From c7c696c23a3bb284e2c1c29abe83737acb3d287a Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 11:09:56 +0200 Subject: [PATCH 01/11] extend tests to py3.10 --- .github/workflows/qiita-plugin-ci.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 7c2ed51..9adb6f3 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -9,7 +9,9 @@ jobs: # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml main: runs-on: ubuntu-latest - + strategy: + matrix: + python-version: ["3.9", "3.10"] steps: # Downloads a copy of the code in your repository before running CI tests - name: Check out repository code @@ -19,12 +21,12 @@ jobs: uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true - python-version: 3.9 + python-version: ${{ matrix.python-version }} - name: Basic dependencies install shell: bash -l {0} run: | - conda create --yes -n qiita-files python=3.9 h5py pandas scipy numpy + conda create --yes -n qiita-files python=${{ matrix.python-version }} h5py pandas scipy numpy conda activate qiita-files pip install . pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click From e1551dc94f13a58ee28b36bf4bfc5caacac08a70 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 11:18:01 +0200 Subject: [PATCH 02/11] try to import current module OR (for older py versions) from deprecated location --- qiita_files/parse/workflow.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/qiita_files/parse/workflow.py b/qiita_files/parse/workflow.py index c1baf16..744e3c8 100644 --- a/qiita_files/parse/workflow.py +++ b/qiita_files/parse/workflow.py @@ -9,7 +9,10 @@ from copy import deepcopy from time import time from functools import update_wrapper -from collections import Iterable +try: + from collections.abc import Iterable +except ImportError: + from collections import Iterable from types import MethodType From 92fdf873bb76e40923564cb1355f1758666b58b4 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 11:24:22 +0200 Subject: [PATCH 03/11] use pytest instead of nose --- .github/workflows/qiita-plugin-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 9adb6f3..d62df3c 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -29,13 +29,13 @@ jobs: conda create --yes -n qiita-files python=${{ matrix.python-version }} h5py pandas scipy numpy conda activate qiita-files pip install . - pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click + pip install sphinx sphinx-bootstrap-theme pytest-cov codecov Click - name: Main tests shell: bash -l {0} run: | conda activate qiita-files - nosetests --with-doctest --with-coverage --cover-package=qiita_files + pytest --with-doctest --cov=qiita_files --cov-report=lcov lint: runs-on: ubuntu-latest From 08a1c997ba352c39b176785d5a51c5936add4866 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 11:27:14 +0200 Subject: [PATCH 04/11] change flag --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index d62df3c..c1949fc 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -35,7 +35,7 @@ jobs: shell: bash -l {0} run: | conda activate qiita-files - pytest --with-doctest --cov=qiita_files --cov-report=lcov + pytest --doctest-modules --cov=qiita_files --cov-report=lcov lint: runs-on: ubuntu-latest From 39e5d77e70fd17c0a8e4518543b64a7afad58dce Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 11:32:02 +0200 Subject: [PATCH 05/11] add classifiers for py3.9 and py3.10 --- setup.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.py b/setup.py index 2f398e5..4b539a4 100644 --- a/setup.py +++ b/setup.py @@ -20,6 +20,8 @@ Programming Language :: Python Programming Language :: Python :: 3.5 Programming Language :: Python :: 3.6 + Programming Language :: Python :: 3.9 + Programming Language :: Python :: 3.10 Programming Language :: Python :: Implementation :: CPython Operating System :: POSIX :: Linux Operating System :: MacOS :: MacOS X From 51bb51abd70fee4e76eef0b2e11a05fbc6369da4 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 16:38:42 +0200 Subject: [PATCH 06/11] trigger tests for even more recent py versions --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index c1949fc..9e5d128 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: # Downloads a copy of the code in your repository before running CI tests - name: Check out repository code From 3a172f07bb268f6a14e06a1035328c905357d872 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 16:55:41 +0200 Subject: [PATCH 07/11] add classifiers --- setup.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.py b/setup.py index 4b539a4..2580547 100644 --- a/setup.py +++ b/setup.py @@ -22,6 +22,8 @@ Programming Language :: Python :: 3.6 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 + Programming Language :: Python :: 3.12 Programming Language :: Python :: Implementation :: CPython Operating System :: POSIX :: Linux Operating System :: MacOS :: MacOS X From 46964c5f3ff0e1e54cf05bf7c0abf55209bee736 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 17:05:29 +0200 Subject: [PATCH 08/11] also test old py versions --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 9e5d128..71c3928 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.5, "3.6", "3.9", "3.10", "3.11", "3.12"] steps: # Downloads a copy of the code in your repository before running CI tests - name: Check out repository code From 0ef315b3a8356b52c4b959e903ff7821f1818be2 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 17:05:57 +0200 Subject: [PATCH 09/11] Update qiita-plugin-ci.yml --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 71c3928..57a168c 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.5, "3.6", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.5", "3.6", "3.9", "3.10", "3.11", "3.12"] steps: # Downloads a copy of the code in your repository before running CI tests - name: Check out repository code From d80ba7956df555ea3ca6a5afbefe0a77222e346e Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 17:10:04 +0200 Subject: [PATCH 10/11] Update qiita-plugin-ci.yml --- .github/workflows/qiita-plugin-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 57a168c..78eb963 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.5", "3.6", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.6", "3.9", "3.10", "3.11", "3.12"] steps: # Downloads a copy of the code in your repository before running CI tests - name: Check out repository code From 194f6a85a2b49d055bf7f0051fc5306005227ac2 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 26 Aug 2025 17:21:40 +0200 Subject: [PATCH 11/11] Update qiita-plugin-ci.yml --- .github/workflows/qiita-plugin-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 78eb963..b88f397 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.6", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.5", "3.6", "3.9", "3.10", "3.11", "3.12"] steps: # Downloads a copy of the code in your repository before running CI tests - name: Check out repository code @@ -35,7 +35,7 @@ jobs: shell: bash -l {0} run: | conda activate qiita-files - pytest --doctest-modules --cov=qiita_files --cov-report=lcov + pytest --doctest-modules --cov=qiita_files `if (( $(echo "${{ matrix.python-version }} > 3.6" | bc -l) )); then echo "--cov-report=lcov"; else echo ""; fi` lint: runs-on: ubuntu-latest