From d95d4de8b75871968f6d30fcc39d7cd35d2386fe Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 21:18:47 +0100 Subject: [PATCH 01/10] ci: update CI test file --- .github/workflows/tests.yml | 32 ++++++++++++++++++++------------ 1 file changed, 20 insertions(+), 12 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5ff4bf9..6e74f7b 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -11,7 +11,7 @@ on: jobs: static-code-analysis: - runs-on: ubuntu-latest + runs-on: ubuntu-20.04 defaults: run: shell: bash -l {0} @@ -21,15 +21,17 @@ jobs: uses: actions/checkout@v4 - name: Setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" + channel-priority: true + auto-update-conda: false activate-environment: mirflowz environment-file: environment.yml 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 -p $CONDA_PREFIX -n mirflowz -f environment.dev.yml - name: display environment info run: | @@ -53,7 +55,7 @@ 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} @@ -64,15 +66,17 @@ jobs: uses: actions/checkout@v4 - name: setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" + channel-priority: true + auto-update-conda: false activate-environment: mirflowz environment-file: environment.yml 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 -p $CONDA_PREFIX -n mirflowz -f environment.dev.yml - name: display environment info run: | @@ -90,7 +94,7 @@ jobs: snakemake-integration-test: - runs-on: ubuntu-latest + runs-on: ubuntu-20.04 defaults: run: shell: bash -l {0} @@ -101,15 +105,17 @@ jobs: uses: actions/checkout@v4 - name: setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" activate-environment: mirflowz + channel-priority: true + auto-update-conda: false environment-file: environment.yml 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 -p $CONDA_PREFIX -n mirflowz -f environment.root.yml - name: display environment info run: | @@ -124,7 +130,7 @@ jobs: unit-testing: - runs-on: ubuntu-latest + runs-on: ubuntu-20.04 defaults: run: shell: bash -l {0} @@ -135,15 +141,17 @@ jobs: uses: actions/checkout@v4 - name: setup Conda/Mamba - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: mamba-version: "*" + channel-priority: true + auto-update-conda: false activate-environment: mirflowz environment-file: environment.yml 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 -p $CONDA_PREFIX -n mirflowz -f environment.dev.yml - name: display environment info run: | From c68e8afe7e084e49cd10646b686766ac170d2b56 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 21:22:38 +0100 Subject: [PATCH 02/10] ci: change conda path --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6e74f7b..29fd654 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -31,7 +31,7 @@ jobs: auto-activate-base: false - name: Update mirflowz env with dev packages - run: mamba env update -p $CONDA_PREFIX -n mirflowz -f environment.dev.yml + run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.dev.yml - name: display environment info run: | @@ -76,7 +76,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -p $CONDA_PREFIX -n mirflowz -f environment.dev.yml + run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.dev.yml - name: display environment info run: | @@ -115,7 +115,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with root packages - run: mamba env update -p $CONDA_PREFIX -n mirflowz -f environment.root.yml + run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.root.yml - name: display environment info run: | @@ -151,7 +151,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -p $CONDA_PREFIX -n mirflowz -f environment.dev.yml + run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.dev.yml - name: display environment info run: | From 7361a808bad369fe34d3a86e997204b89fcad9b8 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 21:24:13 +0100 Subject: [PATCH 03/10] ci: remove 'defaults' channel --- .github/workflows/tests.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 29fd654..d6579fd 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -28,6 +28,7 @@ jobs: 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 @@ -73,6 +74,7 @@ jobs: 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 @@ -112,6 +114,7 @@ jobs: 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 @@ -148,6 +151,7 @@ jobs: 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 From 7338e290e4b386c11ffd9b7fe967a7fe10ab07f5 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 21:25:39 +0100 Subject: [PATCH 04/10] ci: change CLI parameter order --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d6579fd..d2b454d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -32,7 +32,7 @@ jobs: auto-activate-base: false - name: Update mirflowz env with dev packages - run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.dev.yml + run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.dev.yml - name: display environment info run: | @@ -78,7 +78,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.dev.yml + run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.dev.yml - name: display environment info run: | @@ -118,7 +118,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with root packages - run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.root.yml + run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.root.yml - name: display environment info run: | @@ -155,7 +155,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -p $MAMBA_ROOT_PREFIX -n mirflowz -f environment.dev.yml + run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.dev.yml - name: display environment info run: | From ca0bbee64bd3e87fd3f97aa481033e097108f46e Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 21:28:19 +0100 Subject: [PATCH 05/10] ci: change CLI parameter order --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d2b454d..2569545 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -32,7 +32,7 @@ jobs: auto-activate-base: false - name: Update mirflowz env with dev packages - run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.dev.yml + run: mamba env update -n mirflowz -f environment.dev.yml -p $MAMBA_ROOT_PREFIX - name: display environment info run: | @@ -78,7 +78,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.dev.yml + run: mamba env update -n mirflowz -f environment.dev.yml -p $MAMBA_ROOT_PREFIX - name: display environment info run: | @@ -118,7 +118,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with root packages - run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.root.yml + run: mamba env update -n mirflowz -f environment.root.yml -p $MAMBA_ROOT_PREFIX - name: display environment info run: | @@ -155,7 +155,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -n mirflowz -p $MAMBA_ROOT_PREFIX -f environment.dev.yml + run: mamba env update -n mirflowz -f environment.dev.yml -p $MAMBA_ROOT_PREFIX - name: display environment info run: | From f97f123382fe24cce3e9fa901882dfb80efe4192 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 21:33:24 +0100 Subject: [PATCH 06/10] ci: remove mamba prefix --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 2569545..49815db 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -32,7 +32,7 @@ jobs: auto-activate-base: false - name: Update mirflowz env with dev packages - run: mamba env update -n mirflowz -f environment.dev.yml -p $MAMBA_ROOT_PREFIX + run: mamba env update -n mirflowz -f environment.dev.yml - name: display environment info run: | @@ -78,7 +78,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -n mirflowz -f environment.dev.yml -p $MAMBA_ROOT_PREFIX + run: mamba env update -n mirflowz -f environment.dev.yml - name: display environment info run: | @@ -118,7 +118,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with root packages - run: mamba env update -n mirflowz -f environment.root.yml -p $MAMBA_ROOT_PREFIX + run: mamba env update -n mirflowz -f environment.root.yml - name: display environment info run: | @@ -155,7 +155,7 @@ jobs: auto-activate-base: false - name: update mirflowz env with dev packages - run: mamba env update -n mirflowz -f environment.dev.yml -p $MAMBA_ROOT_PREFIX + run: mamba env update -n mirflowz -f environment.dev.yml - name: display environment info run: | From 27246d5c6e815d6cb9896f9463e64a96bf613cc9 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 22:59:03 +0100 Subject: [PATCH 07/10] ci: remove parameter --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 49815db..c865673 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -112,7 +112,7 @@ jobs: mamba-version: "*" activate-environment: mirflowz channel-priority: true - auto-update-conda: false + auto-update-conda: true environment-file: environment.yml conda-remove-defaults: true auto-activate-base: false From eb34b24f3d6bdf86c29cda95e6587bd16f6ce917 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 19 Jan 2025 23:17:01 +0100 Subject: [PATCH 08/10] ci: revert to previous commit --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c865673..49815db 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -112,7 +112,7 @@ jobs: mamba-version: "*" activate-environment: mirflowz channel-priority: true - auto-update-conda: true + auto-update-conda: false environment-file: environment.yml conda-remove-defaults: true auto-activate-base: false From f5feb837709a83ccccc13749b03dd2e89ba28076 Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Mon, 20 Jan 2025 13:50:49 +0100 Subject: [PATCH 09/10] ci: pin mamba version --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 49815db..d839854 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -23,7 +23,7 @@ jobs: - name: Setup Conda/Mamba uses: conda-incubator/setup-miniconda@v3 with: - mamba-version: "*" + mamba-version: "2" channel-priority: true auto-update-conda: false activate-environment: mirflowz @@ -69,7 +69,7 @@ jobs: - name: setup Conda/Mamba uses: conda-incubator/setup-miniconda@v3 with: - mamba-version: "*" + mamba-version: "2" channel-priority: true auto-update-conda: false activate-environment: mirflowz @@ -109,7 +109,7 @@ jobs: - name: setup Conda/Mamba uses: conda-incubator/setup-miniconda@v3 with: - mamba-version: "*" + mamba-version: "2" activate-environment: mirflowz channel-priority: true auto-update-conda: false @@ -146,7 +146,7 @@ jobs: - name: setup Conda/Mamba uses: conda-incubator/setup-miniconda@v3 with: - mamba-version: "*" + mamba-version: "2" channel-priority: true auto-update-conda: false activate-environment: mirflowz From 7f36b0e6a2f1007068317507b3354a30b86395de Mon Sep 17 00:00:00 2001 From: deliaBlue Date: Sun, 26 Jan 2025 16:12:43 +0100 Subject: [PATCH 10/10] ci: add strict channel priority --- .github/workflows/tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d839854..0de44bb 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -129,7 +129,9 @@ 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: