From 0b38067cebef255f59971a8f573d4baf385ad31d Mon Sep 17 00:00:00 2001 From: aschroed Date: Wed, 27 Sep 2023 15:38:54 -0400 Subject: [PATCH 1/6] updates to use python versions 3.8 - 3.11 --- Makefile | 2 +- poetry.lock | 1192 ++++++++++++++++++++++++++++-------------------- pyproject.toml | 6 +- 3 files changed, 710 insertions(+), 490 deletions(-) diff --git a/Makefile b/Makefile index 0785497..42ea758 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ clear-poetry-cache: # clear poetry/pypi cache. for user to do explicitly, never poetry cache clear pypi --all configure: # does any pre-requisite installs - pip install poetry==1.3.2 + pip install poetry==1.4.2 lint: flake8 dcicwrangling diff --git a/poetry.lock b/poetry.lock index 6d645e3..ac09a25 100644 --- a/poetry.lock +++ b/poetry.lock @@ -16,7 +16,6 @@ files = [ exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" -typing-extensions = {version = "*", markers = "python_version < 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ubuntu-22.04 strategy: matrix: - python_version: [3.7, 3.8] + python_version: [3.8, 3.9, 3.10, 3.11] # 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/checkout@v3 - uses: actions/setup-python@v2 with: python-version: ${{ matrix.python_version }} - name: Install Deps run: | - pip install poetry coveralls codacy-coverage + make build + pip install coveralls codacy-coverage - name: QA env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: | - poetry install poetry run coverage run --source=dcicwrangling -m pytest -vv tests poetry run coveralls --service=github diff --git a/notebooks/useful_notebooks/12_geo_submission.ipynb b/notebooks/useful_notebooks/12_geo_submission.ipynb index 52eff34..aefd868 100644 --- a/notebooks/useful_notebooks/12_geo_submission.ipynb +++ b/notebooks/useful_notebooks/12_geo_submission.ipynb @@ -664,7 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"9636a1fe872abe91549a248647bb75317c15bae33847cf3a13f6f775aa15e934" +content-hash = "22d97deea0dd7766cf388d443360afad5f5d7a11b57fe25a610beab38d712e28" diff --git a/pyproject.toml b/pyproject.toml index bbfaf8e..31ba4a3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicwrangling" -version = "2.4.1" +version = "3.0.0" description = "Scripts and Jupyter notebooks for 4DN wrangling" authors = ["4DN-DCIC Team "] license = "MIT" @@ -11,7 +11,7 @@ packages = [{ include="scripts", from="." }] [tool.poetry.dependencies] python = ">=3.8.0, <3.12" -dcicutils = "7.12.0.2b6" +dcicutils = "8.0.0" openpyxl = "^3.0.9" Biopython = "^1.80" GEOparse = "^2.0.1" From dc51d9eb69bd51db07dc624acf4e755e3d1c4a70 Mon Sep 17 00:00:00 2001 From: aschroed Date: Thu, 5 Oct 2023 16:45:05 -0400 Subject: [PATCH 3/6] remove 3.10 from matrix --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2340d54..9cdb839 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-22.04 strategy: matrix: - python_version: [3.8, 3.9, 3.10, 3.11] + python_version: [3.8, 3.9, 3.11] # Steps represent a sequence of tasks that will be executed as part of the job steps: From 9596abee77f3b5b0385aa94669454dbff8e0b9fd Mon Sep 17 00:00:00 2001 From: aschroed Date: Thu, 5 Oct 2023 16:51:43 -0400 Subject: [PATCH 4/6] quoting 3.10 --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9cdb839..f749162 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-22.04 strategy: matrix: - python_version: [3.8, 3.9, 3.11] + python_version: [3.8, 3.9, '3.10', 3.11] # Steps represent a sequence of tasks that will be executed as part of the job steps: From 3144ef7469208686e56048bb371e8992cd0e8a03 Mon Sep 17 00:00:00 2001 From: aschroed Date: Thu, 5 Oct 2023 17:10:50 -0400 Subject: [PATCH 5/6] update publish GA --- .github/workflows/main-publish.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main-publish.yml b/.github/workflows/main-publish.yml index 57ed479..f60d661 100644 --- a/.github/workflows/main-publish.yml +++ b/.github/workflows/main-publish.yml @@ -18,17 +18,17 @@ jobs: # This workflow contains a single job called "build" build: # The type of runner that the job will run on - runs-on: ubuntu-20.04 + 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/checkout@v3 - uses: actions/setup-python@v2 with: - python-version: 3.7 + python-version: 3.11 - name: Install Python dependencies for publish - run: python -m pip install dcicutils==7.5.1 + run: python -m pip install dcicutils==8.0.0 - name: Publish env: PYPI_USER: ${{ secrets.PYPI_USER }} From a6c49d8aa1d2d223eed046126ca4ce35d405950b Mon Sep 17 00:00:00 2001 From: aschroed Date: Tue, 10 Oct 2023 11:55:38 -0400 Subject: [PATCH 6/6] consistently quoting python versions --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f749162..c10d3c8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-22.04 strategy: matrix: - python_version: [3.8, 3.9, '3.10', 3.11] + python_version: ['3.8', '3.9', '3.10', '3.11'] # Steps represent a sequence of tasks that will be executed as part of the job steps: