From 6af898111df5577f6edc71701b1f0be8f27e4399 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 27 Jun 2024 18:11:49 -0400 Subject: [PATCH 1/9] Support Python 3.12 --- .github/workflows/main.yml | 4 +- CHANGELOG.rst | 20 + Makefile | 8 + poetry.lock | 1170 +++++++++++++++++++++--------------- pyproject.toml | 20 +- 5 files changed, 744 insertions(+), 478 deletions(-) create mode 100644 CHANGELOG.rst diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index af6733c..78bc975 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,10 +20,10 @@ jobs: name: Test granite with Python ${{ matrix.python_version }} # The type of runner that the job will run on - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 strategy: matrix: - python_version: [3.6, 3.7, 3.8, 3.9] + python_version: [3.9, 3.12] # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 0000000..18f05a4 --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,20 @@ +============= +granite-suite +============= + +---------- +Change Log +---------- + +0.3.0 +===== +* Added this CHANGELOG.rst. +* Updated to support Python 3.12. + - update pysam ">=0.15.0" -> "^0.22.1" + - update bitarray: ">=1.2.0" -> "^2.9.2" + - update pytabix: ">=0.0.2" -> "^0.1" + - update matplotlib: = "==3.3.4" -> "^3.9.0" + +0.2.0 +===== +* Original. diff --git a/Makefile b/Makefile index 64ac51c..93d57e4 100644 --- a/Makefile +++ b/Makefile @@ -24,3 +24,11 @@ info: $(info - Use 'make update' to update dependencies and the lock file.) $(info - Use 'make build' to install entry point commands.) $(info - Use 'make test' to run tests.) + +publish: + pip install dcicutils + poetry run publish-to-pypi + +publish-for-ga: + pip install dcicutils + python -m dcicutils.scripts.publish_to_pypi --noconfirm diff --git a/poetry.lock b/poetry.lock index 972e3de..25e4b4e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,229 +1,790 @@ -[[package]] -name = "atomicwrites" -version = "1.4.0" -description = "Atomic file writes." -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[[package]] -name = "attrs" -version = "21.4.0" -description = "Classes Without Boilerplate" -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - -[package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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"granite is a collection of software to call, filter and work with genomic variants." authors = ["Michele Berselli ", "Phil Grayson"] readme = "README.md" @@ -19,13 +19,19 @@ packages = [ [tool.poetry.dependencies] -python = "^3.6" -pysam = ">=0.15.0" -bitarray = ">=1.2.0" -pytabix = ">=0.0.2" +# python = "^3.6" +python = "^3.9" +# pysam = ">=0.15.0" +pysam = "^0.22.1" +# bitarray = ">=1.2.0" +bitarray = "^2.9.2" +# pytabix = ">=0.0.2" +pytabix = "^0.1" h5py = ">=2.10.0" -numpy = ">=1.18.0" -matplotlib = "==3.3.4" +# numpy = ">=1.18.0" +numpy = "^2.0.0" +# matplotlib = "==3.3.4" +matplotlib = "^3.9.0" [tool.poetry.dev-dependencies] From f014b565a94673c761771f214998f1aef6612f92 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 27 Jun 2024 18:18:04 -0400 Subject: [PATCH 2/9] Support Python 3.12 --- CHANGELOG.rst | 6 ++++-- poetry.lock | 2 +- pyproject.toml | 11 ++++++----- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 18f05a4..6629cde 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -10,10 +10,12 @@ Change Log ===== * Added this CHANGELOG.rst. * Updated to support Python 3.12. - - update pysam ">=0.15.0" -> "^0.22.1" - update bitarray: ">=1.2.0" -> "^2.9.2" + - update h5py: ">=2.10.0" -> "^3.11.0" + - update matplotlib: "==3.3.4" -> "^3.9.0" + - udpate numpy: ">=1.18.0" -> "^2.0.0" + - update pysam ">=0.15.0" -> "^0.22.1" - update pytabix: ">=0.0.2" -> "^0.1" - - update matplotlib: = "==3.3.4" -> "^3.9.0" 0.2.0 ===== diff --git a/poetry.lock b/poetry.lock index 25e4b4e..2779652 100644 --- a/poetry.lock +++ b/poetry.lock @@ -829,4 +829,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "e60d47abe5892e26258b43431862eeb25ed8f1798bc4a28d226080c76cf0370f" +content-hash = "9bdf5e33f063b2d94da2ae9d69ffb5fd16c3e4e6d3d5437617779a0cd2862236" diff --git a/pyproject.toml b/pyproject.toml index 69eb823..9aa563c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,17 +21,18 @@ packages = [ [tool.poetry.dependencies] # python = "^3.6" python = "^3.9" -# pysam = ">=0.15.0" -pysam = "^0.22.1" # bitarray = ">=1.2.0" bitarray = "^2.9.2" -# pytabix = ">=0.0.2" -pytabix = "^0.1" -h5py = ">=2.10.0" +# h5py = ">=2.10.0" +h5py = "^3.11.0" # numpy = ">=1.18.0" numpy = "^2.0.0" # matplotlib = "==3.3.4" matplotlib = "^3.9.0" +# pysam = ">=0.15.0" +pysam = "^0.22.1" +# pytabix = ">=0.0.2" +pytabix = "^0.1" [tool.poetry.dev-dependencies] From 59e1a44a99f55eeba5aa4a573fe4bbdfce0a396a Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 27 Jun 2024 18:20:20 -0400 Subject: [PATCH 3/9] Support Python 3.12 --- .github/workflows/main-publish.yml | 38 ++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 .github/workflows/main-publish.yml diff --git a/.github/workflows/main-publish.yml b/.github/workflows/main-publish.yml new file mode 100644 index 0000000..4e451b8 --- /dev/null +++ b/.github/workflows/main-publish.yml @@ -0,0 +1,38 @@ +# PyPi publish for granite-suite + +name: publish + +# Controls when the action will run. +on: + + # Publish on all tags + push: + tags: + - '*' + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "build" + build: + # The type of runner that the job will run on + runs-on: ubuntu-22.04 + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: Install Python dependencies for publish + run: pip install requests toml + - name: Publish + env: + PYPI_USER: ${{ secrets.PYPI_USER }} + PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }} + run: | + make configure + make publish-for-ga From a6cf0a46c399b500cddc07f93a0e09ba65a5fc16 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 27 Jun 2024 18:25:24 -0400 Subject: [PATCH 4/9] Support Python 3.12 --- pyproject.toml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 9aa563c..ee30b9f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "granite-suite" -version = "0.2.0.1b1" # TODO: To become 0.3.0 +version = "0.2.0.1b2" # TODO: To become 0.3.0 description = "granite is a collection of software to call, filter and work with genomic variants." authors = ["Michele Berselli ", "Phil Grayson"] readme = "README.md" @@ -19,19 +19,12 @@ packages = [ [tool.poetry.dependencies] -# python = "^3.6" python = "^3.9" -# bitarray = ">=1.2.0" bitarray = "^2.9.2" -# h5py = ">=2.10.0" h5py = "^3.11.0" -# numpy = ">=1.18.0" numpy = "^2.0.0" -# matplotlib = "==3.3.4" matplotlib = "^3.9.0" -# pysam = ">=0.15.0" pysam = "^0.22.1" -# pytabix = ">=0.0.2" pytabix = "^0.1" From 86933454f0a81b15bede32344b6f95d75ddd5cea Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 27 Jun 2024 18:26:50 -0400 Subject: [PATCH 5/9] Support Python 3.12 --- .github/workflows/main-publish.yml | 2 +- CHANGELOG.rst | 12 ++++++------ pyproject.toml | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/main-publish.yml b/.github/workflows/main-publish.yml index 4e451b8..cb46590 100644 --- a/.github/workflows/main-publish.yml +++ b/.github/workflows/main-publish.yml @@ -1,6 +1,6 @@ # PyPi publish for granite-suite -name: publish +name: PUBLISH # Controls when the action will run. on: diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 6629cde..2cf343c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -10,12 +10,12 @@ Change Log ===== * Added this CHANGELOG.rst. * Updated to support Python 3.12. - - update bitarray: ">=1.2.0" -> "^2.9.2" - - update h5py: ">=2.10.0" -> "^3.11.0" - - update matplotlib: "==3.3.4" -> "^3.9.0" - - udpate numpy: ">=1.18.0" -> "^2.0.0" - - update pysam ">=0.15.0" -> "^0.22.1" - - update pytabix: ">=0.0.2" -> "^0.1" + - updated bitarray: ">=1.2.0" -> "^2.9.2" + - updated h5py: ">=2.10.0" -> "^3.11.0" + - updated matplotlib: "==3.3.4" -> "^3.9.0" + - udpated numpy: ">=1.18.0" -> "^2.0.0" + - updated pysam ">=0.15.0" -> "^0.22.1" + - updated pytabix: ">=0.0.2" -> "^0.1" 0.2.0 ===== diff --git a/pyproject.toml b/pyproject.toml index ee30b9f..c7a07cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "granite-suite" -version = "0.2.0.1b2" # TODO: To become 0.3.0 +version = "0.2.0.1b3" # TODO: To become 0.3.0 description = "granite is a collection of software to call, filter and work with genomic variants." authors = ["Michele Berselli ", "Phil Grayson"] readme = "README.md" From c7bc899f8c659a2d277e2b2a30bb8c276ae5876d Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 27 Jun 2024 18:35:03 -0400 Subject: [PATCH 6/9] Support Python 3.12 --- CHANGELOG.rst | 2 +- poetry.lock | 85 ++++++++++++++++++++++---------------------------- pyproject.toml | 4 +-- 3 files changed, 41 insertions(+), 50 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 2cf343c..faef5f6 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -13,7 +13,7 @@ Change Log - updated bitarray: ">=1.2.0" -> "^2.9.2" - updated h5py: ">=2.10.0" -> "^3.11.0" - updated matplotlib: "==3.3.4" -> "^3.9.0" - - udpated numpy: ">=1.18.0" -> "^2.0.0" + - udpated numpy: ">=1.18.0" -> "^1.26.4" - updated pysam ">=0.15.0" -> "^0.22.1" - updated pytabix: ">=0.0.2" -> "^0.1" diff --git a/poetry.lock b/poetry.lock index 2779652..8b9d8fa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -529,56 +529,47 @@ dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6)", "setupto [[package]] name = "numpy" -version = "2.0.0" +version = "1.26.4" description = "Fundamental package for array 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and work with genomic variants." authors = ["Michele Berselli ", "Phil Grayson"] readme = "README.md" @@ -22,7 +22,7 @@ packages = [ python = "^3.9" bitarray = "^2.9.2" h5py = "^3.11.0" -numpy = "^2.0.0" +numpy = "^1.26.4" matplotlib = "^3.9.0" pysam = "^0.22.1" pytabix = "^0.1" From 0f78e3e66628ae154b584a0442402f6f53365f4f Mon Sep 17 00:00:00 2001 From: David Michaels Date: Mon, 1 Jul 2024 15:48:50 -0400 Subject: [PATCH 7/9] Support for Python 3.12 --- .github/workflows/main.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 78bc975..34eafc8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -23,7 +23,7 @@ jobs: runs-on: ubuntu-22.04 strategy: matrix: - python_version: [3.9, 3.12] + python_version: [3.9, 3.11, 3.12] # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/pyproject.toml b/pyproject.toml index 1a4c16c..bee85e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "granite-suite" -version = "0.2.0.1b4" # TODO: To become 0.3.0 +version = "0.2.0.1b5" # TODO: To become 0.3.0 description = "granite is a collection of software to call, filter and work with genomic variants." authors = ["Michele Berselli ", "Phil Grayson"] readme = "README.md" From 35b4f8c787a23523e095f811bd976a605a05a482 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Mon, 1 Jul 2024 15:51:45 -0400 Subject: [PATCH 8/9] Support for Python 3.12 --- CHANGELOG.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index faef5f6..c2b4d39 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -16,6 +16,8 @@ Change Log - udpated numpy: ">=1.18.0" -> "^1.26.4" - updated pysam ">=0.15.0" -> "^0.22.1" - updated pytabix: ">=0.0.2" -> "^0.1" +* Supported Python versions now are: 3.9, 3.10, 3.11, 3.12 +* Note specifically that Python 3.8 is no longer supported (end 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