From ca1d6f0e16a7b140d5b2c89b2eaeb038a59a655d Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Mon, 22 Apr 2024 15:01:21 -0700 Subject: [PATCH 1/8] testing 3.11 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index da01b65..4dafaa5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,7 +5,7 @@ jobs: runs-on: macos-latest strategy: matrix: - python-version: ["3.9", "3.10"] + python-version: ["3.9", "3.10", "3.11"] steps: - uses: actions/checkout@master - name: Set up Python ${{ matrix.python-version }} From b6dc84036acb8a764ef8428f899b62443bca35c1 Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Mon, 22 Apr 2024 15:05:29 -0700 Subject: [PATCH 2/8] changed pytest to 8.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 918167b..b9c54cd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,7 +10,7 @@ pathspec==0.8.0 pluggy==0.13.1 py==1.8.1 pyparsing==2.4.7 -pytest==7.2.2 +pytest==8.1.1 pytest-mock==3.0.0 regex==2020.5.7 six==1.14.0 From ce46cd5f32e7eb63525a66d5c7d413a9dcb29dcd Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Mon, 22 Apr 2024 15:11:26 -0700 Subject: [PATCH 3/8] changed pluggy to 8.1.1 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index b9c54cd..be587e5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ more-itertools==8.2.0 numpy==1.24.0 packaging==20.3 pathspec==0.8.0 -pluggy==0.13.1 +pluggy==1.5.0 py==1.8.1 pyparsing==2.4.7 pytest==8.1.1 From 228d5b0642e8d9b554b2fe9e6e6993892ae72335 Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Mon, 22 Apr 2024 15:17:51 -0700 Subject: [PATCH 4/8] testing biopython 1.82 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index be587e5..5a7b95b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ appdirs==1.4.3 attrs==19.3.0 -biopython==1.81 +biopython==1.82 click==7.1.2 importlib-metadata==1.6.0 more-itertools==8.2.0 From cdc55278fcedff5049ac07500a63eb9f729944bf Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Mon, 22 Apr 2024 15:21:07 -0700 Subject: [PATCH 5/8] removing py from requirements.txt --- requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5a7b95b..8e47a32 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,7 +8,6 @@ numpy==1.24.0 packaging==20.3 pathspec==0.8.0 pluggy==1.5.0 -py==1.8.1 pyparsing==2.4.7 pytest==8.1.1 pytest-mock==3.0.0 From d5f1bbf32b018e70411d63e850a087ac7aa33949 Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Mon, 22 Apr 2024 15:27:12 -0700 Subject: [PATCH 6/8] updated setup.py and change log for support for python version 3.11 --- clipkit/version.py | 2 +- docs/change_log/index.rst | 3 +++ setup.py | 3 ++- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/clipkit/version.py b/clipkit/version.py index a7ecb80..55e4709 100644 --- a/clipkit/version.py +++ b/clipkit/version.py @@ -1 +1 @@ -__version__ = "2.2.6" +__version__ = "2.3.0" diff --git a/docs/change_log/index.rst b/docs/change_log/index.rst index 2c7ba65..6353dd9 100644 --- a/docs/change_log/index.rst +++ b/docs/change_log/index.rst @@ -8,6 +8,9 @@ Change log Major changes to ClipKIT are summarized here. +**2.3.0** +Added support for Python version 3.11 + **2.2.3** Fixed gap character handling. The help message was incongruent with what was happening underneath the hood. diff --git a/setup.py b/setup.py index 2109922..d898386 100644 --- a/setup.py +++ b/setup.py @@ -14,10 +14,11 @@ "Programming Language :: Python", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "Topic :: Scientific/Engineering", ] -REQUIRES = ["biopython>=1.81", "numpy>=1.24.0", "cython"] +REQUIRES = ["biopython>=1.82", "numpy>=1.24.0", "cython"] setup( name="clipkit", From ab7e6986e72ca5cd87b79ecbd05965367698662a Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Mon, 29 Apr 2024 15:03:30 -0700 Subject: [PATCH 7/8] updating python version docs to 3.9 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4dafaa5..dfe1b69 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -72,7 +72,7 @@ jobs: - name: Setup Python 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