From 09f76d686ba45d5550e10aa7fb820540306a8e89 Mon Sep 17 00:00:00 2001 From: Alex Chklovski <54562698+chklovski@users.noreply.github.com> Date: Sun, 22 Jan 2023 18:25:15 +1000 Subject: [PATCH 1/7] full requirements --- setup.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/setup.py b/setup.py index e7cd726..0f1fc52 100644 --- a/setup.py +++ b/setup.py @@ -13,16 +13,23 @@ include_package_data=True, url='https://github.com/chklovski/CheckM2', license='', - install_requires=('h5py==2.10.0', + install_requires=('python>=3.6, <3.9', + 'h5py==2.10.0', 'scikit-learn==0.23.2', - 'numpy>=1.16.4', + 'numpy=1.19.2', + 'diamond=2.0.4', 'scipy', - 'pandas', - 'tensorflow', - 'lightgbm', - 'requests', - 'tqdm' + 'pandas<=1.4.0', + 'tensorflow>=2.1.0, <2.6.0', + 'lightgbm=3.2.1', + 'requests', + 'prodigal>=2.6.3', + 'tqdm', + 'packaging' + 'requests', + 'setuptools' ), + author='Alex Chklovski', scripts=['bin/checkm2'], author_email='chklovski@gmail.com', From c21a767feb724b06e32911e4c2d58d3e4cfcfebe Mon Sep 17 00:00:00 2001 From: Alex Chklovski <54562698+chklovski@users.noreply.github.com> Date: Sun, 22 Jan 2023 18:29:25 +1000 Subject: [PATCH 2/7] fix requirements --- setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index 0f1fc52..8ca5b4d 100644 --- a/setup.py +++ b/setup.py @@ -16,12 +16,12 @@ install_requires=('python>=3.6, <3.9', 'h5py==2.10.0', 'scikit-learn==0.23.2', - 'numpy=1.19.2', - 'diamond=2.0.4', + 'numpy==1.19.2', + 'diamond==2.0.4', 'scipy', 'pandas<=1.4.0', 'tensorflow>=2.1.0, <2.6.0', - 'lightgbm=3.2.1', + 'lightgbm==3.2.1', 'requests', 'prodigal>=2.6.3', 'tqdm', From 28adc9e8f8adebecf585750806e2f158c9fa47dd Mon Sep 17 00:00:00 2001 From: Alex Chklovski <54562698+chklovski@users.noreply.github.com> Date: Sun, 22 Jan 2023 18:34:01 +1000 Subject: [PATCH 3/7] Update setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8ca5b4d..ecaddb3 100644 --- a/setup.py +++ b/setup.py @@ -25,7 +25,7 @@ 'requests', 'prodigal>=2.6.3', 'tqdm', - 'packaging' + 'packaging', 'requests', 'setuptools' ), From d0cdf4bbe7e1619ef0601497602df8c5cad9842b Mon Sep 17 00:00:00 2001 From: Alex Chklovski <54562698+chklovski@users.noreply.github.com> Date: Sun, 22 Jan 2023 18:43:47 +1000 Subject: [PATCH 4/7] Update setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ecaddb3..b2d6589 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,7 @@ 'tensorflow>=2.1.0, <2.6.0', 'lightgbm==3.2.1', 'requests', - 'prodigal>=2.6.3', + 'prodigal', 'tqdm', 'packaging', 'requests', From 03ac7d839940fa980a5766796592c87fc4be7748 Mon Sep 17 00:00:00 2001 From: Alex Chklovski <54562698+chklovski@users.noreply.github.com> Date: Sun, 22 Jan 2023 18:52:07 +1000 Subject: [PATCH 5/7] Update setup.py --- setup.py | 1 - 1 file changed, 1 deletion(-) diff --git a/setup.py b/setup.py index b2d6589..7418dab 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,6 @@ 'tensorflow>=2.1.0, <2.6.0', 'lightgbm==3.2.1', 'requests', - 'prodigal', 'tqdm', 'packaging', 'requests', From d3d1e1034dfb1393fc27cb570823d3a0c824e44b Mon Sep 17 00:00:00 2001 From: Alex Chklovski <54562698+chklovski@users.noreply.github.com> Date: Sun, 22 Jan 2023 18:59:21 +1000 Subject: [PATCH 6/7] Update setup.py --- setup.py | 20 +++++++------------- 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/setup.py b/setup.py index 7418dab..e7cd726 100644 --- a/setup.py +++ b/setup.py @@ -13,22 +13,16 @@ include_package_data=True, url='https://github.com/chklovski/CheckM2', license='', - install_requires=('python>=3.6, <3.9', - 'h5py==2.10.0', + install_requires=('h5py==2.10.0', 'scikit-learn==0.23.2', - 'numpy==1.19.2', - 'diamond==2.0.4', + 'numpy>=1.16.4', 'scipy', - 'pandas<=1.4.0', - 'tensorflow>=2.1.0, <2.6.0', - 'lightgbm==3.2.1', - 'requests', - 'tqdm', - 'packaging', - 'requests', - 'setuptools' + 'pandas', + 'tensorflow', + 'lightgbm', + 'requests', + 'tqdm' ), - author='Alex Chklovski', scripts=['bin/checkm2'], author_email='chklovski@gmail.com', From efb261df2cca011eab935e533cc0ea5f454a682b Mon Sep 17 00:00:00 2001 From: Alex Chklovski <54562698+chklovski@users.noreply.github.com> Date: Sun, 22 Jan 2023 19:03:18 +1000 Subject: [PATCH 7/7] Create publishpackage.yml --- .github/workflows/publishpackage.yml | 29 ++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 .github/workflows/publishpackage.yml diff --git a/.github/workflows/publishpackage.yml b/.github/workflows/publishpackage.yml new file mode 100644 index 0000000..e75c070 --- /dev/null +++ b/.github/workflows/publishpackage.yml @@ -0,0 +1,29 @@ +name: Upload Python Package + +on: + release: + types: [created] + +jobs: + tests: + uses: ./.github/workflows/test_checkm2.yml + publish: + name: publish + needs: [tests] # require tests to pass before deploy runs + runs-on: ubuntu-latest + steps: + - name: Checkout source + uses: actions/checkout@v3 + - name: Set up Python 3.8 + uses: actions/setup-python@v4 + with: + python-version: 3.8 + - name: Build package + run: | + python -m pip install -U pip build + python -m build + - name: Publish + uses: pypa/gh-action-pypi-publish@v1.5.0 + with: + user: __token__ + password: ${{ secrets.PYPI_API_TOKEN }}