From 921106cac5010c63f2b69552d8298e8de3dda506 Mon Sep 17 00:00:00 2001 From: Keisuke Oshima Date: Tue, 26 Nov 2024 09:48:33 -0500 Subject: [PATCH 1/3] Merged all dependencies into env.yaml. --- README.md | 6 +++--- env.yaml | 5 +++++ test/env_dev.yaml | 11 ----------- 3 files changed, 8 insertions(+), 14 deletions(-) delete mode 100644 test/env_dev.yaml diff --git a/README.md b/README.md index 4d6616d..6e6b0c3 100644 --- a/README.md +++ b/README.md @@ -112,10 +112,10 @@ Multiple samples can be provided via the configfile. Each sample should contain See [`docs/ISSUES.md`](docs/ISSUES.md) for edge-cases and effects of parameter tuning. ## Testing -Set up the dev conda environment and pull test data with [`git-lfs`](https://git-lfs.com/). +Set up the conda environment and pull test data with [`git-lfs`](https://git-lfs.com/). ```bash -conda env create --name test_cdr_finder -f test/env_dev.yaml -conda activate test_cdr_finder +conda env create --name cdr_finder -f test/env.yaml +conda activate cdr_finder git lfs install && git lfs pull ``` diff --git a/env.yaml b/env.yaml index 6b775e1..2ccdd2c 100644 --- a/env.yaml +++ b/env.yaml @@ -2,5 +2,10 @@ channels: - conda-forge dependencies: - python==3.12 + - anaconda::git-lfs - pip: - snakemake==8.18.2 + - pytest + - intervaltree==3.1.0 + - polars==0.20.31 + - scipy==1.14.1 diff --git a/test/env_dev.yaml b/test/env_dev.yaml deleted file mode 100644 index 2ccdd2c..0000000 --- a/test/env_dev.yaml +++ /dev/null @@ -1,11 +0,0 @@ -channels: - - conda-forge -dependencies: - - python==3.12 - - anaconda::git-lfs - - pip: - - snakemake==8.18.2 - - pytest - - intervaltree==3.1.0 - - polars==0.20.31 - - scipy==1.14.1 From 1f3409b1300e7ed472f743ae0fa6ba6cd000ae58 Mon Sep 17 00:00:00 2001 From: Keisuke Oshima Date: Tue, 26 Nov 2024 09:51:48 -0500 Subject: [PATCH 2/3] Merged all dependencies into env.yaml. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6e6b0c3..969567a 100644 --- a/README.md +++ b/README.md @@ -114,7 +114,7 @@ See [`docs/ISSUES.md`](docs/ISSUES.md) for edge-cases and effects of parameter t ## Testing Set up the conda environment and pull test data with [`git-lfs`](https://git-lfs.com/). ```bash -conda env create --name cdr_finder -f test/env.yaml +conda env create --name cdr_finder -f env.yaml conda activate cdr_finder git lfs install && git lfs pull ``` From 1639f6678c2e778ec83939faf922f074663eb28b Mon Sep 17 00:00:00 2001 From: Keisuke Oshima Date: Tue, 26 Nov 2024 10:45:03 -0500 Subject: [PATCH 3/3] Update CI to use new yaml. --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index e701cc7..634fe72 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -18,7 +18,7 @@ jobs: - name: Install Snakemake and testing dependencies. run: | - pip install -r <(yq -r '.dependencies[] | select(type == "!!map") | to_entries[].value[]' test/env_dev.yaml) + pip install -r <(yq -r '.dependencies[] | select(type == "!!map") | to_entries[].value[]' env.yaml) - name: Install Singularity. uses: singularityhub/install-singularity@main