From c5cba958168a3087c60a060e30e202e9c2ab321f Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 17 Nov 2023 09:23:19 -0600 Subject: [PATCH 1/4] Switch to mamba for environment installation --- .github/workflows/test.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 1bfacac..5616a8e 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -18,7 +18,9 @@ jobs: activate-environment: nn4dms environment-file: environment.yml auto-activate-base: false - miniconda-version: 'latest' + miniforge-variant: Mambaforge + miniforge-version: 'latest' + use-mamba: true # Tests that the regression training code runs in the conda environment - name: Train regression example shell: bash --login {0} From 075f7a5d5e13321299db7fb81132afebbefee6ff Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 17 Nov 2023 09:26:26 -0600 Subject: [PATCH 2/4] Log conda environment packages --- .github/workflows/test.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5616a8e..cbe9841 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -21,6 +21,10 @@ jobs: miniforge-variant: Mambaforge miniforge-version: 'latest' use-mamba: true + # Log conda environment contents + - name: Log conda environment + shell: bash --login {0} + run: conda list # Tests that the regression training code runs in the conda environment - name: Train regression example shell: bash --login {0} From 6dedf709a2e5376430880b7a76f7808a2dc0341e Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 17 Nov 2023 09:30:52 -0600 Subject: [PATCH 3/4] Switch back to conda and test again --- .github/workflows/test.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index cbe9841..e4e5810 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -18,9 +18,7 @@ jobs: activate-environment: nn4dms environment-file: environment.yml auto-activate-base: false - miniforge-variant: Mambaforge - miniforge-version: 'latest' - use-mamba: true + miniconda-version: 'latest' # Log conda environment contents - name: Log conda environment shell: bash --login {0} From 77953894e6e2ec8688c8b05d9974bc3febc00ede Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Fri, 17 Nov 2023 10:06:57 -0600 Subject: [PATCH 4/4] Pin absl-py version --- environment.yml | 1 + environment_gpu.yml | 1 + 2 files changed, 2 insertions(+) diff --git a/environment.yml b/environment.yml index 69c849c..63e6ef1 100644 --- a/environment.yml +++ b/environment.yml @@ -13,6 +13,7 @@ dependencies: - matplotlib=3.3.1 - seaborn=0.10.1 - pyyaml=5.3.1 + - absl-py=0.15.0 - conda-forge::biopandas=0.2.7 - conda-forge::shortuuid=1.0.1 - conda-forge::umap-learn=0.4.0 diff --git a/environment_gpu.yml b/environment_gpu.yml index edcf86f..77031e0 100644 --- a/environment_gpu.yml +++ b/environment_gpu.yml @@ -13,6 +13,7 @@ dependencies: - matplotlib=3.3.1 - seaborn=0.10.1 - pyyaml=5.3.1 + - absl-py=0.15.0 - conda-forge::biopandas=0.2.7 - conda-forge::shortuuid=1.0.1 - conda-forge::umap-learn=0.4.0