From 714296b695a180c04ae1e80e4516306e04b18c3c Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 10 Mar 2022 14:44:22 +0100 Subject: [PATCH 1/6] adding py310 --- .github/workflows/release-workflow.yml | 30 +++++++++++----------- .github/workflows/sync-with-model-repo.yml | 6 ++--- .github/workflows/test-images.yml | 16 ++++++------ dockerfiles/environment.kipoi.yml | 2 +- environment.ubuntu.singularity.yml | 4 +-- 5 files changed, 29 insertions(+), 29 deletions(-) diff --git a/.github/workflows/release-workflow.yml b/.github/workflows/release-workflow.yml index b9d84f0..1ff11c2 100644 --- a/.github/workflows/release-workflow.yml +++ b/.github/workflows/release-workflow.yml @@ -18,14 +18,14 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUBPAT }} steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 - - name: Install conda environment py39 + python-version: 3.10 + - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: py39 + activate-environment: py310 environment-file: environment.ubuntu.singularity.yml auto-activate-base: false - name: Install dependencies @@ -62,14 +62,14 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUBPAT }} steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 - - name: Install conda environment py39 + python-version: 3.10 + - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: py39 + activate-environment: py310 environment-file: environment.ubuntu.singularity.yml auto-activate-base: false - name: Install dependencies @@ -94,11 +94,11 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUBPAT }} steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 - - name: Install conda environment py39 + python-version: 3.10 + - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: activate-environment: py39 @@ -134,14 +134,14 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUBPAT }} steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 - - name: Install conda environment py39 + python-version: 3.10 + - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: py39 + activate-environment: py310 environment-file: environment.ubuntu.singularity.yml auto-activate-base: false - name: Install dependencies diff --git a/.github/workflows/sync-with-model-repo.yml b/.github/workflows/sync-with-model-repo.yml index 2b26a67..d452324 100644 --- a/.github/workflows/sync-with-model-repo.yml +++ b/.github/workflows/sync-with-model-repo.yml @@ -22,14 +22,14 @@ jobs: # Steps represent a sequence of tasks that will be executed as part of the job steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: 3.10 - name: Install conda dependencies uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: py39 + activate-environment: py310 environment-file: environment.ubuntu.singularity.yml auto-activate-base: false - name: Install pip dependencies diff --git a/.github/workflows/test-images.yml b/.github/workflows/test-images.yml index 31f81a8..c3f1fde 100644 --- a/.github/workflows/test-images.yml +++ b/.github/workflows/test-images.yml @@ -14,10 +14,10 @@ jobs: steps: - uses: actions/checkout@v2 - uses: psf/black@stable - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: 3.10 - name: Install dependencies run: | python -m pip install --upgrade pip @@ -47,16 +47,16 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: 3.10 - name: Install uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: py39 + activate-environment: py310 environment-file: environment.ubuntu.singularity.yml - python-version: 3.9 + python-version: 3.10 auto-activate-base: false - name: Install dependencies shell: bash -l {0} @@ -78,10 +78,10 @@ jobs: ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODOACCESSTOKEN }} steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: 3.10 - name: Install dependencies run: | sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config diff --git a/dockerfiles/environment.kipoi.yml b/dockerfiles/environment.kipoi.yml index fc0cb6c..5b85631 100644 --- a/dockerfiles/environment.kipoi.yml +++ b/dockerfiles/environment.kipoi.yml @@ -4,7 +4,7 @@ channels: - bioconda - defaults dependencies: - - python=3.9 + - python=3.10 - pip - pkgconfig - conda-forge::hdf5 diff --git a/environment.ubuntu.singularity.yml b/environment.ubuntu.singularity.yml index b0dbed8..8d444c6 100644 --- a/environment.ubuntu.singularity.yml +++ b/environment.ubuntu.singularity.yml @@ -1,4 +1,4 @@ -name: py39 +name: py310 channels: - bioconda - conda-forge @@ -6,4 +6,4 @@ channels: dependencies: - pip - singularity>=3.5 - - python=3.9 + - python=3.10 From 55077c22cd89893c291fe03dbf582534ecc4cec9 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 10 Mar 2022 14:49:31 +0100 Subject: [PATCH 2/6] adding test images --- .github/workflows/test-images.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test-images.yml b/.github/workflows/test-images.yml index c3f1fde..72d93dc 100644 --- a/.github/workflows/test-images.yml +++ b/.github/workflows/test-images.yml @@ -17,7 +17,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install dependencies run: | python -m pip install --upgrade pip @@ -50,13 +50,13 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install uses: conda-incubator/setup-miniconda@v2 with: activate-environment: py310 environment-file: environment.ubuntu.singularity.yml - python-version: 3.10 + python-version: '3.10' auto-activate-base: false - name: Install dependencies shell: bash -l {0} @@ -81,7 +81,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install dependencies run: | sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config From 7876402d8de6ad7cecad949682f2ae37b934a9c9 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 10 Mar 2022 14:57:54 +0100 Subject: [PATCH 3/6] Installing kipoi from master branch --- dockerfiles/environment.kipoi.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/dockerfiles/environment.kipoi.yml b/dockerfiles/environment.kipoi.yml index 5b85631..3c9f98c 100644 --- a/dockerfiles/environment.kipoi.yml +++ b/dockerfiles/environment.kipoi.yml @@ -9,5 +9,4 @@ dependencies: - pkgconfig - conda-forge::hdf5 - pip: - - kipoi - + - git+https://github.com/kipoi/kipoi.git #TODO: Add back when kipoi when py3.10 version is available From fc5b56f82a638bfade915e7b396a2522b8a5f4c1 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 10 Mar 2022 15:43:15 +0100 Subject: [PATCH 4/6] adding kipoi installation from master branch --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index f255f79..3be06e8 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ "ruamel.yaml.clib", "pandas", "spython", - "kipoi", + "git+https://github.com/kipoi/kipoi.git", "pre-commit", "click", ] From 66eb0eac7da2c08f4ef2d9f2644d4ecd0ec2eb1f Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 10 Mar 2022 17:54:13 +0100 Subject: [PATCH 5/6] adding kipoi in setuptools --- setup.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 3be06e8..f104c5c 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,6 @@ "ruamel.yaml.clib", "pandas", "spython", - "git+https://github.com/kipoi/kipoi.git", "pre-commit", "click", ] @@ -39,7 +38,10 @@ "update_all_singularity=kipoi_containers.update_all_singularity_images:run_update", ], }, - install_requires=requirements, + install_requires=[ + requirements, + "kipoi @ https://github.com/kipoi/kipoi/archive/master.tar.gz", + ], license="MIT license", include_package_data=True, keywords="kipoi_containers", From 1853a15470ff094ddb0419399e7155cdd24e2c09 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 10 Mar 2022 19:35:20 +0100 Subject: [PATCH 6/6] fixing yaml error --- .github/workflows/release-workflow.yml | 8 ++++---- .github/workflows/sync-with-model-repo.yml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/release-workflow.yml b/.github/workflows/release-workflow.yml index 1ff11c2..78160ef 100644 --- a/.github/workflows/release-workflow.yml +++ b/.github/workflows/release-workflow.yml @@ -21,7 +21,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: @@ -65,7 +65,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: @@ -97,7 +97,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: @@ -137,7 +137,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install conda environment py310 uses: conda-incubator/setup-miniconda@v2 with: diff --git a/.github/workflows/sync-with-model-repo.yml b/.github/workflows/sync-with-model-repo.yml index d452324..f83d6d7 100644 --- a/.github/workflows/sync-with-model-repo.yml +++ b/.github/workflows/sync-with-model-repo.yml @@ -25,7 +25,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v2 with: - python-version: 3.10 + python-version: '3.10' - name: Install conda dependencies uses: conda-incubator/setup-miniconda@v2 with: