From f8cf66c0786c42d12f9fb360fd90dbf9e294310e Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 8 Oct 2024 14:35:14 +0200 Subject: [PATCH 1/5] drop python 3.8 and support 3.13 --- .github/workflows/test.yml | 8 ++++---- pyproject.toml | 2 +- tox.ini | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 55181661..319dd71f 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -38,19 +38,19 @@ jobs: strategy: matrix: os: ['ubuntu-latest', 'macos-latest'] - python-version: [3.8, 3.9, '3.10', '3.11', '3.12'] + python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] dependencies: ['full', 'pre'] include: - os: ubuntu-latest - python-version: 3.8 + python-version: '3.9' dependencies: min exclude: # Drop pre tests for SPEC-0-unsupported Python versions # See https://scientific-python.org/specs/spec-0000/ - - python-version: '3.8' - dependencies: pre - python-version: '3.9' dependencies: pre + - python-version: '3.10' + dependencies: pre fail-fast: false env: diff --git a/pyproject.toml b/pyproject.toml index 8c1bcfec..d566b28b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "pybids" description = "bids: interface with datasets conforming to BIDS" readme = "README.md" -requires-python = ">=3.8" +requires-python = ">=3.9" license = { file="LICENSE" } authors = [ { name = "PyBIDS Developers", email = "bids-discussion@googlegroups.com" }, diff --git a/tox.ini b/tox.ini index b17054b5..01703a82 100644 --- a/tox.ini +++ b/tox.ini @@ -2,18 +2,18 @@ requires = tox>=4 envlist = - py3{8,9,10,11,12}-{full,pre} - py38-min + py3{9,10,11,12,13}-{full,pre} + py39-min skip_missing_interpreters = true # Configuration that allows us to split tests across GitHub runners effectively [gh-actions] python = - 3.8: py38 3.9: py39 3.10: py310 3.11: py311 3.12: py312 + 3.13: py313 [gh-actions:env] DEPENDS = From 546429cdf2ba9a915e2ef656cf9db8e445aee5ac Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 8 Oct 2024 15:03:28 +0200 Subject: [PATCH 2/5] fix dependencies --- pyproject.toml | 6 +++--- tox.ini | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d566b28b..29bfcf54 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,10 +23,10 @@ classifiers = [ "Topic :: Scientific/Engineering", ] dependencies = [ - "numpy >=1.19", # NEP29 + 1yr - "scipy >=1.5", # Scientific Python SPEC 0 + 1yr + "numpy >=1.20", # NEP29 + 1yr + "scipy >=1.7", # Scientific Python SPEC 0 + 1yr "nibabel >=3.0", - "pandas >=0.25.2", # First with Py38 wheel + "pandas >=1.2.0", # First with Py38 wheel "formulaic >=0.2.4, <0.6", # Tested on 0.2.4-0.5.2 "sqlalchemy >=1.3.16", "bids-validator>=1.11", # Keep up-to-date to ensure support for recent modalities diff --git a/tox.ini b/tox.ini index 01703a82..2f2a1a23 100644 --- a/tox.ini +++ b/tox.ini @@ -40,10 +40,10 @@ pass_env = CLICOLOR_FORCE extras = test deps = - min: numpy ==1.19 - min: scipy ==1.5 + min: numpy ==1.20 + min: scipy ==1.7 min: nibabel ==3.0 - min: pandas ==0.25.2 + min: pandas ==1.2.0 # Tested on 0.2.4-0.5.2 min: formulaic ==0.2.4 min: sqlalchemy ==1.3.16 From b7e1c478f5dc234aa0d8d85c5fd6f4641fc16a4a Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 8 Oct 2024 15:18:11 +0200 Subject: [PATCH 3/5] Apply suggestions from code review Co-authored-by: Chris Markiewicz --- pyproject.toml | 10 +++++----- tox.ini | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 29bfcf54..1c4e90b4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,13 +23,13 @@ classifiers = [ "Topic :: Scientific/Engineering", ] dependencies = [ - "numpy >=1.20", # NEP29 + 1yr - "scipy >=1.7", # Scientific Python SPEC 0 + 1yr - "nibabel >=3.0", - "pandas >=1.2.0", # First with Py38 wheel + "numpy >=1.22", # SPEC 0 + 1yr (3yr) + "scipy >=1.8", # SPEC 0 + 1yr (3yr) + "nibabel >=4.0", # SPEC 0 + 1yr (3yr) + "pandas >=1.4.0", # SPEC 0 + 1yr (3yr) "formulaic >=0.2.4, <0.6", # Tested on 0.2.4-0.5.2 "sqlalchemy >=1.3.16", - "bids-validator>=1.11", # Keep up-to-date to ensure support for recent modalities + "bids-validator>=1.14.12", # Keep up-to-date to ensure support for recent modalities "num2words >=0.5.5", "click >=8.0", "universal_pathlib >=0.2.2", diff --git a/tox.ini b/tox.ini index 2f2a1a23..6469ab35 100644 --- a/tox.ini +++ b/tox.ini @@ -40,9 +40,9 @@ pass_env = CLICOLOR_FORCE extras = test deps = - min: numpy ==1.20 - min: scipy ==1.7 - min: nibabel ==3.0 + min: numpy ==1.22 + min: scipy ==1.8 + min: nibabel ==4.0 min: pandas ==1.2.0 # Tested on 0.2.4-0.5.2 min: formulaic ==0.2.4 From 3cea2b924e493a1a999e360abea891bcf7d752cd Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 8 Oct 2024 09:20:47 -0400 Subject: [PATCH 4/5] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 1c4e90b4..5602b721 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ dependencies = [ "pandas >=1.4.0", # SPEC 0 + 1yr (3yr) "formulaic >=0.2.4, <0.6", # Tested on 0.2.4-0.5.2 "sqlalchemy >=1.3.16", - "bids-validator>=1.14.12", # Keep up-to-date to ensure support for recent modalities + "bids-validator>=1.14.7", # Keep up-to-date to ensure support for recent modalities "num2words >=0.5.5", "click >=8.0", "universal_pathlib >=0.2.2", From a7325bcd41535a242a4a5df4cfcb4a6630403050 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 8 Oct 2024 15:51:17 +0200 Subject: [PATCH 5/5] no 3.13 --- .github/workflows/test.yml | 2 +- tox.ini | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 319dd71f..e43ea0ff 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -38,7 +38,7 @@ jobs: strategy: matrix: os: ['ubuntu-latest', 'macos-latest'] - python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] + python-version: ['3.9', '3.10', '3.11', '3.12'] dependencies: ['full', 'pre'] include: - os: ubuntu-latest diff --git a/tox.ini b/tox.ini index 6469ab35..d3012c15 100644 --- a/tox.ini +++ b/tox.ini @@ -2,7 +2,7 @@ requires = tox>=4 envlist = - py3{9,10,11,12,13}-{full,pre} + py3{9,10,11,12}-{full,pre} py39-min skip_missing_interpreters = true @@ -13,7 +13,6 @@ python = 3.10: py310 3.11: py311 3.12: py312 - 3.13: py313 [gh-actions:env] DEPENDS =