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ci: update CI test file #150

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ci: update CI test file #150

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d95d4de
ci: update CI test file
deliaBlue Jan 19, 2025
c68e8af
ci: change conda path
deliaBlue Jan 19, 2025
7361a80
ci: remove 'defaults' channel
deliaBlue Jan 19, 2025
7338e29
ci: change CLI parameter order
deliaBlue Jan 19, 2025
ca0bbee
ci: change CLI parameter order
deliaBlue Jan 19, 2025
f97f123
ci: remove mamba prefix
deliaBlue Jan 19, 2025
27246d5
ci: remove parameter
deliaBlue Jan 19, 2025
eb34b24
ci: revert to previous commit
deliaBlue Jan 19, 2025
f5feb83
ci: pin mamba version
deliaBlue Jan 20, 2025
7f36b0e
ci: add strict channel priority
deliaBlue Jan 26, 2025
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48 changes: 31 additions & 17 deletions .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ on:
jobs:

static-code-analysis:
runs-on: ubuntu-latest
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
Expand All @@ -21,15 +21,18 @@ jobs:
uses: actions/checkout@v4

- name: Setup Conda/Mamba
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
mamba-version: "*"
mamba-version: "2"
channel-priority: true
auto-update-conda: false
activate-environment: mirflowz
environment-file: environment.yml
conda-remove-defaults: true
auto-activate-base: false

- name: Update mirflowz env with dev packages
run: mamba env update -n mirflowz -f environment.dev.yml
run: mamba env update -n mirflowz -f environment.dev.yml

- name: display environment info
run: |
Expand All @@ -53,7 +56,7 @@ jobs:
run: black --check --verbose --line-length=79 ./*.py

snakemake-format-graph-test:
runs-on: ubuntu-latest
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
Expand All @@ -64,15 +67,18 @@ jobs:
uses: actions/checkout@v4

- name: setup Conda/Mamba
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
mamba-version: "*"
mamba-version: "2"
channel-priority: true
auto-update-conda: false
activate-environment: mirflowz
environment-file: environment.yml
conda-remove-defaults: true
auto-activate-base: false

- name: update mirflowz env with dev packages
run: mamba env update -n mirflowz -f environment.dev.yml
run: mamba env update -n mirflowz -f environment.dev.yml

- name: display environment info
run: |
Expand All @@ -90,7 +96,7 @@ jobs:


snakemake-integration-test:
runs-on: ubuntu-latest
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
Expand All @@ -101,15 +107,18 @@ jobs:
uses: actions/checkout@v4

- name: setup Conda/Mamba
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
mamba-version: "*"
mamba-version: "2"
activate-environment: mirflowz
channel-priority: true
auto-update-conda: false
environment-file: environment.yml
conda-remove-defaults: true
auto-activate-base: false

- name: update mirflowz env with root packages
run: mamba env update -n mirflowz -f environment.root.yml
run: mamba env update -n mirflowz -f environment.root.yml

- name: display environment info
run: |
Expand All @@ -120,11 +129,13 @@ jobs:
run: bash test/test_workflow_local_with_singularity.sh

- name: run local test with Conda
run: bash test/test_workflow_local_with_conda.sh
run: |
conda config --set channel_priority strict
bash test/test_workflow_local_with_conda.sh


unit-testing:
runs-on: ubuntu-latest
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -l {0}
Expand All @@ -135,15 +146,18 @@ jobs:
uses: actions/checkout@v4

- name: setup Conda/Mamba
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
mamba-version: "*"
mamba-version: "2"
channel-priority: true
auto-update-conda: false
activate-environment: mirflowz
environment-file: environment.yml
conda-remove-defaults: true
auto-activate-base: false

- name: update mirflowz env with dev packages
run: mamba env update -n mirflowz -f environment.dev.yml
run: mamba env update -n mirflowz -f environment.dev.yml

- name: display environment info
run: |
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