.toml | 3 ++- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 2093630..aa6ecf8 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -12,6 +12,7 @@ jobs: strategy: matrix: python-version: + - "3.7" - "3.8" - "3.9" - "3.10" diff --git a/hicmatrix/lib/cool.py b/hicmatrix/lib/cool.py index 83bf955..84d68a5 100644 --- a/hicmatrix/lib/cool.py +++ b/hicmatrix/lib/cool.py @@ -2,7 +2,10 @@ import os import gc -from importlib.metadata import version +try: + from importlib.metadata import version +except ImportError: + from importlib_metadata import version import cooler import h5py diff --git a/pyproject.toml b/pyproject.toml index 305e1a9..5884686 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,8 @@ dependencies = [ "tables >= 3.5", "pandas >= 0.25", "cooler >= 0.8.9", - "intervaltree >= 3.0" + "intervaltree >= 3.0", + "importlib_metadata; python_version<'3.8'" ] [project.urls] From 7aee53e2d9d85054f9b1acd8fa4c079e2e4396d8 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 11 Apr 2024 15:33:46 +0200 Subject: [PATCH 2/5] bump version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5884686..306f275 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "HiCMatrix" -version = "17.1" +version = "17.2" authors = [ { name = "Lucille Lopez-Delisle, Joachim Wolff, Leily Rabbani, Vivek Bhardwaj, Fidel Ramirez", email = "lucille.delisle@epfl.ch" }, ] From 0958660864e878c65d407307d2807c5aedc1e9c8 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 11 Apr 2024 15:42:09 +0200 Subject: [PATCH 3/5] allow python 3.7 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 306f275..f7fee0e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ authors = [ ] description = "Helper package which implements HiCMatrix class for HiCExplorer, pyGenomeTracks and scHiCExplorer." readme = "README.rst" -requires-python = ">=3.8" +requires-python = ">=3.7" classifiers = [ 'Intended Audience :: Science/Research', 'Topic :: Scientific/Engineering :: Bio-Informatics', From 871331f1632fe82ded910e34d07f50da36ea27f4 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 11 Apr 2024 15:47:30 +0200 Subject: [PATCH 4/5] simplify pytest config --- pytest.ini | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/pytest.ini b/pytest.ini index cc8b80a..fa32b1b 100644 --- a/pytest.ini +++ b/pytest.ini @@ -3,6 +3,4 @@ filterwarnings = ignore::UserWarning ignore::FutureWarning ignore::DeprecationWarning - ignore::ImportWarning - ignore::tables.exceptions.FlavorWarning - ; error::ResourceWarning \ No newline at end of file + ignore::ImportWarning \ No newline at end of file From d600c10215064b1530e173fe4248874ea9fb115b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 11 Apr 2024 15:59:46 +0200 Subject: [PATCH 5/5] pin version of c-blosc2 --- HiCMatrix_env_ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/HiCMatrix_env_ci.yml b/HiCMatrix_env_ci.yml index e774e1b..17761cb 100644 --- a/HiCMatrix_env_ci.yml +++ b/HiCMatrix_env_ci.yml @@ -7,6 +7,7 @@ dependencies: - scipy >= 1.2 - pandas >= 0.25 - pytables >= 3.5 + - c-blosc2<=2.14.1 # Temp fix see https://github.com/Blosc/c-blosc2/issues/601 - cooler >= 0.8.9 - intervaltree >= 3.0 - pytest