Adding OpenMs installation in ci.yml#145
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WalkthroughThe pull request modifies the continuous integration workflow in Changes
Sequence Diagram(s)sequenceDiagram
participant Runner as CI Runner
participant Env as Conda Environment
participant OpenMS as OpenMS Package Installer
Runner->>Runner: Checkout Code
Runner->>Env: Create 'openms' Environment
Env-->>Runner: Environment Ready
Runner->>OpenMS: Configure conda channels (default, bioconda, conda-forge)
Runner->>OpenMS: Install OpenMS
Runner->>Runner: Install remaining dependencies & Run tests
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.github/workflows/ci.yml (1)
20-26: Ensure Conda Availability and Use Non-Interactive Flags
The new "Install OpenMS" step employs several conda commands which may prompt for interactive input. In CI environments—especially on GitHub’subuntu-latestimage—conda is not pre-installed by default. Please consider:
- Verifying or installing Conda: Add a prior step (e.g., using
actions/setup-miniconda) to ensure that the CI environment has conda available.- Adding non-interactive flags: Append the
-yflag to both theconda createandconda installcommands to avoid hanging due to interactive prompts.- Activating the Environment (if required): If subsequent steps depend on the OpenMS installation in the new environment, explicitly activate it via
conda activate openms.For example, you might update the commands as follows:
- conda create -n openms python=3.10 + conda create -n openms python=3.10 -y ... - conda install openms + conda install -n openms openms -y
jcharkow
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Good start! Please see comments.
Also please ensure that the build is actually working as it seems to be failing. https://github.com/subCode321/streamlit-template/actions/runs/13647721004/job/38149552299
In this case, this issue seems to be unrelated to your PR however it is good to take note of this.
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.github/workflows/ci.yml (2)
17-23: Clarify the OpenMS Installation CommandsThe "Install OpenMS" step successfully creates a new Conda environment (
openms) using the matrix-provided Python version and configures the necessary channels. However, please address the following concerns:
- The command
conda install openms openms -ylists the package name twice. Verify whether this duplication is intentional or if it should be simplified toconda install openms -y.- If the OpenMS installation is expected to be used in subsequent steps (such as dependency installation or tests), consider explicitly activating the newly created environment (for example, by adding
conda activate openms) so that subsequent commands run within the correct context.Below is an example diff suggestion:
- conda install openms openms -y + conda install openms -y + conda activate openms # Activate the environment for subsequent steps, if needed.
24-32: Ensure Consistent Environment Use After OpenMS InstallationSince the previous
actions/setup-pythonstep was removed, please verify that subsequent steps (like "Install dependencies" and "Test") run in the intended Python environment. If these steps should leverage theopenmsenvironment, you might need to activate it explicitly as suggested above.🧰 Tools
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[error] 31-31: trailing spaces
(trailing-spaces)
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15-15: Validate the use of the setup-miniconda ActionThe addition of the
conda-incubator/setup-miniconda@v3action is correctly placed to initialize Conda in the CI workflow. Please ensure that this step’s configuration meets your intended environment setup requirements, especially in terms of Python version management.
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Looks good to me! Ready to merge
2 participants
Fixes #137
Adding installation for
OpenMsvia conda. Documentation followed https://openms.readthedocs.io/en/latest/about/installation/installation-on-gnu-linux.html#install-via-condaSummary by CodeRabbit