From e39e6bcd6cfc4a81fea0482d129a0344b410cc8d Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 3 Nov 2023 09:14:47 -0700 Subject: [PATCH 1/6] update ci --- .github/workflows/test.yml | 42 ++++++++++++++++++++++++-------------- 1 file changed, 27 insertions(+), 15 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e786557..7c2774e 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -16,26 +16,38 @@ jobs: if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository steps: - - uses: actions/checkout@v2 - - - name: Set up Python ${{ matrix.python }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python }} - - - run: pip install -U pip setuptools - - - name: Setup conda - uses: s-weigand/setup-conda@v1 + - uses: actions/checkout@v4 with: - activate-conda: true - - run: conda env update -n base -f environment.yml + fetch-depth: 0 + + - name: cache conda + uses: actions/cache@v3 + env: + CACHE_NUMBER: 0 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} + + - name: setup conda + uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 + with: + auto-update-conda: true + python-version: 3.9 + channels: conda-forge,bioconda + miniforge-variant: Mambaforge + miniforge-version: latest + use-mamba: true + mamba-version: "*" + activate-environment: sourmash_dev + auto-activate-base: false + use-only-tar-bz2: true - name: Install coverage dependencies run: pip install pytest-cov pytest-dependency - - name: Build - run: python setup.py build_ext --inplace +# - name: Build +# run: python setup.py build_ext --inplace - name: Install charcoal run: pip install -e . From 0287eccb1f7eea8bd10cafb28a89ed9cc8f3c075 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 3 Nov 2023 09:16:16 -0700 Subject: [PATCH 2/6] upd --- .github/workflows/test.yml | 44 +++++++++++++++++++------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 7c2774e..10f3edf 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -20,28 +20,28 @@ jobs: with: fetch-depth: 0 - - name: cache conda - uses: actions/cache@v3 - env: - CACHE_NUMBER: 0 - with: - path: ~/conda_pkgs_dir - key: - ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} - - - name: setup conda - uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 - with: - auto-update-conda: true - python-version: 3.9 - channels: conda-forge,bioconda - miniforge-variant: Mambaforge - miniforge-version: latest - use-mamba: true - mamba-version: "*" - activate-environment: sourmash_dev - auto-activate-base: false - use-only-tar-bz2: true + - name: cache conda + uses: actions/cache@v3 + env: + CACHE_NUMBER: 0 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} + + - name: setup conda + uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 + with: + auto-update-conda: true + python-version: 3.9 + channels: conda-forge,bioconda + miniforge-variant: Mambaforge + miniforge-version: latest + use-mamba: true + mamba-version: "*" + activate-environment: sourmash_dev + auto-activate-base: false + use-only-tar-bz2: true - name: Install coverage dependencies run: pip install pytest-cov pytest-dependency From 19c7c3b0f779033c0594bf01c965cf4020f42e91 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 3 Nov 2023 09:18:28 -0700 Subject: [PATCH 3/6] add setuptools --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 10f3edf..cd58ad5 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -44,7 +44,7 @@ jobs: use-only-tar-bz2: true - name: Install coverage dependencies - run: pip install pytest-cov pytest-dependency + run: pip install pytest-cov pytest-dependency setuptools # - name: Build # run: python setup.py build_ext --inplace From a7876bebc535d36bc25dcbba7f83bf502ac55d50 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 3 Nov 2023 09:22:14 -0700 Subject: [PATCH 4/6] ?? --- .github/workflows/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index cd58ad5..1948142 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -46,8 +46,8 @@ jobs: - name: Install coverage dependencies run: pip install pytest-cov pytest-dependency setuptools -# - name: Build -# run: python setup.py build_ext --inplace + - name: Build + run: python setup.py build_ext --inplace - name: Install charcoal run: pip install -e . From f223c5e60c62ecb89a38bab0ced450f98b755b61 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 3 Nov 2023 09:24:30 -0700 Subject: [PATCH 5/6] try again --- .github/workflows/test.yml | 4 ++-- setup.py | 5 ++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 1948142..cd58ad5 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -46,8 +46,8 @@ jobs: - name: Install coverage dependencies run: pip install pytest-cov pytest-dependency setuptools - - name: Build - run: python setup.py build_ext --inplace +# - name: Build +# run: python setup.py build_ext --inplace - name: Install charcoal run: pip install -e . diff --git a/setup.py b/setup.py index 2e00da5..5d9ba89 100644 --- a/setup.py +++ b/setup.py @@ -1,4 +1,4 @@ -from setuptools import setup, find_packages +from setuptools import setup CLASSIFIERS = [ "Environment :: Console", @@ -22,7 +22,7 @@ author="C. Titus Brown and Taylor Reiter", author_email="titus@idyll.org,tereiter@ucdavis.edu", license="BSD 3-clause", - packages = find_packages(), + packages = ["charcoal"], classifiers = CLASSIFIERS, entry_points = {'console_scripts': [ 'charcoal = charcoal.__main__:main' @@ -30,6 +30,5 @@ }, include_package_data=True, package_data = { "charcoal": ["Snakefile", "*.yml", "*.ipynb"] }, - setup_requires = [ "setuptools>=68.2.2" ], install_requires = ['snakemake==7.32.4', 'click>=7,<8'] ) From 1b8eec6db44f9499537d687d4492b1e897ce08cf Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Fri, 3 Nov 2023 09:27:25 -0700 Subject: [PATCH 6/6] closer --- .github/workflows/test.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index cd58ad5..b9af934 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -43,6 +43,8 @@ jobs: auto-activate-base: false use-only-tar-bz2: true + - run: conda env update -n base -f environment.yml + - name: Install coverage dependencies run: pip install pytest-cov pytest-dependency setuptools