diff --git a/.github/workflows/release-workflow.yml b/.github/workflows/release-workflow.yml index ae67fcf..137b4b2 100644 --- a/.github/workflows/release-workflow.yml +++ b/.github/workflows/release-workflow.yml @@ -34,7 +34,7 @@ jobs: mkdir -p /home/runner/singularity/ sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config python -m pip install --upgrade pip - pip install -e . + pip install . - name: Build and test ${{ matrix.image }} shell: bash -l {0} run: | @@ -97,7 +97,7 @@ jobs: mkdir -p /home/runner/singularity/ sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config python -m pip install --upgrade pip - pip install -e . + pip install . - name: Build sharedpy3keras2 and kipoi-base-env shell: bash -l {0} run: | diff --git a/.github/workflows/sync-with-model-repo.yml b/.github/workflows/sync-with-model-repo.yml index c818f5d..af26cbf 100644 --- a/.github/workflows/sync-with-model-repo.yml +++ b/.github/workflows/sync-with-model-repo.yml @@ -40,7 +40,7 @@ jobs: run: | sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config python -m pip install --upgrade pip - pip install -e . + pip install . - name: Sync with kipoi model repo shell: bash -l {0} run: | diff --git a/.github/workflows/test-images.yml b/.github/workflows/test-images.yml index a213f26..0e69cba 100644 --- a/.github/workflows/test-images.yml +++ b/.github/workflows/test-images.yml @@ -22,7 +22,7 @@ jobs: run: | python -m pip install --upgrade pip pip install flake8 - pip install -e . + pip install . - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names @@ -63,7 +63,7 @@ jobs: mkdir -p /home/runner/singularity/ sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config python -m pip install --upgrade pip - pip install -e . + pip install . - name: Test with pytest shell: bash -l {0} run: | @@ -85,7 +85,7 @@ jobs: run: | sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config python -m pip install --upgrade pip - pip install -e . + pip install . - name: Test kipoi_containers and send coverage report to coveralls.io run: |- pip install coveralls diff --git a/README.md b/README.md index 8b1e1ed..60db7c5 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ kipoi predict Basset \ - Install [singularity](https://sylabs.io/guides/3.0/user-guide/installation.html) -- Install kipoi_containers using ```pip install -e .``` +- Install kipoi_containers using ```pip install .``` ## Environment variables diff --git a/kipoi_containers/update_all_singularity_images.py b/kipoi_containers/update_all_singularity_images.py index 92d58a4..ebc9b94 100644 --- a/kipoi_containers/update_all_singularity_images.py +++ b/kipoi_containers/update_all_singularity_images.py @@ -25,7 +25,7 @@ def run_update(docker_image: str) -> None: kipoi_containers/container-info/model-group-to-singularity.json will be updated. """ - click.echo(f"Testing {docker_image}") + click.echo(f"Updating {docker_image}") model_group_to_singularity_dict = populate_json( MODEL_GROUP_TO_SINGULARITY_JSON ) diff --git a/setup.py b/setup.py index 5aaa60e..f255f79 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ boilerplate you need to create a Python package.", entry_points={ "console_scripts": [ - "update_all_singularity=kipoi_containers.update_all_singularity_containers:run_update", + "update_all_singularity=kipoi_containers.update_all_singularity_images:run_update", ], }, install_requires=requirements,