From 2ac9dd5f98d3b1b1520315c1d0b77b6320985664 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Mon, 22 May 2023 09:46:43 +0200 Subject: [PATCH 1/7] update pystardb dependency to 0.4.2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cffa132..fc22a46 100644 --- a/setup.py +++ b/setup.py @@ -29,7 +29,7 @@ "numpy >= 1.20.0", "scikit-learn", "scikit-image", - "pystardb==0.3.1", + "pystardb>=0.4.2", "pandas >= 1.3", "pytorch-metric-learning==1.6.3", "numba", From fe97ef0e652aaeaee82a1b0fbe12e92bee98b76b Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Mon, 22 May 2023 09:47:18 +0200 Subject: [PATCH 2/7] update to cuda 11.8, cuml 23.04 and pytorch 1.13.1 --- conda_env.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conda_env.yml b/conda_env.yml index a3878aa..acdbd6a 100644 --- a/conda_env.yml +++ b/conda_env.yml @@ -6,15 +6,15 @@ channels: - nvidia - defaults dependencies: - - pytorch==1.12 + - pytorch==1.13.1 - torchvision - pandas - scipy - numpy - matplotlib - pytables - - cuml=22.06 - - cudatoolkit=11.6 + - cuml=23.04 + - cudatoolkit=11.8 - protobuf[version='>3.20'] - tensorboard - optuna From 87f02dd2415145cfd5e769add22f26e4342563d0 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Mon, 22 May 2023 09:48:10 +0200 Subject: [PATCH 3/7] update to python 3.10 --- .github/workflows/checks_tests_deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/checks_tests_deploy.yml b/.github/workflows/checks_tests_deploy.yml index ce1ce87..d1a51f3 100644 --- a/.github/workflows/checks_tests_deploy.yml +++ b/.github/workflows/checks_tests_deploy.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9"] + python-version: ["3.10"] defaults: run: shell: bash -el {0} From e7be48f4bb8609e3fdb6535bfa2520c48a899f74 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Mon, 22 May 2023 10:04:07 +0200 Subject: [PATCH 4/7] update installation instructions --- docs/installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/installation.rst b/docs/installation.rst index 7b09832..200ade2 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -13,7 +13,7 @@ There are three main steps to install TomoTwin: .. prompt:: bash $ - mamba create -n tomotwin -c pytorch -c rapidsai -c nvidia -c conda-forge python=3.9 pytorch==1.12 torchvision pandas scipy numpy matplotlib pytables cuML=22.06 cudatoolkit=11.6 'protobuf>3.20' tensorboard optuna mysql-connector-python + mamba create -n tomotwin -c pytorch -c rapidsai -c nvidia -c conda-forge python=3.10 pytorch==1.13.1 torchvision pandas scipy numpy matplotlib pytables cuML=23.04 cudatoolkit=11.8 'protobuf>3.20' tensorboard optuna mysql-connector-python conda activate tomotwin pip install tomotwin-cryoet From f61692f2157c529a39ffbf4b41fcbafb684e846e Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Mon, 22 May 2023 10:32:11 +0200 Subject: [PATCH 5/7] make sure that pandas is < 2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index fc22a46..f93bf3d 100644 --- a/setup.py +++ b/setup.py @@ -30,7 +30,7 @@ "scikit-learn", "scikit-image", "pystardb>=0.4.2", - "pandas >= 1.3", + "pandas <= 2", # Because rapids does not support pandas > 1.5.3 "pytorch-metric-learning==1.6.3", "numba", "tabulate", From 965341939fccf2553f4ca502bc1cd5d3a5f5a0d2 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Mon, 22 May 2023 10:36:26 +0200 Subject: [PATCH 6/7] make sure that pandas is < 2 --- conda_env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda_env.yml b/conda_env.yml index acdbd6a..c492480 100644 --- a/conda_env.yml +++ b/conda_env.yml @@ -8,7 +8,7 @@ channels: dependencies: - pytorch==1.13.1 - torchvision - - pandas + - pandas[version='<2'] - scipy - numpy - matplotlib From 5c73b472f902a35c8b6de4df2b2be614568c78d5 Mon Sep 17 00:00:00 2001 From: thorstenwagner Date: Mon, 22 May 2023 10:45:50 +0200 Subject: [PATCH 7/7] add changelog for 0.4.3 --- docs/changes.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/changes.rst b/docs/changes.rst index 25b4e69..86c8dbd 100644 --- a/docs/changes.rst +++ b/docs/changes.rst @@ -1,6 +1,15 @@ Changes ======= +Version 0.4.3 +************* + +* Fix numba related issue by updating various dependencies (https://github.com/MPI-Dortmund/tomotwin-cryoet/issues/20): + - Python 3.9 -> Python 3.10 + - Rapids 22.04 -> 23.04 + - CUDA 11.6 -> CUDA 11.8 +* Updating pyStarDB from 0.3.2 -> 0.4.2 + Version 0.4.0 *************